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commit/galaxy-central: dannon: =Use tabs instead of spaces for sample lines in bowtie_indices.loc.sample
by Bitbucket 23 Mar '12

23 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/732c10115fdf/ changeset: 732c10115fdf user: dannon date: 2012-03-23 13:24:42 summary: =Use tabs instead of spaces for sample lines in bowtie_indices.loc.sample affected #: 1 file diff -r 1adcc1b43718a0abc925061fdb6403a60bde2ddb -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e tool-data/bowtie_indices.loc.sample --- a/tool-data/bowtie_indices.loc.sample +++ b/tool-data/bowtie_indices.loc.sample @@ -7,11 +7,11 @@ # #<unique_build_id><dbkey><display_name><file_base_path> # -#So, for example, if you had hg18 indexed stored in -#/depot/data2/galaxy/bowtie/hg18/, +#So, for example, if you had hg18 indexed stored in +#/depot/data2/galaxy/bowtie/hg18/, #then the bowtie_indices.loc entry would look like this: # -#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 +#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 # #and your /depot/data2/galaxy/bowtie/hg18/ directory #would contain hg18.*.ebwt files: @@ -25,9 +25,9 @@ #index set you have stored. The "file" in the path does not actually #exist, but it is the prefix for the actual index files. For example: # -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon -#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full -#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon +#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full +#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 #...etc... # #Note that for backwards compatibility with workflows, the unique ID of Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Remove the EMBOSS tools from Main's tool_conf.
by Bitbucket 22 Mar '12

22 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1adcc1b43718/ changeset: 1adcc1b43718 user: natefoo date: 2012-03-23 03:16:22 summary: Remove the EMBOSS tools from Main's tool_conf. affected #: 1 file diff -r 9e4fe7f46c621e1b79a33d223b3c9b807135b62c -r 1adcc1b43718a0abc925061fdb6403a60bde2ddb tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -218,115 +218,6 @@ <tool file="genome_diversity/select_restriction_enzymes.xml" /><tool file="genome_diversity/extract_flanking_dna.xml" /></section> - <section name="EMBOSS" id="EMBOSSLite"> - <tool file="emboss_5/emboss_antigenic.xml" /> - <tool file="emboss_5/emboss_backtranseq.xml" /> - <tool file="emboss_5/emboss_banana.xml" /> - <tool file="emboss_5/emboss_biosed.xml" /> - <tool file="emboss_5/emboss_btwisted.xml" /> - <tool file="emboss_5/emboss_cai_custom.xml" /> - <tool file="emboss_5/emboss_cai.xml" /> - <tool file="emboss_5/emboss_chaos.xml" /> - <tool file="emboss_5/emboss_charge.xml" /> - <tool file="emboss_5/emboss_checktrans.xml" /> - <tool file="emboss_5/emboss_chips.xml" /> - <tool file="emboss_5/emboss_cirdna.xml" /> - <tool file="emboss_5/emboss_codcmp.xml" /> - <tool file="emboss_5/emboss_coderet.xml" /> - <tool file="emboss_5/emboss_compseq.xml" /> - <tool file="emboss_5/emboss_cpgplot.xml" /> - <tool file="emboss_5/emboss_cpgreport.xml" /> - <tool file="emboss_5/emboss_cusp.xml" /> - <tool file="emboss_5/emboss_cutseq.xml" /> - <tool file="emboss_5/emboss_dan.xml" /> - <tool file="emboss_5/emboss_degapseq.xml" /> - <tool file="emboss_5/emboss_descseq.xml" /> - <tool file="emboss_5/emboss_diffseq.xml" /> - <tool file="emboss_5/emboss_digest.xml" /> - <tool file="emboss_5/emboss_dotmatcher.xml" /> - <tool file="emboss_5/emboss_dotpath.xml" /> - <tool file="emboss_5/emboss_dottup.xml" /> - <tool file="emboss_5/emboss_dreg.xml" /> - <tool file="emboss_5/emboss_einverted.xml" /> - <tool file="emboss_5/emboss_epestfind.xml" /> - <tool file="emboss_5/emboss_equicktandem.xml" /> - <tool file="emboss_5/emboss_est2genome.xml" /> - <tool file="emboss_5/emboss_etandem.xml" /> - <tool file="emboss_5/emboss_extractfeat.xml" /> - <tool file="emboss_5/emboss_extractseq.xml" /> - <tool file="emboss_5/emboss_freak.xml" /> - <tool file="emboss_5/emboss_fuzznuc.xml" /> - <tool file="emboss_5/emboss_fuzzpro.xml" /> - <tool file="emboss_5/emboss_fuzztran.xml" /> - <tool file="emboss_5/emboss_garnier.xml" /> - <tool file="emboss_5/emboss_geecee.xml" /> - <tool file="emboss_5/emboss_getorf.xml" /> - <tool file="emboss_5/emboss_helixturnhelix.xml" /> - <tool file="emboss_5/emboss_hmoment.xml" /> - <tool file="emboss_5/emboss_iep.xml" /> - <tool file="emboss_5/emboss_infoseq.xml" /> - <tool file="emboss_5/emboss_isochore.xml" /> - <tool file="emboss_5/emboss_lindna.xml" /> - <tool file="emboss_5/emboss_marscan.xml" /> - <tool file="emboss_5/emboss_maskfeat.xml" /> - <tool file="emboss_5/emboss_maskseq.xml" /> - <tool file="emboss_5/emboss_matcher.xml" /> - <tool file="emboss_5/emboss_megamerger.xml" /> - <tool file="emboss_5/emboss_merger.xml" /> - <tool file="emboss_5/emboss_msbar.xml" /> - <tool file="emboss_5/emboss_needle.xml" /> - <tool file="emboss_5/emboss_newcpgreport.xml" /> - <tool file="emboss_5/emboss_newcpgseek.xml" /> - <tool file="emboss_5/emboss_newseq.xml" /> - <tool file="emboss_5/emboss_noreturn.xml" /> - <tool file="emboss_5/emboss_notseq.xml" /> - <tool file="emboss_5/emboss_nthseq.xml" /> - <tool file="emboss_5/emboss_octanol.xml" /> - <tool file="emboss_5/emboss_oddcomp.xml" /> - <tool file="emboss_5/emboss_palindrome.xml" /> - <tool file="emboss_5/emboss_pasteseq.xml" /> - <tool file="emboss_5/emboss_patmatdb.xml" /> - <tool file="emboss_5/emboss_pepcoil.xml" /> - <tool file="emboss_5/emboss_pepinfo.xml" /> - <tool file="emboss_5/emboss_pepnet.xml" /> - <tool file="emboss_5/emboss_pepstats.xml" /> - <tool file="emboss_5/emboss_pepwheel.xml" /> - <tool file="emboss_5/emboss_pepwindow.xml" /> - <tool file="emboss_5/emboss_pepwindowall.xml" /> - <tool file="emboss_5/emboss_plotcon.xml" /> - <tool file="emboss_5/emboss_plotorf.xml" /> - <tool file="emboss_5/emboss_polydot.xml" /> - <tool file="emboss_5/emboss_preg.xml" /> - <tool file="emboss_5/emboss_prettyplot.xml" /> - <tool file="emboss_5/emboss_prettyseq.xml" /> - <tool file="emboss_5/emboss_primersearch.xml" /> - <tool file="emboss_5/emboss_revseq.xml" /> - <tool file="emboss_5/emboss_seqmatchall.xml" /> - <tool file="emboss_5/emboss_seqret.xml" /> - <tool file="emboss_5/emboss_showfeat.xml" /> - <tool file="emboss_5/emboss_shuffleseq.xml" /> - <tool file="emboss_5/emboss_sigcleave.xml" /> - <tool file="emboss_5/emboss_sirna.xml" /> - <tool file="emboss_5/emboss_sixpack.xml" /> - <tool file="emboss_5/emboss_skipseq.xml" /> - <tool file="emboss_5/emboss_splitter.xml" /> - <tool file="emboss_5/emboss_supermatcher.xml" /> - <tool file="emboss_5/emboss_syco.xml" /> - <tool file="emboss_5/emboss_tcode.xml" /> - <tool file="emboss_5/emboss_textsearch.xml" /> - <tool file="emboss_5/emboss_tmap.xml" /> - <tool file="emboss_5/emboss_tranalign.xml" /> - <tool file="emboss_5/emboss_transeq.xml" /> - <tool file="emboss_5/emboss_trimest.xml" /> - <tool file="emboss_5/emboss_trimseq.xml" /> - <tool file="emboss_5/emboss_twofeat.xml" /> - <tool file="emboss_5/emboss_union.xml" /> - <tool file="emboss_5/emboss_vectorstrip.xml" /> - <tool file="emboss_5/emboss_water.xml" /> - <tool file="emboss_5/emboss_wobble.xml" /> - <tool file="emboss_5/emboss_wordcount.xml" /> - <tool file="emboss_5/emboss_wordmatch.xml" /> - </section><label text="NGS Toolbox Beta" id="ngs" /><section name="NGS: QC and manipulation" id="cshl_library_information"><label text="Illumina data" id="illumina" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Pack script.
by Bitbucket 22 Mar '12

22 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9e4fe7f46c62/ changeset: 9e4fe7f46c62 user: jgoecks date: 2012-03-23 02:17:09 summary: Pack script. affected #: 1 file diff -r b7d0ea8cf2334a840b9bef195c06b30e99fcbaba -r 9e4fe7f46c621e1b79a33d223b3c9b807135b62c static/scripts/packed/galaxy.panels.js --- a/static/scripts/packed/galaxy.panels.js +++ b/static/scripts/packed/galaxy.panels.js @@ -1,1 +1,1 @@ -!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}};var b=150,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o<n){if(!this.hidden){this.do_toggle();this.hidden_by_tool=true}}else{if(this.hidden_by_tool){this.do_toggle();this.hidden_by_tool=false}}},force_panel:function(n){if((this.hidden&&n=="show")||(!this.hidden&&n=="hide")){this.do_toggle()}},init:function(){var n=this;this.$toggle.remove().appendTo("body");this.$drag.on("dragstart",function(o,p){d("#DD-helper").show();p.width=n.$panel.width()}).on("dragend",function(){d("#DD-helper").hide()}).on("drag",function(p,q){var o;if(n.left){o=q.width+q.deltaX}else{o=q.width-q.deltaX}o=Math.min(h,Math.max(b,o));n.resize(o)});n.$toggle.on("click",function(){n.do_toggle()})}});var f=function(n){this.$overlay=n.overlay;this.$dialog=n.dialog;this.$header=this.$dialog.find(".modal-header");this.$body=this.$dialog.find(".modal-body");this.$footer=this.$dialog.find(".modal-footer");this.$backdrop=n.backdrop};d.extend(f.prototype,{setContent:function(p){if(p.title){this.$header.find(".title").html(p.title);this.$header.show()}else{this.$header.hide()}this.$footer.hide();console.log(this.$footer,p.buttons);var o=this.$footer.find(".buttons").html("");if(p.buttons){d.each(p.buttons,function(r,s){o.append(d("<button></button> ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("<button></button>").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("<div class='progress progress-striped active'><div class='bar' style='width: 100%'></div></div>")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$body.css("min-width",this.$body.width())}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#overlay"),dialog:d("#dialog-box"),backdrop:d("#overlay-background")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function g(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:false},q)}function j(p){var q=p.width||"600";var o=p.height||"400";var n=p.scroll||"auto";d("#overlay-background").bind("click.overlay",function(){a();d("#overlay-background").unbind("click.overlay")});l(null,d("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+image_path+"/closebox.png'><iframe style='margin: 0; 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commit/galaxy-central: jgoecks: Reinstate dialog-box class in modal.
by Bitbucket 22 Mar '12

22 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b7d0ea8cf233/ changeset: b7d0ea8cf233 user: jgoecks date: 2012-03-22 23:53:55 summary: Reinstate dialog-box class in modal. affected #: 1 file diff -r 423d7f6e7b80cc294a9324133a49e1cd385c36ae -r b7d0ea8cf2334a840b9bef195c06b30e99fcbaba templates/base_panels.mako --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -178,7 +178,7 @@ <div id="overlay-background" class="modal-backdrop fade ${overlay_class}"></div> - <div id="dialog-box" class="modal" border="0" ${display}> + <div id="dialog-box" class="modal dialog-box" border="0" ${display}><div class="modal-header"><span><h3 class='title'>${title}</h3></span></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Remove debugging statement.
by Bitbucket 22 Mar '12

22 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/423d7f6e7b80/ changeset: 423d7f6e7b80 user: jgoecks date: 2012-03-22 23:00:54 summary: Remove debugging statement. affected #: 1 file diff -r bb19e940a03c7120674b2ba1ebf1588cbea95f74 -r 423d7f6e7b80cc294a9324133a49e1cd385c36ae static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js +++ b/static/scripts/galaxy.panels.js @@ -140,7 +140,6 @@ } // Buttons this.$footer.hide(); - console.log( this.$footer, options.buttons ); var $buttons = this.$footer.find( ".buttons" ).html( "" ); if ( options.buttons ) { $.each( options.buttons, function( name, value ) { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: richard_burhans: fix get_file_peek() to better support datasets with very long lines
by Bitbucket 22 Mar '12

22 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/bb19e940a03c/ changeset: bb19e940a03c user: richard_burhans date: 2012-03-22 21:15:24 summary: fix get_file_peek() to better support datasets with very long lines affected #: 1 file diff -r fa40b8f3f385f67d57294d98a036e483775d873f -r bb19e940a03c7120674b2ba1ebf1588cbea95f74 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -433,13 +433,13 @@ if line and not line.startswith( '#' ): data_lines += 1 return data_lines - def set_peek( self, dataset, line_count=None, is_multi_byte=False, skipchars=[] ): + def set_peek( self, dataset, line_count=None, is_multi_byte=False, WIDTH=256, skipchars=[] ): """ Set the peek. This method is used by various subclasses of Text. """ if not dataset.dataset.purged: # The file must exist on disk for the get_file_peek() method - dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte, skipchars=skipchars ) + dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte, WIDTH=WIDTH, skipchars=skipchars ) if line_count is None: # See if line_count is stored in the metadata if dataset.metadata.data_lines: @@ -567,6 +567,11 @@ ## >>> get_file_peek(fname) ## 'chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 +\n' """ + # Set size for file.readline() to a negative number to force it to + # read until either a newline or EOF. Needed for datasets with very + # long lines. + if WIDTH == 'unlimited': + WIDTH = -1 lines = [] count = 0 file_type = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: richard_burhans: changes to aaChanges tool
by Bitbucket 22 Mar '12

22 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fa40b8f3f385/ changeset: fa40b8f3f385 user: richard_burhans date: 2012-03-22 18:19:31 summary: changes to aaChanges tool affected #: 2 files diff -r 1f6c7be22ba9059d8fd8e05148466bb005a7fbd1 -r fa40b8f3f385f67d57294d98a036e483775d873f tools/evolution/codingSnps.pl --- a/tools/evolution/codingSnps.pl +++ b/tools/evolution/codingSnps.pl @@ -7,11 +7,15 @@ # and a gene bed file with cds start and stop. # It then checks for changes in coding regions, reporting # those that cause a frameshift or substitution in the amino acid. +# Output columns: +# chrom, start, end, allele as given (amb code translated) +# Gene ID from genes file, ref amino acid:variant amino acids, +# codon number, (in strand of gene)ref nt, refCodon:variantCodons ######################################################################### my $seqFlag = "2bit"; #flag to set sequence type 2bit|nib if (!@ARGV or scalar @ARGV < 3) { - print "Usage: codingSnps.pl snps.bed genes.bed (/dir/*$seqFlag|Galaxy build= loc=) [chr=# start=# end=# snp=# keepColumns=1] > codingSnps.txt\n"; + print "Usage: codingSnps.pl snps.bed genes.bed (/dir/*$seqFlag|Galaxy build= loc=) [chr=# start=# end=# snp=# strand=#|-|+ keepColumns=1 synon=1 unique=1] > codingSnps.txt\n"; exit; } my $uniq = 0; #flag for whether want uniq positions @@ -25,6 +29,7 @@ my $col1 = 1; my $col2 = 2; my $col3 = 3; +my $strand = -1; #column positions 1 based coming in (for Galaxy) foreach (@ARGV) { if (/chr=(\d+)/) { $col0 = $1 -1; } @@ -32,6 +37,10 @@ elsif (/end=(\d+)/) { $col2 = $1 -1; } elsif (/snp=(\d+)/) { $col3 = $1 -1; } elsif (/keepColumns=1/) { $keep = 1; } + elsif (/synon=1/) { $syn = 1; } + elsif (/unique=1/) { $uniq = 1; } + elsif (/strand=(\d+)/) { $strand = $1 -1; } #0 based column + elsif (/strand=-/) { $strand = -99; } #special case of all minus } if ($col0 < 0 || $col1 < 0 || $col2 < 0 || $col3 < 0) { print STDERR "ERROR column numbers are given with origin 1\n"; @@ -42,6 +51,7 @@ my %codon; #hash of codon amino acid conversions my $ends = 0; #ends vs sizes in bed 11 position, starts relative to chrom my $ignoreN = 1; #skip N +my $origAll; #alleles from input file (before changes for strand) my %amb = ( "R" => "A/G", @@ -90,6 +100,10 @@ print STDERR "ERROR file has fewer columns than requested, requested columns (0 based) $col0 $col1 $col2 $col3, file has $size\n"; exit 1; } + if ($strand >= 0 && $strand > $size) { + print STDERR "ERROR file has fewer columns than requested, requested strand in $strand (0 based), file has $size\n"; + exit 1; + } if ($s[$col1] =~ /\D/) { print STDERR "ERROR the start point must be an integer not $s[$col1]\n"; exit 1; @@ -100,6 +114,11 @@ } if ($s[$col3] eq 'N' && $ignoreN) { next; } if (exists $amb{$s[$col3]}) { $s[$col3] = $amb{$s[$col3]}; } + if (($strand >= 0 && $s[$strand] eq '-') or $strand == -99) { + #reverse complement nts + $origAll = $s[$col3]; + $s[$col3] = reverseCompAlleles($s[$col3]); + }else { undef $origAll } if (!@g && exists $chrSt{$s[$col0]}) { #need to fetch first gene row $i = $chrSt{$s[$col0]}; @g = split(/\t/, $genes[$i]); @@ -287,36 +306,45 @@ } #now compute amino acids my $oldaa = getaa($oldnts); + my $codon = "$oldnts:"; my @newaa; my $change = 0; #flag for if there is a change foreach my $v (@newnts) { my $t = getaa($v); if ($t ne $oldaa) { $change = 1; } - push(@newaa, $t); + push(@newaa, "$t"); + $codon .= "$v/"; } + $codon =~ s/\/$//; if (!$change && $syn) { if (!$keep) { print "$sref->[$col0]\t$sref->[$col1]\t$sref->[$col2]\t$sref->[$col3]"; - print "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\n"; + print "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\t$cdNum\t$changed\t$codon\n"; }else { my @s = @{$sref}; print join("\t", @s), - "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\n"; + "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\t$cdNum\t$changed\t$codon\n"; } + $done{"$sref->[$col0] $sref->[$col1] $sref->[$col2]"}++; return; }elsif ($syn) { return; } #only want synonymous changes if (!$change) { return; } #no change in amino acids if (!$keep) { - print "$sref->[$col0]\t$sref->[$col1]\t$sref->[$col2]\t$sref->[$col3]"; - if ($gref->[5] eq '-') { $changed = compl($changed); } #use plus for ref + my $a = $sref->[$col3]; + if (($strand >= 0 && $origAll) or $strand == -99) { $a = $origAll; } + print "$sref->[$col0]\t$sref->[$col1]\t$sref->[$col2]\t$a"; + #my $minus = $changed; #in case minus strand and change back + #if ($gref->[5] eq '-') { $changed = compl($changed); } #use plus for ref if (!$changed) { return; } #skip this one - print "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\t$cdNum\t$changed\n"; + print "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\t$cdNum\t$changed\t$codon\n"; }else { my @s = @{$sref}; + if (($strand >= 0 && $origAll) or $strand == -99) { $s[$col3] = $origAll; } print join("\t", @s); - if ($gref->[5] eq '-') { $changed = compl($changed); } #use plus for ref + #my $minus = $changed; #in case minus strand and change back + #if ($gref->[5] eq '-') { $changed = compl($changed); } #use plus for ref if (!$changed) { return; } #skip this one - print "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\t$cdNum\t$changed\n"; + print "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\t$cdNum\t$changed\t$codon\n"; } $done{"$sref->[$col0] $sref->[$col1] $sref->[$col2]"}++; } @@ -418,6 +446,19 @@ return $comp; } +sub reverseCompAlleles { + my $all = shift; + my @nt = split(/\//, $all); + my $rv = ''; + foreach my $n (@nt) { + $n = reverse(split(/ */, $n)); #needed for indels + $n = compl($n); + $rv .= "$n/"; + } + $rv =~ s/\/$//; + return $rv; +} + sub getaa { my $nts = shift; #in multiples of 3 my $aa = ''; diff -r 1f6c7be22ba9059d8fd8e05148466bb005a7fbd1 -r fa40b8f3f385f67d57294d98a036e483775d873f tools/evolution/codingSnps.xml --- a/tools/evolution/codingSnps.xml +++ b/tools/evolution/codingSnps.xml @@ -2,7 +2,7 @@ <description>amino-acid changes caused by a set of SNPs</description><command interpreter="perl"> - codingSnps.pl $input1 $input2 Galaxy build=${input1.metadata.dbkey} loc=${GALAXY_DATA_INDEX_DIR}/codingSnps.loc chr=${input1.metadata.chromCol} start=${input1.metadata.startCol} end=${input1.metadata.endCol} snp=$col1 keepColumns=$keep > $out_file1 + codingSnps.pl $input1 $input2 Galaxy build=${input1.metadata.dbkey} loc=${GALAXY_DATA_INDEX_DIR}/codingSnps.loc chr=${input1.metadata.chromCol} start=${input1.metadata.startCol} end=${input1.metadata.endCol} snp=$col1 keepColumns=$keep strand=${strand_source.strand_col} > $out_file1 </command><inputs> @@ -17,6 +17,22 @@ <option value="0" selected="true">No</option><option value="1">Yes</option></param> + <conditional name="strand_source"> + <param name="strand_choice" type="select" label="Strand info"> + <option value="data_column">a column in the dataset</option> + <option value="all_pos" selected="true">all on sense/forward/+ strand</option> + <option value="all_neg">all on antisense/reverse/- strand</option> + </param> + <when value="data_column"> + <param name="strand_col" type="data_column" data_ref="input1" label="Column with strand"/> + </when> + <when value="all_pos"> + <param name="strand_col" type="hidden" value="+"/> + </when> + <when value="all_neg"> + <param name="strand_col" type="hidden" value="-"/> + </when> + </conditional></inputs><outputs> @@ -36,14 +52,26 @@ <param name="input1" ftype="interval" value="codingSnps_input1.interval" dbkey="hg18" /><param name="col1" value="6" /><param name="input2" ftype="interval" value="codingSnps_inputGenes1.bed" dbkey="hg18" /> + <param name="strand_choice" value="all_pos" /> + <param name="strand_col" value="+" /><output name="output" file="codingSnps_output1.interval" /></test><test><param name="input1" ftype="interval" value="codingSnps_input2.interval" dbkey="hg18" /><param name="input2" ftype="interval" value="codingSnps_inputGenes2.bed" dbkey="hg18" /><param name="col1" value="4" /> + <param name="strand_choice" value="all_pos" /> + <param name="strand_col" value="+" /><output name="output" file="codingSnps_output2.interval" /></test> + <test> + <param name="input1" ftype="interval" value="codingSnps_input2.interval" dbkey="hg18" /> + <param name="input2" ftype="interval" value="codingSnps_inputGenes2.bed" dbkey="hg18" /> + <param name="col1" value="4" /> + <param name="strand_choice" value="all_neg" /> + <param name="strand_col" value="-" /> + <output name="output" file="codingSnps_output3.interval" /> + </test></tests><help> @@ -79,8 +107,9 @@ the first 12 columns standard BED columns. The output is the same as the first input file with several columns added: the name field from the line of the gene input file -used, the amino acids, the codon number, and the reference nucleotide that -changed in the amino acid. +used, the amino acids, the codon number, the reference nucleotide that +changed in the amino acid (in the same strand as the gene), and the codons +that go with the amino acids. The amino acids are listed with the reference amino acid first, then a colon, and then the amino acids for the alleles. If a SNP is not in a coding region or is synonymous then it is not included in the output file. @@ -128,15 +157,15 @@ - output file, showing non-synonymous substitutions in coding regions:: - chr22 15825725 15825726 G/T uc002zlw.1 Gln:Pro/Gln 469 T - chr22 15827035 15827036 G uc002zlw.1 Glu:Asp 414 C - chr22 15827135 15827136 C/G uc002zlw.1 Gly:Gly/Ala 381 C - chr22 15830928 15830929 A/G uc002zlw.1 Ala:Ser/Pro 281 C - chr22 15830951 15830952 G uc002zlw.1 Leu:Pro 273 A - chr22 15830955 15830956 C/T uc002zlw.1 Ser:Gly/Ser 272 T - chr22 15848885 15848886 C/T uc002zlw.1 Ser:Trp/Stop 217 G - chr22 15848885 15848886 C/T uc010gqs.1 Ser:Trp/Stop 200 G - chr22 15849048 15849049 A/C uc002zlw.1 Gly:Stop/Gly 163 C + chr22 15825725 15825726 G/T uc002zlw.1 Gln:Pro/Gln 469 A CAA:CCA/CAA + chr22 15827035 15827036 G uc002zlw.1 Glu:Asp 414 G GAG:GAC + chr22 15827135 15827136 C/G uc002zlw.1 Gly:Gly/Ala 381 G GGT:GGT/GCT + chr22 15830928 15830929 A/G uc002zlw.1 Ala:Ser/Pro 281 G GCA:TCA/CCA + chr22 15830951 15830952 G uc002zlw.1 Leu:Pro 273 T CTT:CCT + chr22 15830955 15830956 C/T uc002zlw.1 Ser:Gly/Ser 272 A AGC:GGC/AGC + chr22 15848885 15848886 C/T uc002zlw.1 Ser:Trp/Stop 217 C TCG:TGG/TAG + chr22 15848885 15848886 C/T uc010gqs.1 Ser:Trp/Stop 200 C TCG:TGG/TAG + chr22 15849048 15849049 A/C uc002zlw.1 Gly:Stop/Gly 163 G GGA:TGA/GGA etc. </help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: richard_burhans: Updates to Human Genome Variation tools
by Bitbucket 22 Mar '12

22 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1f6c7be22ba9/ changeset: 1f6c7be22ba9 user: richard_burhans date: 2012-03-22 18:03:01 summary: Updates to Human Genome Variation tools Rename Human Genome Variation to Phenotype Association affected #: 76 files Diff too large to display. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 22 Mar '12

22 Mar '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b00471c0ffe8/ changeset: b00471c0ffe8 user: jgoecks date: 2012-03-22 15:10:18 summary: Remove debugging statement. affected #: 1 file diff -r 4d48285fcaa65c7895768069ea197acf9d66b1ed -r b00471c0ffe864c1223d39ca4fd5b4836d73f4c7 templates/base_panels.mako --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -69,7 +69,7 @@ %if self.has_right_panel: var rp = new Panel( { panel: $("#right"), center: $("#center"), drag: $("#right > .unified-panel-footer > .drag" ), toggle: $("#right > .unified-panel-footer > .panel-collapse" ), right: true } ); - window.handle_minwidth_hint = function( x ) { console.log( "hint", x ); rp.handle_minwidth_hint( x ) }; + window.handle_minwidth_hint = function( x ) { rp.handle_minwidth_hint( x ) }; force_right_panel = function( x ) { rp.force_panel( x ) }; %endif https://bitbucket.org/galaxy/galaxy-central/changeset/164eef0d7693/ changeset: 164eef0d7693 user: jgoecks date: 2012-03-22 15:40:47 summary: Add spacing for checkboxes, radio buttons; use webkit default of 0.5ex affected #: 1 file diff -r b00471c0ffe864c1223d39ca4fd5b4836d73f4c7 -r 164eef0d76931e20135fdb908136e599d351599e static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -14,6 +14,7 @@ button,input[type="button"],input[type="reset"],input[type="submit"]{cursor:pointer;-webkit-appearance:button;} input[type="search"]{-webkit-appearance:textfield;-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box;} input[type="search"]::-webkit-search-decoration,input[type="search"]::-webkit-search-cancel-button{-webkit-appearance:none;} +input[type="checkbox"],input[type="radio"]{margin-left:0.5ex;margin-right:0.5ex;} textarea{overflow:auto;vertical-align:top;} body{margin:0;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:12px;line-height:16px;color:#111111;background-color:#ffffff;} a{color:#303030;text-decoration:none;} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Convert dbkeys from string to dict before checking for dbkey when including chrom info in jobs. Thanks Andrew Warren.
by Bitbucket 22 Mar '12

22 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4d48285fcaa6/ changeset: 4d48285fcaa6 user: jgoecks date: 2012-03-22 14:58:42 summary: Convert dbkeys from string to dict before checking for dbkey when including chrom info in jobs. Thanks Andrew Warren. affected #: 1 file diff -r ee4a47ed53712fe87c5372f667c9058147415c04 -r 4d48285fcaa65c7895768069ea197acf9d66b1ed lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -195,7 +195,7 @@ else: # For custom builds, chrom info resides in converted dataset; for built-in builds, chrom info resides in tool-data/shared. chrom_info = None - if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in trans.user.preferences[ 'dbkeys' ] ): + if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ): # Custom build. custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ input_dbkey ] if 'fasta' in custom_build_dict: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for checker for certain tools eliminated from the distribution.
by Bitbucket 21 Mar '12

21 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ee4a47ed5371/ changeset: ee4a47ed5371 user: greg date: 2012-03-21 22:50:25 summary: Fix for checker for certain tools eliminated from the distribution. affected #: 1 file diff -r e439813f0748dd615b2a7ad18b5de9cbd68b4f9d -r ee4a47ed53712fe87c5372f667c9058147415c04 lib/galaxy/tool_shed/migrate/common.py --- a/lib/galaxy/tool_shed/migrate/common.py +++ b/lib/galaxy/tool_shed/migrate/common.py @@ -9,7 +9,7 @@ from galaxy.tool_shed import install_manager from galaxy.tool_shed.migrate.common import * -def check_for_missing_tools( tool_panel_config, latest_tool_migration_script_number ): +def check_for_missing_tools( tool_panel_configs, latest_tool_migration_script_number ): # Get the 000x_tools.xml file associated with the current migrate_tools version number. tools_xml_file_path = os.path.abspath( os.path.join( 'scripts', 'migrate_tools', '%04d_tools.xml' % latest_tool_migration_script_number ) ) # Parse the XML and load the file attributes for later checking against the proprietary tool_panel_config. @@ -20,17 +20,18 @@ if elem.tag == 'repository': for tool_elem in elem.findall( 'tool' ): migrated_tool_configs.append( tool_elem.get( 'file' ) ) - # Parse the proprietary tool_panel_config (the default is tool_conf.xml) and generate the list of missing tool config file names. + # Parse the proprietary tool_panel_configs (the default is tool_conf.xml) and generate the list of missing tool config file names. missing_tool_configs = [] - tree = util.parse_xml( tool_panel_config ) - root = tree.getroot() - for elem in root: - if elem.tag == 'tool': - missing_tool_configs = check_tool_tag_set( elem, migrated_tool_configs, missing_tool_configs ) - elif elem.tag == 'section': - for section_elem in elem: - if section_elem.tag == 'tool': - missing_tool_configs = check_tool_tag_set( section_elem, migrated_tool_configs, missing_tool_configs ) + for tool_panel_config in tool_panel_configs: + tree = util.parse_xml( tool_panel_config ) + root = tree.getroot() + for elem in root: + if elem.tag == 'tool': + missing_tool_configs = check_tool_tag_set( elem, migrated_tool_configs, missing_tool_configs ) + elif elem.tag == 'section': + for section_elem in elem: + if section_elem.tag == 'tool': + missing_tool_configs = check_tool_tag_set( section_elem, migrated_tool_configs, missing_tool_configs ) return missing_tool_configs def check_tool_tag_set( elem, migrated_tool_configs, missing_tool_configs ): file_path = elem.get( 'file', None ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: james_taylor: pack scripts
by Bitbucket 21 Mar '12

21 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e439813f0748/ changeset: e439813f0748 user: james_taylor date: 2012-03-21 22:46:55 summary: pack scripts affected #: 3 files diff -r 79236000c5bdceaf98546d66f002d5a40b006f74 -r e439813f0748dd615b2a7ad18b5de9cbd68b4f9d static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function make_popupmenu(b,c){var 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d=function(k){$(a).css("width",k);$(e).css("right",k+9);$(h).css("right",k).css("left","");if(document.recalc){document.recalc()}};var i=function(){if(j){$(h).removeClass("hover");$(h).animate({right:c},"fast");$(a).css("right",-c).show().animate({right:0},"fast",function(){d(c);$(h).removeClass("hidden")});j=false}else{c=$(document).width()-$(h).position().left-$(h).outerWidth();$(e).css("right",$(h).innerWidth()+1);if(document.recalc){document.recalc()}$(h).removeClass("hover");$(a).animate({right:-c},"fast");$(h).animate({right:-1},"fast",function(){$(this).addClass("hidden")});j=true}g=false};var b=function(k){var l=$(e).width()-(j?c:0);if(l<k){if(!j){i();g=true}}else{if(g){i();g=false}}};$(h).hover(function(){$(this).addClass("hover")},function(){$(this).removeClass("hover")}).bind("dragstart",function(){$("#DD-helper").show()}).bind("dragend",function(){$("#DD-helper").hide()}).bind("drag",function(k,l){x=l.offsetX;w=$(window).width();x=Math.min(w-MIN_PANEL_WIDTH,x);x=Math.max(w-MAX_PANEL_WIDTH,x);if(j){$(a).css("right",0);$(h).removeClass("hidden");j=false}d(w-x-$(this).outerWidth())}).bind("dragclickonly",function(){i()}).find("div").show();var f=function(k){if((j&&k=="show")||(!j&&k=="hide")){i()}};return{handle_minwidth_hint:b,force_panel:f}}function hide_modal(){$(".dialog-box-container").hide(0,function(){$("#overlay").hide();$("#overlay").removeClass("modal");$(".dialog-box").find(".body").children().remove()})}function show_modal(){$("#overlay").addClass("modal");_show_modal.apply(this,arguments)}function show_message(){_show_modal.apply(this,arguments)}function _show_modal(h,c,f,d,g){if(h){$(".dialog-box").find(".title").html(h);$(".dialog-box").find(".unified-panel-header").show()}else{$(".dialog-box").find(".unified-panel-header").hide()}var a=$(".dialog-box").find(".buttons").html("");if(f){$.each(f,function(b,i){a.append($("<button/>").text(b).click(i));a.append(" ")});a.show()}else{a.hide()}var a=$(".dialog-box").find(".extra_buttons").html("");if(d){$.each(d,function(b,i){a.append($("<button/>").text(b).click(i));a.append(" ")});a.show()}else{a.hide()}if(c=="progress"){c=$("<img/>").attr("src",image_path+"/yui/rel_interstitial_loading.gif")}var e=$(".dialog-box").find(".body");e.css("min-width","0px");$(".dialog-box").find(".body").html(c);if(!$(".dialog-box-container").is(":visible")){$("#overlay").show();$(".dialog-box-container").show()}e.css("min-width",e.width());if(g){g()}}function show_in_overlay(c){var d=c.width||"600";var b=c.height||"400";var a=c.scroll||"auto";$("#overlay-background").bind("click.overlay",function(){hide_modal();$("#overlay-background").unbind("click.overlay")});show_modal(null,$("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+image_path+"/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+c.url+"' width='"+d+"' height='"+b+"' scrolling='"+a+"' frameborder='0'></iframe></div>"));$("#close_button").bind("click",function(){hide_modal()})}$(function(){$(".tab").each(function(){var a=$(this).children(".submenu");if(a.length>0){if($.browser.msie){a.prepend("<iframe style=\"position: absolute; top: 0; left: 0; width: 100%; height: 100%; z-index: -1; filter:Alpha(Opacity='0');\"></iframe>")}$(this).hover(function(){a.show()},function(){a.hide()});a.click(function(){a.hide()})}})});function user_changed(a,b){if(a){$(".loggedin-only").show();$(".loggedout-only").hide();$("#user-email").text(a);if(b){$(".admin-only").show()}}else{$(".loggedin-only").hide();$(".loggedout-only").show();$(".admin-only").hide()}}; \ No newline at end of file +!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}};var b=150,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o<n){if(!this.hidden){this.do_toggle();this.hidden_by_tool=true}}else{if(this.hidden_by_tool){this.do_toggle();this.hidden_by_tool=false}}},force_panel:function(n){if((this.hidden&&n=="show")||(!this.hidden&&n=="hide")){this.do_toggle()}},init:function(){var n=this;this.$toggle.remove().appendTo("body");this.$drag.on("dragstart",function(o,p){d("#DD-helper").show();p.width=n.$panel.width()}).on("dragend",function(){d("#DD-helper").hide()}).on("drag",function(p,q){var o;if(n.left){o=q.width+q.deltaX}else{o=q.width-q.deltaX}o=Math.min(h,Math.max(b,o));n.resize(o)});n.$toggle.on("click",function(){n.do_toggle()})}});var f=function(n){this.$overlay=n.overlay;this.$dialog=n.dialog;this.$header=this.$dialog.find(".modal-header");this.$body=this.$dialog.find(".modal-body");this.$footer=this.$dialog.find(".modal-footer");this.$backdrop=n.backdrop};d.extend(f.prototype,{setContent:function(p){if(p.title){this.$header.find(".title").html(p.title);this.$header.show()}else{this.$header.hide()}this.$footer.hide();console.log(this.$footer,p.buttons);var o=this.$footer.find(".buttons").html("");if(p.buttons){d.each(p.buttons,function(r,s){o.append(d("<button></button> ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("<button></button>").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("<div class='progress progress-striped active'><div class='bar' style='width: 100%'></div></div>")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$body.css("min-width",this.$body.width())}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#overlay"),dialog:d("#dialog-box"),backdrop:d("#overlay-background")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function g(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:false},q)}function j(p){var q=p.width||"600";var o=p.height||"400";var n=p.scroll||"auto";d("#overlay-background").bind("click.overlay",function(){a();d("#overlay-background").unbind("click.overlay")});l(null,d("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+image_path+"/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+p.url+"' width='"+q+"' height='"+o+"' scrolling='"+n+"' frameborder='0'></iframe></div>"));d("#close_button").bind("click",function(){a()})}function i(n,o){if(n){d(".loggedin-only").show();d(".loggedout-only").hide();d("#user-email").text(n);if(o){d(".admin-only").show()}}else{d(".loggedin-only").hide();d(".loggedout-only").show();d(".admin-only").hide()}}d(function(){var n=d("#masthead ul.nav > li.dropdown > .dropdown-menu");d("body").on("click.nav_popups",function(p){n.hide();d("#DD-helper").hide();if(d(p.target).closest("#masthead ul.nav > li.dropdown > .dropdown-menu").length){return}var o=d(p.target).closest("#masthead ul.nav > li.dropdown");if(o.length){d("#DD-helper").show();o.children(".dropdown-menu").show();p.preventDefault()}})});c.ensure_dd_helper=e;c.Panel=k;c.Modal=f;c.hide_modal=a;c.show_modal=l;c.show_message=g;c.show_in_overlay=j;c.user_changed=i}(window,window.jQuery); \ No newline at end of file diff -r 79236000c5bdceaf98546d66f002d5a40b006f74 -r e439813f0748dd615b2a7ad18b5de9cbd68b4f9d static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +1,1 @@ -var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(var j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tipsy({gravity:"s"}).click(a)};var trackster_module=function(e,U){var p=e("class").extend,s=e("slotting"),J=e("painters");var ab=function(ac,ad){this.document=ac;this.default_font=ad!==undefined?ad:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ab.prototype,{load_pattern:function(ac,ag){var ad=this.patterns,ae=this.dummy_context,af=new Image();af.src=image_path+ag;af.onload=function(){ad[ac]=ae.createPattern(af,"repeat")}},get_pattern:function(ac){return this.patterns[ac]},new_canvas:function(){var ac=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ac)}ac.manager=this;return ac}});var n={};var l=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this);var at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}var aj;for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};U.moveable=m;var aa=16,D=9,A=20,x=100,G=12000,R=400,I=5000,u=100,o="There was an error in indexing this dataset. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",t="Currently indexing... please wait",v="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",O=10,F=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var c=function(ac){this.num_elements=ac;this.clear()};p(c.prototype,{get:function(ad){var ac=this.key_ary.indexOf(ad);if(ac!==-1){if(this.obj_cache[ad].stale){this.key_ary.splice(ac,1);delete this.obj_cache[ad]}else{this.move_key_to_end(ad,ac)}}return this.obj_cache[ad]},set:function(ad,ae){if(!this.obj_cache[ad]){if(this.key_ary.length>=this.num_elements){var ac=this.key_ary.shift();delete this.obj_cache[ac]}this.key_ary.push(ad)}this.obj_cache[ad]=ae;return ae},move_key_to_end:function(ad,ac){this.key_ary.splice(ac,1);this.key_ary.push(ad)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var P=function(ad,ac){c.call(this,ad);this.track=ac};p(P.prototype,c.prototype,{load_data:function(al,ag,aj,ad,ai){var ak=this.track.view.chrom,af={chrom:ak,low:al,high:ag,mode:aj,resolution:ad,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(af,ai);if(this.track.filters_manager){var am=[];var ac=this.track.filters_manager.filters;for(var ah=0;ah<ac.length;ah++){am.push(ac[ah].name)}af.filter_cols=JSON.stringify(am)}var ae=this;return $.getJSON(this.track.data_url,af,function(an){ae.set_data(al,ag,an)})},get_data:function(ak,ae,ai,ad,ah){var al=this.get(ak,ae);if(al&&(is_deferred(al)||this.track.data_and_mode_compatible(al,ai))){return al}var am,aj,ac,ag,ai,al;for(var af=0;af<this.key_ary.length;af++){am=this.key_ary[af];aj=this.split_key(am);ac=aj[0];ag=aj[1];if(ak>=ac&&ae<=ag){var al=this.obj_cache[am];if(is_deferred(al)||(this.track.data_and_mode_compatible(al,ai)&&this.track.can_subset(al))){this.move_key_to_end(am,af);return al}}}al=this.load_data(ak,ae,ai,ad,ah);this.set_data(ak,ae,al);return al},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ak,af,aj,ae,ai,ag){var al=this.get(ak,af);if(!(al&&this.track.data_and_mode_compatible(al,aj))){console.log("ERROR: no current data for: ",this.track,ak,af,aj,ae,ai);return}al.stale=true;var ad=ak;if(ag===this.DEEP_DATA_REQ){$.extend(ai,{start_val:al.data.length+1})}else{if(ag===this.BROAD_DATA_REQ){ad=(al.max_high?al.max_high:al.data[al.data.length-1][2])+1}}var ac=this,ah=this.load_data(ad,af,aj,ae,ai);new_data_available=$.Deferred();this.set_data(ak,af,new_data_available);$.when(ah).then(function(am){if(am.data){am.data=al.data.concat(am.data);if(am.max_low){am.max_low=al.max_low}if(am.message){am.message=am.message.replace(/[0-9]+/,am.data.length)}}ac.set_data(ak,af,am);new_data_available.resolve(am)});return new_data_available},get:function(ac,ad){return c.prototype.get.call(this,this.gen_key(ac,ad))},set_data:function(ad,ae,ac){return this.set(this.gen_key(ad,ae),ac)},gen_key:function(ac,ae){var ad=ac+"_"+ae;return ad},split_key:function(ac){return ac.split("_")}});var E=function(ad,ac,ae){P.call(this,ad,ac,ae)};p(E.prototype,P.prototype,c.prototype,{get:P.prototype.get,load_data:function(ac,af,ag,ad,ae){if(ad>1){return{data:null}}return P.prototype.load_data.call(this,ac,af,ag,ad,ae)}});var q=function(ad,ac,af){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tipsy").remove();ac.remove()}}];p(q.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},update_icons:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tipsy({gravity:"s"}).click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var w=function(ad,ac,ae){q.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};p(w.prototype,q.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=object_from_template(ae[ac],this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false}});var N=function(ad,ac,af){p(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});w.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new X(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new X(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};p(N.prototype,q.prototype,w.prototype,{action_icons_def:[q.prototype.action_icons_def[0],q.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},q.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof h){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(var al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(var al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new S({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ag=[];for(var ad=0;ad<this.drawables.length;ad++){ag.push(this.drawables[ad].name)}var ae="Composite Track of "+this.drawables.length+" tracks ("+ag.join(", ")+")";var af=new h(this.view,this.view,{name:ae,drawables:this.drawables});var ac=this.container.replace_drawable(this,af,true);af.request_draw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){w.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=p(w.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=function(ac){p(ac,{obj_type:"View"});w.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ab(this.container.get(0).ownerDocument);this.reset()};p(Z.prototype,w.prototype,{init:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new Y(this,{content_div:this.top_labeltrack}));this.add_label_track(new Y(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ac.resize_window()});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(ac,ad){this.location_span.text(commatize(ac)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ad))},load_chroms:function(ae){ae.num=u;ae.dbkey=this.dbkey;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){alert("Invalid chromosome: "+ae.chrom);return}if(ag.reference){ac.add_label_track(new y(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+u+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+u+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){if(!ah||ah==="None"){return}var ae=this;if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-u});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+u});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(ae){var ac=this;var ad=ac.high-ac.low;if(ac.low-ae<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ad}else{if(ac.high-ae>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ad}else{ac.high-=ae;ac.low-=ae}}ac.request_redraw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){w.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,ad){var ai=this,ag=(ad?[ad]:ai.drawables),ae;var ad;for(var ah=0;ah<ag.length;ah++){ad=ag[ah];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ah][1]=ac;ai.tracks_to_be_redrawn[ah][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(ak)});this.requested_redraw=true}},_redraw:function(am){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}this.update_location(this.low,this.high);if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new f(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new L(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);var ak=this;ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};p(r.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=JSON.stringify(ae)});return ac},get_param_values:function(){var ad=[];var ac={};this.parent_div.find(":input").each(function(){var ae=$(this).attr("name"),af=$(this).val();if(ae){ad[ad.length]=af}});return ad},run_on_dataset:function(){var ac=this;ac.run({dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ad={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ad.chrom,ad.low,ad.high),ac;if(ah.container===view){var ag=new N(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var ai=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});ai.init_for_tool_data();ai.change_mode(ah.mode);ai.set_filters_manager(ah.filters_manager.copy(ai));ai.update_icons();ac.add_drawable(ai);ai.content_div.text("Starting job.");this.update_params();this.run(ad,ai,function(aj){ai.dataset_id=aj.dataset_id;ai.content_div.text("Running job.");ai.init()})},run:function(ad,ae,af){$.extend(ad,this.get_param_values_dict());var ac=function(){$.getJSON(rerun_tool_url,ad,function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(v+ag.message)}else{if(ag==="pending"){ae.container_div.addClass("pending");ae.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ac,2000)}else{af(ag)}}}})};ac()}});var L=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};p(L.prototype,{update_value:function(){this.value=$(this.html).val()}});var f=function(ae,ad,ag,ah,af,ac){L.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};p(f.prototype,L.prototype,{update_value:function(){L.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var g=function(ac){this.manager=null;this.name=ac.name;this.index=ac.index;this.tool_id=ac.tool_id;this.tool_exp_name=ac.tool_exp_name};p(g.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var S=function(al){g.call(this,al);this.low=("low" in al?al.low:-Number.MAX_VALUE);this.high=("high" in al?al.high:Number.MAX_VALUE);this.min=("min" in al?al.min:Number.MAX_VALUE);this.max=("max" in al?al.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var ah=function(am,an,ao){am.click(function(){var au=an.text(),ar=parseFloat(ao.slider("option","max")),aq=(ar<=1?4:ar<=1000000?ar.toString().length:6),at=false,ap=$(this).parents(".slider-row");ap.addClass("input");if(ao.slider("option","values")){aq=2*aq+1;at=true}an.text("");$("<input type='text'/>").attr("size",aq).attr("maxlength",aq).attr("value",au).appendTo(an).focus().select().click(function(av){av.stopPropagation()}).blur(function(){$(this).remove();an.text(au);ap.removeClass("input")}).keyup(function(az){if(az.keyCode===27){$(this).trigger("blur")}else{if(az.keyCode===13){var ax=ao.slider("option","min"),av=ao.slider("option","max"),ay=function(aA){return(isNaN(aA)||aA>av||aA<ax)},aw=$(this).val();if(!at){aw=parseFloat(aw);if(ay(aw)){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}else{aw=aw.split("-");aw=[parseFloat(aw[0]),parseFloat(aw[1])];if(ay(aw[0])||ay(aw[1])){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}ao.slider((at?"values":"value"),aw);ap.removeClass("input")}}})})};var ad=this;ad.parent_div=$("<div/>").addClass("filter-row slider-row");var ac=$("<div/>").addClass("elt-label").appendTo(ad.parent_div),aj=$("<span/>").addClass("slider-name").text(ad.name+" ").appendTo(ac),ae=$("<span/>").text(this.low+"-"+this.high),af=$("<span/>").addClass("slider-value").appendTo(ac).append("[").append(ae).append("]");ad.values_span=ae;var ai=$("<div/>").addClass("slider").appendTo(ad.parent_div);ad.control_element=$("<div/>").attr("id",ad.name+"-filter-control").appendTo(ai);var ag=[0,0];ad.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(am,an){ad.slide(am,an)},change:function(am,an){ad.control_element.slider("option","slide").call(ad.control_element,am,an)}});ad.slider=ad.control_element;ad.slider_label=ae;ah(af,ae,ad.control_element);var ak=$("<div/>").addClass("display-controls").appendTo(ad.parent_div);this.transparency_icon=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(ad.manager.alpha_filter!==ad){ad.manager.alpha_filter=ad;ad.manager.parent_div.find(".layer-transparent").removeClass("active").hide();ad.transparency_icon.addClass("active").show()}else{ad.manager.alpha_filter=null;ad.transparency_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();this.height_icon=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(ad.manager.height_filter!==ad){ad.manager.height_filter=ad;ad.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();ad.height_icon.addClass("active").show()}else{ad.manager.height_filter=null;ad.height_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();ad.parent_div.hover(function(){ad.transparency_icon.show();ad.height_icon.show()},function(){if(ad.manager.alpha_filter!==ad){ad.transparency_icon.hide()}if(ad.manager.height_filter!==ad){ad.height_icon.hide()}});$("<div style='clear: both;'/>").appendTo(ad.parent_div)};p(S.prototype,{to_dict:function(){var ac=g.prototype.to_dict.call(this);return p(ac,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new S({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ae,ac){var ad=ac-ae;return(ad<=2?0.01:1)},slide:function(ad,ae){var ac=ae.values;this.values_span.text(ac[0]+"-"+ac[1]);this.low=ac[0];this.high=ac[1];this.manager.track.request_draw(true,true)},applies_to:function(ac){if(ac.length>this.index){return true}return false},_keep_val:function(ac){return(isNaN(ac)||(ac>=this.low&&ac<=this.high))},keep:function(ad){if(!this.applies_to(ad)){return true}var af=this;var ag=ad[this.index];if(ag instanceof Array){var ae=true;for(var ac=0;ac<ag.length;ac++){if(!this._keep_val(ag[ac])){ae=false;break}}return ae}else{return this._keep_val(ad[this.index])}},update_attrs:function(af){var ac=false;if(!this.applies_to(af)){return ac}var ad=af[this.index];if(!(ad instanceof Array)){ad=[ad]}for(var ae=0;ae<ad.length;ae++){var ag=ad[ae];if(ag<this.min){this.min=Math.floor(ag);ac=true}if(ag>this.max){this.max=Math.ceil(ag);ac=true}}return ac},update_ui_elt:function(){if(this.min!==this.max){this.parent_div.show()}else{this.parent_div.hide()}var ad=this.slider.slider("option","min"),ac=this.slider.slider("option","max");if(this.min<ad||this.max>ac){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var X=function(ae,ak){this.track=ae;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(am){am.stopPropagation()}).click(function(am){am.stopPropagation()}).bind("dblclick",function(am){am.stopPropagation()}).bind("keydown",function(am){am.stopPropagation()});if(ak&&"filters" in ak){var ac=("alpha_filter" in ak?ak.alpha_filter:null),af=("height_filter" in ak?ak.height_filter:null),ah=ak.filters,ad;for(var ai=0;ai<ah.length;ai++){if(ah[ai].type==="number"){ad=new S(ah[ai]);this.add_filter(ad);if(ad.name===ac){this.alpha_filter=ad;ad.transparency_icon.addClass("active").show()}if(ad.name===af){this.height_filter=ad;ad.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in ak&&ak.visible){this.parent_div.show()}}if(this.filters.length!==0){var al=$("<div/>").addClass("param-row").appendTo(this.parent_div);var aj=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(al);var ag=this;aj.click(function(){ag.run_on_dataset()})}};p(X.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var af={},ae=[],ad;for(var ac=0;ac<this.filters.length;ac++){ad=this.filters[ac];ae.push(ad.to_dict())}af.filters=ae;af.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);af.height_filter=(this.height_filter?this.height_filter.name:null);af.visible=this.parent_div.is(":visible");return af},copy:function(ad){var ae=new X(ad);for(var ac=0;ac<this.filters.length;ac++){ae.add_filter(this.filters[ac].copy())}return ae},add_filter:function(ac){ac.manager=this;this.parent_div.append(ac.parent_div);this.filters.push(ac)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.update_ui_elt()}},clear_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.slider.slider("option","values",[ad.min,ad.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var ak=function(ao,am,an){if(!(am in ao)){ao[am]=an}return ao[am]};var ae={},ac,ad,af;for(var ag=0;ag<this.filters.length;ag++){ac=this.filters[ag];if(ac.tool_id){if(ac.min!==ac.low){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" >= "+ac.low}if(ac.max!==ac.high){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" <= "+ac.high}}}var ai=[];for(var al in ae){ai[ai.length]=[al,ae[al]]}var aj=ai.length;(function ah(at,ap){var an=ap[0],ao=an[0],ar=an[1],aq="("+ar.join(") and (")+")",am={cond:aq,input:at,target_dataset_id:at,tool_id:ao},ap=ap.slice(1);$.getJSON(run_tool_url,am,function(au){if(au.error){show_modal("Filter Dataset","Error running tool "+ao,{Close:hide_modal})}else{if(ap.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ah(au.dataset_id,ap)}}})})(this.track.dataset_id,ai)}});var z=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};z.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var C=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};p(C.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(aj,ag){for(var an=0;an<aj.length;an++){ae=aj[an];if(ae.hidden){continue}var ah="param_"+an;var ar=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ah).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ah).attr("name",ah).attr("checked",ar))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ah).val(ar).click(function(){$(this).select()}))}else{if(ae.type==="select"){var ap=$("<select />").attr("id",ah);for(var al=0;al<ae.options.length;al++){$("<option/>").text(ae.options[al].label).attr("value",ae.options[al].value).appendTo(ap)}ap.val(ar);av.append(ap)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ao=$("<input />").attr("id",ah).attr("name",ah).val(ar).css("float","left").appendTo(au).click(function(ax){$(".tipsy").hide();var aw=$(this).siblings(".tipsy");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),am=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tipsy({gravity:"s"}),aq=$("<div class='tipsy tipsy-west' style='position: absolute;' />").appendTo(au).hide(),ai=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(aq),at=$("<div/>").appendTo(ai),ak=$.farbtastic(at,{width:100,height:100,callback:ao,color:ar});au.append($("<div/>").css("clear","both"));(function(aw){am.click(function(){aw.setColor(get_random_color())})})(ak)}else{av.append($("<input />").attr("id",ah).attr("name",ah).val(ar))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,af,ae,ad,ag){this.track=ac;this.index=af;var ah=this.track._get_tile_bounds(af,ae);this.low=ah[0];this.high=ah[1];this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(ac,af,ae,ad,ag,ah){b.call(this,ac,af,ae,ad,ag);this.max_val=ah};p(k.prototype,b.prototype);var M=function(af,ak,ag,ae,ai,ao,aj,ap,ad,am){b.call(this,af,ak,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(ap){this.has_icons=true;var al=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:A-1,width:ae.width}).prependTo(this.html_elt);var an=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tipsy({gravity:"s"}).appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tipsy({gravity:"s"}).appendTo(message_div);ah.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};p(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var i=function(ad,ac,ae){p(ae,{drag_handle_class:"draghandle"});q.call(this,ad,ac,ae);this.data_url=("data_url" in ae?ae.data_url:default_data_url);this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.dataset_check_url=converted_datasets_state_url;this.data_manager=("data_manager" in ae?ae.data_manager:new P(F,this));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);this.add_resize_handle()}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tools",css_class:"toolbox",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},on_resize:function(){},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof y){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Q){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.tiles_div.children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred();$.getJSON(converted_datasets_state_url,{hda_ldda:ad.hda_ldda,dataset_id:ad.dataset_id,chrom:ad.view.chrom},function(ae){if(!ae||ae==="error"||ae.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ae.message){var af=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ae.message+"</pre>",{Close:hide_modal})});ad.tiles_div.append(af)}}else{if(ae==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(H)}else{if(ae==="no data"||(ae.data!==undefined&&(ae.data===null||ae.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(B)}else{if(ae==="pending"){ad.container_div.addClass("pending");ad.tiles_div.text(t);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ae.status==="data"){if(ae.valid_chroms){ad.valid_chroms=ae.valid_chroms;ad.update_icons()}ad.tiles_div.text(V);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){}});var K=function(ae,ad,af){i.call(this,ae,ad,af);var ac=this,ae=ac.view;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new X(this,("filters" in af?af.filters:null));this.filters_available=false;this.tool=("tool" in af&&af.tool?new r(this,af.tool,af.tool_state):null);this.tile_cache=new c(O);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};p(K.prototype,q.prototype,i.prototype,{action_icons_def:i.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tipsy").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();p(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.tile_cache.clear();ac.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show()}else{ac.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_"+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},before_draw:function(){},_draw:function(ad,an){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=Math.pow(RESOLUTION,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(RESOLUTION)));ap=ae/(view.max_high-view.max_low)}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*R)),ak=true,ao=[],ai=function(aq){return(aq&&"track" in aq)};while((ac*R*ag)<ah){var am=this.draw_helper(ad,ae,ac,ag,this.tiles_div,ap);if(ai(am)){ao.push(am)}else{ak=false}ac+=1}if(!an){this.tiles_div.children(".remove").remove()}var af=this;if(ak){this.tiles_div.children(".remove").remove();af.postdraw_actions(ao,ae,ap,an)}},postdraw_actions:function(af,ag,ai,ac){var ae=this;var ah=false;for(var ad=0;ad<af.length;ad++){if(af[ad].has_icons){ah=true;break}}if(ah){for(var ad=0;ad<af.length;ad++){tile=af[ad];if(!tile.has_icons){tile.html_elt.css("padding-top",A)}}}},draw_helper:function(ac,ao,au,ar,ah,ai,ap){var an=this,ax=this._gen_tile_cache_key(ao,ai,au),af=this._get_tile_bounds(au,ar),av=af[0],ad=af[1];if(!ap){ap={}}var aw=(ac?undefined:an.tile_cache.get(ax));if(aw){an.show_tile(aw,ah,ai);return aw}var al=true;var at=an.data_manager.get_data(av,ad,an.mode,ar,an.data_url_extra_params);if(is_deferred(at)){al=false}var aj;if(view.reference_track&&ai>view.canvas_manager.char_width_px){aj=view.reference_track.data_manager.get_data(av,ad,an.mode,ar,view.reference_track.data_url_extra_params);if(is_deferred(aj)){al=false}}if(al){p(at,ap.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),af=an._get_tile_bounds(au,ar),av=af[0],ad=af[1],ao=Math.ceil((ad-av)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ao);ae.width=ao;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var aw=an.draw_tile(at,aq,ak,ar,au,ai,aj);if(aw!==undefined){an.tile_cache.set(ax,aw);an.show_tile(aw,ah,ai)}return aw}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},draw_tile:function(ac,ae,ah,ag,ad,ai,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ag,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var af=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){af-=this.left_offset}ac.css({position:"absolute",top:0,left:af,height:""});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ag.append(ac)}ad.after_show_tile(ae)},after_show_tile:function(ac){},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*R*ad),ag=Math.ceil(R*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return[af,ae]},tool_region_and_parameters_str:function(ae,ac,af){var ad=this,ag=(ae!==undefined&&ac!==undefined&&af!==undefined?ae+":"+ac+"-"+af:"all");return" - region=["+ag+"], parameters=["+ad.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ad=this;var ac=function(){if(ad.data_manager.size()===0){setTimeout(ac,300)}else{ad.data_url=default_data_url;ad.data_query_wait=I;ad.dataset_state_url=converted_datasets_state_url;$.getJSON(ad.dataset_state_url,{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},function(ae){})}};ac()}}});var Y=function(ad,ac){var ae={todo:"label",todo:false};i.call(this,ad,ac,ae);this.container_div.addClass("label-track")};p(Y.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var h=function(ad,ac,ag){K.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=object_from_template(af);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,K.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_group()}}].concat(K.prototype.action_icons_def),to_dict:w.prototype.to_dict,add_drawable:w.prototype.add_drawable,unpack_drawables:w.prototype.unpack_drawables,change_mode:function(ac){K.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(ad,ar,ay,av,aj,al,at){var aq=this,aC=this._gen_tile_cache_key(ar,al,ay),ah=this._get_tile_bounds(ay,av),az=ah[0],ae=ah[1];if(!at){at={}}var aB=(ad?undefined:aq.tile_cache.get(aC));if(aB){aq.show_tile(aB,aj,al);return aB}var ak=[],aq,ao=true,aw,am;for(var ax=0;ax<this.drawables.length;ax++){aq=this.drawables[ax];aw=aq.data_manager.get_data(az,ae,aq.mode,av,aq.data_url_extra_params);if(is_deferred(aw)){ao=false}ak.push(aw);am=null;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(az,ae,aq.mode,av,view.reference_track.data_url_extra_params);if(is_deferred(am)){ao=false}}ak.push(am)}if(ao){p(aw,at.more_tile_data);this.tile_predraw_init();var ag=aq.view.canvas_manager.new_canvas(),ah=aq._get_tile_bounds(ay,av),az=ah[0],ae=ah[1],aA=0,ar=Math.ceil((ae-az)*al)+this.left_offset,ap=0,af=[];var ac=0;for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}af.push(an);ac=aq.get_canvas_height(aw,an,al,ar);if(ac>ap){ap=ac}}ag.width=ar;ag.height=(at.height?at.height:ap);aA=0;var au=ag.getContext("2d");au.translate(this.left_offset,0);au.globalAlpha=0.5;au.globalCompositeOperation="source-over";for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];am=ak[aA+1];aB=aq.draw_tile(aw,au,af[ax],av,ay,al,am)}this.tile_cache.set(aC,aB);this.show_tile(aB,aj,al);return aB}var ai=$.Deferred(),aq=this;$.when.apply($,ak).then(function(){view.request_redraw(false,false,false,aq);ai.resolve()});return ai},show_group:function(){var af=new N(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof j){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){K.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ah,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var y=function(ac){K.call(this,"reference",ac,{content_div:ac.top_labeltrack},{});ac.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ac.dbkey};this.data_manager=new E(F,this,false)};p(y.prototype,q.prototype,K.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(ak,al,ah,ag,ad,am){var af=this;if(am>this.view.canvas_manager.char_width_px){if(ak.data===null){af.content_div.css("height","0px");return}var ae=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";ak=ak.data;for(var ai=0,aj=ak.length;ai<aj;ai++){var ac=Math.floor(ai*am);al.fillText(ak[ai],ac,10)}return new b(af,ad,ag,ae,ak)}this.content_div.css("height","0px")}});var j=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";K.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};p(j.prototype,q.prototype,K.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.data_url,{stats:true,chrom:ac.view.chrom,low:null,high:null,hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min;var ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div/>").text(W(ac.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".tipsy").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=$("<div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".tipsy").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(am,ak,ah,af,ad,al){var ae=ak.canvas,ac=this._get_tile_bounds(ad,af),ag=ac[0],aj=ac[1],ai=new J.LinePainter(am.data,ag,aj,this.prefs,ah);ai.draw(ak,ae.width,ae.height,al);return new b(this,ad,af,ae,am.data)},can_subset:function(ac){return false},});var d=function(ae,ad,af){var ac=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];K.call(this,ae,ad,af);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.tile_cache.clear();ac.set_painter_from_config();ac.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=af.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(d.prototype,q.prototype,K.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},after_show_tile:function(ac){this.max_height_px=Math.max(this.max_height_px,ac.html_elt.height());ac.html_elt.parent().children().css("height",this.max_height_px+"px");var ad=this.max_height_px;if(this.visible_height_px!==0){ad=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ad+"px")},postdraw_actions:function(ar,am,ah,ag){K.prototype.postdraw_actions.call(this,ar,ag);var al=this;if(al.mode==="Histogram"){var ad=-1;for(var ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(var ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){au.html_elt.remove();al.draw_helper(true,am,au.index,au.resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(var ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof k){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=$("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){$(".tipsy").remove();var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanceof M){var ap=true;for(var ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,x,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_summary_tree_data:function(ag,aj,ae,ar){if(ar>ae-aj){ar=ae-aj}var an=Math.floor((ae-aj)/ar),aq=[],af=0;var ah=0,ai=0,am,ap=0,ak=[],ao,al;var ad=function(av,au,aw,at){av[0]=au+aw*at;av[1]=au+(aw+1)*at};while(ap<ar&&ah!==ag.length){var ac=false;for(;ap<ar&&!ac;ap++){ad(ak,aj,ap,an);for(ai=ah;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ac=true;break}}if(ac){break}}data_start_index=ai;aq[aq.length]=ao=[ak[0],0];for(;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ao[1]++}else{break}}if(ao[1]>af){af=ao[1]}ap++}return{max:af,delta:an,data:aq}},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Histogram"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(an,ar,ap,at,ax,aj,ae){var aq=this,ad=ar.canvas,ag=this._get_tile_bounds(ax,at),aA=ag[0],ac=ag[1],aF=25,af=this.left_offset;if(ap==="summary_tree"||ap==="Histogram"){if(an.dataset_type!=="summary_tree"){var ak=this.get_summary_tree_data(an.data,aA,ac,200);if(an.max){ak.max=an.max}an=ak}var aC=new J.SummaryTreePainter(an,aA,ac,this.prefs);aC.draw(ar,ad.width,ad.height,aj);return new k(aq,ax,at,ad,an.data,an.max)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ah=an.data[au];var av=false;var am;for(var az=0,aE=al.length;az<aE;az++){am=al[az];am.update_attrs(ah);if(!am.keep(ah)){av=true;break}}if(!av){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aD=(this.filters_manager.alpha_filter?new z(this.filters_manager.alpha_filter):null);var aB=(this.filters_manager.height_filter?new z(this.filters_manager.height_filter):null);var aC=new (this.painter)(ai,aA,ac,this.prefs,ap,aD,aB,ae);var ay=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ay=aC.draw(ar,ad.width,ad.height,aj,ao);ay.translation=-af}return new M(aq,ax,at,ad,an.data,aj,ap,an.message,all_slotted,ay)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message){return false}return true},});var Q=function(ad,ac,ae){d.call(this,ad,ac,ae);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter};p(Q.prototype,q.prototype,K.prototype,d.prototype);var T=function(ae,ad,ag){d.call(this,ae,ad,ag);var af=get_random_color(),ac=get_random_color([af,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter;this.update_icons()};p(T.prototype,q.prototype,K.prototype,d.prototype);U.View=Z;U.DrawableGroup=N;U.LineTrack=j;U.FeatureTrack=d;U.ReadTrack=T;U.VcfTrack=Q;U.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};l.prototype.draw=function(z,A,y,B){};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(L,z,K,M){var E=this.view_start,N=this.view_end-this.view_start,I=this.data.data,G=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),B=K;delta_x_px=Math.ceil(this.data.delta*M);L.save();for(var C=0,D=I.length;C<D;C++){var H=Math.floor((I[C][0]-E)*M);var F=I[C][1];if(!F){continue}var J=F/G*K;if(F!==0&&J<1){J=1}L.fillStyle=this.prefs.block_color;L.fillRect(H,B-J,delta_x_px,J);var A=4;if(this.prefs.show_counts&&(L.measureText(F).width+A)<delta_x_px){L.fillStyle=this.prefs.label_color;L.textAlign="center";L.fillText(F,H+(delta_x_px/2),10)}}L.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(S,Q,N,D){var I=false,K=this.prefs.min_value,F=this.prefs.max_value,M=F-K,B=N,C=this.view_start,P=this.view_end-this.view_start,L=this.mode,aa=this.data;S.save();var ac=Math.round(N+K/M*N);if(L!=="Intensity"){S.fillStyle="#aaa";S.fillRect(0,ac,Q,1)}S.beginPath();var Y,G,E;if(aa.length>1){E=Math.ceil((aa[1][0]-aa[0][0])*D)}else{E=10}var A=parseInt(this.prefs.color.slice(1),16),H=(A&16711680)>>16,R=(A&65280)>>8,V=A&255;for(var T=0,U=aa.length;T<U;T++){S.fillStyle=S.strokeStyle=this.prefs.color;Y=Math.round((aa[T][0]-C)*D);G=aa[T][1];var W=false,J=false;if(G===null){if(I&&L==="Filled"){S.lineTo(Y,B)}I=false;continue}if(G<K){J=true;G=K}else{if(G>F){W=true;G=F}}if(L==="Histogram"){G=Math.round(G/M*B);S.fillRect(Y,ac,E,-G)}else{if(L==="Intensity"){var z=(G-K)/M,O=Math.round(H+(255-H)*(1-z)),X=Math.round(R+(255-R)*(1-z)),ab=Math.round(V+(255-V)*(1-z));S.fillStyle="rgb("+O+","+X+","+ab+")";S.fillRect(Y,0,E,B)}else{G=Math.round(B-(G-K)/M*B);if(I){S.lineTo(Y,G)}else{I=true;if(L==="Filled"){S.moveTo(Y,B);S.lineTo(Y,G)}else{S.moveTo(Y,G)}}}}S.fillStyle=this.prefs.overflow_color;if(W||J){var Z;if(L==="Histogram"||L==="Intensity"){Z=E}else{Y-=2;Z=4}if(W){S.fillRect(Y,0,Z,3)}if(J){S.fillRect(Y,B-3,Z,3)}}S.fillStyle=this.prefs.color}if(L==="Filled"){if(I){S.lineTo(Y,ac);S.lineTo(0,ac)}S.fill()}else{S.stroke()}S.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,E,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode==="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2]-1,Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-1-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length===1&&D==="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences){if(this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}else{continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai==="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file +var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(var j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tipsy({gravity:"s"}).click(a)};var trackster_module=function(e,U){var p=e("class").extend,s=e("slotting"),J=e("painters");var ab=function(ac,ad){this.document=ac;this.default_font=ad!==undefined?ad:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ab.prototype,{load_pattern:function(ac,ag){var ad=this.patterns,ae=this.dummy_context,af=new Image();af.src=image_path+ag;af.onload=function(){ad[ac]=ae.createPattern(af,"repeat")}},get_pattern:function(ac){return this.patterns[ac]},new_canvas:function(){var ac=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ac)}ac.manager=this;return ac}});var n={};var l=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this);var at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}var aj;for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};U.moveable=m;var aa=16,D=9,A=20,x=100,G=12000,R=400,I=5000,u=100,o="There was an error in indexing this dataset. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",t="Preparing data. This takes seconds for a small dataset but longer for a large dataset.<br/> You can save and close the visualization and preparation will continue.<br/>",v="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",O=10,F=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var c=function(ac){this.num_elements=ac;this.clear()};p(c.prototype,{get:function(ad){var ac=this.key_ary.indexOf(ad);if(ac!==-1){if(this.obj_cache[ad].stale){this.key_ary.splice(ac,1);delete this.obj_cache[ad]}else{this.move_key_to_end(ad,ac)}}return this.obj_cache[ad]},set:function(ad,ae){if(!this.obj_cache[ad]){if(this.key_ary.length>=this.num_elements){var ac=this.key_ary.shift();delete this.obj_cache[ac]}this.key_ary.push(ad)}this.obj_cache[ad]=ae;return ae},move_key_to_end:function(ad,ac){this.key_ary.splice(ac,1);this.key_ary.push(ad)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var P=function(ad,ac){c.call(this,ad);this.track=ac};p(P.prototype,c.prototype,{load_data:function(al,ag,aj,ad,ai){var ak=this.track.view.chrom,af={chrom:ak,low:al,high:ag,mode:aj,resolution:ad,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(af,ai);if(this.track.filters_manager){var am=[];var ac=this.track.filters_manager.filters;for(var ah=0;ah<ac.length;ah++){am.push(ac[ah].name)}af.filter_cols=JSON.stringify(am)}var ae=this;return $.getJSON(this.track.data_url,af,function(an){ae.set_data(al,ag,an)})},get_data:function(ak,ae,ai,ad,ah){var al=this.get(ak,ae);if(al&&(is_deferred(al)||this.track.data_and_mode_compatible(al,ai))){return al}var am,aj,ac,ag,ai,al;for(var af=0;af<this.key_ary.length;af++){am=this.key_ary[af];aj=this.split_key(am);ac=aj[0];ag=aj[1];if(ak>=ac&&ae<=ag){var al=this.obj_cache[am];if(is_deferred(al)||(this.track.data_and_mode_compatible(al,ai)&&this.track.can_subset(al))){this.move_key_to_end(am,af);return al}}}al=this.load_data(ak,ae,ai,ad,ah);this.set_data(ak,ae,al);return al},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ak,af,aj,ae,ai,ag){var al=this.get(ak,af);if(!(al&&this.track.data_and_mode_compatible(al,aj))){console.log("ERROR: no current data for: ",this.track,ak,af,aj,ae,ai);return}al.stale=true;var ad=ak;if(ag===this.DEEP_DATA_REQ){$.extend(ai,{start_val:al.data.length+1})}else{if(ag===this.BROAD_DATA_REQ){ad=(al.max_high?al.max_high:al.data[al.data.length-1][2])+1}}var ac=this,ah=this.load_data(ad,af,aj,ae,ai);new_data_available=$.Deferred();this.set_data(ak,af,new_data_available);$.when(ah).then(function(am){if(am.data){am.data=al.data.concat(am.data);if(am.max_low){am.max_low=al.max_low}if(am.message){am.message=am.message.replace(/[0-9]+/,am.data.length)}}ac.set_data(ak,af,am);new_data_available.resolve(am)});return new_data_available},get:function(ac,ad){return c.prototype.get.call(this,this.gen_key(ac,ad))},set_data:function(ad,ae,ac){return this.set(this.gen_key(ad,ae),ac)},gen_key:function(ac,ae){var ad=ac+"_"+ae;return ad},split_key:function(ac){return ac.split("_")}});var E=function(ad,ac,ae){P.call(this,ad,ac,ae)};p(E.prototype,P.prototype,c.prototype,{get:P.prototype.get,load_data:function(ac,af,ag,ad,ae){if(ad>1){return{data:null}}return P.prototype.load_data.call(this,ac,af,ag,ad,ae)}});var q=function(ad,ac,af){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tipsy").remove();ac.remove()}}];p(q.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},update_icons:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tipsy({gravity:"s"}).click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var w=function(ad,ac,ae){q.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};p(w.prototype,q.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=object_from_template(ae[ac],this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false}});var N=function(ad,ac,af){p(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});w.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new X(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new X(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};p(N.prototype,q.prototype,w.prototype,{action_icons_def:[q.prototype.action_icons_def[0],q.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},q.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof h){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(var al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(var al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new S({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ag=[];for(var ad=0;ad<this.drawables.length;ad++){ag.push(this.drawables[ad].name)}var ae="Composite Track of "+this.drawables.length+" tracks ("+ag.join(", ")+")";var af=new h(this.view,this.view,{name:ae,drawables:this.drawables});var ac=this.container.replace_drawable(this,af,true);af.request_draw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){w.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=p(w.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=function(ac){p(ac,{obj_type:"View"});w.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ab(this.container.get(0).ownerDocument);this.reset()};p(Z.prototype,w.prototype,{init:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new Y(this,{content_div:this.top_labeltrack}));this.add_label_track(new Y(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ac.resize_window()});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(ac,ad){this.location_span.text(commatize(ac)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ad))},load_chroms:function(ae){ae.num=u;ae.dbkey=this.dbkey;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){alert("Invalid chromosome: "+ae.chrom);return}if(ag.reference){ac.add_label_track(new y(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+u+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+u+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){if(!ah||ah==="None"){return}var ae=this;if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-u});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+u});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(ae){var ac=this;var ad=ac.high-ac.low;if(ac.low-ae<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ad}else{if(ac.high-ae>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ad}else{ac.high-=ae;ac.low-=ae}}ac.request_redraw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){w.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,ad){var ai=this,ag=(ad?[ad]:ai.drawables),ae;var ad;for(var ah=0;ah<ag.length;ah++){ad=ag[ah];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ah][1]=ac;ai.tracks_to_be_redrawn[ah][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(ak)});this.requested_redraw=true}},_redraw:function(am){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}this.update_location(this.low,this.high);if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new f(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new L(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);var ak=this;ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};p(r.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=JSON.stringify(ae)});return ac},get_param_values:function(){var ad=[];var ac={};this.parent_div.find(":input").each(function(){var ae=$(this).attr("name"),af=$(this).val();if(ae){ad[ad.length]=af}});return ad},run_on_dataset:function(){var ac=this;ac.run({dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ad={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ad.chrom,ad.low,ad.high),ac;if(ah.container===view){var ag=new N(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var ai=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});ai.init_for_tool_data();ai.change_mode(ah.mode);ai.set_filters_manager(ah.filters_manager.copy(ai));ai.update_icons();ac.add_drawable(ai);ai.tiles_div.text("Starting job.");this.update_params();this.run(ad,ai,function(aj){ai.dataset_id=aj.dataset_id;ai.tiles_div.text("Running job.");ai.init()})},run:function(ad,ae,af){$.extend(ad,this.get_param_values_dict());var ac=function(){$.getJSON(rerun_tool_url,ad,function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(v+ag.message)}else{if(ag==="pending"){ae.container_div.addClass("pending");ae.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ac,2000)}else{af(ag)}}}})};ac()}});var L=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};p(L.prototype,{update_value:function(){this.value=$(this.html).val()}});var f=function(ae,ad,ag,ah,af,ac){L.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};p(f.prototype,L.prototype,{update_value:function(){L.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var g=function(ac){this.manager=null;this.name=ac.name;this.index=ac.index;this.tool_id=ac.tool_id;this.tool_exp_name=ac.tool_exp_name};p(g.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var S=function(al){g.call(this,al);this.low=("low" in al?al.low:-Number.MAX_VALUE);this.high=("high" in al?al.high:Number.MAX_VALUE);this.min=("min" in al?al.min:Number.MAX_VALUE);this.max=("max" in al?al.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var ah=function(am,an,ao){am.click(function(){var au=an.text(),ar=parseFloat(ao.slider("option","max")),aq=(ar<=1?4:ar<=1000000?ar.toString().length:6),at=false,ap=$(this).parents(".slider-row");ap.addClass("input");if(ao.slider("option","values")){aq=2*aq+1;at=true}an.text("");$("<input type='text'/>").attr("size",aq).attr("maxlength",aq).attr("value",au).appendTo(an).focus().select().click(function(av){av.stopPropagation()}).blur(function(){$(this).remove();an.text(au);ap.removeClass("input")}).keyup(function(az){if(az.keyCode===27){$(this).trigger("blur")}else{if(az.keyCode===13){var ax=ao.slider("option","min"),av=ao.slider("option","max"),ay=function(aA){return(isNaN(aA)||aA>av||aA<ax)},aw=$(this).val();if(!at){aw=parseFloat(aw);if(ay(aw)){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}else{aw=aw.split("-");aw=[parseFloat(aw[0]),parseFloat(aw[1])];if(ay(aw[0])||ay(aw[1])){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}ao.slider((at?"values":"value"),aw);ap.removeClass("input")}}})})};var ad=this;ad.parent_div=$("<div/>").addClass("filter-row slider-row");var ac=$("<div/>").addClass("elt-label").appendTo(ad.parent_div),aj=$("<span/>").addClass("slider-name").text(ad.name+" ").appendTo(ac),ae=$("<span/>").text(this.low+"-"+this.high),af=$("<span/>").addClass("slider-value").appendTo(ac).append("[").append(ae).append("]");ad.values_span=ae;var ai=$("<div/>").addClass("slider").appendTo(ad.parent_div);ad.control_element=$("<div/>").attr("id",ad.name+"-filter-control").appendTo(ai);var ag=[0,0];ad.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(am,an){ad.slide(am,an)},change:function(am,an){ad.control_element.slider("option","slide").call(ad.control_element,am,an)}});ad.slider=ad.control_element;ad.slider_label=ae;ah(af,ae,ad.control_element);var ak=$("<div/>").addClass("display-controls").appendTo(ad.parent_div);this.transparency_icon=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(ad.manager.alpha_filter!==ad){ad.manager.alpha_filter=ad;ad.manager.parent_div.find(".layer-transparent").removeClass("active").hide();ad.transparency_icon.addClass("active").show()}else{ad.manager.alpha_filter=null;ad.transparency_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();this.height_icon=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(ad.manager.height_filter!==ad){ad.manager.height_filter=ad;ad.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();ad.height_icon.addClass("active").show()}else{ad.manager.height_filter=null;ad.height_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();ad.parent_div.hover(function(){ad.transparency_icon.show();ad.height_icon.show()},function(){if(ad.manager.alpha_filter!==ad){ad.transparency_icon.hide()}if(ad.manager.height_filter!==ad){ad.height_icon.hide()}});$("<div style='clear: both;'/>").appendTo(ad.parent_div)};p(S.prototype,{to_dict:function(){var ac=g.prototype.to_dict.call(this);return p(ac,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new S({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ae,ac){var ad=ac-ae;return(ad<=2?0.01:1)},slide:function(ad,ae){var ac=ae.values;this.values_span.text(ac[0]+"-"+ac[1]);this.low=ac[0];this.high=ac[1];this.manager.track.request_draw(true,true)},applies_to:function(ac){if(ac.length>this.index){return true}return false},_keep_val:function(ac){return(isNaN(ac)||(ac>=this.low&&ac<=this.high))},keep:function(ad){if(!this.applies_to(ad)){return true}var af=this;var ag=ad[this.index];if(ag instanceof Array){var ae=true;for(var ac=0;ac<ag.length;ac++){if(!this._keep_val(ag[ac])){ae=false;break}}return ae}else{return this._keep_val(ad[this.index])}},update_attrs:function(af){var ac=false;if(!this.applies_to(af)){return ac}var ad=af[this.index];if(!(ad instanceof Array)){ad=[ad]}for(var ae=0;ae<ad.length;ae++){var ag=ad[ae];if(ag<this.min){this.min=Math.floor(ag);ac=true}if(ag>this.max){this.max=Math.ceil(ag);ac=true}}return ac},update_ui_elt:function(){if(this.min!==this.max){this.parent_div.show()}else{this.parent_div.hide()}var ad=this.slider.slider("option","min"),ac=this.slider.slider("option","max");if(this.min<ad||this.max>ac){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var X=function(ae,ak){this.track=ae;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(am){am.stopPropagation()}).click(function(am){am.stopPropagation()}).bind("dblclick",function(am){am.stopPropagation()}).bind("keydown",function(am){am.stopPropagation()});if(ak&&"filters" in ak){var ac=("alpha_filter" in ak?ak.alpha_filter:null),af=("height_filter" in ak?ak.height_filter:null),ah=ak.filters,ad;for(var ai=0;ai<ah.length;ai++){if(ah[ai].type==="number"){ad=new S(ah[ai]);this.add_filter(ad);if(ad.name===ac){this.alpha_filter=ad;ad.transparency_icon.addClass("active").show()}if(ad.name===af){this.height_filter=ad;ad.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in ak&&ak.visible){this.parent_div.show()}}if(this.filters.length!==0){var al=$("<div/>").addClass("param-row").appendTo(this.parent_div);var aj=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(al);var ag=this;aj.click(function(){ag.run_on_dataset()})}};p(X.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var af={},ae=[],ad;for(var ac=0;ac<this.filters.length;ac++){ad=this.filters[ac];ae.push(ad.to_dict())}af.filters=ae;af.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);af.height_filter=(this.height_filter?this.height_filter.name:null);af.visible=this.parent_div.is(":visible");return af},copy:function(ad){var ae=new X(ad);for(var ac=0;ac<this.filters.length;ac++){ae.add_filter(this.filters[ac].copy())}return ae},add_filter:function(ac){ac.manager=this;this.parent_div.append(ac.parent_div);this.filters.push(ac)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.update_ui_elt()}},clear_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.slider.slider("option","values",[ad.min,ad.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var ak=function(ao,am,an){if(!(am in ao)){ao[am]=an}return ao[am]};var ae={},ac,ad,af;for(var ag=0;ag<this.filters.length;ag++){ac=this.filters[ag];if(ac.tool_id){if(ac.min!==ac.low){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" >= "+ac.low}if(ac.max!==ac.high){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" <= "+ac.high}}}var ai=[];for(var al in ae){ai[ai.length]=[al,ae[al]]}var aj=ai.length;(function ah(at,ap){var an=ap[0],ao=an[0],ar=an[1],aq="("+ar.join(") and (")+")",am={cond:aq,input:at,target_dataset_id:at,tool_id:ao},ap=ap.slice(1);$.getJSON(run_tool_url,am,function(au){if(au.error){show_modal("Filter Dataset","Error running tool "+ao,{Close:hide_modal})}else{if(ap.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ah(au.dataset_id,ap)}}})})(this.track.dataset_id,ai)}});var z=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};z.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var C=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};p(C.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(aj,ag){for(var an=0;an<aj.length;an++){ae=aj[an];if(ae.hidden){continue}var ah="param_"+an;var ar=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ah).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ah).attr("name",ah).attr("checked",ar))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ah).val(ar).click(function(){$(this).select()}))}else{if(ae.type==="select"){var ap=$("<select />").attr("id",ah);for(var al=0;al<ae.options.length;al++){$("<option/>").text(ae.options[al].label).attr("value",ae.options[al].value).appendTo(ap)}ap.val(ar);av.append(ap)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ao=$("<input />").attr("id",ah).attr("name",ah).val(ar).css("float","left").appendTo(au).click(function(ax){$(".tipsy").hide();var aw=$(this).siblings(".tipsy");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),am=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tipsy({gravity:"s"}),aq=$("<div class='tipsy tipsy-west' style='position: absolute;' />").appendTo(au).hide(),ai=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(aq),at=$("<div/>").appendTo(ai),ak=$.farbtastic(at,{width:100,height:100,callback:ao,color:ar});au.append($("<div/>").css("clear","both"));(function(aw){am.click(function(){aw.setColor(get_random_color())})})(ak)}else{av.append($("<input />").attr("id",ah).attr("name",ah).val(ar))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,af,ae,ad,ag){this.track=ac;this.index=af;var ah=this.track._get_tile_bounds(af,ae);this.low=ah[0];this.high=ah[1];this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(ac,af,ae,ad,ag,ah){b.call(this,ac,af,ae,ad,ag);this.max_val=ah};p(k.prototype,b.prototype);var M=function(af,ak,ag,ae,ai,ao,aj,ap,ad,am){b.call(this,af,ak,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(ap){this.has_icons=true;var al=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:A-1,width:ae.width}).prependTo(this.html_elt);var an=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tipsy({gravity:"s"}).appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tipsy({gravity:"s"}).appendTo(message_div);ah.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};p(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var i=function(ad,ac,ae){p(ae,{drag_handle_class:"draghandle"});q.call(this,ad,ac,ae);this.data_url=("data_url" in ae?ae.data_url:default_data_url);this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.dataset_check_url=converted_datasets_state_url;this.data_manager=("data_manager" in ae?ae.data_manager:new P(F,this));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},on_resize:function(){},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof y){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Q){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.tiles_div.children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred();$.getJSON(converted_datasets_state_url,{hda_ldda:ad.hda_ldda,dataset_id:ad.dataset_id,chrom:ad.view.chrom},function(ae){if(!ae||ae==="error"||ae.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ae.message){var af=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ae.message+"</pre>",{Close:hide_modal})});ad.tiles_div.append(af)}}else{if(ae==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(H)}else{if(ae==="no data"||(ae.data!==undefined&&(ae.data===null||ae.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(B)}else{if(ae==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(t);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ae.status==="data"){if(ae.valid_chroms){ad.valid_chroms=ae.valid_chroms;ad.update_icons()}ad.tiles_div.text(V);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){}});var K=function(ae,ad,af){i.call(this,ae,ad,af);var ac=this,ae=ac.view;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new X(this,("filters" in af?af.filters:null));this.filters_available=false;this.tool=("tool" in af&&af.tool?new r(this,af.tool,af.tool_state):null);this.tile_cache=new c(O);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};p(K.prototype,q.prototype,i.prototype,{action_icons_def:i.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tipsy").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();p(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.tile_cache.clear();ac.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show()}else{ac.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_"+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},before_draw:function(){},_draw:function(ad,an){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=Math.pow(RESOLUTION,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(RESOLUTION)));ap=ae/(view.max_high-view.max_low)}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*R)),ak=true,ao=[],ai=function(aq){return(aq&&"track" in aq)};while((ac*R*ag)<ah){var am=this.draw_helper(ad,ae,ac,ag,this.tiles_div,ap);if(ai(am)){ao.push(am)}else{ak=false}ac+=1}if(!an){this.tiles_div.children(".remove").remove()}var af=this;if(ak){this.tiles_div.children(".remove").remove();af.postdraw_actions(ao,ae,ap,an)}},postdraw_actions:function(af,ag,ai,ac){var ae=this;var ah=false;for(var ad=0;ad<af.length;ad++){if(af[ad].has_icons){ah=true;break}}if(ah){for(var ad=0;ad<af.length;ad++){tile=af[ad];if(!tile.has_icons){tile.html_elt.css("padding-top",A)}}}},draw_helper:function(ac,ao,au,ar,ah,ai,ap){var an=this,ax=this._gen_tile_cache_key(ao,ai,au),af=this._get_tile_bounds(au,ar),av=af[0],ad=af[1];if(!ap){ap={}}var aw=(ac?undefined:an.tile_cache.get(ax));if(aw){an.show_tile(aw,ah,ai);return aw}var al=true;var at=an.data_manager.get_data(av,ad,an.mode,ar,an.data_url_extra_params);if(is_deferred(at)){al=false}var aj;if(view.reference_track&&ai>view.canvas_manager.char_width_px){aj=view.reference_track.data_manager.get_data(av,ad,an.mode,ar,view.reference_track.data_url_extra_params);if(is_deferred(aj)){al=false}}if(al){p(at,ap.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),af=an._get_tile_bounds(au,ar),av=af[0],ad=af[1],ao=Math.ceil((ad-av)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ao);ae.width=ao;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var aw=an.draw_tile(at,aq,ak,ar,au,ai,aj);if(aw!==undefined){an.tile_cache.set(ax,aw);an.show_tile(aw,ah,ai)}return aw}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},draw_tile:function(ac,ae,ah,ag,ad,ai,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ag,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var af=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){af-=this.left_offset}ac.css({position:"absolute",top:0,left:af,height:""});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ag.append(ac)}ad.after_show_tile(ae)},after_show_tile:function(ac){},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*R*ad),ag=Math.ceil(R*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return[af,ae]},tool_region_and_parameters_str:function(ae,ac,af){var ad=this,ag=(ae!==undefined&&ac!==undefined&&af!==undefined?ae+":"+ac+"-"+af:"all");return" - region=["+ag+"], parameters=["+ad.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ad=this;var ac=function(){if(ad.data_manager.size()===0){setTimeout(ac,300)}else{ad.data_url=default_data_url;ad.data_query_wait=I;ad.dataset_state_url=converted_datasets_state_url;$.getJSON(ad.dataset_state_url,{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},function(ae){})}};ac()}}});var Y=function(ad,ac){var ae={resize:false};i.call(this,ad,ac,ae);this.container_div.addClass("label-track")};p(Y.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var h=function(ad,ac,ag){K.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=object_from_template(af);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,K.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_group()}}].concat(K.prototype.action_icons_def),to_dict:w.prototype.to_dict,add_drawable:w.prototype.add_drawable,unpack_drawables:w.prototype.unpack_drawables,change_mode:function(ac){K.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(ad,ar,ay,av,aj,al,at){var aq=this,aC=this._gen_tile_cache_key(ar,al,ay),ah=this._get_tile_bounds(ay,av),az=ah[0],ae=ah[1];if(!at){at={}}var aB=(ad?undefined:aq.tile_cache.get(aC));if(aB){aq.show_tile(aB,aj,al);return aB}var ak=[],aq,ao=true,aw,am;for(var ax=0;ax<this.drawables.length;ax++){aq=this.drawables[ax];aw=aq.data_manager.get_data(az,ae,aq.mode,av,aq.data_url_extra_params);if(is_deferred(aw)){ao=false}ak.push(aw);am=null;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(az,ae,aq.mode,av,view.reference_track.data_url_extra_params);if(is_deferred(am)){ao=false}}ak.push(am)}if(ao){p(aw,at.more_tile_data);this.tile_predraw_init();var ag=aq.view.canvas_manager.new_canvas(),ah=aq._get_tile_bounds(ay,av),az=ah[0],ae=ah[1],aA=0,ar=Math.ceil((ae-az)*al)+this.left_offset,ap=0,af=[];var ac=0;for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}af.push(an);ac=aq.get_canvas_height(aw,an,al,ar);if(ac>ap){ap=ac}}ag.width=ar;ag.height=(at.height?at.height:ap);aA=0;var au=ag.getContext("2d");au.translate(this.left_offset,0);au.globalAlpha=0.5;au.globalCompositeOperation="source-over";for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];am=ak[aA+1];aB=aq.draw_tile(aw,au,af[ax],av,ay,al,am)}this.tile_cache.set(aC,aB);this.show_tile(aB,aj,al);return aB}var ai=$.Deferred(),aq=this;$.when.apply($,ak).then(function(){view.request_redraw(false,false,false,aq);ai.resolve()});return ai},show_group:function(){var af=new N(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof j){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){K.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ah,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var y=function(ac){K.call(this,ac,{content_div:ac.top_labeltrack,resize:false},{});ac.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ac.dbkey};this.data_manager=new E(F,this,false)};p(y.prototype,q.prototype,K.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(ak,al,ah,ag,ad,am){var af=this;if(am>this.view.canvas_manager.char_width_px){if(ak.data===null){af.content_div.css("height","0px");return}var ae=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";ak=ak.data;for(var ai=0,aj=ak.length;ai<aj;ai++){var ac=Math.floor(ai*am);al.fillText(ak[ai],ac,10)}return new b(af,ad,ag,ae,ak)}this.content_div.css("height","0px")},after_show_tile:function(ac){if(ac){this.content_div.css("height","12px")}}});var j=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";K.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};p(j.prototype,q.prototype,K.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.data_url,{stats:true,chrom:ac.view.chrom,low:null,high:null,hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min;var ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div/>").text(W(ac.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".tipsy").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=$("<div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".tipsy").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(am,ak,ah,af,ad,al){var ae=ak.canvas,ac=this._get_tile_bounds(ad,af),ag=ac[0],aj=ac[1],ai=new J.LinePainter(am.data,ag,aj,this.prefs,ah);ai.draw(ak,ae.width,ae.height,al);return new b(this,ad,af,ae,am.data)},can_subset:function(ac){return false},});var d=function(ae,ad,af){var ac=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];K.call(this,ae,ad,af);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.tile_cache.clear();ac.set_painter_from_config();ac.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=af.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(d.prototype,q.prototype,K.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},after_show_tile:function(ac){this.max_height_px=Math.max(this.max_height_px,ac.html_elt.height());ac.html_elt.parent().children().css("height",this.max_height_px+"px");var ad=this.max_height_px;if(this.visible_height_px!==0){ad=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ad+"px")},postdraw_actions:function(ar,am,ah,ag){K.prototype.postdraw_actions.call(this,ar,ag);var al=this;if(al.mode==="Histogram"){var ad=-1;for(var ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(var ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){au.html_elt.remove();al.draw_helper(true,am,au.index,au.resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(var ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof k){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=$("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){$(".tipsy").remove();var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanceof M){var ap=true;for(var ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,x,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_summary_tree_data:function(ag,aj,ae,ar){if(ar>ae-aj){ar=ae-aj}var an=Math.floor((ae-aj)/ar),aq=[],af=0;var ah=0,ai=0,am,ap=0,ak=[],ao,al;var ad=function(av,au,aw,at){av[0]=au+aw*at;av[1]=au+(aw+1)*at};while(ap<ar&&ah!==ag.length){var ac=false;for(;ap<ar&&!ac;ap++){ad(ak,aj,ap,an);for(ai=ah;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ac=true;break}}if(ac){break}}data_start_index=ai;aq[aq.length]=ao=[ak[0],0];for(;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ao[1]++}else{break}}if(ao[1]>af){af=ao[1]}ap++}return{max:af,delta:an,data:aq}},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Histogram"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(an,ar,ap,at,ax,aj,ae){var aq=this,ad=ar.canvas,ag=this._get_tile_bounds(ax,at),aA=ag[0],ac=ag[1],aF=25,af=this.left_offset;if(ap==="summary_tree"||ap==="Histogram"){if(an.dataset_type!=="summary_tree"){var ak=this.get_summary_tree_data(an.data,aA,ac,200);if(an.max){ak.max=an.max}an=ak}var aC=new J.SummaryTreePainter(an,aA,ac,this.prefs);aC.draw(ar,ad.width,ad.height,aj);return new k(aq,ax,at,ad,an.data,an.max)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ah=an.data[au];var av=false;var am;for(var az=0,aE=al.length;az<aE;az++){am=al[az];am.update_attrs(ah);if(!am.keep(ah)){av=true;break}}if(!av){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aD=(this.filters_manager.alpha_filter?new z(this.filters_manager.alpha_filter):null);var aB=(this.filters_manager.height_filter?new z(this.filters_manager.height_filter):null);var aC=new (this.painter)(ai,aA,ac,this.prefs,ap,aD,aB,ae);var ay=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ay=aC.draw(ar,ad.width,ad.height,aj,ao);ay.translation=-af}return new M(aq,ax,at,ad,an.data,aj,ap,an.message,all_slotted,ay)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message){return false}return true},});var Q=function(ad,ac,ae){d.call(this,ad,ac,ae);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter};p(Q.prototype,q.prototype,K.prototype,d.prototype);var T=function(ae,ad,ag){d.call(this,ae,ad,ag);var af=get_random_color(),ac=get_random_color([af,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter;this.update_icons()};p(T.prototype,q.prototype,K.prototype,d.prototype);U.View=Z;U.DrawableGroup=N;U.LineTrack=j;U.FeatureTrack=d;U.ReadTrack=T;U.VcfTrack=Q;U.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};l.prototype.draw=function(z,A,y,B){};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(L,z,K,M){var E=this.view_start,N=this.view_end-this.view_start,I=this.data.data,G=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),B=K;delta_x_px=Math.ceil(this.data.delta*M);L.save();for(var C=0,D=I.length;C<D;C++){var H=Math.floor((I[C][0]-E)*M);var F=I[C][1];if(!F){continue}var J=F/G*K;if(F!==0&&J<1){J=1}L.fillStyle=this.prefs.block_color;L.fillRect(H,B-J,delta_x_px,J);var A=4;if(this.prefs.show_counts&&(L.measureText(F).width+A)<delta_x_px){L.fillStyle=this.prefs.label_color;L.textAlign="center";L.fillText(F,H+(delta_x_px/2),10)}}L.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(S,Q,N,D){var I=false,K=this.prefs.min_value,F=this.prefs.max_value,M=F-K,B=N,C=this.view_start,P=this.view_end-this.view_start,L=this.mode,aa=this.data;S.save();var ac=Math.round(N+K/M*N);if(L!=="Intensity"){S.fillStyle="#aaa";S.fillRect(0,ac,Q,1)}S.beginPath();var Y,G,E;if(aa.length>1){E=Math.ceil((aa[1][0]-aa[0][0])*D)}else{E=10}var A=parseInt(this.prefs.color.slice(1),16),H=(A&16711680)>>16,R=(A&65280)>>8,V=A&255;for(var T=0,U=aa.length;T<U;T++){S.fillStyle=S.strokeStyle=this.prefs.color;Y=Math.round((aa[T][0]-C)*D);G=aa[T][1];var W=false,J=false;if(G===null){if(I&&L==="Filled"){S.lineTo(Y,B)}I=false;continue}if(G<K){J=true;G=K}else{if(G>F){W=true;G=F}}if(L==="Histogram"){G=Math.round(G/M*B);S.fillRect(Y,ac,E,-G)}else{if(L==="Intensity"){var z=(G-K)/M,O=Math.round(H+(255-H)*(1-z)),X=Math.round(R+(255-R)*(1-z)),ab=Math.round(V+(255-V)*(1-z));S.fillStyle="rgb("+O+","+X+","+ab+")";S.fillRect(Y,0,E,B)}else{G=Math.round(B-(G-K)/M*B);if(I){S.lineTo(Y,G)}else{I=true;if(L==="Filled"){S.moveTo(Y,B);S.lineTo(Y,G)}else{S.moveTo(Y,G)}}}}S.fillStyle=this.prefs.overflow_color;if(W||J){var Z;if(L==="Histogram"||L==="Intensity"){Z=E}else{Y-=2;Z=4}if(W){S.fillRect(Y,0,Z,3)}if(J){S.fillRect(Y,B-3,Z,3)}}S.fillStyle=this.prefs.color}if(L==="Filled"){if(I){S.lineTo(Y,ac);S.lineTo(0,ac)}S.fill()}else{S.stroke()}S.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,E,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode==="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2]-1,Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-1-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length===1&&D==="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences){if(this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}else{continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai==="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Enable the installation of the emboss_5 repository from the tool shed under the condition that any of its contained tools are defined in a local tool_conf.xml file.
by Bitbucket 21 Mar '12

21 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/79236000c5bd/ changeset: 79236000c5bd user: greg date: 2012-03-21 21:53:26 summary: Enable the installation of the emboss_5 repository from the tool shed under the condition that any of its contained tools are defined in a local tool_conf.xml file. affected #: 2 files diff -r b1d33edc5dffc055867abefa7a666d0957eb0d00 -r 79236000c5bdceaf98546d66f002d5a40b006f74 lib/galaxy/tool_shed/migrate/versions/0002_tools.py --- /dev/null +++ b/lib/galaxy/tool_shed/migrate/versions/0002_tools.py @@ -0,0 +1,17 @@ +""" +The Emboss 5.0.0 tools have been eliminated from the distribution and the Emboss datatypes have been removed from +datatypes_conf.xml.sample. You should remove the Emboss datatypes from your version of datatypes_conf.xml. The +repositories named emboss_5 and emboss_datatypes from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu +will be installed into your local Galaxy instance at the location discussed above by running the following command. + +vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv +sh ./scripts/migrate_tools/0002_tools.sh +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +""" + +import sys + +def upgrade(): + print __doc__ +def downgrade(): + pass diff -r b1d33edc5dffc055867abefa7a666d0957eb0d00 -r 79236000c5bdceaf98546d66f002d5a40b006f74 scripts/migrate_tools/0002_tools.xml --- a/scripts/migrate_tools/0002_tools.xml +++ b/scripts/migrate_tools/0002_tools.xml @@ -1,7 +1,7 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository name="emboss_datatypes" description="Datatypes for Emboss tools" changeset_revision="a89163f31369" /> - <repository name="emboss_5" description="Galaxy wrappers for EMBOSS version 5.0.0 tools" changeset_revision="b94ca591877b"> + <repository name="emboss_5" description="Galaxy wrappers for EMBOSS version 5.0.0 tools" changeset_revision="7334f6d0ac17"><tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" /><tool id="EMBOSS: backtranseq2" version="5.0.0" file="emboss_backtranseq.xml" /><tool id="EMBOSS: banana3" version="5.0.0" file="emboss_banana.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Add a link to the documentation about managing datasets to the disk usage display on the user prefs page.
by Bitbucket 21 Mar '12

21 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b1d33edc5dff/ changeset: b1d33edc5dff user: natefoo date: 2012-03-21 21:52:12 summary: Add a link to the documentation about managing datasets to the disk usage display on the user prefs page. affected #: 1 file diff -r 17ca70b3cc5fdafa895488d3d24a2c89204acd47 -r b1d33edc5dffc055867abefa7a666d0957eb0d00 templates/user/index.mako --- a/templates/user/index.mako +++ b/templates/user/index.mako @@ -37,6 +37,7 @@ %if trans.app.config.enable_quotas: Your disk quota is: <strong>${trans.app.quota_agent.get_quota( trans.user, nice_size=True )}</strong>. %endif + Is your usage more than expected? See the <a href="http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets" target="_blank">documentation</a> for tips on how to find all of the data in your account. </p> %endif %else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Eliminate the commented out emboss 5 tools from tool_conf.xml.sample.
by Bitbucket 21 Mar '12

21 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/17ca70b3cc5f/ changeset: 17ca70b3cc5f user: greg date: 2012-03-21 21:50:37 summary: Eliminate the commented out emboss 5 tools from tool_conf.xml.sample. affected #: 1 file diff -r a4e31b10221d4872a3fff63ee9114df5dfffe023 -r 17ca70b3cc5fdafa895488d3d24a2c89204acd47 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -491,121 +491,4 @@ <tool file="vcf_tools/filter.xml" /><tool file="vcf_tools/extract.xml" /></section> -  - </toolbox> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Eliminate the emboss 5 datatypes from datatypes_conf.xml.sample
by Bitbucket 21 Mar '12

21 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a4e31b10221d/ changeset: a4e31b10221d user: greg date: 2012-03-21 21:47:58 summary: Eliminate the emboss 5 datatypes from datatypes_conf.xml.sample affected #: 1 file diff -r 806f0f2d066d9aa36cdf58aa601b3710d6db8343 -r a4e31b10221d4872a3fff63ee9114df5dfffe023 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -186,104 +186,6 @@ <display file="igv/vcf.xml" /><converter file="vcf_bgzip_to_tabix_converter.xml" target_datatype="tabix"/></datatype> -  - <datatype extension="acedb" type="galaxy.datatypes.data:Text"/> - <datatype extension="asn1" type="galaxy.datatypes.data:Text"/> - <datatype extension="btwisted" type="galaxy.datatypes.data:Text"/> - <datatype extension="cai" type="galaxy.datatypes.data:Text"/> - <datatype extension="charge" type="galaxy.datatypes.data:Text"/> - <datatype extension="checktrans" type="galaxy.datatypes.data:Text"/> - <datatype extension="chips" type="galaxy.datatypes.data:Text"/> - <datatype extension="clustal" type="galaxy.datatypes.data:Text"/> - <datatype extension="codata" type="galaxy.datatypes.data:Text"/> - <datatype extension="codcmp" type="galaxy.datatypes.data:Text"/> - <datatype extension="coderet" type="galaxy.datatypes.data:Text"/> - <datatype extension="compseq" type="galaxy.datatypes.data:Text"/> - <datatype extension="cpgplot" type="galaxy.datatypes.data:Text"/> - <datatype extension="cpgreport" type="galaxy.datatypes.data:Text"/> - <datatype extension="cusp" type="galaxy.datatypes.data:Text"/> - <datatype extension="cut" type="galaxy.datatypes.data:Text"/> - <datatype extension="dan" type="galaxy.datatypes.data:Text"/> - <datatype extension="dbmotif" type="galaxy.datatypes.data:Text"/> - <datatype extension="diffseq" type="galaxy.datatypes.data:Text"/> - <datatype extension="digest" type="galaxy.datatypes.data:Text"/> - <datatype extension="dreg" type="galaxy.datatypes.data:Text"/> - <datatype extension="einverted" type="galaxy.datatypes.data:Text"/> - <datatype extension="embl" type="galaxy.datatypes.data:Text"/> - <datatype extension="epestfind" type="galaxy.datatypes.data:Text"/> - <datatype extension="equicktandem" type="galaxy.datatypes.data:Text"/> - <datatype extension="est2genome" type="galaxy.datatypes.data:Text"/> - <datatype extension="etandem" type="galaxy.datatypes.data:Text"/> - <datatype extension="excel" type="galaxy.datatypes.data:Text"/> - <datatype extension="feattable" type="galaxy.datatypes.data:Text"/> - <datatype extension="fitch" type="galaxy.datatypes.data:Text"/> - <datatype extension="freak" type="galaxy.datatypes.data:Text"/> - <datatype extension="fuzznuc" type="galaxy.datatypes.data:Text"/> - <datatype extension="fuzzpro" type="galaxy.datatypes.data:Text"/> - <datatype extension="fuzztran" type="galaxy.datatypes.data:Text"/> - <datatype extension="garnier" type="galaxy.datatypes.data:Text"/> - <datatype extension="gcg" type="galaxy.datatypes.data:Text"/> - <datatype extension="geecee" type="galaxy.datatypes.data:Text"/> - <datatype extension="genbank" type="galaxy.datatypes.data:Text"/> - <datatype extension="helixturnhelix" type="galaxy.datatypes.data:Text"/> - <datatype extension="hennig86" type="galaxy.datatypes.data:Text"/> - <datatype extension="hmoment" type="galaxy.datatypes.data:Text"/> - <datatype extension="ig" type="galaxy.datatypes.data:Text"/> - <datatype extension="isochore" type="galaxy.datatypes.data:Text"/> - <datatype extension="jackknifer" type="galaxy.datatypes.data:Text"/> - <datatype extension="jackknifernon" type="galaxy.datatypes.data:Text"/> - <datatype extension="markx10" type="galaxy.datatypes.data:Text"/> - <datatype extension="markx1" type="galaxy.datatypes.data:Text"/> - <datatype extension="markx0" type="galaxy.datatypes.data:Text"/> - <datatype extension="markx3" type="galaxy.datatypes.data:Text"/> - <datatype extension="markx2" type="galaxy.datatypes.data:Text"/> - <datatype extension="match" type="galaxy.datatypes.data:Text"/> - <datatype extension="mega" type="galaxy.datatypes.data:Text"/> - <datatype extension="meganon" type="galaxy.datatypes.data:Text"/> - <datatype extension="motif" type="galaxy.datatypes.data:Text"/> - <datatype extension="msf" type="galaxy.datatypes.data:Text"/> - <datatype extension="nametable" type="galaxy.datatypes.data:Text"/> - <datatype extension="ncbi" type="galaxy.datatypes.data:Text"/> - <datatype extension="needle" type="galaxy.datatypes.data:Text"/> - <datatype extension="newcpgreport" type="galaxy.datatypes.data:Text"/> - <datatype extension="newcpgseek" type="galaxy.datatypes.data:Text"/> - <datatype extension="nexus" type="galaxy.datatypes.data:Text"/> - <datatype extension="nexusnon" type="galaxy.datatypes.data:Text"/> - <datatype extension="noreturn" type="galaxy.datatypes.data:Text"/> - <datatype extension="pair" type="galaxy.datatypes.data:Text"/> - <datatype extension="palindrome" type="galaxy.datatypes.data:Text"/> - <datatype extension="pepcoil" type="galaxy.datatypes.data:Text"/> - <datatype extension="pepinfo" type="galaxy.datatypes.data:Text"/> - <datatype extension="pepstats" type="galaxy.datatypes.data:Text"/> - <datatype extension="phylip" type="galaxy.datatypes.data:Text"/> - <datatype extension="phylipnon" type="galaxy.datatypes.data:Text"/> - <datatype extension="pir" type="galaxy.datatypes.data:Text"/> - <datatype extension="polydot" type="galaxy.datatypes.data:Text"/> - <datatype extension="preg" type="galaxy.datatypes.data:Text"/> - <datatype extension="prettyseq" type="galaxy.datatypes.data:Text"/> - <datatype extension="primersearch" type="galaxy.datatypes.data:Text"/> - <datatype extension="regions" type="galaxy.datatypes.data:Text"/> - <datatype extension="score" type="galaxy.datatypes.data:Text"/> - <datatype extension="selex" type="galaxy.datatypes.data:Text"/> - <datatype extension="seqtable" type="galaxy.datatypes.data:Text"/> - <datatype extension="showfeat" type="galaxy.datatypes.data:Text"/> - <datatype extension="showorf" type="galaxy.datatypes.data:Text"/> - <datatype extension="simple" type="galaxy.datatypes.data:Text"/> - <datatype extension="sixpack" type="galaxy.datatypes.data:Text"/> - <datatype extension="srs" type="galaxy.datatypes.data:Text"/> - <datatype extension="srspair" type="galaxy.datatypes.data:Text"/> - <datatype extension="staden" type="galaxy.datatypes.data:Text"/> - <datatype extension="strider" type="galaxy.datatypes.data:Text"/> - <datatype extension="supermatcher" type="galaxy.datatypes.data:Text"/> - <datatype extension="swiss" type="galaxy.datatypes.data:Text"/> - <datatype extension="syco" type="galaxy.datatypes.data:Text"/> - <datatype extension="table" type="galaxy.datatypes.data:Text"/> - <datatype extension="textsearch" type="galaxy.datatypes.data:Text"/> - <datatype extension="vectorstrip" type="galaxy.datatypes.data:Text"/> - <datatype extension="wobble" type="galaxy.datatypes.data:Text"/> - <datatype extension="wordcount" type="galaxy.datatypes.data:Text"/> - <datatype extension="tagseq" type="galaxy.datatypes.data:Text"/> - <datatype extension="affybatch" type="galaxy.datatypes.genetics:Affybatch" display_in_upload="true"/> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Eliminte the emboss_5 tools.
by Bitbucket 21 Mar '12

21 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/806f0f2d066d/ changeset: 806f0f2d066d user: greg date: 2012-03-21 21:46:39 summary: Eliminte the emboss_5 tools. affected #: 113 files Diff too large to display. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Eliminate teh emboss 5 functional test output data since it is now available in the emboss_5 repository in the tool shed.
by Bitbucket 21 Mar '12

21 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4dd1e50e78ef/ changeset: 4dd1e50e78ef user: greg date: 2012-03-21 21:41:45 summary: Eliminate teh emboss 5 functional test output data since it is now available in the emboss_5 repository in the tool shed. affected #: 78 files diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_antigenic_out.tabular --- a/test-data/emboss_antigenic_out.tabular +++ /dev/null @@ -1,23 +0,0 @@ -SeqName Start End Score Strand Max_score_pos -Sequence 196 225 1.340 + 221 -Sequence 253 283 1.263 + 266 -Sequence 27 45 1.241 + 32 -Sequence 60 72 1.236 + 66 -Sequence 357 368 1.214 + 360 -Sequence 130 159 1.191 + 148 -Sequence 83 93 1.186 + 87 -Sequence 165 175 1.147 + 173 -Sequence 6 22 1.147 + 20 -Sequence 293 301 1.147 + 299 -Sequence 324 343 1.147 + 330 -Sequence 473 481 1.142 + 479 -Sequence 540 551 1.119 + 545 -Sequence 501 510 1.114 + 504 -Sequence 409 415 1.097 + 412 -Sequence 48 56 1.097 + 51 -Sequence 553 558 1.092 + 558 -Sequence 106 112 1.087 + 110 -Sequence 488 494 1.075 + 490 -Sequence 423 429 1.075 + 426 -Sequence 118 123 1.070 + 118 -Sequence 239 247 1.042 + 245 diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_backtranseq_out.fasta --- a/test-data/emboss_backtranseq_out.fasta +++ /dev/null @@ -1,30 +0,0 @@ ->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -GGCACCACCTGCGGCGCCACCGGCTGCTGCACCGCCGCCGCCGCCACCGCCTGCTGCACC -ACCTGCACCACCACCACCGGCACCTGCTGCTGCACCGCCTGCGCCTGCGCCGGCGCCTGC -TGCGCCTGCGCCGGCACCACCACCACCTGCTGCACCGCCGCCACCGGCGGCTGCACCACC -ACCGCCTGCGCCTGCTGCGGCGCCTGCACCGCCGGCGCCGCCGCCACCACCTGCACCACC -GGCACCGGCTGCGCCGCCGGCTGCGCCTGCACCGCCGCCACCACCGGCGCCGCCGCCGGC -TGCGGCGGCACCACCGGCGGCTGCTGCACCGCCGGCGCCGGCACCGGCACCACCGCCTGC -TGCGGCGGCACCACCACCGGCACCGCCACCGCCGGCTGCACCGGCGCCGGCTGCGGCTGC -GGCACCTGCACCTGCACCACCGGCTGCTGCTGCACCGGCGCCACCTGCGCCGCCGCCGGC -GGCACCACCTGCGCCACCACCACCACCTGCACCTGCACCGCCTGCACCACCACCGGCGGC -GCCGCCGGCGCCTGCGGCACCACCGGCACCGGCGGCGCCGCCGGCGCCGCCACCGCCTGC -GCCGCCTGCGCCGCCGGCACCGCCTGCGGCGCCGGCACCTGCACCTGCACCTGCTGCTGC -TGCTGCTGCACCGGCGGCACCACCACCGGCTGCACCGGCGCCACCACCGCCTGCACCGGC -GGCGCCACCGCCTGCGCCGGCACCACCGGCACCGCCGCCACCGCCTGCTGCTGCACCACC -TGCGGCTGCGCCGCCTGCGCCTGCTGCGGCTGCGGCACCGCCGCCTGCACCGCCACCTGC -ACCGCCACCGCCACCGGCGCCGCCACCACCGCCACCACCACCACCTGCTGCTGCACCACC -ACCGCCACCACCGCCACCGCCACCGGCACCGCCGGCACCGCCGGCGGCACCACCTGCGGC -ACCTGCACCACCACCGCCGCCACCTGCACCACCTGCTGCACCACCACCGCCGGCTGCGCC -GCCGGCACCTGCACCACCACCACCGCCTGCACCGGCACCACCACCACCTGCGGCGCCTGC -TGCACCTGCGCCGCCACCGGCACCACCTGCGCCACCGGCACCACCTGCACCACCGCCGGC -GGCACCACCGGCACCACCACCACCGGCGGCGCCACCGCCGCCACCGCCACCGGCTGCGGC -GGCACCTGCGCCGGCACCACCACCGCCGCCACCTGCACCACCTGCGGCACCACCGGCACC -ACCACCTGCACCACCTGCACCACCGCCGCCGCCGCCACCGCCACCACCACCGCCACCACC -TGCGCCACCGGCGGCACCACCACCGCCGCCACCACCACCACCACCGGCGGCACCACCACC -GGCACCGCCTGCACCACCGGCACCACCTGCGCCGGCGGCGGCGGCTGCTGCGCCGGCACC -ACCTGCGCCACCACCGCCACCACCACCGCCTGCACCTGCACCGGCACCACCACCGGCACC -GCCACCGCCTGCGCCGGCTGCGCCGGCACCACCTGCACCACCACCACCGCCACCACCACC -ACCACCGCCGGCACCGCCACCGGCGCCACCACCACCACCGCCGCCACCACCACCGCCGCC -GCCGCCTGCGCCGCCACCACCTGCACCGCCGCCACCGGCGGCACCTGCGCCGCCGCCGCC -GCC diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_banana_out.txt --- a/test-data/emboss_banana_out.txt +++ /dev/null @@ -1,562 +0,0 @@ -Base Bend Curve -g 0.0 0.0 -t 10.8 0.0 -t 18.5 0.0 -c 26.9 0.0 -g 22.1 0.0 -a 19.5 0.0 -t 20.7 0.0 -g 26.2 0.0 -c 25.2 0.0 -c 12.5 0.0 -t 6.8 0.0 -a 3.4 0.0 -a 0.0 0.0 -a 1.3 0.0 -a 5.9 0.0 -t 10.6 0.0 -a 14.9 0.0 -c 17.7 0.0 -c 17.3 0.0 -t 13.3 0.0 -t 10.2 23.2 -c 13.9 22.5 -t 8.8 21.7 -t 0.0 20.6 -t 5.7 19.2 -t 13.9 17.7 -g 17.3 16.5 -t 15.1 15.5 -c 16.1 14.7 -c 18.7 13.9 -c 12.5 13.2 -t 9.7 12.5 -a 14.5 11.8 -c 19.1 11.1 -a 19.1 10.6 -c 15.3 10.0 -a 12.2 9.2 -g 14.3 7.9 -a 17.7 6.4 -c 17.7 5.0 -c 19.5 3.5 -a 19.1 2.9 -c 15.3 3.9 -a 16.3 5.5 -g 15.5 6.8 -t 6.3 7.8 -t 0.0 8.5 -t 5.0 9.3 -t 11.0 10.0 -c 15.1 10.8 -c 12.5 11.6 -t 6.8 12.5 -a 4.5 13.4 -a 12.4 14.3 -t 19.7 15.1 -g 25.2 15.7 -g 28.5 16.2 -c 20.7 16.6 -t 8.8 17.0 -t 3.4 17.5 -t 9.3 18.1 -a 14.5 18.5 -c 19.1 18.6 -a 19.5 18.5 -c 16.5 18.3 -c 21.1 18.0 -g 22.3 17.4 -a 18.3 16.3 -c 13.2 15.1 -t 7.2 13.8 -a 9.0 12.6 -g 10.2 11.4 -a 5.0 10.9 -a 1.3 11.0 -a 2.4 11.4 -t 6.1 11.9 -t 10.2 12.3 -c 13.9 12.5 -t 13.9 12.4 -t 13.9 12.4 -g 19.1 12.6 -t 20.5 12.9 -g 19.7 13.2 -c 15.3 13.1 -a 13.9 12.7 -a 20.7 12.2 -g 22.1 11.8 -c 20.5 11.5 -a 20.1 11.3 -c 13.2 10.9 -t 6.8 10.2 -a 4.5 9.6 -a 2.4 9.9 -t 6.7 10.9 -t 14.3 12.1 -g 13.7 13.2 -a 5.0 13.8 -a 8.8 13.6 -a 20.7 12.9 -g 24.5 12.1 -c 19.9 11.3 -g 16.5 10.3 -g 14.9 9.0 -t 11.4 7.5 -t 14.3 6.2 -g 25.2 5.2 -g 32.5 4.4 -c 25.2 4.0 -c 12.5 3.8 -t 7.2 3.4 -a 9.0 2.8 -g 14.3 2.4 -a 18.3 2.5 -g 20.1 2.8 -t 19.1 3.1 -g 14.5 3.2 -t 9.3 3.1 -t 9.3 2.6 -a 14.9 2.5 -c 16.5 2.7 -c 15.3 2.7 -g 16.5 2.6 -g 14.9 2.8 -t 6.3 2.9 -t 5.7 2.8 -t 13.9 2.3 -g 14.5 1.6 -t 10.6 0.6 -a 9.2 0.7 -t 8.2 1.8 -a 16.1 2.7 -g 24.5 3.7 -c 19.1 4.6 -t 15.7 5.6 -g 17.7 6.4 -a 21.1 7.1 -g 24.5 7.7 -c 24.5 8.1 -g 24.5 8.2 -c 21.1 8.0 -g 17.7 7.8 -t 14.3 7.7 -c 14.3 7.7 -t 14.3 7.9 -c 13.9 8.4 -t 13.9 9.1 -t 15.3 10.2 -g 26.2 11.3 -c 26.2 12.2 -c 18.7 12.7 -c 15.7 12.9 -t 15.7 12.9 -g 17.5 12.9 -a 17.3 13.0 -t 17.5 13.2 -c 14.3 13.3 -a 5.7 13.3 -a 8.8 13.2 -a 17.3 13.0 -g 17.7 12.9 -g 14.9 12.7 -t 10.8 12.6 -t 13.7 12.6 -c 19.7 12.6 -a 12.4 12.7 -t 1.3 12.9 -t 0.0 13.1 -t 5.0 13.1 -t 10.2 12.9 -c 14.3 12.6 -t 14.3 12.3 -c 9.0 11.9 -t 9.7 11.6 -a 15.5 11.2 -c 17.9 10.6 -t 8.8 9.9 -t 5.7 9.0 -t 14.3 8.1 -g 15.1 7.4 -g 11.0 6.8 -a 13.3 6.3 -a 13.9 5.9 -g 14.3 5.6 -a 17.7 5.3 -c 17.7 5.1 -g 14.9 5.0 -t 11.4 5.1 -t 13.9 5.2 -g 19.1 5.2 -t 19.5 5.0 -g 15.1 4.9 -g 11.0 4.9 -a 13.3 4.9 -a 13.9 4.9 -g 10.2 5.1 -a 6.1 5.5 -a 5.9 6.3 -t 10.6 7.0 -a 14.5 7.8 -c 13.9 8.4 -a 11.4 8.6 -a 14.5 8.7 -c 13.9 8.8 -a 13.9 8.9 -a 17.9 9.0 -g 15.5 9.0 -t 12.0 8.8 -a 14.9 8.9 -c 22.3 9.1 -g 22.3 9.3 -a 18.3 9.6 -g 18.3 9.9 -t 14.3 10.1 -c 14.3 10.2 -t 14.3 10.5 -c 14.3 11.2 -t 15.1 12.3 -c 16.1 13.4 -c 19.7 14.2 -c 19.7 14.9 -c 19.7 15.1 -c 18.7 15.0 -c 15.7 14.8 -t 15.7 14.4 -g 17.7 14.1 -g 14.9 13.5 -t 6.3 12.9 -t 5.7 12.4 -t 15.3 11.9 -g 22.1 11.5 -c 19.1 11.1 -t 15.7 10.4 -g 17.5 9.4 -a 10.1 8.3 -t 4.5 7.2 -t 9.3 6.2 -a 15.5 5.2 -c 16.3 4.2 -t 15.7 3.2 -g 15.1 2.5 -g 14.9 2.3 -a 13.3 2.9 -t 10.6 3.7 -a 14.5 4.5 -c 15.3 5.3 -a 16.3 6.1 -g 15.5 7.0 -t 11.4 7.5 -t 13.9 7.7 -g 14.5 7.9 -t 9.3 8.3 -a 4.5 8.6 -a 5.9 9.1 -t 10.6 9.7 -a 14.9 10.4 -c 18.7 11.1 -c 18.7 11.7 -c 17.3 12.1 -t 13.3 12.6 -t 18.5 12.9 -c 25.7 12.9 -g 22.1 12.6 -c 15.3 12.2 -a 11.4 11.7 -a 14.5 11.0 -c 19.1 10.3 -a 19.5 9.7 -c 16.5 9.0 -c 19.9 8.1 -g 24.5 7.2 -c 21.1 6.4 -g 14.9 5.5 -t 9.3 4.5 -a 9.3 3.5 -a 15.5 2.5 -c 13.2 1.7 -t 8.2 1.0 -a 13.3 0.8 -t 14.1 1.6 -c 9.0 2.9 -t 8.2 4.5 -a 9.2 6.0 -t 9.2 7.4 -a 15.6 8.8 -t 19.7 10.3 -g 13.7 11.7 -a 6.1 12.9 -a 2.4 14.1 -t 4.5 15.4 -t 7.8 16.6 -a 5.9 17.4 -t 1.3 17.8 -t 0.0 18.0 -t 5.0 18.0 -t 11.0 18.0 -c 16.1 17.9 -c 18.7 17.9 -c 17.3 17.6 -t 8.8 17.4 -t 3.4 17.4 -t 7.8 17.4 -a 5.9 17.5 -t 4.5 17.6 -t 7.8 17.6 -a 9.2 17.8 -t 9.2 18.3 -a 15.6 18.7 -t 19.3 18.8 -g 14.5 18.5 -t 9.7 17.9 -a 13.2 17.3 -g 15.5 16.7 -t 9.7 16.4 -a 12.5 16.0 -g 17.7 15.7 -g 14.9 15.6 -t 10.8 15.7 -t 18.5 15.7 -c 22.3 15.8 -g 17.7 15.6 -t 14.3 15.3 -c 13.9 15.2 -t 8.8 15.3 -t 3.4 15.6 -t 6.4 15.9 -a 4.5 16.4 -a 10.1 17.0 -t 14.1 18.0 -c 13.9 18.9 -t 13.3 19.6 -t 11.0 20.1 -c 15.1 20.5 -c 17.3 20.8 -t 8.8 21.1 -t 3.4 21.3 -t 6.8 21.4 -a 16.1 20.9 -g 22.1 19.9 -c 15.3 18.9 -a 13.9 18.1 -a 17.9 17.4 -g 18.3 16.9 -t 14.3 16.5 -c 13.9 16.5 -t 8.8 16.6 -t 0.0 16.6 -t 3.4 16.6 -t 9.3 16.7 -a 15.5 16.6 -c 16.3 16.4 -t 15.3 16.1 -g 14.5 15.8 -t 6.3 15.5 -t 0.0 15.3 -t 5.0 15.1 -t 18.5 15.2 -c 26.9 15.3 -g 22.3 15.6 -a 17.7 16.2 -c 17.7 16.7 -c 17.7 16.9 -t 17.7 17.1 -c 14.3 17.0 -a 6.7 16.9 -a 12.4 16.5 -t 19.3 16.1 -g 14.5 16.1 -t 10.8 16.2 -t 13.7 16.1 -c 19.7 16.0 -a 21.7 15.7 -t 19.3 15.3 -g 14.5 14.7 -t 10.8 14.3 -t 10.2 14.0 -c 13.9 13.8 -t 11.7 13.5 -t 6.8 12.9 -a 12.5 12.3 -g 17.7 11.7 -g 14.9 11.2 -t 11.4 10.6 -t 13.9 10.3 -g 14.5 10.2 -t 6.3 10.2 -t 0.0 10.2 -t 5.7 10.4 -t 14.3 11.0 -g 15.1 11.5 -g 14.9 11.9 -a 13.3 12.0 -t 7.8 12.0 -a 4.5 12.0 -a 5.9 12.0 -t 9.2 12.1 -a 15.6 12.2 -t 20.7 11.8 -g 22.1 11.3 -c 19.9 10.5 -g 16.5 9.8 -g 17.7 8.9 -t 17.7 7.9 -c 15.7 6.9 -a 16.3 5.8 -g 15.5 5.0 -t 6.3 4.5 -t 3.4 4.5 -t 6.4 5.1 -a 4.5 6.2 -a 10.1 7.8 -t 14.1 9.7 -c 13.9 11.7 -t 13.3 13.4 -t 18.5 14.9 -c 22.3 15.9 -g 14.9 16.5 -t 11.4 16.9 -t 13.9 17.0 -g 14.5 16.8 -t 6.3 16.2 -t 5.0 15.3 -t 10.2 14.0 -c 13.9 12.6 -t 13.3 11.1 -t 10.2 9.7 -c 13.9 8.5 -t 11.7 7.2 -t 6.4 6.1 -a 3.4 5.5 -a 0.0 5.7 -a 1.3 6.7 -a 5.9 7.9 -t 9.2 9.1 -a 5.9 9.8 -t 1.3 10.1 -t 3.4 10.3 -t 7.8 10.7 -a 5.9 11.0 -t 6.1 11.3 -t 13.7 11.4 -c 19.7 11.2 -a 21.7 10.8 -t 19.7 10.4 -g 17.7 10.4 -g 14.9 10.8 -t 6.3 11.3 -t 3.4 11.8 -t 6.4 12.2 -a 4.5 12.6 -a 2.4 12.9 -t 1.3 13.2 -t 0.0 13.3 -t 0.0 13.2 -t 5.7 12.8 -t 14.3 12.3 -g 17.7 12.1 -g 14.9 12.0 -t 6.3 12.0 -t 5.7 12.1 -t 13.9 12.2 -g 14.5 12.3 -t 12.0 12.4 -a 15.5 12.5 -c 17.9 12.9 -t 13.9 13.2 -t 13.9 12.8 -g 14.5 11.9 -t 10.8 10.9 -t 13.7 10.1 -c 15.7 9.7 -a 15.7 9.7 -g 18.7 9.8 -g 19.7 9.7 -g 26.2 9.2 -g 32.5 8.8 -c 25.2 8.6 -c 15.7 8.5 -a 16.3 8.4 -g 15.5 8.4 -t 10.8 8.4 -t 13.7 8.6 -c 19.7 8.8 -a 12.4 8.7 -t 4.5 8.5 -t 7.8 8.1 -a 5.9 7.9 -t 1.3 7.8 -t 3.4 7.8 -t 9.3 7.9 -a 15.5 8.2 -c 18.3 8.5 -t 14.3 8.8 -c 12.2 9.1 -t 15.3 9.2 -g 14.5 9.0 -t 6.3 8.4 -t 5.7 7.5 -t 13.9 6.4 -g 14.5 5.5 -t 10.6 4.9 -a 9.2 4.5 -t 10.6 4.1 -a 14.5 3.8 -c 15.3 3.7 -a 19.1 3.8 -g 22.1 3.9 -c 16.7 4.2 -a 16.3 4.8 -g 15.5 5.6 -t 10.8 6.6 -t 10.2 7.6 -c 13.9 8.6 -t 8.8 9.7 -t 0.0 10.8 -t 3.4 11.8 -t 7.8 12.6 -a 5.9 12.8 -t 1.3 12.4 -t 0.0 11.8 -t 0.0 11.2 -t 3.4 10.6 -t 6.8 9.8 -a 13.2 9.0 -g 15.5 8.2 -t 10.6 7.8 -a 15.6 7.8 -t 19.7 8.2 -g 17.5 8.8 -a 10.1 9.2 -t 1.3 9.3 -t 0.0 9.0 -t 3.4 8.5 -t 6.4 7.9 -a 4.5 7.1 -a 2.4 6.1 -t 1.3 5.0 -t 3.4 3.8 -t 6.4 2.6 -a 3.4 2.4 -a 0.0 90.8 -a 6.3 0.0 -a 14.5 0.0 -c 13.9 0.0 -a 6.7 0.0 -a 2.4 0.0 -t 6.1 0.0 -t 10.2 0.0 -c 9.0 0.0 -t 6.8 0.0 -a 4.5 0.0 -a 12.4 0.0 -t 19.7 0.0 -g 17.7 0.0 -g 17.7 0.0 -t 17.7 0.0 -c 14.3 0.0 -a 5.7 0.0 -a 0.0 0.0 -a 0.0 0.0 -a 0.0 0.0 -a 0.0 0.0 diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_biosed_out.fasta --- a/test-data/emboss_biosed_out.fasta +++ /dev/null @@ -1,11 +0,0 @@ ->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -GTTCGAGTCCTAAAATACCTTCTTTTGTCCCTACACAGACCACAGTTTTCCTAAGTGCTT -TACACCGACTAGAAATTCTTGTGCAAGCACTAATTGAAAGCGGTTGGCCTAGAGTGTTAC -CGGTTTGTATAGCTGAGCGCGTCTCTTGCCCTGATCAAAGGTTCATTTTCTCTACTTTGG -AAGACGTTGTGGAAGAATACAACAAGTACGAGTCTCTCCCCCCTGGTTTGCTGATTACTG -GATACAGTTGTAATACCCTTCGCAACACCGCGTAACTATCTATAGTAATTATTTTCCCTT -TATTATAGTTAGTAGGTTCGTCTTTAATCTTCCTTTAGCAAGTCTTTTACTGTTTTCGAC -CTCAAGTTTCAGTTTCTTAGGTTGTTTTGGATAATAGTCGGTCAGTTTAATCTTCGTTGT -TTCTTCTTAAAATATTTATTCAGTGTTTAATTTTTGGTTTGTACTTGTTCAGGGGCCAGT -TCATTATTTACTCTGTTTGTATACAGCAGTTCTTTTATTTTTAGTAGTATTTTAATTTAA -AACAATTCTAAGTGTCAAAAA diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_btwisted_out.btwisted --- a/test-data/emboss_btwisted_out.btwisted +++ /dev/null @@ -1,7 +0,0 @@ -# Output from BTWISTED -# Twisting calculated from 1 to 561 of Sequence -Total twist (degrees): 19085.5 -Total turns : 53.02 -Average bases per turn: 10.58 -Total stacking energy : -4107.68 -Average stacking energy per dinucleotide: -7.34 diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_cai_out.cai --- a/test-data/emboss_cai_out.cai +++ /dev/null @@ -1,1 +0,0 @@ -Sequence: Sequence CAI: 0.188 \ No newline at end of file diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_charge_out.charge --- a/test-data/emboss_charge_out.charge +++ /dev/null @@ -1,560 +0,0 @@ -CHARGE of Sequence from 1 to 561: window 5 - -Position Residue Charge -1 G 0.000 -2 T 0.000 -3 T 0.000 -4 C 0.000 -5 G 0.000 -6 A 0.000 -7 T 0.000 -8 G 0.000 -9 C 0.000 -10 C 0.000 -11 T 0.000 -12 A 0.000 -13 A 0.000 -14 A 0.000 -15 A 0.000 -16 T 0.000 -17 A 0.000 -18 C 0.000 -19 C 0.000 -20 T 0.000 -21 T 0.000 -22 C 0.000 -23 T 0.000 -24 T 0.000 -25 T 0.000 -26 T 0.000 -27 G 0.000 -28 T 0.000 -29 C 0.000 -30 C 0.000 -31 C 0.000 -32 T 0.000 -33 A 0.000 -34 C 0.000 -35 A 0.000 -36 C 0.000 -37 A 0.000 -38 G 0.000 -39 A 0.000 -40 C 0.000 -41 C 0.000 -42 A 0.000 -43 C 0.000 -44 A 0.000 -45 G 0.000 -46 T 0.000 -47 T 0.000 -48 T 0.000 -49 T 0.000 -50 C 0.000 -51 C 0.000 -52 T 0.000 -53 A 0.000 -54 A 0.000 -55 T 0.000 -56 G 0.000 -57 G 0.000 -58 C 0.000 -59 T 0.000 -60 T 0.000 -61 T 0.000 -62 A 0.000 -63 C 0.000 -64 A 0.000 -65 C 0.000 -66 C 0.000 -67 G 0.000 -68 A 0.000 -69 C 0.000 -70 T 0.000 -71 A 0.000 -72 G 0.000 -73 A 0.000 -74 A 0.000 -75 A 0.000 -76 T 0.000 -77 T 0.000 -78 C 0.000 -79 T 0.000 -80 T 0.000 -81 G 0.000 -82 T 0.000 -83 G 0.000 -84 C 0.000 -85 A 0.000 -86 A 0.000 -87 G 0.000 -88 C 0.000 -89 A 0.000 -90 C 0.000 -91 T 0.000 -92 A 0.000 -93 A 0.000 -94 T 0.000 -95 T 0.000 -96 G 0.000 -97 A 0.000 -98 A 0.000 -99 A 0.000 -100 G 0.000 -101 C 0.000 -102 G 0.000 -103 G 0.000 -104 T 0.000 -105 T 0.000 -106 G 0.000 -107 G 0.000 -108 C 0.000 -109 C 0.000 -110 T 0.000 -111 A 0.000 -112 G 0.000 -113 A 0.000 -114 G 0.000 -115 T 0.000 -116 G 0.000 -117 T 0.000 -118 T 0.000 -119 A 0.000 -120 C 0.000 -121 C 0.000 -122 G 0.000 -123 G 0.000 -124 T 0.000 -125 T 0.000 -126 T 0.000 -127 G 0.000 -128 T 0.000 -129 A 0.000 -130 T 0.000 -131 A 0.000 -132 G 0.000 -133 C 0.000 -134 T 0.000 -135 G 0.000 -136 A 0.000 -137 G 0.000 -138 C 0.000 -139 G 0.000 -140 C 0.000 -141 G 0.000 -142 T 0.000 -143 C 0.000 -144 T 0.000 -145 C 0.000 -146 T 0.000 -147 T 0.000 -148 G 0.000 -149 C 0.000 -150 C 0.000 -151 C 0.000 -152 T 0.000 -153 G 0.000 -154 A 0.000 -155 T 0.000 -156 C 0.000 -157 A 0.000 -158 A 0.000 -159 A 0.000 -160 G 0.000 -161 G 0.000 -162 T 0.000 -163 T 0.000 -164 C 0.000 -165 A 0.000 -166 T 0.000 -167 T 0.000 -168 T 0.000 -169 T 0.000 -170 C 0.000 -171 T 0.000 -172 C 0.000 -173 T 0.000 -174 A 0.000 -175 C 0.000 -176 T 0.000 -177 T 0.000 -178 T 0.000 -179 G 0.000 -180 G 0.000 -181 A 0.000 -182 A 0.000 -183 G 0.000 -184 A 0.000 -185 C 0.000 -186 G 0.000 -187 T 0.000 -188 T 0.000 -189 G 0.000 -190 T 0.000 -191 G 0.000 -192 G 0.000 -193 A 0.000 -194 A 0.000 -195 G 0.000 -196 A 0.000 -197 A 0.000 -198 T 0.000 -199 A 0.000 -200 C 0.000 -201 A 0.000 -202 A 0.000 -203 C 0.000 -204 A 0.000 -205 A 0.000 -206 G 0.000 -207 T 0.000 -208 A 0.000 -209 C 0.000 -210 G 0.000 -211 A 0.000 -212 G 0.000 -213 T 0.000 -214 C 0.000 -215 T 0.000 -216 C 0.000 -217 T 0.000 -218 C 0.000 -219 C 0.000 -220 C 0.000 -221 C 0.000 -222 C 0.000 -223 C 0.000 -224 T 0.000 -225 G 0.000 -226 G 0.000 -227 T 0.000 -228 T 0.000 -229 T 0.000 -230 G 0.000 -231 C 0.000 -232 T 0.000 -233 G 0.000 -234 A 0.000 -235 T 0.000 -236 T 0.000 -237 A 0.000 -238 C 0.000 -239 T 0.000 -240 G 0.000 -241 G 0.000 -242 A 0.000 -243 T 0.000 -244 A 0.000 -245 C 0.000 -246 A 0.000 -247 G 0.000 -248 T 0.000 -249 T 0.000 -250 G 0.000 -251 T 0.000 -252 A 0.000 -253 A 0.000 -254 T 0.000 -255 A 0.000 -256 C 0.000 -257 C 0.000 -258 C 0.000 -259 T 0.000 -260 T 0.000 -261 C 0.000 -262 G 0.000 -263 C 0.000 -264 A 0.000 -265 A 0.000 -266 C 0.000 -267 A 0.000 -268 C 0.000 -269 C 0.000 -270 G 0.000 -271 C 0.000 -272 G 0.000 -273 T 0.000 -274 A 0.000 -275 A 0.000 -276 C 0.000 -277 T 0.000 -278 A 0.000 -279 T 0.000 -280 C 0.000 -281 T 0.000 -282 A 0.000 -283 T 0.000 -284 A 0.000 -285 T 0.000 -286 G 0.000 -287 A 0.000 -288 A 0.000 -289 T 0.000 -290 T 0.000 -291 A 0.000 -292 T 0.000 -293 T 0.000 -294 T 0.000 -295 T 0.000 -296 C 0.000 -297 C 0.000 -298 C 0.000 -299 T 0.000 -300 T 0.000 -301 T 0.000 -302 A 0.000 -303 T 0.000 -304 T 0.000 -305 A 0.000 -306 T 0.000 -307 A 0.000 -308 T 0.000 -309 G 0.000 -310 T 0.000 -311 A 0.000 -312 G 0.000 -313 T 0.000 -314 A 0.000 -315 G 0.000 -316 G 0.000 -317 T 0.000 -318 T 0.000 -319 C 0.000 -320 G 0.000 -321 T 0.000 -322 C 0.000 -323 T 0.000 -324 T 0.000 -325 T 0.000 -326 A 0.000 -327 A 0.000 -328 T 0.000 -329 C 0.000 -330 T 0.000 -331 T 0.000 -332 C 0.000 -333 C 0.000 -334 T 0.000 -335 T 0.000 -336 T 0.000 -337 A 0.000 -338 G 0.000 -339 C 0.000 -340 A 0.000 -341 A 0.000 -342 G 0.000 -343 T 0.000 -344 C 0.000 -345 T 0.000 -346 T 0.000 -347 T 0.000 -348 T 0.000 -349 A 0.000 -350 C 0.000 -351 T 0.000 -352 G 0.000 -353 T 0.000 -354 T 0.000 -355 T 0.000 -356 T 0.000 -357 C 0.000 -358 G 0.000 -359 A 0.000 -360 C 0.000 -361 C 0.000 -362 T 0.000 -363 C 0.000 -364 A 0.000 -365 A 0.000 -366 T 0.000 -367 G 0.000 -368 T 0.000 -369 T 0.000 -370 C 0.000 -371 A 0.000 -372 T 0.000 -373 G 0.000 -374 T 0.000 -375 T 0.000 -376 C 0.000 -377 T 0.000 -378 T 0.000 -379 A 0.000 -380 G 0.000 -381 G 0.000 -382 T 0.000 -383 T 0.000 -384 G 0.000 -385 T 0.000 -386 T 0.000 -387 T 0.000 -388 T 0.000 -389 G 0.000 -390 G 0.000 -391 A 0.000 -392 T 0.000 -393 A 0.000 -394 A 0.000 -395 T 0.000 -396 A 0.000 -397 T 0.000 -398 G 0.000 -399 C 0.000 -400 G 0.000 -401 G 0.000 -402 T 0.000 -403 C 0.000 -404 A 0.000 -405 G 0.000 -406 T 0.000 -407 T 0.000 -408 T 0.000 -409 A 0.000 -410 A 0.000 -411 T 0.000 -412 C 0.000 -413 T 0.000 -414 T 0.000 -415 C 0.000 -416 G 0.000 -417 T 0.000 -418 T 0.000 -419 G 0.000 -420 T 0.000 -421 T 0.000 -422 T 0.000 -423 C 0.000 -424 T 0.000 -425 T 0.000 -426 C 0.000 -427 T 0.000 -428 T 0.000 -429 A 0.000 -430 A 0.000 -431 A 0.000 -432 A 0.000 -433 T 0.000 -434 A 0.000 -435 T 0.000 -436 T 0.000 -437 T 0.000 -438 A 0.000 -439 T 0.000 -440 T 0.000 -441 C 0.000 -442 A 0.000 -443 T 0.000 -444 G 0.000 -445 G 0.000 -446 T 0.000 -447 T 0.000 -448 T 0.000 -449 A 0.000 -450 A 0.000 -451 T 0.000 -452 T 0.000 -453 T 0.000 -454 T 0.000 -455 T 0.000 -456 G 0.000 -457 G 0.000 -458 T 0.000 -459 T 0.000 -460 T 0.000 -461 G 0.000 -462 T 0.000 -463 A 0.000 -464 C 0.000 -465 T 0.000 -466 T 0.000 -467 G 0.000 -468 T 0.000 -469 T 0.000 -470 C 0.000 -471 A 0.000 -472 G 0.000 -473 G 0.000 -474 G 0.000 -475 G 0.000 -476 C 0.000 -477 C 0.000 -478 A 0.000 -479 G 0.000 -480 T 0.000 -481 T 0.000 -482 C 0.000 -483 A 0.000 -484 T 0.000 -485 T 0.000 -486 A 0.000 -487 T 0.000 -488 T 0.000 -489 T 0.000 -490 A 0.000 -491 C 0.000 -492 T 0.000 -493 C 0.000 -494 T 0.000 -495 G 0.000 -496 T 0.000 -497 T 0.000 -498 T 0.000 -499 G 0.000 -500 T 0.000 -501 A 0.000 -502 T 0.000 -503 A 0.000 -504 C 0.000 -505 A 0.000 -506 G 0.000 -507 C 0.000 -508 A 0.000 -509 G 0.000 -510 T 0.000 -511 T 0.000 -512 C 0.000 -513 T 0.000 -514 T 0.000 -515 T 0.000 -516 T 0.000 -517 A 0.000 -518 T 0.000 -519 T 0.000 -520 T 0.000 -521 T 0.000 -522 T 0.000 -523 A 0.000 -524 G 0.000 -525 T 0.000 -526 A 0.000 -527 T 0.000 -528 G 0.000 -529 A 0.000 -530 T 0.000 -531 T 0.000 -532 T 0.000 -533 T 0.000 -534 A 0.000 -535 A 0.000 -536 T 0.000 -537 T 0.000 -538 T 0.000 -539 A 0.000 -540 A 0.000 -541 A 0.000 -542 A 0.000 -543 C 0.000 -544 A 0.000 -545 A 0.000 -546 T 0.000 -547 T 0.000 -548 C 0.000 -549 T 0.000 -550 A 0.000 -551 A 0.000 -552 T 0.000 -553 G 0.000 -554 G 0.000 -555 T 0.000 -556 C 0.000 -557 A 0.000 diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_chips_out.chips --- a/test-data/emboss_chips_out.chips +++ /dev/null @@ -1,3 +0,0 @@ -# CHIPS codon usage statistics - -Nc = 61.000 diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_codcmp_out.codcmp --- a/test-data/emboss_codcmp_out.codcmp +++ /dev/null @@ -1,9 +0,0 @@ -# CODCMP codon usage table comparison -# Ehum.cut vs Eacc.cut - -Sum Squared Difference = 3.044 -Mean Squared Difference = 0.048 -Root Mean Squared Difference = 0.218 -Sum Difference = 11.470 -Mean Difference = 0.179 -Codons not appearing = 0 diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_coderet_out.coderet --- a/test-data/emboss_coderet_out.coderet +++ /dev/null @@ -1,3 +0,0 @@ - CDS mRNA non-c Trans Total Sequence - ===== ===== ===== ===== ===== ======== - 0 0 0 0 0 Sequence diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_compseq_out.compseq --- a/test-data/emboss_compseq_out.compseq +++ /dev/null @@ -1,34 +0,0 @@ -# -# Output from 'compseq' -# -# The Expected frequencies are calculated on the (false) assumption that every -# word has equal frequency. -# -# The input sequences are: -# Sequence - - -Word size 2 -Total count 560 - -# -# Word Obs Count Obs Frequency Exp Frequency Obs/Exp Frequency -# -AA 40 0.0714286 0.0625000 1.1428571 -AC 27 0.0482143 0.0625000 0.7714286 -AG 26 0.0464286 0.0625000 0.7428571 -AT 41 0.0732143 0.0625000 1.1714286 -CA 26 0.0464286 0.0625000 0.7428571 -CC 24 0.0428571 0.0625000 0.6857143 -CG 15 0.0267857 0.0625000 0.4285714 -CT 41 0.0732143 0.0625000 1.1714286 -GA 19 0.0339286 0.0625000 0.5428571 -GC 17 0.0303571 0.0625000 0.4857143 -GG 19 0.0339286 0.0625000 0.5428571 -GT 43 0.0767857 0.0625000 1.2285714 -TA 50 0.0892857 0.0625000 1.4285714 -TC 38 0.0678571 0.0625000 1.0857143 -TG 37 0.0660714 0.0625000 1.0571429 -TT 97 0.1732143 0.0625000 2.7714286 - -Other 0 0.0000000 0.0000000 10000000000.0000000 diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_cpgreport_out1.gff --- a/test-data/emboss_cpgreport_out1.gff +++ /dev/null @@ -1,13 +0,0 @@ -##gff-version 2.0 -##date 2007-10-15 -##Type DNA Sequence -Sequence cpgreport misc_feature 4 5 17.000 + . Sequence "Sequence.1" -Sequence cpgreport misc_feature 66 67 17.000 + . Sequence "Sequence.2" -Sequence cpgreport misc_feature 101 102 17.000 + . Sequence "Sequence.3" -Sequence cpgreport misc_feature 121 141 34.000 + . Sequence "Sequence.4" -Sequence cpgreport misc_feature 185 186 17.000 + . Sequence "Sequence.5" -Sequence cpgreport misc_feature 209 210 17.000 + . Sequence "Sequence.6" -Sequence cpgreport misc_feature 261 272 43.000 + . Sequence "Sequence.7" -Sequence cpgreport misc_feature 319 320 17.000 + . Sequence "Sequence.8" -Sequence cpgreport misc_feature 357 358 17.000 + . Sequence "Sequence.9" -Sequence cpgreport misc_feature 399 416 19.000 + . Sequence "Sequence.10" diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_cpgreport_out2.cpgreport --- a/test-data/emboss_cpgreport_out2.cpgreport +++ /dev/null @@ -1,15 +0,0 @@ - - -CPGREPORT of Sequence from 1 to 561 - -Sequence Begin End Score CpG %CG CG/GC -Sequence 4 5 17 1 100.0 - -Sequence 66 67 17 1 100.0 - -Sequence 101 102 17 1 100.0 - -Sequence 121 141 34 3 57.1 1.00 -Sequence 185 186 17 1 100.0 - -Sequence 209 210 17 1 100.0 - -Sequence 261 272 43 3 75.0 1.00 -Sequence 319 320 17 1 100.0 - -Sequence 357 358 17 1 100.0 - -Sequence 399 416 19 2 44.4 - diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_cusp_out.cusp --- a/test-data/emboss_cusp_out.cusp +++ /dev/null @@ -1,72 +0,0 @@ -#CdsCount: 10 - -#Coding GC 36.36% -#1st letter GC 34.22% -#2nd letter GC 35.29% -#3rd letter GC 39.57% - -#Codon AA Fraction Frequency Number -GCA A 0.200 5.348 1 -GCC A 0.400 10.695 2 -GCG A 0.400 10.695 2 -GCT A 0.000 0.000 0 -TGC C 0.500 21.390 4 -TGT C 0.500 21.390 4 -GAC D 0.667 10.695 2 -GAT D 0.333 5.348 1 -GAA E 0.500 5.348 1 -GAG E 0.500 5.348 1 -TTC F 0.316 32.086 6 -TTT F 0.684 69.519 13 -GGA G 0.000 0.000 0 -GGC G 0.200 5.348 1 -GGG G 0.200 5.348 1 -GGT G 0.600 16.043 3 -CAC H 0.667 10.695 2 -CAT H 0.333 5.348 1 -ATA I 0.429 16.043 3 -ATC I 0.143 5.348 1 -ATT I 0.429 16.043 3 -AAA K 0.600 32.086 6 -AAG K 0.400 21.390 4 -CTA L 0.152 26.738 5 -CTC L 0.061 10.695 2 -CTG L 0.152 26.738 5 -CTT L 0.273 48.128 9 -TTA L 0.182 32.086 6 -TTG L 0.182 32.086 6 -ATG M 1.000 16.043 3 -AAC N 0.286 10.695 2 -AAT N 0.714 26.738 5 -CCA P 0.250 5.348 1 -CCC P 0.500 10.695 2 -CCG P 0.250 5.348 1 -CCT P 0.000 0.000 0 -CAA Q 0.333 5.348 1 -CAG Q 0.667 10.695 2 -AGA R 0.143 5.348 1 -AGG R 0.143 5.348 1 -CGA R 0.143 5.348 1 -CGC R 0.000 0.000 0 -CGG R 0.143 5.348 1 -CGT R 0.429 16.043 3 -AGC S 0.136 16.043 3 -AGT S 0.227 26.738 5 -TCA S 0.136 16.043 3 -TCC S 0.227 26.738 5 -TCG S 0.000 0.000 0 -TCT S 0.273 32.086 6 -ACA T 0.400 21.390 4 -ACC T 0.100 5.348 1 -ACG T 0.200 10.695 2 -ACT T 0.300 16.043 3 -GTA V 0.231 16.043 3 -GTC V 0.000 0.000 0 -GTG V 0.000 0.000 0 -GTT V 0.769 53.476 10 -TGG W 1.000 21.390 4 -TAC Y 0.444 21.390 4 -TAT Y 0.556 26.738 5 -TAA * 0.500 26.738 5 -TAG * 0.400 21.390 4 -TGA * 0.100 5.348 1 diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_cutseq_out.fasta --- a/test-data/emboss_cutseq_out.fasta +++ /dev/null @@ -1,11 +0,0 @@ ->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -ttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggcttt -acaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttacc -ggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgga -agacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactgg -atacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttcccttt -attatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgacc -tcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgtt -tcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagtt -cattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaaa -acaattctaatggtcaaaaa diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_dan_out.png Binary file test-data/emboss_dan_out.png has changed diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_degapseq_out.fasta --- a/test-data/emboss_degapseq_out.fasta +++ /dev/null @@ -1,11 +0,0 @@ ->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt -tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac -cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg -aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg -gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt -tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac -ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt -ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt -tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa -aacaattctaatggtcaaaaa diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_descseq_out.fasta --- a/test-data/emboss_descseq_out.fasta +++ /dev/null @@ -1,11 +0,0 @@ ->Sequencetest 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;test -gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt -tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac -cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg -aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg -gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt -tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac -ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt -ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt -tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa -aacaattctaatggtcaaaaa diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_einverted_out.einverted --- a/test-data/emboss_einverted_out.einverted +++ /dev/null @@ -1,20 +0,0 @@ - -hg17: Score 97: 63/77 ( 81%) matches, 3 gaps - 2684 gtggcaggctcggttcaccaacgtcatttgcagttccccgctttatgttatggg-t--tttgttttgttttgtttttttt 2760 - |||| |||| | |||||| || |||| |||||||||||||| | ||||| | |||||||||||||||||| ||| - 3298 caccatccgtacaaagtggacatagcaaacatcaaggggcgaaatgtactacccaaccaaacaaaacaaaacaaaacaaa 3219 - -hg17: Score 94: 34/36 ( 94%) matches, 0 gaps - 7058 gacacacacacacacacacacacacacacacacaca 7093 - |||||||| ||||||||||| ||||||||||||||| - 7888 ctgtgtgtatgtgtgtgtgtctgtgtgtgtgtgtgt 7853 - -hg17: Score 139: 213/305 ( 69%) matches, 11 gaps - 8604 ggtggctcatgcctgtaatcccagcattttgggaggccgaggcgggtggatcac--gaggtcaggagtttgagaccagcctggccaagatggtgaagcctcgtctctactaaaaatacaaa-aattagccaggt-gcggtg-gtgggcgcctgtatttccagctacccgggaggctgaggaggctgaggcaggagaatcgcttgaacccgggaggcggaggttgcagtgagccgaggtcacgccactgcactctagcctgggcaacagagcaagactccgtcaaaaaaaaaataaaaaaataaaaaaataaaaaaa 8914 - ||||||||| |||| ||||||||| ||||||||||| |||| || ||||| | ||| |||||||| |||||||||||| | | | | | || | |||||| ||||||| ||| || | | | || | | |||| || || | | ||| | || |||||| ||| |||| | || ||| ||| ||| | |||| ||||||||| | |||| || ||||||| |||||| | ||| |||||||| || || ||||| |||| ||||| |||| ||| - 9563 ccaccgagt-cggatattagggtcccgaaaccctccggttccgtcctcctagcgaactcgggtcctcaagttctggtcggacccgctgtgtcgttctggggtagagattttttttatttttatttttatttttatcgactcacaccaccgtttgcgaa-cacca-ggg-tcgatgaaccctccggttccaccctccaaacggactcgggtcctacagctccgacgtcactccatactagtg-tgtcacgtgaggtcggacacactgtgtcgttctggggtag-agaatttttgttttcggttttttctattacttt 9254 - -hg17: Score 202: 70/72 ( 97%) matches, 0 gaps - 18075 tgcattttattctggatggatttgaagcaaagcaccagcttctccaggctctttggggtcagccagggccag 18146 - ||| |||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||| - 18677 acgcaaaataagacctacctaaacttcgtttcgtagtcgaagaggtccgagaaaccccagtcggtcccggtc 18606 diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_epestfind_out.epestfind --- a/test-data/emboss_epestfind_out.epestfind +++ /dev/null @@ -1,41 +0,0 @@ -PEST-find: Finds PEST motifs as potential proteolytic cleavage sites. - - No PEST motif was identified in Sequence from 1 to 561. - - - ---------+---------+---------+---------+---------+---------+ - - 1 GTTCGATGCCTAAAATACCTTCTTTTGTCCCTACACAGACCACAGTTTTCCTAATGGCTT 60 - - - 61 TACACCGACTAGAAATTCTTGTGCAAGCACTAATTGAAAGCGGTTGGCCTAGAGTGTTAC 120 - - - 121 CGGTTTGTATAGCTGAGCGCGTCTCTTGCCCTGATCAAAGGTTCATTTTCTCTACTTTGG 180 - - - 181 AAGACGTTGTGGAAGAATACAACAAGTACGAGTCTCTCCCCCCTGGTTTGCTGATTACTG 240 - - - 241 GATACAGTTGTAATACCCTTCGCAACACCGCGTAACTATCTATATGAATTATTTTCCCTT 300 - - - 301 TATTATATGTAGTAGGTTCGTCTTTAATCTTCCTTTAGCAAGTCTTTTACTGTTTTCGAC 360 - - - 361 CTCAATGTTCATGTTCTTAGGTTGTTTTGGATAATATGCGGTCAGTTTAATCTTCGTTGT 420 - - - 421 TTCTTCTTAAAATATTTATTCATGGTTTAATTTTTGGTTTGTACTTGTTCAGGGGCCAGT 480 - - - 481 TCATTATTTACTCTGTTTGTATACAGCAGTTCTTTTATTTTTAGTATGATTTTAATTTAA 540 - - - 541 AACAATTCTAATGGTCAAAAA 561 - - - Symbols PEST motifs - +++++++ potential - OOOOOOO poor - diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_equicktandem_out.equicktandem --- a/test-data/emboss_equicktandem_out.equicktandem +++ /dev/null @@ -1,16 +0,0 @@ - 22 8881 8915 1 35 - 33 7059 7093 2 17 - 29 7847 7891 2 22 - 27 3213 3248 5 7 - 20 9430 9457 6 4 - 39 19631 19709 36 2 - 39 19851 19927 36 2 - 37 20067 20141 36 2 - 21 19550 19630 60 1 - 21 19770 19850 60 1 - 79 19928 20066 60 2 - 24 8595 8793 133 1 - 26 2844 3045 134 1 - 35 10945 11179 136 1 - 22 15264 15435 138 1 - 29 11181 11429 168 1 diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_est2genome_out.est2genome --- a/test-data/emboss_est2genome_out.est2genome +++ /dev/null @@ -1,1 +0,0 @@ -Note Best alignment is between reversed est and forward genome, and splice sites imply forward gene diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_etandem_out.table --- a/test-data/emboss_etandem_out.table +++ /dev/null @@ -1,2 +0,0 @@ - 24 7847 7886 10 4 92.5 tgtgtgtgtg - 22 7059 7098 10 4 90.0 acacacacac diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_extractseq_out.fasta --- a/test-data/emboss_extractseq_out.fasta +++ /dev/null @@ -1,11 +0,0 @@ ->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt -tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac -cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg -aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg -gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt -tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac -ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt -ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt -tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa -aacaattctaatggtcaaaaa diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_freak_out.freak --- a/test-data/emboss_freak_out.freak +++ /dev/null @@ -1,534 +0,0 @@ -FREAK of Sequence from 1 to 561 Window 30 Step 1 - -1 0.400000 -2 0.400000 -3 0.400000 -4 0.400000 -5 0.400000 -6 0.366667 -7 0.400000 -8 0.400000 -9 0.400000 -10 0.366667 -11 0.366667 -12 0.400000 -13 0.400000 -14 0.433333 -15 0.433333 -16 0.466667 -17 0.466667 -18 0.466667 -19 0.433333 -20 0.400000 -21 0.433333 -22 0.466667 -23 0.433333 -24 0.433333 -25 0.433333 -26 0.433333 -27 0.466667 -28 0.466667 -29 0.500000 -30 0.466667 -31 0.433333 -32 0.400000 -33 0.400000 -34 0.433333 -35 0.400000 -36 0.433333 -37 0.433333 -38 0.466667 -39 0.433333 -40 0.466667 -41 0.433333 -42 0.400000 -43 0.433333 -44 0.400000 -45 0.400000 -46 0.366667 -47 0.366667 -48 0.366667 -49 0.400000 -50 0.400000 -51 0.366667 -52 0.366667 -53 0.366667 -54 0.400000 -55 0.433333 -56 0.433333 -57 0.400000 -58 0.400000 -59 0.400000 -60 0.400000 -61 0.433333 -62 0.433333 -63 0.433333 -64 0.400000 -65 0.400000 -66 0.366667 -67 0.366667 -68 0.333333 -69 0.333333 -70 0.300000 -71 0.333333 -72 0.366667 -73 0.366667 -74 0.400000 -75 0.400000 -76 0.400000 -77 0.433333 -78 0.466667 -79 0.466667 -80 0.500000 -81 0.500000 -82 0.466667 -83 0.500000 -84 0.466667 -85 0.466667 -86 0.466667 -87 0.500000 -88 0.466667 -89 0.433333 -90 0.433333 -91 0.433333 -92 0.466667 -93 0.500000 -94 0.533333 -95 0.533333 -96 0.533333 -97 0.500000 -98 0.533333 -99 0.533333 -100 0.533333 -101 0.500000 -102 0.466667 -103 0.466667 -104 0.466667 -105 0.466667 -106 0.500000 -107 0.466667 -108 0.466667 -109 0.466667 -110 0.466667 -111 0.500000 -112 0.533333 -113 0.500000 -114 0.533333 -115 0.500000 -116 0.533333 -117 0.500000 -118 0.500000 -119 0.533333 -120 0.566667 -121 0.566667 -122 0.566667 -123 0.533333 -124 0.533333 -125 0.533333 -126 0.533333 -127 0.566667 -128 0.533333 -129 0.533333 -130 0.533333 -131 0.566667 -132 0.600000 -133 0.566667 -134 0.533333 -135 0.566667 -136 0.533333 -137 0.533333 -138 0.500000 -139 0.466667 -140 0.433333 -141 0.433333 -142 0.400000 -143 0.433333 -144 0.400000 -145 0.400000 -146 0.400000 -147 0.400000 -148 0.400000 -149 0.366667 -150 0.366667 -151 0.366667 -152 0.333333 -153 0.333333 -154 0.333333 -155 0.333333 -156 0.366667 -157 0.366667 -158 0.366667 -159 0.366667 -160 0.400000 -161 0.366667 -162 0.366667 -163 0.400000 -164 0.400000 -165 0.366667 -166 0.400000 -167 0.400000 -168 0.400000 -169 0.400000 -170 0.400000 -171 0.400000 -172 0.400000 -173 0.366667 -174 0.400000 -175 0.400000 -176 0.366667 -177 0.400000 -178 0.400000 -179 0.400000 -180 0.400000 -181 0.400000 -182 0.400000 -183 0.433333 -184 0.400000 -185 0.433333 -186 0.400000 -187 0.400000 -188 0.400000 -189 0.433333 -190 0.433333 -191 0.466667 -192 0.466667 -193 0.466667 -194 0.500000 -195 0.500000 -196 0.500000 -197 0.533333 -198 0.533333 -199 0.533333 -200 0.533333 -201 0.533333 -202 0.566667 -203 0.566667 -204 0.566667 -205 0.566667 -206 0.566667 -207 0.533333 -208 0.533333 -209 0.566667 -210 0.533333 -211 0.533333 -212 0.566667 -213 0.533333 -214 0.533333 -215 0.500000 -216 0.533333 -217 0.500000 -218 0.533333 -219 0.500000 -220 0.466667 -221 0.466667 -222 0.433333 -223 0.400000 -224 0.366667 -225 0.366667 -226 0.333333 -227 0.333333 -228 0.366667 -229 0.400000 -230 0.400000 -231 0.366667 -232 0.366667 -233 0.400000 -234 0.400000 -235 0.400000 -236 0.400000 -237 0.433333 -238 0.433333 -239 0.433333 -240 0.466667 -241 0.466667 -242 0.466667 -243 0.500000 -244 0.500000 -245 0.500000 -246 0.466667 -247 0.500000 -248 0.466667 -249 0.466667 -250 0.466667 -251 0.466667 -252 0.466667 -253 0.466667 -254 0.466667 -255 0.466667 -256 0.466667 -257 0.466667 -258 0.433333 -259 0.400000 -260 0.400000 -261 0.400000 -262 0.366667 -263 0.333333 -264 0.300000 -265 0.300000 -266 0.300000 -267 0.300000 -268 0.333333 -269 0.333333 -270 0.300000 -271 0.266667 -272 0.233333 -273 0.200000 -274 0.200000 -275 0.200000 -276 0.200000 -277 0.166667 -278 0.166667 -279 0.166667 -280 0.200000 -281 0.166667 -282 0.166667 -283 0.200000 -284 0.200000 -285 0.200000 -286 0.233333 -287 0.233333 -288 0.233333 -289 0.233333 -290 0.266667 -291 0.300000 -292 0.300000 -293 0.333333 -294 0.333333 -295 0.333333 -296 0.333333 -297 0.300000 -298 0.266667 -299 0.233333 -300 0.266667 -301 0.266667 -302 0.266667 -303 0.300000 -304 0.333333 -305 0.333333 -306 0.333333 -307 0.333333 -308 0.333333 -309 0.366667 -310 0.366667 -311 0.366667 -312 0.366667 -313 0.366667 -314 0.366667 -315 0.400000 -316 0.366667 -317 0.333333 -318 0.333333 -319 0.333333 -320 0.300000 -321 0.300000 -322 0.300000 -323 0.300000 -324 0.300000 -325 0.300000 -326 0.300000 -327 0.300000 -328 0.333333 -329 0.366667 -330 0.333333 -331 0.366667 -332 0.400000 -333 0.366667 -334 0.366667 -335 0.366667 -336 0.366667 -337 0.366667 -338 0.400000 -339 0.366667 -340 0.333333 -341 0.366667 -342 0.366667 -343 0.333333 -344 0.366667 -345 0.333333 -346 0.333333 -347 0.366667 -348 0.366667 -349 0.366667 -350 0.366667 -351 0.366667 -352 0.400000 -353 0.366667 -354 0.366667 -355 0.400000 -356 0.400000 -357 0.400000 -358 0.366667 -359 0.333333 -360 0.366667 -361 0.366667 -362 0.333333 -363 0.333333 -364 0.300000 -365 0.300000 -366 0.300000 -367 0.300000 -368 0.266667 -369 0.300000 -370 0.333333 -371 0.333333 -372 0.366667 -373 0.366667 -374 0.366667 -375 0.366667 -376 0.400000 -377 0.366667 -378 0.366667 -379 0.366667 -380 0.366667 -381 0.333333 -382 0.300000 -383 0.333333 -384 0.333333 -385 0.300000 -386 0.333333 -387 0.366667 -388 0.366667 -389 0.366667 -390 0.366667 -391 0.333333 -392 0.333333 -393 0.333333 -394 0.366667 -395 0.366667 -396 0.366667 -397 0.400000 -398 0.400000 -399 0.366667 -400 0.333333 -401 0.300000 -402 0.266667 -403 0.266667 -404 0.233333 -405 0.233333 -406 0.200000 -407 0.200000 -408 0.200000 -409 0.200000 -410 0.200000 -411 0.200000 -412 0.233333 -413 0.200000 -414 0.200000 -415 0.233333 -416 0.233333 -417 0.200000 -418 0.200000 -419 0.200000 -420 0.166667 -421 0.166667 -422 0.166667 -423 0.166667 -424 0.133333 -425 0.133333 -426 0.133333 -427 0.133333 -428 0.166667 -429 0.166667 -430 0.166667 -431 0.166667 -432 0.200000 -433 0.200000 -434 0.200000 -435 0.233333 -436 0.233333 -437 0.233333 -438 0.266667 -439 0.266667 -440 0.266667 -441 0.300000 -442 0.266667 -443 0.300000 -444 0.333333 -445 0.333333 -446 0.333333 -447 0.366667 -448 0.400000 -449 0.400000 -450 0.433333 -451 0.433333 -452 0.433333 -453 0.466667 -454 0.466667 -455 0.466667 -456 0.466667 -457 0.433333 -458 0.400000 -459 0.400000 -460 0.400000 -461 0.400000 -462 0.400000 -463 0.400000 -464 0.433333 -465 0.400000 -466 0.433333 -467 0.433333 -468 0.400000 -469 0.400000 -470 0.433333 -471 0.400000 -472 0.400000 -473 0.366667 -474 0.333333 -475 0.333333 -476 0.300000 -477 0.300000 -478 0.300000 -479 0.300000 -480 0.300000 -481 0.300000 -482 0.300000 -483 0.300000 -484 0.300000 -485 0.300000 -486 0.300000 -487 0.300000 -488 0.300000 -489 0.300000 -490 0.300000 -491 0.300000 -492 0.266667 -493 0.266667 -494 0.233333 -495 0.266667 -496 0.233333 -497 0.233333 -498 0.233333 -499 0.266667 -500 0.233333 -501 0.233333 -502 0.233333 -503 0.233333 -504 0.233333 -505 0.200000 -506 0.200000 -507 0.166667 -508 0.133333 -509 0.133333 -510 0.100000 -511 0.100000 -512 0.100000 -513 0.066667 -514 0.100000 -515 0.100000 -516 0.100000 -517 0.100000 -518 0.100000 -519 0.133333 -520 0.133333 -521 0.133333 -522 0.133333 -523 0.133333 -524 0.166667 -525 0.166667 -526 0.166667 -527 0.200000 -528 0.200000 -529 0.166667 -530 0.166667 -531 0.166667 -532 0.166667 diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_fuzznuc_out.tabular --- a/test-data/emboss_fuzznuc_out.tabular +++ /dev/null @@ -1,41 +0,0 @@ -SeqName Start End Score Strand Pattern_name Mismatch -Sequence 12 13 2 + pattern1 . -Sequence 13 14 2 + pattern1 . -Sequence 14 15 2 + pattern1 . -Sequence 53 54 2 + pattern1 . -Sequence 73 74 2 + pattern1 . -Sequence 74 75 2 + pattern1 . -Sequence 85 86 2 + pattern1 . -Sequence 92 93 2 + pattern1 . -Sequence 97 98 2 + pattern1 . -Sequence 98 99 2 + pattern1 . -Sequence 157 158 2 + pattern1 . -Sequence 158 159 2 + pattern1 . -Sequence 181 182 2 + pattern1 . -Sequence 193 194 2 + pattern1 . -Sequence 196 197 2 + pattern1 . -Sequence 201 202 2 + pattern1 . -Sequence 204 205 2 + pattern1 . -Sequence 252 253 2 + pattern1 . -Sequence 264 265 2 + pattern1 . -Sequence 274 275 2 + pattern1 . -Sequence 287 288 2 + pattern1 . -Sequence 326 327 2 + pattern1 . -Sequence 340 341 2 + pattern1 . -Sequence 364 365 2 + pattern1 . -Sequence 393 394 2 + pattern1 . -Sequence 409 410 2 + pattern1 . -Sequence 429 430 2 + pattern1 . -Sequence 430 431 2 + pattern1 . -Sequence 431 432 2 + pattern1 . -Sequence 449 450 2 + pattern1 . -Sequence 534 535 2 + pattern1 . -Sequence 539 540 2 + pattern1 . -Sequence 540 541 2 + pattern1 . -Sequence 541 542 2 + pattern1 . -Sequence 544 545 2 + pattern1 . -Sequence 550 551 2 + pattern1 . -Sequence 557 558 2 + pattern1 . -Sequence 558 559 2 + pattern1 . -Sequence 559 560 2 + pattern1 . -Sequence 560 561 2 + pattern1 . diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_fuzzpro_out.tabular --- a/test-data/emboss_fuzzpro_out.tabular +++ /dev/null @@ -1,41 +0,0 @@ -SeqName Start End Score Strand Pattern_name Mismatch -Sequence 12 13 2 + pattern1 . -Sequence 13 14 2 + pattern1 . -Sequence 14 15 2 + pattern1 . -Sequence 53 54 2 + pattern1 . -Sequence 73 74 2 + pattern1 . -Sequence 74 75 2 + pattern1 . -Sequence 85 86 2 + pattern1 . -Sequence 92 93 2 + pattern1 . -Sequence 97 98 2 + pattern1 . -Sequence 98 99 2 + pattern1 . -Sequence 157 158 2 + pattern1 . -Sequence 158 159 2 + pattern1 . -Sequence 181 182 2 + pattern1 . -Sequence 193 194 2 + pattern1 . -Sequence 196 197 2 + pattern1 . -Sequence 201 202 2 + pattern1 . -Sequence 204 205 2 + pattern1 . -Sequence 252 253 2 + pattern1 . -Sequence 264 265 2 + pattern1 . -Sequence 274 275 2 + pattern1 . -Sequence 287 288 2 + pattern1 . -Sequence 326 327 2 + pattern1 . -Sequence 340 341 2 + pattern1 . -Sequence 364 365 2 + pattern1 . -Sequence 393 394 2 + pattern1 . -Sequence 409 410 2 + pattern1 . -Sequence 429 430 2 + pattern1 . -Sequence 430 431 2 + pattern1 . -Sequence 431 432 2 + pattern1 . -Sequence 449 450 2 + pattern1 . -Sequence 534 535 2 + pattern1 . -Sequence 539 540 2 + pattern1 . -Sequence 540 541 2 + pattern1 . -Sequence 541 542 2 + pattern1 . -Sequence 544 545 2 + pattern1 . -Sequence 550 551 2 + pattern1 . -Sequence 557 558 2 + pattern1 . -Sequence 558 559 2 + pattern1 . -Sequence 559 560 2 + pattern1 . -Sequence 560 561 2 + pattern1 . diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_fuzztran_out.tabular --- a/test-data/emboss_fuzztran_out.tabular +++ /dev/null @@ -1,133 +0,0 @@ -SeqName Start End Score Strand Pattern_name Mismatch Frame PStart PEnd Translation -hg17 3958 3963 2 + pattern1 . 1 1320 1321 AA -hg17 3961 3966 2 + pattern1 . 1 1321 1322 AA -hg17 4099 4104 2 + pattern1 . 1 1367 1368 AA -hg17 4315 4320 2 + pattern1 . 1 1439 1440 AA -hg17 5194 5199 2 + pattern1 . 1 1732 1733 AA -hg17 8584 8589 2 + pattern1 . 1 2862 2863 AA -hg17 9232 9237 2 + pattern1 . 1 3078 3079 AA -hg17 9343 9348 2 + pattern1 . 1 3115 3116 AA -hg17 9715 9720 2 + pattern1 . 1 3239 3240 AA -hg17 9769 9774 2 + pattern1 . 1 3257 3258 AA -hg17 9841 9846 2 + pattern1 . 1 3281 3282 AA -hg17 9994 9999 2 + pattern1 . 1 3332 3333 AA -hg17 10045 10050 2 + pattern1 . 1 3349 3350 AA -hg17 10048 10053 2 + pattern1 . 1 3350 3351 AA -hg17 12157 12162 2 + pattern1 . 1 4053 4054 AA -hg17 12487 12492 2 + pattern1 . 1 4163 4164 AA -hg17 12688 12693 2 + pattern1 . 1 4230 4231 AA -hg17 12691 12696 2 + pattern1 . 1 4231 4232 AA -hg17 15010 15015 2 + pattern1 . 1 5004 5005 AA -hg17 17521 17526 2 + pattern1 . 1 5841 5842 AA -hg17 17551 17556 2 + pattern1 . 1 5851 5852 AA -hg17 1148 1153 2 + pattern1 . 2 383 384 AA -hg17 2078 2083 2 + pattern1 . 2 693 694 AA -hg17 2432 2437 2 + pattern1 . 2 811 812 AA -hg17 3080 3085 2 + pattern1 . 2 1027 1028 AA -hg17 3593 3598 2 + pattern1 . 2 1198 1199 AA -hg17 3692 3697 2 + pattern1 . 2 1231 1232 AA -hg17 4055 4060 2 + pattern1 . 2 1352 1353 AA -hg17 5018 5023 2 + pattern1 . 2 1673 1674 AA -hg17 5147 5152 2 + pattern1 . 2 1716 1717 AA -hg17 8276 8281 2 + pattern1 . 2 2759 2760 AA -hg17 9587 9592 2 + pattern1 . 2 3196 3197 AA -hg17 9668 9673 2 + pattern1 . 2 3223 3224 AA -hg17 9920 9925 2 + pattern1 . 2 3307 3308 AA -hg17 9971 9976 2 + pattern1 . 2 3324 3325 AA -hg17 10112 10117 2 + pattern1 . 2 3371 3372 AA -hg17 10115 10120 2 + pattern1 . 2 3372 3373 AA -hg17 11837 11842 2 + pattern1 . 2 3946 3947 AA -hg17 12026 12031 2 + pattern1 . 2 4009 4010 AA -hg17 12944 12949 2 + pattern1 . 2 4315 4316 AA -hg17 12953 12958 2 + pattern1 . 2 4318 4319 AA -hg17 13229 13234 2 + pattern1 . 2 4410 4411 AA -hg17 13232 13237 2 + pattern1 . 2 4411 4412 AA -hg17 15356 15361 2 + pattern1 . 2 5119 5120 AA -hg17 15482 15487 2 + pattern1 . 2 5161 5162 AA -hg17 16061 16066 2 + pattern1 . 2 5354 5355 AA -hg17 17822 17827 2 + pattern1 . 2 5941 5942 AA -hg17 15 20 2 + pattern1 . 3 5 6 AA -hg17 33 38 2 + pattern1 . 3 11 12 AA -hg17 3669 3674 2 + pattern1 . 3 1223 1224 AA -hg17 3759 3764 2 + pattern1 . 3 1253 1254 AA -hg17 5646 5651 2 + pattern1 . 3 1882 1883 AA -hg17 5847 5852 2 + pattern1 . 3 1949 1950 AA -hg17 5850 5855 2 + pattern1 . 3 1950 1951 AA -hg17 5853 5858 2 + pattern1 . 3 1951 1952 AA -hg17 7674 7679 2 + pattern1 . 3 2558 2559 AA -hg17 9699 9704 2 + pattern1 . 3 3233 3234 AA -hg17 9891 9896 2 + pattern1 . 3 3297 3298 AA -hg17 10074 10079 2 + pattern1 . 3 3358 3359 AA -hg17 10407 10412 2 + pattern1 . 3 3469 3470 AA -hg17 12675 12680 2 + pattern1 . 3 4225 4226 AA -hg17 13746 13751 2 + pattern1 . 3 4582 4583 AA -hg17 17115 17120 2 + pattern1 . 3 5705 5706 AA -hg17 17421 17426 2 + pattern1 . 3 5807 5808 AA -hg17 19122 19127 2 + pattern1 . 3 6374 6375 AA -hg17 19353 19358 2 + pattern1 . 3 6451 6452 AA -hg17 -2312 -2317 2 - pattern1 . 1 772 773 AA -hg17 -4073 -4078 2 - pattern1 . 1 1359 1360 AA -hg17 -4652 -4657 2 - pattern1 . 1 1552 1553 AA -hg17 -4778 -4783 2 - pattern1 . 1 1594 1595 AA -hg17 -6902 -6907 2 - pattern1 . 1 2302 2303 AA -hg17 -6905 -6910 2 - pattern1 . 1 2303 2304 AA -hg17 -7181 -7186 2 - pattern1 . 1 2395 2396 AA -hg17 -7190 -7195 2 - pattern1 . 1 2398 2399 AA -hg17 -8108 -8113 2 - pattern1 . 1 2704 2705 AA -hg17 -8297 -8302 2 - pattern1 . 1 2767 2768 AA -hg17 -10019 -10024 2 - pattern1 . 1 3341 3342 AA -hg17 -10022 -10027 2 - pattern1 . 1 3342 3343 AA -hg17 -10163 -10168 2 - pattern1 . 1 3389 3390 AA -hg17 -10214 -10219 2 - pattern1 . 1 3406 3407 AA -hg17 -10466 -10471 2 - pattern1 . 1 3490 3491 AA -hg17 -10547 -10552 2 - pattern1 . 1 3517 3518 AA -hg17 -11858 -11863 2 - pattern1 . 1 3954 3955 AA -hg17 -14987 -14992 2 - pattern1 . 1 4997 4998 AA -hg17 -15116 -15121 2 - pattern1 . 1 5040 5041 AA -hg17 -16079 -16084 2 - pattern1 . 1 5361 5362 AA -hg17 -16442 -16447 2 - pattern1 . 1 5482 5483 AA -hg17 -16541 -16546 2 - pattern1 . 1 5515 5516 AA -hg17 -17054 -17059 2 - pattern1 . 1 5686 5687 AA -hg17 -17702 -17707 2 - pattern1 . 1 5902 5903 AA -hg17 -18056 -18061 2 - pattern1 . 1 6020 6021 AA -hg17 -18986 -18991 2 - pattern1 . 1 6330 6331 AA -hg17 -783 -788 2 - pattern1 . 2 262 263 AA -hg17 -1014 -1019 2 - pattern1 . 2 339 340 AA -hg17 -2715 -2720 2 - pattern1 . 2 906 907 AA -hg17 -3021 -3026 2 - pattern1 . 2 1008 1009 AA -hg17 -6390 -6395 2 - pattern1 . 2 2131 2132 AA -hg17 -7461 -7466 2 - pattern1 . 2 2488 2489 AA -hg17 -9729 -9734 2 - pattern1 . 2 3244 3245 AA -hg17 -10062 -10067 2 - pattern1 . 2 3355 3356 AA -hg17 -10245 -10250 2 - pattern1 . 2 3416 3417 AA -hg17 -10437 -10442 2 - pattern1 . 2 3480 3481 AA -hg17 -12462 -12467 2 - pattern1 . 2 4155 4156 AA -hg17 -14283 -14288 2 - pattern1 . 2 4762 4763 AA -hg17 -14286 -14291 2 - pattern1 . 2 4763 4764 AA -hg17 -14289 -14294 2 - pattern1 . 2 4764 4765 AA -hg17 -14490 -14495 2 - pattern1 . 2 4831 4832 AA -hg17 -16377 -16382 2 - pattern1 . 2 5460 5461 AA -hg17 -16467 -16472 2 - pattern1 . 2 5490 5491 AA -hg17 -20103 -20108 2 - pattern1 . 2 6702 6703 AA -hg17 -20121 -20126 2 - pattern1 . 2 6708 6709 AA -hg17 17553 17548 2 - pattern1 . 3 863 864 AA -hg17 17523 17518 2 - pattern1 . 3 873 874 AA -hg17 15012 15007 2 - pattern1 . 3 1710 1711 AA -hg17 12693 12688 2 - pattern1 . 3 2483 2484 AA -hg17 12690 12685 2 - pattern1 . 3 2484 2485 AA -hg17 12489 12484 2 - pattern1 . 3 2551 2552 AA -hg17 12159 12154 2 - pattern1 . 3 2661 2662 AA -hg17 10050 10045 2 - pattern1 . 3 3364 3365 AA -hg17 10047 10042 2 - pattern1 . 3 3365 3366 AA -hg17 9996 9991 2 - pattern1 . 3 3382 3383 AA -hg17 9843 9838 2 - pattern1 . 3 3433 3434 AA -hg17 9771 9766 2 - pattern1 . 3 3457 3458 AA -hg17 9717 9712 2 - pattern1 . 3 3475 3476 AA -hg17 9345 9340 2 - pattern1 . 3 3599 3600 AA -hg17 9234 9229 2 - pattern1 . 3 3636 3637 AA -hg17 8586 8581 2 - pattern1 . 3 3852 3853 AA -hg17 5196 5191 2 - pattern1 . 3 4982 4983 AA -hg17 4317 4312 2 - pattern1 . 3 5275 5276 AA -hg17 4101 4096 2 - pattern1 . 3 5347 5348 AA -hg17 3963 3958 2 - pattern1 . 3 5393 5394 AA -hg17 3960 3955 2 - pattern1 . 3 5394 5395 AA diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_garnier_out.tabular --- a/test-data/emboss_garnier_out.tabular +++ /dev/null @@ -1,102 +0,0 @@ -SeqName Start End Score Strand helix sheet turns coil -Sequence 1 9 0.000 + . . T . -Sequence 10 10 0.000 + . E . . -Sequence 11 16 0.000 + H . . . -Sequence 17 39 0.000 + . . T . -Sequence 40 40 0.000 + H . . . -Sequence 41 42 0.000 + . E . . -Sequence 43 48 0.000 + . . T . -Sequence 49 52 0.000 + . E . . -Sequence 53 68 0.000 + . . T . -Sequence 69 75 0.000 + H . . . -Sequence 76 78 0.000 + . E . . -Sequence 79 87 0.000 + . . T . -Sequence 88 90 0.000 + . E . . -Sequence 91 96 0.000 + H . . . -Sequence 97 98 0.000 + . E . . -Sequence 99 99 0.000 + . . . C -Sequence 100 107 0.000 + . . T . -Sequence 108 111 0.000 + . E . . -Sequence 112 116 0.000 + . . T . -Sequence 117 120 0.000 + . E . . -Sequence 121 123 0.000 + . . T . -Sequence 124 126 0.000 + . . . C -Sequence 127 131 0.000 + . E . . -Sequence 132 153 0.000 + . . T . -Sequence 154 157 0.000 + . E . . -Sequence 158 161 0.000 + . . T . -Sequence 162 162 0.000 + . . . C -Sequence 163 164 0.000 + . E . . -Sequence 165 172 0.000 + . . T . -Sequence 173 176 0.000 + . E . . -Sequence 177 180 0.000 + . . T . -Sequence 181 183 0.000 + . . . C -Sequence 184 187 0.000 + . E . . -Sequence 188 194 0.000 + . . . C -Sequence 195 206 0.000 + H . . . -Sequence 207 234 0.000 + . . T . -Sequence 235 237 0.000 + . E . . -Sequence 238 241 0.000 + . . T . -Sequence 242 242 0.000 + . . . C -Sequence 243 246 0.000 + . E . . -Sequence 247 247 0.000 + . . T . -Sequence 248 249 0.000 + . . . C -Sequence 250 275 0.000 + . . T . -Sequence 276 282 0.000 + . E . . -Sequence 283 283 0.000 + H . . . -Sequence 284 289 0.000 + . . . C -Sequence 290 301 0.000 + . . T . -Sequence 302 307 0.000 + . E . . -Sequence 308 313 0.000 + . . . C -Sequence 314 321 0.000 + . . T . -Sequence 322 322 0.000 + . E . . -Sequence 323 344 0.000 + . . T . -Sequence 345 348 0.000 + . E . . -Sequence 349 360 0.000 + . . T . -Sequence 361 363 0.000 + . E . . -Sequence 364 374 0.000 + . . T . -Sequence 375 378 0.000 + . E . . -Sequence 379 381 0.000 + . . T . -Sequence 382 384 0.000 + . . . C -Sequence 385 386 0.000 + . E . . -Sequence 387 392 0.000 + . . . C -Sequence 393 396 0.000 + . E . . -Sequence 397 401 0.000 + . . T . -Sequence 402 402 0.000 + . . . C -Sequence 403 403 0.000 + . E . . -Sequence 404 406 0.000 + . . T . -Sequence 407 407 0.000 + . . . C -Sequence 408 409 0.000 + . . T . -Sequence 410 412 0.000 + . E . . -Sequence 413 422 0.000 + . . T . -Sequence 423 427 0.000 + . E . . -Sequence 428 436 0.000 + H . . . -Sequence 437 441 0.000 + . E . . -Sequence 442 444 0.000 + . . T . -Sequence 445 447 0.000 + . . . C -Sequence 448 452 0.000 + . E . . -Sequence 453 455 0.000 + . . . C -Sequence 456 457 0.000 + . . T . -Sequence 458 460 0.000 + . . . C -Sequence 461 463 0.000 + . E . . -Sequence 464 467 0.000 + . . T . -Sequence 468 469 0.000 + . E . . -Sequence 470 480 0.000 + . . T . -Sequence 481 484 0.000 + . E . . -Sequence 485 490 0.000 + . . T . -Sequence 491 491 0.000 + . E . . -Sequence 492 496 0.000 + . . T . -Sequence 497 497 0.000 + . . . C -Sequence 498 500 0.000 + . . T . -Sequence 501 504 0.000 + . E . . -Sequence 505 510 0.000 + . . T . -Sequence 511 514 0.000 + . E . . -Sequence 515 517 0.000 + . . . C -Sequence 518 520 0.000 + . E . . -Sequence 521 532 0.000 + . . . C -Sequence 533 534 0.000 + . E . . -Sequence 535 547 0.000 + H . . . -Sequence 548 549 0.000 + . E . . -Sequence 550 554 0.000 + . . T . -Sequence 555 555 0.000 + . . . C -Sequence 556 561 0.000 + H . . . diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_geecee_out.geecee --- a/test-data/emboss_geecee_out.geecee +++ /dev/null @@ -1,2 +0,0 @@ -#Sequence GC content -Sequence 0.36 diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_getorf_out.fasta --- a/test-data/emboss_getorf_out.fasta +++ /dev/null @@ -1,65 +0,0 @@ ->Sequence_1 [1 - 51] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -VRCLKYLLLSLHRPQFS ->Sequence_2 [14 - 94] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -NTFFCPYTDHSFPNGFTPTRNSCASTN ->Sequence_3 [94 - 129] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -LKAVGLECYRFV ->Sequence_4 [133 - 231] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -LSASLALIKGSFSLLWKTLWKNTTSTSLSPLVC ->Sequence_5 [155 - 250] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -SKVHFLYFGRRCGRIQQVRVSPPWFADYWIQL ->Sequence_6 [3 - 272] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -SMPKIPSFVPTQTTVFLMALHRLEILVQALIESGWPRVLPVCIAERVSCPDQRFIFSTLE -DVVEEYNKYESLPPGLLITGYSCNTLRNTA ->Sequence_7 [235 - 309] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -LLDTVVIPFATPRNYLYELFSLYYM ->Sequence_8 [288 - 335] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -IIFPLLYVVGSSLIFL ->Sequence_9 [339 - 377] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -QVFYCFRPQCSCS ->Sequence_10 [254 - 391] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -YPSQHRVTIYMNYFPFIICSRFVFNLPLASLLLFSTSMFMFLGCFG ->Sequence_11 [395 - 427] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -YAVSLIFVVSS ->Sequence_12 [328 - 447] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -SSFSKSFTVFDLNVHVLRLFWIICGQFNLRCFFLKYLFMV ->Sequence_13 [411 - 521] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -SSLFLLKIFIHGLIFGLYLFRGQFIIYSVCIQQFFYF ->Sequence_14 [431 - 526] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -NIYSWFNFWFVLVQGPVHYLLCLYTAVLLFLV ->Sequence_15 [451 - 537] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -FLVCTCSGASSLFTLFVYSSSFIFSMILI ->Sequence_16 [531 - 487] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -NHTKNKRTAVYKQSK ->Sequence_17 [536 - 450] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -IKIILKIKELLYTNRVNNELAPEQVQTKN ->Sequence_18 [487 - 443] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -IMNWPLNKYKPKIKP ->Sequence_19 [468 - 439] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -TSTNQKLNHE ->Sequence_20 [439 - 410] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -INILRRNNED ->Sequence_21 [446 - 405] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -TMNKYFKKKQRRLN ->Sequence_22 [401 - 372] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -PHIIQNNLRT ->Sequence_23 [368 - 327] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -TLRSKTVKDLLKED ->Sequence_24 [426 - 292] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -EETTKIKLTAYYPKQPKNMNIEVENSKRLAKGRLKTNLLHIIKGK ->Sequence_25 [279 - 238] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -IVTRCCEGYYNCIQ ->Sequence_26 [234 - 175] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -SANQGGETRTCCILPQRLPK ->Sequence_27 [334 - 158] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -RKIKDEPTTYNKGKIIHIDSYAVLRRVLQLYPVISKPGGRDSYLLYSSTTSSKVEKMNL ->Sequence_28 [275 - 120] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -LRGVAKGITTVSSNQQTRGERLVLVVFFHNVFQSRENEPLIRARDALSYTNR ->Sequence_29 [162 - 112] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -TFDQGKRRAQLYKPVTL ->Sequence_30 [108 - 34] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -ANRFQLVLAQEFLVGVKPLGKLWSV ->Sequence_31 [50 - 3] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -ENCGLCRDKRRYFRHR ->Sequence_32 [154 - 2] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -SGQETRSAIQTGNTLGQPLSISACTRISSRCKAIRKTVVCVGTKEGILGIE diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_helixturnhelix_out.tabular --- a/test-data/emboss_helixturnhelix_out.tabular +++ /dev/null @@ -1,1 +0,0 @@ -SeqName Start End Score Strand Maximum_score_at Standard_deviations diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_hmoment_out.hmoment --- a/test-data/emboss_hmoment_out.hmoment +++ /dev/null @@ -1,556 +0,0 @@ -HMOMENT of Sequence from 1 to 561 - -Window: 10 Angle: 100 Max uH: 0.205 -Position uH -1 0.100 -2 0.071 -3 0.127 -4 0.152 -5 0.127 -6 0.056 -7 0.049 -8 0.032 -9 0.066 -10 0.041 -11 0.019 -12 0.020 -13 0.081 -14 0.125 -15 0.092 -16 0.044 -17 0.040 -18 0.051 -19 0.063 -20 0.038 -21 0.063 -22 0.052 -23 0.065 -24 0.086 -25 0.106 -26 0.073 -27 0.048 -28 0.088 -29 0.082 -30 0.044 -31 0.007 -32 0.035 -33 0.041 -34 0.094 -35 0.035 -36 0.045 -37 0.073 -38 0.069 -39 0.024 -40 0.055 -41 0.040 -42 0.007 -43 0.066 -44 0.009 -45 0.071 -46 0.111 -47 0.095 -48 0.144 -49 0.138 -50 0.143 -51 0.113 -52 0.120 -53 0.078 -54 0.051 -55 0.042 -56 0.035 -57 0.055 -58 0.027 -59 0.037 -60 0.029 -61 0.032 -62 0.077 -63 0.148 -64 0.108 -65 0.035 -66 0.098 -67 0.128 -68 0.118 -69 0.083 -70 0.108 -71 0.112 -72 0.076 -73 0.116 -74 0.102 -75 0.043 -76 0.090 -77 0.073 -78 0.025 -79 0.031 -80 0.058 -81 0.043 -82 0.066 -83 0.075 -84 0.146 -85 0.173 -86 0.140 -87 0.142 -88 0.200 -89 0.154 -90 0.089 -91 0.140 -92 0.121 -93 0.063 -94 0.055 -95 0.051 -96 0.057 -97 0.075 -98 0.136 -99 0.132 -100 0.068 -101 0.067 -102 0.076 -103 0.055 -104 0.019 -105 0.043 -106 0.041 -107 0.022 -108 0.064 -109 0.060 -110 0.085 -111 0.090 -112 0.111 -113 0.049 -114 0.083 -115 0.131 -116 0.137 -117 0.099 -118 0.119 -119 0.120 -120 0.054 -121 0.064 -122 0.059 -123 0.042 -124 0.026 -125 0.032 -126 0.078 -127 0.104 -128 0.117 -129 0.096 -130 0.116 -131 0.108 -132 0.084 -133 0.056 -134 0.063 -135 0.058 -136 0.050 -137 0.048 -138 0.025 -139 0.047 -140 0.093 -141 0.072 -142 0.027 -143 0.021 -144 0.053 -145 0.022 -146 0.049 -147 0.040 -148 0.103 -149 0.154 -150 0.105 -151 0.076 -152 0.127 -153 0.126 -154 0.105 -155 0.088 -156 0.107 -157 0.131 -158 0.095 -159 0.052 -160 0.114 -161 0.088 -162 0.041 -163 0.071 -164 0.067 -165 0.008 -166 0.056 -167 0.060 -168 0.064 -169 0.059 -170 0.055 -171 0.046 -172 0.030 -173 0.092 -174 0.062 -175 0.036 -176 0.019 -177 0.038 -178 0.032 -179 0.037 -180 0.051 -181 0.100 -182 0.051 -183 0.036 -184 0.088 -185 0.090 -186 0.039 -187 0.080 -188 0.076 -189 0.079 -190 0.061 -191 0.074 -192 0.090 -193 0.042 -194 0.024 -195 0.063 -196 0.065 -197 0.050 -198 0.061 -199 0.077 -200 0.136 -201 0.116 -202 0.037 -203 0.092 -204 0.120 -205 0.066 -206 0.026 -207 0.070 -208 0.075 -209 0.041 -210 0.075 -211 0.082 -212 0.034 -213 0.031 -214 0.023 -215 0.048 -216 0.047 -217 0.098 -218 0.098 -219 0.083 -220 0.059 -221 0.103 -222 0.099 -223 0.085 -224 0.110 -225 0.127 -226 0.163 -227 0.132 -228 0.190 -229 0.194 -230 0.197 -231 0.154 -232 0.205 -233 0.171 -234 0.166 -235 0.148 -236 0.161 -237 0.106 -238 0.035 -239 0.026 -240 0.026 -241 0.038 -242 0.084 -243 0.016 -244 0.060 -245 0.121 -246 0.061 -247 0.028 -248 0.076 -249 0.046 -250 0.050 -251 0.072 -252 0.042 -253 0.033 -254 0.083 -255 0.031 -256 0.093 -257 0.106 -258 0.042 -259 0.055 -260 0.053 -261 0.008 -262 0.030 -263 0.062 -264 0.078 -265 0.037 -266 0.114 -267 0.108 -268 0.078 -269 0.107 -270 0.134 -271 0.117 -272 0.091 -273 0.150 -274 0.147 -275 0.071 -276 0.025 -277 0.064 -278 0.022 -279 0.069 -280 0.072 -281 0.044 -282 0.107 -283 0.170 -284 0.176 -285 0.116 -286 0.110 -287 0.128 -288 0.078 -289 0.059 -290 0.055 -291 0.061 -292 0.020 -293 0.051 -294 0.048 -295 0.055 -296 0.112 -297 0.139 -298 0.083 -299 0.055 -300 0.105 -301 0.100 -302 0.049 -303 0.087 -304 0.086 -305 0.069 -306 0.131 -307 0.096 -308 0.090 -309 0.095 -310 0.134 -311 0.102 -312 0.098 -313 0.062 -314 0.055 -315 0.111 -316 0.098 -317 0.106 -318 0.131 -319 0.132 -320 0.098 -321 0.097 -322 0.096 -323 0.059 -324 0.089 -325 0.083 -326 0.088 -327 0.025 -328 0.103 -329 0.065 -330 0.028 -331 0.086 -332 0.109 -333 0.100 -334 0.094 -335 0.116 -336 0.109 -337 0.111 -338 0.063 -339 0.043 -340 0.074 -341 0.099 -342 0.090 -343 0.073 -344 0.067 -345 0.086 -346 0.092 -347 0.089 -348 0.092 -349 0.044 -350 0.045 -351 0.066 -352 0.039 -353 0.019 -354 0.013 -355 0.059 -356 0.069 -357 0.070 -358 0.045 -359 0.079 -360 0.117 -361 0.081 -362 0.138 -363 0.135 -364 0.083 -365 0.034 -366 0.096 -367 0.071 -368 0.034 -369 0.029 -370 0.038 -371 0.083 -372 0.105 -373 0.112 -374 0.070 -375 0.096 -376 0.096 -377 0.079 -378 0.078 -379 0.072 -380 0.088 -381 0.036 -382 0.059 -383 0.056 -384 0.043 -385 0.114 -386 0.114 -387 0.107 -388 0.101 -389 0.089 -390 0.079 -391 0.029 -392 0.098 -393 0.100 -394 0.036 -395 0.106 -396 0.075 -397 0.085 -398 0.090 -399 0.091 -400 0.096 -401 0.048 -402 0.032 -403 0.049 -404 0.070 -405 0.110 -406 0.059 -407 0.107 -408 0.102 -409 0.106 -410 0.081 -411 0.138 -412 0.143 -413 0.112 -414 0.138 -415 0.136 -416 0.127 -417 0.113 -418 0.107 -419 0.111 -420 0.092 -421 0.134 -422 0.098 -423 0.055 -424 0.044 -425 0.055 -426 0.056 -427 0.040 -428 0.041 -429 0.095 -430 0.158 -431 0.153 -432 0.106 -433 0.186 -434 0.187 -435 0.118 -436 0.167 -437 0.162 -438 0.168 -439 0.108 -440 0.155 -441 0.121 -442 0.121 -443 0.059 -444 0.053 -445 0.098 -446 0.087 -447 0.119 -448 0.149 -449 0.149 -450 0.113 -451 0.069 -452 0.083 -453 0.084 -454 0.095 -455 0.119 -456 0.117 -457 0.100 -458 0.102 -459 0.096 -460 0.100 -461 0.116 -462 0.187 -463 0.150 -464 0.080 -465 0.106 -466 0.115 -467 0.085 -468 0.036 -469 0.098 -470 0.095 -471 0.112 -472 0.061 -473 0.077 -474 0.119 -475 0.141 -476 0.099 -477 0.154 -478 0.184 -479 0.185 -480 0.136 -481 0.194 -482 0.178 -483 0.177 -484 0.138 -485 0.132 -486 0.087 -487 0.055 -488 0.057 -489 0.051 -490 0.037 -491 0.087 -492 0.035 -493 0.031 -494 0.080 -495 0.053 -496 0.023 -497 0.045 -498 0.033 -499 0.030 -500 0.087 -501 0.089 -502 0.035 -503 0.064 -504 0.125 -505 0.132 -506 0.069 -507 0.085 -508 0.072 -509 0.088 -510 0.050 -511 0.049 -512 0.043 -513 0.064 -514 0.071 -515 0.111 -516 0.109 -517 0.082 -518 0.089 -519 0.054 -520 0.038 -521 0.032 -522 0.032 -523 0.038 -524 0.054 -525 0.059 -526 0.015 -527 0.068 -528 0.073 -529 0.026 -530 0.106 -531 0.055 -532 0.047 -533 0.103 -534 0.091 -535 0.049 -536 0.031 -537 0.032 -538 0.038 -539 0.068 -540 0.130 -541 0.077 -542 0.043 -543 0.104 -544 0.058 -545 0.045 -546 0.108 -547 0.084 -548 0.139 -549 0.189 -550 0.130 -551 0.062 -552 0.136 diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_iep_out.iep --- a/test-data/emboss_iep_out.iep +++ /dev/null @@ -1,31 +0,0 @@ -IEP of Sequence from 1 to 561 -Isoelectric Point = 5.0278 - - pH Bound Charge - 1.00 108.00 1.00 - 1.50 107.99 0.99 - 2.00 107.98 0.98 - 2.50 107.93 0.93 - 3.00 107.80 0.80 - 3.50 107.56 0.56 - 4.00 107.28 0.28 - 4.50 107.10 0.10 - 5.00 107.00 0.00 - 5.50 106.91 -0.09 - 6.00 106.67 -0.33 - 6.50 105.94 -1.06 - 7.00 103.73 -3.27 - 7.50 97.29 -9.71 - 8.00 81.33 -25.67 - 8.50 53.56 -53.44 - 9.00 25.75 -81.25 - 9.50 9.75 -97.25 - 10.00 3.29 -103.71 - 10.50 1.06 -105.94 - 11.00 0.34 -106.66 - 11.50 0.11 -106.89 - 12.00 0.03 -106.97 - 12.50 0.01 -106.99 - 13.00 0.00 -107.00 - 13.50 0.00 -107.00 - 14.00 0.00 -107.00 diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_isochore_out.isochore --- a/test-data/emboss_isochore_out.isochore +++ /dev/null @@ -1,7 +0,0 @@ -Position Percent G+C 1 .. 561 -140 0.446 -196 0.414 -252 0.396 -308 0.357 -364 0.332 -420 0.282 diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_marscan_out.tabular --- a/test-data/emboss_marscan_out.tabular +++ /dev/null @@ -1,4 +0,0 @@ -SeqName Start End Score Strand type start8bp end8bp start16bp end16bp -hg17 440 492 0.000 + MAR/SAR recognition site (MRS) 440 447 477 492 -hg17 13640 13750 0.000 + MAR/SAR recognition site (MRS) 13640 13647 13735 13750 -hg17 15229 15392 0.000 + MAR/SAR recognition site (MRS) 15385 15392 15229 15244 diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_maskfeat_out.fasta --- a/test-data/emboss_maskfeat_out.fasta +++ /dev/null @@ -1,11 +0,0 @@ ->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt -tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac -cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg -aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg -gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt -tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac -ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt -ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt -tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa -aacaattctaatggtcaaaaa diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_maskseq_out.fasta --- a/test-data/emboss_maskseq_out.fasta +++ /dev/null @@ -1,11 +0,0 @@ ->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -NNNcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt -tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac -cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg -aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg -gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt -tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac -ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt -ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt -tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa -aacaattctaatggtcaaaaa diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_matcher_out.fasta --- a/test-data/emboss_matcher_out.fasta +++ /dev/null @@ -1,6 +0,0 @@ ->Sequence -CTTTAGCAAGTCTTTTACTGTTTTCGACCTCAATGTTCATGTTCTTAGGTTGTTTTGGAT -A ->hg17 -CTTCAGCAAGTTCCTTACTGTCTTTAAGCCTTGTTTTCATCATCT--GGATAATGGGGAT -A diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_msbar_out.fasta --- a/test-data/emboss_msbar_out.fasta +++ /dev/null @@ -1,11 +0,0 @@ ->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt -tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac -cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg -aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg -gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt -tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac -ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt -ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt -tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa -aacaattctaatggtcaaaaa diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_needle_out.score --- a/test-data/emboss_needle_out.score +++ /dev/null @@ -1,4 +0,0 @@ -Sequence hg17 20190 (604.5) - -#--------------------------------------- -#--------------------------------------- diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_newcpgreport_out.newcpgreport --- a/test-data/emboss_newcpgreport_out.newcpgreport +++ /dev/null @@ -1,11 +0,0 @@ -ID Sequence 561 BP. -XX -DE CpG Island report. -XX -CC Obs/Exp ratio > 0.60. -CC % C + % G > 50.00. -CC Length > 200. -XX -FH Key Location/Qualifiers -FT no islands detected -// diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_newcpgseek_out.newcpgseek --- a/test-data/emboss_newcpgseek_out.newcpgseek +++ /dev/null @@ -1,9 +0,0 @@ - - -NEWCPGSEEK of Sequence from 1 to 561 -with score > 17 - - Begin End Score CpG %CG CG/GC - 121 141 34 3 57.1 1.00 - 261 272 43 3 75.0 1.00 -------------------------------------------- \ No newline at end of file diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_newseq_out.fasta --- a/test-data/emboss_newseq_out.fasta +++ /dev/null @@ -1,2 +0,0 @@ ->cytoc fragment of cytochrome c -KKKEERADLIAY diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_noreturn_out.noreturn --- a/test-data/emboss_noreturn_out.noreturn +++ /dev/null @@ -1,11 +0,0 @@ ->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gttcgatgcc taaaatacct tcttttgtcc ctacacagac cacagttttc ctaatggctt -tacaccgact agaaattctt gtgcaagcac taattgaaag cggttggcct agagtgttac -cggtttgtat agctgagcgc gtctcttgcc ctgatcaaag gttcattttc tctactttgg -aagacgttgt ggaagaatac aacaagtacg agtctctccc ccctggtttg ctgattactg -gatacagttg taataccctt cgcaacaccg cgtaactatc tatatgaatt attttccctt -tattatatgt agtaggttcg tctttaatct tcctttagca agtcttttac tgttttcgac -ctcaatgttc atgttcttag gttgttttgg ataatatgcg gtcagtttaa tcttcgttgt -ttcttcttaa aatatttatt catggtttaa tttttggttt gtacttgttc aggggccagt -tcattattta ctctgtttgt atacagcagt tcttttattt ttagtatgat tttaatttaa -aacaattcta atggtcaaaa a diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_notseq_out.fasta --- a/test-data/emboss_notseq_out.fasta +++ /dev/null @@ -1,11 +0,0 @@ ->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt -tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac -cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg -aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg -gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt -tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac -ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt -ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt -tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa -aacaattctaatggtcaaaaa diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_nthseq_out.fasta --- a/test-data/emboss_nthseq_out.fasta +++ /dev/null @@ -1,11 +0,0 @@ ->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt -tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac -cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg -aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg -gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt -tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac -ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt -ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt -tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa -aacaattctaatggtcaaaaa diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_palindrome_out.palindrome --- a/test-data/emboss_palindrome_out.palindrome +++ /dev/null @@ -1,15 +0,0 @@ -Palindromes of: Sequence -Sequence length is: 561 -Start at position: 1 -End at position: 561 -Minimum length of Palindromes is: 10 -Maximum length of Palindromes is: 100 -Maximum gap between elements is: 100 -Number of mismatches allowed in Palindrome: 0 - - - -Palindromes: - - - diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_pasteseq_out.fasta --- a/test-data/emboss_pasteseq_out.fasta +++ /dev/null @@ -1,371 +0,0 @@ ->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccag -gctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagt -caggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagcca -ctaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTG -ACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCC---------------- ----------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------T -GAA-------------------AACATCCACTAAAATTTGTGGTTTATTCATTTTTCATT -ATTTTGTTTAAGGAGGTCTATAGTGGAAGAGGGAGATATTTGGggaaatt---ttgtata -gactagctttcacgatgttagggaattattattgtgtgataatggtcttgcagttaca-c -agaaattcttccttattttttgggaa---gcaccaaag----tagggat---aaaatgtc -atgatgtgtgcaatacactttaaaatgtttttg-----ccaaaataatt----------- ------aatgaagc--aaatatggaaa-ataataattattaaatctaggtgatgggtatat -tgtagttcactatagtattgcacacttttctgtatgtttaaatttttcatttaaaaaaaa -actttgagc-----tagacaccaggctatgagctaggagcatagcaatgaccaa------ ------------------------------------------------------------- -----------------------------atagactcctaccaa----------------- ----------------------------------ctc-aaagaatgcacattctCTGGGAA -ACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACCTG-TGTG -ATCCTGGCTTTTCCTGTTCCCTCCG---CATCATCACTGCAGGTGTGTTTTCCCAAGTTT -TAAACATTTA------CCTTCCCAGTGGCCTTGCGTCTAGAGGAATCCCTGTATAGTGGT --ACATGAATATAACACATAACAAA-AATCATCTCTATGGTGTGTGTTGTTCCTGGGGTTC -Aattcagcaaattttccctg-ggcacccatgtgttcttggcactggaaaagtaccgggac -tgaaacagttgatggccca-atccctgtcctct---taaaacctaagggaggagaTGGAA -AGGGG-CACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGC -TTCTTTA---AGGATGGAGAGGCCCTAGTGGAAT-GGGGAGATTCTTCCGGGAGAAGCGA -TGGATGCACAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATC -AATGTG-------CAATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta- -aagggccaggtagaaaacattttaggctttctaagccaag--gcaaaat-tgaggatatt -acatgggtacttatacaacaagaataaacaatt---tacacaattttttgttgacagaat -tcaaaactttat----agacacagaaatgcaaatttcctgtaattttcccat-gagaact -attcttct--tttgttttgttttgcgacAGGGTTGCGCtgatcctcccgcctcagtctcc -ctaagtgctgagatgttgcaggaagtcagggaccccgaacagagagatcggctggagccg -tggcagaggaacataaattttgaagatttcattttaatatggacacttatcagttcccaa -ataatacttttataattttttatgcctgtctttgctttaatctcttaatcctgttatctt -cataagctaaggatgtacgtcacctcaggaccactgtgataattgtgttaactgtacaga -ttgattgcaaaacatgtgtgtttgaacaatatgaaatcagtgcaccttgaaaaagagcag -aataacagcaatttttagggaacaagggaagacaactataaggtctgactgcctgcgggg -tcgggcaaagggagccatatttttcttcttgcagagagcctataaatagacctgcaagta -ggagagatattgctaatttcttttgctagcatggaatattaatattaacaccctgggaaa -ggaatgcattcctggggggaggtctataaatggccgctctgggaatgtctatcctacgca -atggagataaggactgagatacgccctggtctcctgcagtaccctcaggcttactagggt -ggtgaaaaactccgccctggtaaatttgtggtcagaccagttttctgctctcgaacactg -ttttctgttgtttaagatgtttatcaagacaatacgtgcaccgctgaacacagaccctta -tcagtagttctcctttttgccctttgaagcatgtgatctactccctgttttacaccccct -caccttttgaaacccttaataaaaaacttgctggttt-gaggctcaggtgggcatcacag -tactaccgatatgtgatgtcacccccggcggcccagctgtaaaattcctctctttgtact -ctctctctttatttctcagccagctgacacttatggaaaatagaaagaacctacgttgaa -atattgggggcaggttcccccaataTCTGGTGCCCAACGTGGGAtactgagattacaagc -atgagccactgcatctggcctcttcttttgatttttttttttcaaacttttacaaatgta -gaaaccattcttagcttttgggcattaccaaacccggcagtgg-caggctcggttcacca -acgtcatttgcagttccccgCTTTATGTTATGGgttttgttttgttttgtttttttt-at -tgagacagagtttcactcttgttgcccaggctgtagtgcaatggtctgatcttggctcac -tgcaacctccacttcccaggttcaagccattctcctgcctcagcctctcaagtagctggg -attacagacactcaccaccacacctggctaattttgtatttttagtagagatgaggtttc -accatgttggccaggctggtctcgaaatcctgacctcaggtgatccacccaccttggcct -cccaaagtgctgggattacaggcttgagctaccacgcctggctGGGTTGGTTCTCAATGG -AGTGGTTTGTTTTTGGAGCTGCTCT-GCGCAGtggggaccagaataggcctg-------- ------------ggttcctagcccattgctattcctt----accagctgtggattctaagg -aaagtcatttaacctcgctggaccttag-attcctcatccctgaaGCCCAAGGGTaaaac -aaaacaaaacaaaacaaaacaaaccaaCCCATCATGTAAAGCGGGGAACTACAAACGATA -CAGGTGAAACATGCCTACCACACCACTCACAGGCT--ATGATGACAAAAACGTGGCTACA -TCTGGGACCACCCCCCAACCCCCACTTTGTACGTAGGAAATACGGAGTTGAGGATGGAGA -CCCACAGTATGTCCAGAGTGTCCCCAAAGGCCACAGTGCCCGCCTGGAGCCCTCCAGAGA -GCGTGCACTCCCTGGGGTGCCAGCCAGAGACAACTTGCCCTGAGGCTTGGAACTCGATTC -TCCGCGTGCCAGAGAAGGGGTGGGACTTCAGAACCCCCAACCCCGCAATCTGGGTCGGGG -AGCCTGGCGCACTGCGGGCCGCTCCCTCTAACCCTGGGCTTCCCTG------GCGTCCAG -GGCCGTCGG-----------GGCCGAGTCCCGATTCGCTCCCACCCCGAAGCCGCGCCAG -GACCAACGAGGGCGCAGCCGTATGCCCCAGCCCGCTCCGCGGAGCCCCTCACAGCCAccc -ccgccccgaccgcgccccgcgcggcTCGAAGCACCTTCCCAAGGGGCTGGTCCTTGC--- --------GCCATAGTCGCGCCGGAGCCTCTGGAGGGACATCAAGGATTTCTC-GCTCCTA -CCAGCCACCCCCAAATTTTTGGGAGGTACCCAAGGGTGCGCGCGTGGCTCCTGGCGCGCC -GAGGCCCTCCCTCGAGGCCCCGCGAGGTGCACACTGC---------GGGCCCAGGGCTAG -CAGCCGCCCGGCACGTCGCTACCCTGAGGGGCGGGGCGGGAGCTGGCGCTAGAAATGCGC -CGGGGCCTGCGGGGCAGTTGCGCAAGTTGTGATCGGGCCGCTATAAGAGGGGCGGGCAGG -CATGGAGCCCCGTAGGAATCGCAGCGCCAGCGGTTGCAAGGTAAGGCCC-CGGCGCGCTC -CTTCCTCCTTCTCTGCTGGTCTTTCTTGGCAGGCCACAGGGCCCCACACAACTCTGGATC -CCGGGGAAACTGAGTCAGG-AGGGATGCAGGGCGGATGGCTTAGTTCTGGACTATGATAG -CTTTGTACCGAG-----TTCTAGCCAGATAGAAGGTTACCGGGAGCTGGGGAGCGTTGGA -TTTGCTGCTGGGCTGTGCCGGTGCCCAGAAGGCA------GGACCTTGCAGAACCAGCCA -GGTCCCTGGGAGACTGTCAGACCCACCAACCTGGTGGCATTCGCAGAGCTGAGATGCATT -GGAAATTGCCTTGGGCACATCCCCAAAGATCAGGATGTCCCACCCCAGTCTGAAGGAGA- ---TAAAGTTGGGGGTAGGAGAGACGCAG-ATGCAAGTGATCAGTCTC---AGTCCCAGAC -ATTGCCTTGCTCTGCGGGTAGGAATTCAGGATTCATTTTCCAGGGAAG--------TTCC -TGACCTCTGAATGAGAGGGGCTGTGTAAGGCCAATGCCTGGG-AGGAAGGCAAGGATGAG -TAGAGGTGGGGGGAAACAAGTGTCAGGAAGA----------------------------- ----------------CTCAAA---------ATCTTC------------------------ ---------------------------------------CAGAGAAATTGT-----GCAGG -GTCTTACCAGATCTGTCCTCAAAGCCATGCAAATTGCCTTCTTTGCAATGCAT-ACAATG -AGGTGTCTCTGGGGGTCAGAACTGG-----------------------TTATTAGGGAAC -TTCTAGCCAGGACTGCTAAATACGCGCTGTTGG---------CCCACCAGGCTCACCTAT -AGCCT-TCCTTCAGTCTGGGCTTGGTTTGGATTTCACTGTGGGTGCCATCGCCTTTACAC -TCCTGTTTCTATAGTTTAAAGATAGTGGTGCTTTGGGAAAG---TGACTCCTTAAATACA -GTTAGGTCCAAGTGA-GACAAGTGGCCTGGCTGTCATTTCAGAATAGCAGCTTCCAAGAG -G----------TGATTAATTTCTGTTGGAAGGGTGAT-CTTTGGGGAGGT--GGGTGAAG -AGCAGAGACTTGGTGGTACCGTTCCAGGAGCACAGGCTCTCT-----TCCTTTGCA--GT -GCAGAATGACCTCTGGCAGCCGGAGTTGTGTTTGTT--------CTGTAGGATTCTGAGG -TGGGCCATGGGCAGCTGGAACTGGG-----GAATTTTGCCAATCTCTTTCATATTAGGAT -TGTCTGCAGAACCAGATATGGAGG------CTTCTAGCAACGTGAGTGCTCCTGTTCTAA -TGCCCTTAGAAACAAGAAGGCCACACTGATCATTTCTCTCACTTAGGCAGGGAGACAAGG -CAAGAGAGAAACAGT-----------------GGATGC--TTTTAGGTTCTTTCCCTTCC -CAAGCAGTTGTGGACATTGGGCTGA-GGGGAACATTTCCACATTGGCTAAAGGAGCGTCC -TCCTCATATTTTGTACATTTTATACCCAA--AATAA-CTCTTCTTGGTATTT-GGGGAAA -TATTTTCCTCCCCGTCC------------ATTCCAGGAAATGGCTCCAAGTGCCAAGGAC -AGAGCCAGGGAAGTTGCAATGAATTCCTGCCCGTCAGCCCCAGGCAGATGCCTTGCACGT -CTGAGTGGCCCATGCAGAGCGTGGAGGTGGCCGCC----------------ACGGAACC- -TGGGTCAATGT-CCCACCCCCG----CTTAGATGCCA-CCAGGGG--CGTGGGAGCCAAG -GAG--AGAAGAGGGGCTCCAGGAAGGTAGAGTCCTTGTGTCTTGTGCATCTGTGAACAGC -ACTGGTATGATTTAAAGGAAAATTGAGCCAAATTTTCCGGCAGTCAGTT-----ACCCCA -TCCCCACCGGGGTAGGAGTCTGGCAGCCGCAGCTCCATTCTGGCCAGTCGGCAGAGAGCC -TTGAAATTCTTCTTTGTCCACACAGTTGTCTCAGAGAAACAG--AGAGGTT-GTTTCTGC -TTAAAAACAACACACTTGGTGTCTGGGCCCACAGACTCCTTTGCACTTATTCCACGTGTG -ACAGCCAATGTGCCTCGTTGCTTAGCAGACAGCATGTTACCGTCTTTCCTGCTCAGTTTG -TTAG--------------CTCTATGGAATGGAATTTATAATCAATGCCCATACCAACATT -TCACTAATATCATAGGAGATTTAGTCTCCATCTGGGTGTACATTACATTTGC--TCTGGG -G-TGCTCCAGGC--TGGGGGGTTGCCAAGGAAGAGAAGAGAAACCGCAGAGAAGAC---G -GGAGGGCAGGGCAGGGGTCTCTGAGAAGGGGAGGGGTCCCAGAGTGCAGGAGCAGGAGCC -AGGCTC---------ATGAAAGGGGCCACGGGCGGGAGTATCCAGGGACGGCAGTCAAGA -TGGAGCACAGCTTAGG--AAGCTGAAGGGAATCCTGGCCCACCTGGGTGCTAGAGGGCAC -ATAGGAAGTGCAGGAAGCAGACCAAGGTCCCCAAGAGAGGGAGACCTGGACGCTGAAGCA -TTTTCTGTCTTTATTAAG-------------ACAACTCCGTAAGAATTCCTGCTGGGCCA -AAGTGAATTCTAGGATGCGACTTTAAGATGGGAGCAAGCGAACCATTGAGGAGGCAGGTT -ACCCTAGTTAGCCAATGCAGATCGAGAATGGGAAATCTTTCatttattcatgcaacagat -atttaacgaagccctgccgtgttccaggcctgtgatagatgctggaacaggtacagaga- ----------tAc-------aggtgtcattaattgatcaggg--caacctctc---cttct -gagt--cttgctggagcttcagatgc-ccctcacacagagctcgagggagcctc-aacaa -ttgatcagaagtcaggcaccatggctcacgcatataatcccagcactttgggaggccaag -gcaggtggatcactggagcccaggagttccagatcagctggggcaacatggcaaaacccc -atctctattaaaaaaaaaaaaagtaactggatgtgatggtacacacctgtagtcccagct -acttgggaggctgagaggtgggagaattgcttgagcccgggaagtcgggggtccagtgag -ccttgatcacaccactgcactccagcctgagtgacagagcaagaccctgacacacacaca -cacacacacacacacacacacacagattagagctgaaacaggagtagaaacctatctg-t -atctctgATGA-GATCAGATC---------TTTCTGATGAACAGAAAGAATGTAACCCCT -GTACTCACACCCTCTCTGCTGGTTACATATGTTAACACGATTTCTCAAATGAGGCTTTTG -GTTGCAAATAAGAGAAAATCACTCACGCT-GGCCCTGTG--TTTTTCAAATTGTTTATTG -TGATCAACATTTGAAAAAAGAGCCGAGACTCTCAAGAGTGCATTACCCACGGTAAGGGTG -AATTTT-ACTTCTTGACACTTATTTCTCTTACATGTATCTATCTGTCTC-----AAATGA -AAAATATATTTAGAAAGTTGAAAGCTATCCAAGTGAGTATAAGAAAAGAGTATCTCACCC -TGAAGGCTAAGGACAGGGAGGGC---------------------------CACCAGGCCT -CACGAGGACCCAGGAACCACAAAGAAGGCT-AGGAAGGAGCACAGGCGGTGACCATACTC -TGGCTCAGTGGCTATGTGGGCTCTGGTCTCTCTCAGCTGTTCCATGCATATGAGGCCAAA -TGTGGCTACCCTAGAGCTTCTGAGCCCTCAACAGAGATGAACTGGACTCTCTGCAGCCCC -ACTCTAAATTCCTAAGAGAGAAGTTGATTGACCCAATCAGGGTCAGGAGAAGGAAGGGAG -GAGGAAAGGGAGGAGAGAAGAGCCTCTTCGTCTCTTGCCTACCACTGGCCAGGCAATTGT -AGCCAAGGGGGCTGGAGTGTAAATGCAAACATAGCCATCAAGGGTtgtgtatgtgtgtgt -gtgtgtctgtgtgtgtgtatgtgtgtCTCTTGGGTAGGTTAGA-TCTCCCAGGAGGTCCC -TACTAAACAGACTTAAGCCCGCAAAATTTTAGCTCTCCAGCCTCACACACTCCACCCCTC -TACCATATTGAATCTTCCCAAACCAACTATGGCTTTCCCTAACTCCGGAGc------ttg -gcctggaatgccctgcttcccctctttcccctggggaacgcctgtccttcaggcctcagt -tcacacactgcctcccttgcaaagctctccTCCCATCCCCGGAGTCCCT--CTTCCCCTT -TGTTCTTTGGGTTCTATGCTTCTTCCCTCATAACTCCCACCAGGTTGTGTTAAAATGAGT -TGTTCAAGGTCCTGTCTGTTCCACTAGATTCTGAGCAACTTGGAGAACGAAGATCCAAAC -TTCGCTGCCTTTATTTCCTCCTTTGTTCTTTTCTCATCCCCAAGTCCCTTCCAACTTGGA -GTTATgaagaaaggaaggaaggaagggtgggagggaagaaCAGGAGGGGATCCCACAGG- -AGAATGTGTATAGGGAGAGGACTCAGACTAGCTAAAGCTTTTCCCTCATAATTAATAGCA -AATACCATGTTACCTGAATTTAATTCACAGTAGCATACAAAAGACTCGCTTTGTTCT--- -----CCCCA---------TTGATGTCATCAGAGG--------------------GCTGTG -GG--------------CAGGCCTAATCTTGGCTCAGGAGGCCCTCCAGCCTGGATCTAAA -GAGCAGCAGATGggccaggctcggtggctcatgcctgtaatcccagcattttgggaggcc -gaggcgggtggatcacgaggtcaggagtttgagaccagcctggccaagatggtgaagcct -cgtctctactaaaaatacaaaaattagccaggtgcggtggtgggcgcctgtatttccagc -tacccgggaggctgaggaggctgaggcaggagaatcgcttgaacccgggaggcggaggtt -gcagtgagccgaggtcacgccactgcactctagcctgggcaacagagcaagactccgtca -aaaaaaaaataaaaaaataaaaaaataaaaaaaataaaGAGGAGCACACATCTCTGCCCA -TCCTAACTCCCACTTTGACATTGAGGTCCCCAGGATGGAGGGTCTGCCTCCATCTGCCTT -GTCCCCTG-CAATGGTGGGAAGGTGATGGAGCTCAAGTCTAGAGGCCACCAGCTTCTTAG -GGAGG--TAGGAGGTG---------------GAGGGTGGGGTGC-GGGCCCTGCACACAA -CTGCCAAGTGAGGATGGGGGTGGG-GTCCACCTGAGGATAAGTAACAGTGAGGCTGGTGC -AGAGGACCCAGGTGGAGGTAGACAGCAGAATTTGTGGTGGGGT--GGATGGCAC-ATTAT -ATAAGCCTCTCTTGC------TGCCCTGT---TTACTGAGATTGTTTCAttatctttttt -ggcttttgtttttaagagatggggtcttgctgtgtcacacaggctggagtgcactgtgtg -atcatacctcactgcagcctcgacatcctgggctcaggcaaacctcccaccttggcctcc -caagtagctgggaccacaagcgtttgccaccacactcagctatttttatttttattttta ---ttttttttagagatggggtcttgctgtgtcgcccaggctggtcttgaactcctgggct -caagcgatcctcctgccttggcctcccaaagccctgggattataggctgagccaccacac -ccagccACATTTCATCTGTGCAGCTCCAGGGGCTCCACATTCT-ACTCTTCTCATTTCTT -CTCCAGGGTACCC----------ATGGCAAGGGATGAGGGT--AGAAGATGGGGCA--GC -CAGGCCTTGATTAAAGGAGAAGGAAGGCAGCCTGTGGAGAGG---GCAGCC---C---AG -GGAG---TGCAGAGAGAAGTGGGCCATGAGGGAGA---CAGCAGAGTGCAGGCTGCGTCC ----CAAATGAGCATACAGCCCACTGTGAGCCCACC--ATCTTCCTAGA-GA--CCCCTCT -CCTCTCC-AGGAGCTGCTTCAGTAGCACTCA---------GAGGAAAGAATGATGC---- -----TGTATCAACATTTCAGCAGCTCATCTTTTAACTCTAAGAAAATGGCAGCTCCTAAA -TGTTCAA--AACTGCTTTGGAAACTTCT---GGAGAGAGGTTTTGCAGCTCAGGCAGACA -GCTGATCGCGGCCTTTCTTCCACCCCAACCCATGCTCTCCCCATGCT--CTCCTGCCACA -GCTGCAGCGGGCCCCTGGGTCCTACATTTGCAG-CCCTTTGTCTCTGAGCT-----CAGA -CTTCCAATTCCAAGCGGCAGCTGGGCAGGCTCACCAGCATGT---CCAGCCAGTACTAGG -ACATCAGCAGGAGC----CCAACCACCTCTTTCCAAAATCTCTCCTCATGTCTCTCCTAG -TTTCCATCTCCATCCTTCTAGTCAGCCAGGCTGAAAACATT-----------------TG -CTCCTCAGGGTGCAGAAGGGAAAGCTTTGCCTCCCTTCCTGGTGCTCACTGCCCCTGCGA -TTCCAGCCCAAGCCCTCCCCGGCTCCTCACC----------CTGGTGTCAGCTGGAAGCC -ACCATCTCCTAAACCCACCTGtgttcttccacctctgc--------cagggctgc-cctc -tcctccaccttcacaaactcaattcctacccattctcaggtcccttatcaaatgccatct -cctccatgatgcctccctgattccccTGCTGGAaataatggtgataacagctaag--gca -ttggggttggctacgtgccaggcaaggagttggcactttacatgctttatctcatttcag -ccacataacatcgacaggt-ggcattatgattcatatcatccccatctgatagccaggaa -aactgagtcccagagaggttagc-cactttcctagggccCTGTGCTCTGACTCAAGCATA -GCTCTGAGGAACTCTAGCATTCATCAGTTTAAGCACCATGACTTTCTTTGCTGAGTCACC -CAAGGCAT-TTCTTCATTTAAATGTTCTTCCTTGGCCAGGCGCAGTGGCTCAggcccaat -gcggtggctcacgcctgtaatctcaacactttgggaggccgaggtgggcagataatctga -ggtcaggagttcaagaccagcctggccaacatggtgaaaccccatctctactaaaaatac -aaaaaaatgaggctgggcgtgatgactcacacctgtaatcccagcactttgggaggccaa -ggcaggtggattacatgaggtcaggagttcgagaccagcctggccaacatggtgaaatcc -tatctctattaaaaatacaaaaaattagccaggcatggtggcaggcacctgtaatcccag -ctacttgggaggctgaggcaggaaaatggcttgaacccgggaggtggaggttgcagtgag -ccaaggttgcaccattgcactccagcctgggcaaaaagagggaaacatcgtctaaaaaag -aaaaaaaaaaaattagccaggctgggtggtgcatgcccgtaattccagctactcaggagg -atgaagcaagagaattgcttgaacccaggaggcagagattacagtgagctgagatcacaa -cactgcactccagcctaggtaaagaacaagactccatctcaaaaataaataaataaaaat -aaaTGTTCTTCCTTGCAATGAAGTTAAATATGTAAATTCTCAAACCAGTTGCTTAAGGGC -ACAGTTTTGTTCTTTACCTATATTTTTAACAAATATTTTATGTAAGTAGTTGAC-AAAAT -CAAATACTGT-GTACACTACCGAGGCTTCCCTGGGAAAGCCATCAG-CCTCTGCCCCATC -CCTTCCCACTCCTGATT-CCACTTTCCTGTGTTTCCATATCTTTTTCATGTCTGTTTCTG -GCCCACAGTGGGCGATCAATACATGTTAGCCACCAACCATCAAACCTATATTGAGTAATT -ATGGTATGTCAGGCACTATGCTCAATGAAATTGTAttaggcttgtacaaaagtaattgtg -gtttttaagagtaatggcaaaaacggcagttactttcgcaccaacTATTTGCTGCCTTGA -ATTATTCCTCCTCTC-CTCATCCCTAAACCCTGCTCCTCCCAGCCATTCTTCCTCCCCTT -CTTGGGCCATGGCCAGGCCCCACCCAGGTACTAAGACTCAGGTGAACCAAGGAAGACTTA -ATGCCCACTCTTTTCTGATGCCCATGTT--GGCATGTGTTAAGtcggttagcattaagtt -tggctgcatttagcagagacccaaaagaacagtgccttttaaaaggcagaggttatgtct -ctcacacacacccagcacaagtccaag-------------------------accagcat -ggcatctcagctccatcaa--cctcaggaaccgagctcctgcagctccctgccctgcagt -tgataaggtgaggtctttgtcctcctggttcaagatggtgctagaatgttggctaccata -tctatagtccaggcatcagaatggagcaagggatgaaaaaggaagagatgaaggcacacg -acaggttcctgagagctggcacaggacacttctgcttatatttcactggccagaacttag -tcacatggtcacacctagttgggagactctgagaagtaa----agtatttattctagatg -gccatatccctacc-taagacttggagttttctatgactggggaagaacggaagacaaga -tattgggaaagactagcagcctctactaAAAGGGTGATCtgtgttgatgtgcgtgtgtgt -gtgatgtttgtatg---agcatgtgtgt-tatgtgttgt--gtgtTGGTGGGGCA--GAT -TCTTGCGAGCACTTTGGTCTCAGATGGACCTGCTACCAGTTCTCTCTGCAGACCCCCATA -GGTTTCTCCTAAACCTGGCCT-CTCCTATTAGGCAGCCTTACTCAGCGGCAGCTTCTCAG -CTCCATGTTTTCAAGGAACCACAATTTATTTCCAGCATCCACTGAAGCATATTATCAGTG -GTGATAGAGGGGGCTTGTAAAACTGTTTTTCCACTTAGGTATTAGAGGGTGGCCATTATT -TGAGAGTGAC-----TATGACCACAGTTAATCTGGTAATAAATTCTCTTGGGTAGGAGGG -GGAAAGGAAAGGATGCTTTAAGGAAGCATCTTGCCAGGAGACACAAAGCTAACAAGAGTG -GAGCCTGCAG----------------------------CTGGAGCCGCAGAGCCTAATCA -CTACACCCGCCCATCTCTGCTAGGGTTTCATGACTTCGTATCGGGGATTAGCAGTATTTA -ACTCTGTTGCACAAACATTTGGTGTA-----TTATTCAGGTAACAAGTAGCTAATAGAGG -AAGTTTTACTTTTTTAAGACATAA--------------------ATTTGCCTTTTCCCAA -ATTACTTGGTACATAGTAC-TTTTCATGTTTGAAGTTGAGATGTGGGTACAATACCATAG -CTTTATTCCAGAGCAGGGTATTTGTTTCCAAATGCCATGTTCCCAGCAGCTGCCCTTGAC -TGGGAATTGGGGTG-----TGATTTGGGCTTTTCCTTAAATCCTTGA-----GGAGCTGG -A---GGGGTGGGTGGCTCGCACTCCTGCTTTctgg---------atctgaatc------- --------ctgactctgtcatggacctgtt-tgactttgggcaagttgactcctattcctg -agccccatat-ttttctcttctgtgaaattcagattaaaaA-AACATGGCTTTGATCAAA -CATTATAAATAATATATAGACAGACTGCTTGTTTTTATTGTATTGCCAG-AAATGAATCC -TACTAATATTGCCATCTATGGACAGAAAATGTATTACCTGTCTTCATCAAGACCCAGACG -AGGAAGAACACGAAAAGCGGAGATTAATTTTACTGCCATCTCCAGAACCGTCATCCTAAT -ATTTACTTACAT-TTTATTATTATTTCAGGCTCATGCACATATACTTAGCATGGATCATT -GGCCACAGACTCGCATACATTTAACTTTATTACCTTT-TGCCTCATGTATCTCATTAAAA -TTTTGCTGCTTAATCAAGGATCTGCATATTATTTTAATTTTAGAATTCACAGTTCCAAGA -CTTTGAAAGTTTCAAGCGTTCTGGGTGaatgtgttatgc--tctctcccgccaccatgtc -tttataccccctgatttctcagccact-atggcaaccactttctactcttagtagcccat -atttag--tccaatccccagctcaggagacacttcttccaggg--agccccctgtgcctt -ccagtagtatcttgtacctgccctttttgcaaagctctttcctcctggcttagaatggcc -cattgacctgtttgtttctcctattaaactgtaagccactcgagggtagagagcatctgt -tgttcaccattgcatcctcggtgctgagcactgcgtctgacatattatttagaaggtcag -taagtgctagtgggatTCAGGCTCCCAGTGGGTGGGAGAGAAAGGACGTAAGGAAGCAAG -TGGTAAAGGCCCTCACAGA-GTATCAGCAGGCTGGTGTGA-GGGAGAAATGCAGAGGATG -GGTGAGTAGCA-----TAATCGCTAATGAT-AGGGTAATGATAGAGCACATTTCACAACA -CCTTt-aagccctttcacgtgcatcagataatttgatcctcataaaagcctagagataga -tatattacagg-gatgaaggtggagtattttgtggttatgtgatatg-tttaaaattatg -cagtgagtaaatgactgggttcaaaccagaccttaaaagtctgttatctttccCTCG-AG -CATGCAATGAAGTCTACATCATCCCTACCATGTCCATTTGATCACACCCTGGCCTCACAG -CTCTGTGGTCTACAGGATACCTCATGGTGGTTTTATTGACCAGACAATAATCCTCTTTCT -AAGGGGATGCATTTCATTAATACATATGTAGATCATGAATTGTCTTTGACTTTGAGGGGA -TGGTAGC----CAGAGCAGAAAGCAAAGCTGATTTTCATCCCCGTCTGGTAATGTGGTTG -GTAATGTGAAGA-TGGGTGTATTCTGAGATACCGGCTCCTTGCAGTGTGTGGTTCCTTCT -GTTTTCAGGCCC------AAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTG -TGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAA -GTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCA -CACACGGTAAGGAG---AGTATGCGGGGACAAA---GTAGAACTGCAGCCAGCCCAGCAC -TGGCTCCTAGTGGCACT-GGACC-CAGATAGtccaagaaacatttattgaacgcctcctg -aatgccaggcacctactggaagctgagaaGGATTTGAAAGCACAGGGC-TCCACTCTTTC -TGGTTGTTTCTTTTGGCCCCTCTGCCTGCTGAGATTCCAGGGGTTAGTGG---------- -----------------------------------------------TTCTAATTCTAAAC -CACTCCAAGAACATTTGATTTTGCTACATGTTTCCATTTAAAAATCATAGGATTTGggct -gggtgtggtggcttgtacctgtcatcccagcactttgggaggccaaagcaggaggatcat -tcgagcccaagagttcgagaccagcctgggcagcatagggagaccccatctctacaaaaa -taataaaaaatgttagctgggcatggtggtgtgtacctgtggtcccagctaggggaggct -gagatggaaggatcacctgagcctgggaggttgaggctgcagtgggccctgatcatgcca -ccgtgctccagcctgggtgacagagtgagaccttgtctcaaaataaataaataaataaat -aaaAGTCATAGGATTTgatcaggcatgatgggtcacatctgtaagcccattgctttagga -ggccaaggtaggaggatcagttgaggccaggagttcaagaccagcctgggcaacatggca -agacctctctctctaatttttaaaaaaataaaaaTTAAAGATAAGAAAAAAATCATAGGA -TTCTCATGAGGCCTCACGTGCTTATTTTCAACCTACCAAGGGGAAACCCAGGCCTCAGCG -ATTAGCTGAGC----------CACATGCAGGCACAG------------------------ -CCACTG-----TCTCTTTCCTTCCTGTCCCCTCTGTCCCCACCTTCTGCGCTCGCCTTCC -TCCCTGACTTCACTTCCTTGAATCTTAGTGCCTACGACCAGAGGGAGCTGTGAAGTTCCT -TG----TGTCCCATTGGCAGGAA-CAAGACCCCCAGAAGCATCTCCTCAGGGC------C -TCTA-----TCCCATCTC-TAGATGTGCTTGTCATTAGG-Gttct-------------tg -tagttccagctgatctctggccctgccgctcaaagatacccaaaagagcgagtctaccct -ttttcacattcaaccctctactgatttgcaaatagcagtcagtgcccaccctggtctttt -ctctggggtccagcaggcctagaccttcagccattttcctgatgaGGTCTGTAtttgaaa -ttaggaagattaagtttgaatcttcacacttctgat----gtctgtgagatcttcagcaa -gttccttact--gtctttaagccttgt-tttcatcatctggataatggggatatcacaca -cta-ttcacaaggttgttatgaggcctaaattagctaaagcaATTGAATCCTCCTTACCC -CCTGCATGGAGCTCTCTGGAGACTTCCACGTCTCCTGGTCATTGTGGGTGTCTTATGGTA --GTCTTGGGCAGTTAGGGAGAAGTTAGGTGTCTGGAAGCAAAGATGGCTCAGAACTAGAT -AGAGTC-TTGGGCATTTTATA-GATAAAAACTCTT--GTCTCCtttaaaaataataaaaa -aaaattaGCTGGGCATATTAGCCACTCAGCAAGACTGCACGTGATAGATCCCGAGTGCCC -CACCTTGGGTGGTGTAATACACAATATCACGGGAGCCCCGGGTAGTAACCACGGAGGTGT -CAGCCTCAGTGCTGTGGGCAGATG-GATGGGGAGAGCC--TCCCGG-AACTGGAGTCACT -GGAGCA----------------------------GGGTTGGGGGGCCTCACTGAGGGTAC -GGCCTTGATCTCTAAGGAGGAGGGACTGCCTGGAAAAGC-TGACTGGGAGGGAGGACTCG -GCTGGGGGTAGAAGGGA----------CTAGGGAAGGCTGGGGGTGGGGGTGCTTATGGA -GGACCTCAGATGCCTGGGGAACAGACTCCACTAAATAAAACATATGAAACCATGGCTGGT -TCTTCAGCAGAGGCCATGTAGAGAAAGGAATGACCTAGGAAAGTTGGCCTGGAAGTGGAG -GGAAGGATGGTGTGGGAAAAGCAGGAA--------TCTCGGAGACCAGCTTAGAGGCTTG -GCAGTCACCTGGGTGCAGG-ATACAAGGGCCTGAGCCAAAGTGGTGAGGGAGGGTGGAAG -GAGGCAGCCCAGAGAATGACCCTCCATGCCCACGGGGAAGGCAGAGGGCTCT-GAGAGCG -A--TTCCTCCCACATG-CT-GAGCACTTGTTCTCCCTCTTCCTCCTGCATAGCAGTCAGT -CTCCTCCAAACAGAAAGTCACCGGTTTGGACTTCATTCCTGGGCTCCACCCCATCCTGAC -CTTATCCAAGATGGACCAGACACTGGCAGTCTACCAACAGATCCTCACCAGTATGCCTTC -CAGAAACGTGATCCAAATATCCAACGACCTGGAGAACCTCCGGGATCTTCTTCACGTGCT -GGCCTTCTCTAAGAGCTGCCACTTGCCCTGGGCCAGTGGCCTGGAGACCTTGGACAGCCT -GGGGGGTGTCCTGGAAGCTTCAGGCTACTCCACAGAGGTGGTGGCCCTGAGCAGGCTGCA -GGGGTCTCTGCAGGACATGCTGTGGCAGCTGGACCTCAGCCCTGGGTGCTGAGGCCTTGA -AGGTCACTCTTCCTGCAAGGACTACGTTAAGGGAAGGAACTCTGGCTTCCAGGTATCTCC -AGGATTGAAGAGCATTGCATGGACACCCCTTATCCAGGACTCTGTCAATT--TCCCTGAC -TCCTCTAAGCCACTCTTCCAAAGGCATAAGACCCTAAGCCTCCTTTTGCTTGAAACCAAA -GATATATACACAGGATCCTATTCTCACCAGGAAGGGGG-TCCACCC-AGCAAAGAGTGGG -CTGCATCTGGGATTCCCACCAAGGTCTTCAGCCATCA---ACAAGAGTTGTCTTGTCCCC -TCT-TGACCCATCT-----------------CCCCCTCACTGAATGCCTCAATGTGACCA -GGGGTGATTTCAGAGAGGGCAGAGGGGTAGGCAGAGCCTTTGGATGACCA--GAACAAGG -TTCCCTCTGAGAATTCCAAGGAGTTCCATGAAGACCACATCCACACACG--CAGGAACTC -CC--AGCAACACAAGCTGGAA---GCACATGTTTATTTATTCTGCATTTTATTCTGGATG -GATTTGAAGCAAAGCACCAGCTTCTCCAGGCTCTTTGGGGTCAGCCAGGGCCAGGGGTCT -CCCTGGAGTGCAGTTTCCAATCCCATAGATGGGTC-TGGCTGAGCTGAACCCA---TTTT -GAGTGACT----CGAGGGTTGGG-TTCATCTGAGCAAGAGCTGGCAAAGGTGGCTCTCCA -GTTAGTTCTCTCGTAACTGGTTTCATTTCTACTGTGACTGATGTTACATCACAGTGTTTG -CAATGGTGTTGCCCTGAGTGGATCTCCAAGGACCAGGTTATTTTAAAA---AGATTTGTT -TTGTCAAGTGTCATATGTAGGTGTCTGCACCCAGGGGTGGG-GAATGTTTGGGCAGAAGG -GAGAAGGATCTAGAATGTGTTTTCTGAATAACATTTGTGTGGTGGGTTCTTTGGAAGGAG -TGAGA-TCATTTTCTTATCTTCTGCAATTGCTTAGGATGTTTTTCATGAAAA-------- -----TAGCTCTTTCAG-GGGGGTTGTGAGGCCTGGCCAGGCACCCCCTGGAGAGAAGTTT -CTGGCCCTGGCTGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCA -GAATAAAACGCAAAGGGCTGAAAGCCATTTGTTGGGGCAGTGGTAAGCTCTGGCTTTCTC -CGACTGCTAGGGAGTGGTCTTTCCTATCATGGAGTGACGGTCCCACACTGGTGACTGCGA -TCTTCAGAGCAGGGGTCCTTGGTGT-GACCCTCTGAATGGTCCAGGGTTGATCACACTCT -GGGTTTATTACATGGCAG-----TGTTCCTATTTGGGGCTTGCATGCCAAATTGTAGTTC -TTGTCTGATTGGCTCACCC-AAGCAAGGCCAAAATTACCAAAAATCTTGGGGGG--TTTT -TACTC-CAGTGGTGAAGAAAACTCCTTTAGCAGG-TGGTCCTGAGACCT-GACAAGCACT -GCTAGGCGAGTGCCAGGACTCCCCAGGCCAGGCCACCAGGATGGCCCTTCCCACTGGAGG -TCACATTCAGGAAGATGAAAGAGGAGGTTTGGGGTCTGCCACCATCCTGCTGCTGTGTTT -TTGCTATCACACAGTGGGTGGTGGATCTGTCCAAGGAAACTTGAATCAAAGCAGTTAAC- -TTTAAGactgagcacctgcttcatgctcagccctgactggtgctataggctggagaagct -cacccaataaacattaagatt-gaggcctgccctcagggatcttgcattcccagtggTCA -AACC-GCACTCACCCATGTGCCAAGGTGGGGTA-TTTACCACAGCAG--CTGAACAGCCA -AATGCATGGTGCAGTTGACAGCAGGTGGGAAATGGTATGAGCTGAGGGGGGCCGTGCCCA -GGGGCCCACAGG-GAACCCTGCTTGCACTTTGTAACATGTTTA-----CTTTTCagggca -tcttagctt---ctatta-----tagccacatccctttga---aacaagataactgagaa -tttaaaaataagaa-----aata--TGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGC -TTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGC -TTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACG -CAAATGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAA -ACGCATGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAA -AACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAA -AACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGA -GAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGA -GAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGA -GAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATC -CATCCAGAATAAAACGCAgttcgatgcctaaaataccttcttttgtccctacacagacca -cagttttcctaatggctttacaccgactagaaattcttgtgcaagcactaattgaaagcg -gttggcctagagtgttaccggtttgtatagctgagcgcgtctcttgccctgatcaaaggt -tcattttctctactttggaagacgttgtggaagaatacaacaagtacgagtctctccccc -ctggtttgctgattactggatacagttgtaatacccttcgcaacaccgcgtaactatcta -tatgaattattttccctttattatatgtagtaggttcgtctttaatcttcctttagcaag -tcttttactgttttcgacctcaatgttcatgttcttaggttgttttggataatatgcggt -cagtttaatcttcgttgtttcttcttaaaatatttattcatggtttaatttttggtttgt -acttgttcaggggccagttcattatttactctgtttgtatacagcagttcttttattttt -agtatgattttaatttaaaacaattctaatggtcaaaaa diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_patmatdb_out.tabular --- a/test-data/emboss_patmatdb_out.tabular +++ /dev/null @@ -1,41 +0,0 @@ -SeqName Start End Score Strand -Sequence 560 561 2 + -Sequence 559 560 2 + -Sequence 558 559 2 + -Sequence 557 558 2 + -Sequence 550 551 2 + -Sequence 544 545 2 + -Sequence 541 542 2 + -Sequence 540 541 2 + -Sequence 539 540 2 + -Sequence 534 535 2 + -Sequence 449 450 2 + -Sequence 431 432 2 + -Sequence 430 431 2 + -Sequence 429 430 2 + -Sequence 409 410 2 + -Sequence 393 394 2 + -Sequence 364 365 2 + -Sequence 340 341 2 + -Sequence 326 327 2 + -Sequence 287 288 2 + -Sequence 274 275 2 + -Sequence 264 265 2 + -Sequence 252 253 2 + -Sequence 204 205 2 + -Sequence 201 202 2 + -Sequence 196 197 2 + -Sequence 193 194 2 + -Sequence 181 182 2 + -Sequence 158 159 2 + -Sequence 157 158 2 + -Sequence 98 99 2 + -Sequence 97 98 2 + -Sequence 92 93 2 + -Sequence 85 86 2 + -Sequence 74 75 2 + -Sequence 73 74 2 + -Sequence 53 54 2 + -Sequence 14 15 2 + -Sequence 13 14 2 + -Sequence 12 13 2 + diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_pepcoil_out.pepcoil --- a/test-data/emboss_pepcoil_out.pepcoil +++ /dev/null @@ -1,6 +0,0 @@ -PEPCOIL of Sequence - using a window of 28 residues - - -Other structures from 1 to 561 (561 residues) - Max score: 0.827 (probability 0.00) diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_pepstats_out.pepstats --- a/test-data/emboss_pepstats_out.pepstats +++ /dev/null @@ -1,48 +0,0 @@ -PEPSTATS of Sequence from 1 to 561 - -Molecular weight = 48582.66 Residues = 561 -Average Residue Weight = 86.600 Charge = 0.0 -Isoelectric Point = 5.0278 -A280 Molar Extinction Coefficient = 0 -A280 Extinction Coefficient 1mg/ml = 0.00 -Improbability of expression in inclusion bodies = 0.520 - -Residue Number Mole% DayhoffStat -A = Ala 135 24.064 2.798 -B = Asx 0 0.000 0.000 -C = Cys 106 18.895 6.515 -D = Asp 0 0.000 0.000 -E = Glu 0 0.000 0.000 -F = Phe 0 0.000 0.000 -G = Gly 98 17.469 2.080 -H = His 0 0.000 0.000 -I = Ile 0 0.000 0.000 -J = --- 0 0.000 0.000 -K = Lys 0 0.000 0.000 -L = Leu 0 0.000 0.000 -M = Met 0 0.000 0.000 -N = Asn 0 0.000 0.000 -O = --- 0 0.000 0.000 -P = Pro 0 0.000 0.000 -Q = Gln 0 0.000 0.000 -R = Arg 0 0.000 0.000 -S = Ser 0 0.000 0.000 -T = Thr 222 39.572 6.487 -U = --- 0 0.000 0.000 -V = Val 0 0.000 0.000 -W = Trp 0 0.000 0.000 -X = Xaa 0 0.000 0.000 -Y = Tyr 0 0.000 0.000 -Z = Glx 0 0.000 0.000 - -Property Residues Number Mole% -Tiny (A+C+G+S+T) 561 100.000 -Small (A+B+C+D+G+N+P+S+T+V) 561 100.000 -Aliphatic (A+I+L+V) 135 24.064 -Aromatic (F+H+W+Y) 0 0.000 -Non-polar (A+C+F+G+I+L+M+P+V+W+Y) 339 60.428 -Polar (D+E+H+K+N+Q+R+S+T+Z) 222 39.572 -Charged (B+D+E+H+K+R+Z) 0 0.000 -Basic (H+K+R) 0 0.000 -Acidic (B+D+E+Z) 0 0.000 - diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_plotorf_out.png Binary file test-data/emboss_plotorf_out.png has changed diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_plotorf_out1.png Binary file test-data/emboss_plotorf_out1.png has changed diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_polydot_out.png Binary file test-data/emboss_polydot_out.png has changed diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_prettyseq_out.prettyseq --- a/test-data/emboss_prettyseq_out.prettyseq +++ /dev/null @@ -1,42 +0,0 @@ -PRETTYSEQ of Sequence from 1 to 561 - - ---------|---------|---------|---------|---------|---------| - 1 gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt 60 - 1 V R C L K Y L L L S L H R P Q F S * W L 2 - - ---------|---------|---------|---------|---------|---------| - 61 tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac 120 - 3 Y T D * K F L C K H * L K A V G L E C Y 9 - - ---------|---------|---------|---------|---------|---------| - 121 cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg 180 - 10 R F V * L S A S L A L I K G S F S L L W 16 - - ---------|---------|---------|---------|---------|---------| - 181 aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg 240 - 17 K T L W K N T T S T S L S P L V C * L L 2 - - ---------|---------|---------|---------|---------|---------| - 241 gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt 300 - 3 D T V V I P F A T P R N Y L Y E L F S L 22 - - ---------|---------|---------|---------|---------|---------| - 301 tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac 360 - 23 Y Y M * * V R L * S S F S K S F T V F D 11 - - ---------|---------|---------|---------|---------|---------| - 361 ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt 420 - 12 L N V H V L R L F W I I C G Q F N L R C 31 - - ---------|---------|---------|---------|---------|---------| - 421 ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt 480 - 32 F F L K Y L F M V * F L V C T C S G A S 10 - - ---------|---------|---------|---------|---------|---------| - 481 tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa 540 - 11 S L F T L F V Y S S S F I F S M I L I * 29 - - ---------|---------|- - 541 aacaattctaatggtcaaaaa 561 - 1 N N S N G Q K 7 - diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_primersearch.fasta --- a/test-data/emboss_primersearch.fasta +++ /dev/null @@ -1,7 +0,0 @@ -# This is my primer file -D1S243 cacacaggctcacatgcc gctccagcgtcatggact -D1S468 aattaaccgttttggtcct gcgacacacacttccc -D1S2845 ccaaagggtgcttctc gtggcattccaacctc -D1S1608 gatggcttttggggactatt cactgagccaagtgacacag -D1S2893 aaaacatcaactctcccctg ctcaaaccccaataagcctt -D1S2660 cacacatgcacatgcac agtgacaccagcaggg diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_primersearch_out.primersearch --- a/test-data/emboss_primersearch_out.primersearch +++ /dev/null @@ -1,12 +0,0 @@ - -Primer name D1S243 - -Primer name D1S468 - -Primer name D1S2845 - -Primer name D1S1608 - -Primer name D1S2893 - -Primer name D1S2660 diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_revseq_out.fasta --- a/test-data/emboss_revseq_out.fasta +++ /dev/null @@ -1,11 +0,0 @@ ->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -tttttgaccattagaattgttttaaattaaaatcatactaaaaataaaagaactgctgta -tacaaacagagtaaataatgaactggcccctgaacaagtacaaaccaaaaattaaaccat -gaataaatattttaagaagaaacaacgaagattaaactgaccgcatattatccaaaacaa -cctaagaacatgaacattgaggtcgaaaacagtaaaagacttgctaaaggaagattaaag -acgaacctactacatataataaagggaaaataattcatatagatagttacgcggtgttgc -gaagggtattacaactgtatccagtaatcagcaaaccaggggggagagactcgtacttgt -tgtattcttccacaacgtcttccaaagtagagaaaatgaacctttgatcagggcaagaga -cgcgctcagctatacaaaccggtaacactctaggccaaccgctttcaattagtgcttgca -caagaatttctagtcggtgtaaagccattaggaaaactgtggtctgtgtagggacaaaag -aaggtattttaggcatcgaac diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_seqmatchall_out.fasta --- a/test-data/emboss_seqmatchall_out.fasta +++ /dev/null @@ -1,3 +0,0 @@ - -#--------------------------------------- -#--------------------------------------- diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_seqret_out.fasta --- a/test-data/emboss_seqret_out.fasta +++ /dev/null @@ -1,11 +0,0 @@ ->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt -tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac -cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg -aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg -gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt -tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac -ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt -ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt -tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa -aacaattctaatggtcaaaaa diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_sigcleave_out.tabular --- a/test-data/emboss_sigcleave_out.tabular +++ /dev/null @@ -1,6 +0,0 @@ -SeqName Start End Score Strand mature_peptide -Sequence 27 39 5.175 + CCACAGTTTTCCTAATGGCTTTACACCGACTAGAAATTCTTGTGCAAGCA -Sequence 253 265 4.809 + CACCGCGTAACTATCTATATGAATTATTTTCCCTTTATTATATGTAGTAG -Sequence 29 41 4.790 + ACAGTTTTCCTAATGGCTTTACACCGACTAGAAATTCTTGTGCAAGCACT -Sequence 541 553 3.820 + GTCAAAAA -Sequence 30 42 3.530 + CAGTTTTCCTAATGGCTTTACACCGACTAGAAATTCTTGTGCAAGCACTA diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_sirna_out.fasta --- a/test-data/emboss_sirna_out.fasta +++ /dev/null @@ -1,158 +0,0 @@ ->Sequence_92 %GC 50.0 Score 9 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -aattgaaagcggttggcctagag ->Sequence_53 %GC 45.0 Score 8 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -aatggctttacaccgactagaaa ->Sequence_97 %GC 55.0 Score 8 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -aaagcggttggcctagagtgtta ->Sequence_98 %GC 55.0 Score 8 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -aagcggttggcctagagtgttac ->Sequence_201 %GC 55.0 Score 8 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -aacaagtacgagtctctcccccc ->Sequence_14 %GC 40.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -aataccttcttttgtccctacac ->Sequence_85 %GC 40.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -aagcactaattgaaagcggttgg ->Sequence_181 %GC 40.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -aagacgttgtggaagaatacaac ->Sequence_196 %GC 40.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -aatacaacaagtacgagtctctc ->Sequence_204 %GC 60.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -aagtacgagtctctcccccctgg ->Sequence_252 %GC 60.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -aatacccttcgcaacaccgcgta ->Sequence_264 %GC 40.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -aacaccgcgtaactatctatatg ->Sequence_38 %GC 45.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gaccacagttttcctaatggctt ->Sequence_73 %GC 35.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -aaattcttgtgcaagcactaatt ->Sequence_96 %GC 55.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gaaagcggttggcctagagtgtt ->Sequence_118 %GC 50.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -taccggtttgtatagctgagcgc ->Sequence_200 %GC 50.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -caacaagtacgagtctctccccc ->Sequence_326 %GC 35.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -aatcttcctttagcaagtctttt ->Sequence_364 %GC 35.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -aatgttcatgttcttaggttgtt ->Sequence_12 %GC 35.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -aaaataccttcttttgtccctac ->Sequence_13 %GC 35.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -aaataccttcttttgtccctaca ->Sequence_16 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -taccttcttttgtccctacacag ->Sequence_32 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -tacacagaccacagttttcctaa ->Sequence_52 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -taatggctttacaccgactagaa ->Sequence_74 %GC 35.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -aattcttgtgcaagcactaattg ->Sequence_88 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -cactaattgaaagcggttggcct ->Sequence_91 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -taattgaaagcggttggcctaga ->Sequence_128 %GC 55.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -tatagctgagcgcgtctcttgcc ->Sequence_173 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -tactttggaagacgttgtggaag ->Sequence_193 %GC 35.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -aagaatacaacaagtacgagtct ->Sequence_198 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -tacaacaagtacgagtctctccc ->Sequence_243 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -tacagttgtaatacccttcgcaa ->Sequence_251 %GC 55.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -taatacccttcgcaacaccgcgt ->Sequence_313 %GC 40.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -taggttcgtctttaatcttcctt ->Sequence_340 %GC 35.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -aagtcttttactgttttcgacct ->Sequence_393 %GC 35.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -aatatgcggtcagtttaatcttc ->Sequence_489 %GC 40.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -tactctgtttgtatacagcagtt ->Sequence_34 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -cacagaccacagttttcctaatg ->Sequence_36 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -cagaccacagttttcctaatggc ->Sequence_61 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -tacaccgactagaaattcttgtg ->Sequence_63 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -caccgactagaaattcttgtgca ->Sequence_70 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -tagaaattcttgtgcaagcacta ->Sequence_84 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -caagcactaattgaaagcggttg ->Sequence_110 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -tagagtgttaccggtttgtatag ->Sequence_112 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gagtgttaccggtttgtatagct ->Sequence_135 %GC 60.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gagcgcgtctcttgccctgatca ->Sequence_180 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gaagacgttgtggaagaatacaa ->Sequence_183 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gacgttgtggaagaatacaacaa ->Sequence_203 %GC 60.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -caagtacgagtctctcccccctg ->Sequence_210 %GC 60.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gagtctctcccccctggtttgct ->Sequence_245 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -cagttgtaatacccttcgcaaca ->Sequence_254 %GC 60.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -tacccttcgcaacaccgcgtaac ->Sequence_263 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -caacaccgcgtaactatctatat ->Sequence_266 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -caccgcgtaactatctatatgaa ->Sequence_348 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -tactgttttcgacctcaatgttc ->Sequence_395 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -tatgcggtcagtttaatcttcgt ->Sequence_157 %GC 30.0 Score 3 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -aaaggttcattttctctactttg ->Sequence_158 %GC 30.0 Score 3 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -aaggttcattttctctactttgg ->Sequence_207 %GC 65.0 Score 3 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -tacgagtctctcccccctggttt ->Sequence_325 %GC 35.0 Score 3 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -taatcttcctttagcaagtcttt ->Sequence_392 %GC 35.0 Score 3 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -taatatgcggtcagtttaatctt ->Sequence_409 %GC 30.0 Score 3 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -aatcttcgttgtttcttcttaaa ->Sequence_11 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -taaaataccttcttttgtcccta ->Sequence_41 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -cacagttttcctaatggctttac ->Sequence_43 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -cagttttcctaatggctttacac ->Sequence_67 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gactagaaattcttgtgcaagca ->Sequence_72 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gaaattcttgtgcaagcactaat ->Sequence_130 %GC 65.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -tagctgagcgcgtctcttgccct ->Sequence_192 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gaagaatacaacaagtacgagtc ->Sequence_195 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gaatacaacaagtacgagtctct ->Sequence_236 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -tactggatacagttgtaataccc ->Sequence_241 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gatacagttgtaatacccttcgc ->Sequence_304 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -tatatgtagtaggttcgtcttta ->Sequence_306 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -tatgtagtaggttcgtctttaat ->Sequence_310 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -tagtaggttcgtctttaatcttc ->Sequence_358 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gacctcaatgttcatgttcttag ->Sequence_370 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -catgttcttaggttgttttggat ->Sequence_156 %GC 30.0 Score 1 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -caaaggttcattttctctacttt ->Sequence_403 %GC 30.0 Score 1 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -cagtttaatcttcgttgtttctt diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_sixpack_out2.sixpack --- a/test-data/emboss_sixpack_out2.sixpack +++ /dev/null @@ -1,134 +0,0 @@ - - - V R C L K Y L L L S L H R P Q F S * W L F1 - F D A * N T F F C P Y T D H S F P N G F F2 - S M P K I P S F V P T Q T T V F L M A L F3 - gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt - 10 20 30 40 50 60 - ----:----|----:----|----:----|----:----|----:----|----:----| - caagctacggattttatggaagaaaacagggatgtgtctggtgtcaaaaggattaccgaa - T R H R F Y R R K D R C L G C N E * H S F6 - X E I G L I G E K T G V C V V T K R I A F5 - N S A * F V K K Q G * V S W L K G L P K F4 - - - Y T D * K F L C K H * L K A V G L E C Y F1 - T P T R N S C A S T N * K R L A * S V T F2 - H R L E I L V Q A L I E S G W P R V L P F3 - tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac - 70 80 90 100 110 120 - ----:----|----:----|----:----|----:----|----:----|----:----| - atgtggctgatctttaagaacacgttcgtgattaactttcgccaaccggatctcacaatg - * V S * F N K H L C * N F A T P R S H * F6 - K C R S S I R T C A S I S L P Q G L T N F5 - V G V L F E Q A L V L Q F R N A * L T V F4 - - - R F V * L S A S L A L I K G S F S L L W F1 - G L Y S * A R L L P * S K V H F L Y F G F2 - V C I A E R V S C P D Q R F I F S T L E F3 - cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg - 130 140 150 160 170 180 - ----:----|----:----|----:----|----:----|----:----|----:----| - gccaaacatatcgactcgcgcagagaacgggactagtttccaagtaaaagagatgaaacc - R N T Y S L A D R A R I L P E N E R S Q F6 - G T Q I A S R T E Q G S * L N M K E V K F5 - P K Y L Q A R R K G Q D F T * K R * K P F4 - - - K T L W K N T T S T S L S P L V C * L L F1 - R R C G R I Q Q V R V S P P W F A D Y W F2 - D V V E E Y N K Y E S L P P G L L I T G F3 - aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg - 190 200 210 220 230 240 - ----:----|----:----|----:----|----:----|----:----|----:----| - ttctgcaacaccttcttatgttgttcatgctcagagaggggggaccaaacgactaatgac - F V N H F F V V L V L R E G R T Q Q N S F6 - S S T T S S Y L L Y S D R G G P K S I V F5 - L R Q P L I C C T R T E G G Q N A S * Q F4 - - - D T V V I P F A T P R N Y L Y E L F S L F1 - I Q L * Y P S Q H R V T I Y M N Y F P F F2 - Y S C N T L R N T A * L S I * I I F P L F3 - gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt - 250 260 270 280 290 300 - ----:----|----:----|----:----|----:----|----:----|----:----| - ctatgtcaacattatgggaagcgttgtggcgcattgatagatatacttaataaaagggaa - S V T T I G K A V G R L * R Y S N N E R F6 - P Y L Q L V R R L V A Y S D I H I I K G F5 - I C N Y Y G E C C R T V I * I F * K G K F4 - - - Y Y M * * V R L * S S F S K S F T V F D F1 - I I C S R F V F N L P L A S L L L F S T F2 - L Y V V G S S L I F L * Q V F Y C F R P F3 - tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac - 310 320 330 340 350 360 - ----:----|----:----|----:----|----:----|----:----|----:----| - ataatatacatcatccaagcagaaattagaaggaaatcgttcagaaaatgacaaaagctg - * * I Y Y T R R * D E K L L D K V T K S F6 - K N Y T T P E D K I K R * C T K * Q K R F5 - I I H L L N T K L R G K A L R K S N E V F4 - - - L N V H V L R L F W I I C G Q F N L R C F1 - S M F M F L G C F G * Y A V S L I F V V F2 - Q C S C S * V V L D N M R S V * S S L F F3 - ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt - 370 380 390 400 410 420 - ----:----|----:----|----:----|----:----|----:----|----:----| - gagttacaagtacaagaatccaacaaaacctattatacgccagtcaaattagaagcaaca - R L T * T R L N N Q I I H P * N L R R Q F6 - G * H E H E * T T K S L I R D T * D E N F5 - E I N M N K P Q K P Y Y A T L K I K T T F4 - - - F F L K Y L F M V * F L V C T C S G A S F1 - S S * N I Y S W F N F W F V L V Q G P V F2 - L L K I F I H G L I F G L Y L F R G Q F F3 - ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt - 430 440 450 460 470 480 - ----:----|----:----|----:----|----:----|----:----|----:----| - aagaagaattttataaataagtaccaaattaaaaaccaaacatgaacaagtccccggtca - K K K F Y K N M T * N K T Q V Q E P A L F6 - N R R L I N I * P K I K P K Y K N L P W F5 - E E * F I * E H N L K Q N T S T * P G T F4 - - - S L F T L F V Y S S S F I F S M I L I * F1 - H Y L L C L Y T A V L L F L V * F * F K F2 - I I Y S V C I Q Q F F Y F * Y D F N L K F3 - tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa - 490 500 510 520 530 540 - ----:----|----:----|----:----|----:----|----:----|----:----| - agtaataaatgagacaaacatatgtcgtcaagaaaataaaaatcatactaaaattaaatt - E N N V R N T Y L L E K I K L I I K I * F6 - N M I * E T Q I C C N K * K * Y S K L K F5 - * * K S Q K Y V A T R K N K T H N * N L F4 - - - N N S N G Q K F1 - T I L M V K X F2 - Q F * W S K X F3 - aacaattctaatggtcaaaaa - 550 560 - ----:----|----:----|- - ttgttaagattaccagttttt - F L E L P * F F6 - F C N * H D F F5 - V I R I T L F F4 - -############################## -Minimum size of ORFs : 1 - -Total ORFs in frame 1 : 10 -Total ORFs in frame 2 : 11 -Total ORFs in frame 3 : 8 -Total ORFs in frame 4 : 14 -Total ORFs in frame 5 : 12 -Total ORFs in frame 6 : 14 - -Total ORFs : 69 -############################## - diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_skipseq_out.fasta --- a/test-data/emboss_skipseq_out.fasta +++ /dev/null @@ -1,11 +0,0 @@ ->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt -tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac -cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg -aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg -gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt -tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac -ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt -ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt -tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa -aacaattctaatggtcaaaaa diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_splitter_out.fasta --- a/test-data/emboss_splitter_out.fasta +++ /dev/null @@ -1,11 +0,0 @@ ->Sequence_1-561 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt -tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac -cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg -aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg -gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt -tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac -ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt -ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt -tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa -aacaattctaatggtcaaaaa diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_supermatcher_out.fasta --- a/test-data/emboss_supermatcher_out.fasta +++ /dev/null @@ -1,24 +0,0 @@ ->hg17 -CCCTAGAGCTTCTGAGCCCTCAACAG--------AGATGAACTGGACTCTCTGCAGCCCC -ACTCTAAATTC-----------CTAAGAGAGAAGTTGATTGACCCAATCAG-------GG -TCAGGAGAAGGAAGGGAGGAGGAAAGGGAG---------GAGAGAAGAGCCTCTTCGTCT -CTTGCCTACCAC--TGGCCAGGCAATTGTAG---------CCAAGGGGGCT-GGAGTGTA -AATGCAAACATAGCC----------ATCAAGGGTt---gtgtatgtgtgtgtgt------ -----gtgtctgtgtgtgtgtatgtgtgtCTCTTGGGTAGGTTAGATCTCCC--------- ----AGGAGGTCCCTAC--TAAACAGACTTAAGCCCGCAAAA---TTTTA--GCTCTCCAG -CCTCACACACTCCACCCCTCTAC-----CATA-------TTGAATCTTCCCAAACCAACT -ATG-GCT---TTCCCTAA-CTCCGGAGcttggcctggaa--------tgccctgcttccc -ct--ctttcccctgg---ggaacgcctgtccttcaggcctcagttca-----cacactgc -ctcccttgca-----aagctct ->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -ccctaca----caga-----ccacagttttcctaa-------tgg---ctttaca--ccg -actagaaattcttgtgcaagcactaattga-aag-cggttggccta--gagtgttaccgg -tttgta------------tagctgagcgcgtctcttgccctgatcaaaggttcattttct -ct--------actttgg--aagacgttgtggaagaatacaacaag-----tacgagtctc -tcccc--------cctggtttgctgattactggatacagt-----------tgtaatacc -cttcgcaacaccgcgtaactatctatat-------gaa--tta-ttttccctttattata -tgtagtaggttcgt-ctttaatcttcctttagc------aagtcttttactgttttcga- -cctca------------atgttcatgttcttaggttgttttggat------------aat -atgcggtcagtt---taatcttcgttgtttcttcttaaaatatttatt--catggtt--- --taatttt----tggtttgta---cttg---ttcaggggccagttcattatttactctg- -----tttgtatacagcagttct diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_syco_out.syco --- a/test-data/emboss_syco_out.syco +++ /dev/null @@ -1,484 +0,0 @@ -SYCO of Sequence from 1 to 561 - - -Frame 1 -Mid base Gribskov value -46 1.007 -49 1.014 -52 1.012 -55 1.002 -58 1.003 -61 0.997 -64 0.998 -67 0.996 -70 1.005 -73 1.006 -76 1.007 -79 1.020 -82 1.008 -85 1.000 -88 0.995 -91 1.005 -94 1.023 -97 1.011 -100 1.008 -103 1.003 -106 1.017 -109 1.028 -112 1.029 -115 1.019 -118 1.013 -121 1.014 -124 1.003 -127 1.003 -130 0.990 -133 0.981 -136 0.975 -139 0.981 -142 0.983 -145 0.981 -148 0.987 -151 1.000 -154 0.989 -157 0.997 -160 0.995 -163 0.998 -166 0.988 -169 0.981 -172 0.993 -175 1.007 -178 1.016 -181 1.016 -184 0.994 -187 1.006 -190 1.017 -193 1.008 -196 1.016 -199 0.995 -202 0.987 -205 0.982 -208 0.983 -211 0.978 -214 0.989 -217 1.000 -220 1.006 -223 1.013 -226 1.008 -229 0.992 -232 1.002 -235 1.002 -238 0.996 -241 0.987 -244 0.988 -247 0.972 -250 0.966 -253 0.973 -256 0.972 -259 0.968 -262 0.956 -265 0.951 -268 0.942 -271 0.923 -274 0.923 -277 0.907 -280 0.897 -283 0.908 -286 0.888 -289 0.896 -292 0.891 -295 0.911 -298 0.923 -301 0.924 -304 0.914 -307 0.904 -310 0.896 -313 0.901 -316 0.910 -319 0.928 -322 0.918 -325 0.914 -328 0.915 -331 0.911 -334 0.910 -337 0.927 -340 0.926 -343 0.917 -346 0.922 -349 0.920 -352 0.917 -355 0.923 -358 0.917 -361 0.926 -364 0.931 -367 0.937 -370 0.937 -373 0.929 -376 0.930 -379 0.931 -382 0.940 -385 0.915 -388 0.908 -391 0.908 -394 0.899 -397 0.909 -400 0.918 -403 0.904 -406 0.896 -409 0.885 -412 0.884 -415 0.884 -418 0.885 -421 0.889 -424 0.889 -427 0.884 -430 0.892 -433 0.903 -436 0.902 -439 0.906 -442 0.900 -445 0.890 -448 0.893 -451 0.903 -454 0.903 -457 0.899 -460 0.910 -463 0.932 -466 0.935 -469 0.925 -472 0.915 -475 0.926 -478 0.925 -481 0.929 -484 0.943 -487 0.934 -490 0.920 -493 0.925 -496 0.925 -499 0.935 -502 0.936 -505 0.939 -508 0.940 -511 0.936 -514 0.932 - - -Frame 2 -Mid base Gribskov value -47 1.003 -50 0.992 -53 1.002 -56 0.997 -59 1.006 -62 1.005 -65 1.007 -68 0.997 -71 1.001 -74 0.996 -77 0.997 -80 0.982 -83 0.975 -86 0.965 -89 0.971 -92 0.977 -95 0.975 -98 0.968 -101 0.979 -104 0.968 -107 0.978 -110 0.982 -113 0.984 -116 0.994 -119 0.984 -122 0.983 -125 0.984 -128 0.996 -131 1.004 -134 0.986 -137 0.992 -140 0.997 -143 0.980 -146 0.972 -149 0.966 -152 0.971 -155 0.956 -158 0.950 -161 0.943 -164 0.944 -167 0.933 -170 0.944 -173 0.944 -176 0.955 -179 0.949 -182 0.944 -185 0.945 -188 0.952 -191 0.941 -194 0.952 -197 0.946 -200 0.934 -203 0.943 -206 0.935 -209 0.940 -212 0.952 -215 0.953 -218 0.937 -221 0.923 -224 0.934 -227 0.938 -230 0.930 -233 0.936 -236 0.949 -239 0.943 -242 0.944 -245 0.946 -248 0.950 -251 0.954 -254 0.968 -257 0.968 -260 0.962 -263 0.960 -266 0.949 -269 0.943 -272 0.946 -275 0.956 -278 0.963 -281 0.963 -284 0.952 -287 0.947 -290 0.950 -293 0.930 -296 0.934 -299 0.936 -302 0.925 -305 0.915 -308 0.939 -311 0.943 -314 0.928 -317 0.930 -320 0.936 -323 0.941 -326 0.938 -329 0.943 -332 0.949 -335 0.939 -338 0.935 -341 0.934 -344 0.924 -347 0.929 -350 0.929 -353 0.932 -356 0.930 -359 0.934 -362 0.930 -365 0.911 -368 0.916 -371 0.925 -374 0.921 -377 0.917 -380 0.916 -383 0.924 -386 0.922 -389 0.919 -392 0.921 -395 0.930 -398 0.912 -401 0.916 -404 0.920 -407 0.909 -410 0.908 -413 0.908 -416 0.898 -419 0.890 -422 0.880 -425 0.885 -428 0.899 -431 0.907 -434 0.912 -437 0.904 -440 0.901 -443 0.901 -446 0.893 -449 0.897 -452 0.894 -455 0.903 -458 0.890 -461 0.886 -464 0.894 -467 0.894 -470 0.894 -473 0.885 -476 0.884 -479 0.875 -482 0.870 -485 0.879 -488 0.878 -491 0.875 -494 0.875 -497 0.876 -500 0.881 -503 0.878 -506 0.876 -509 0.883 -512 0.891 -515 0.896 - - -Frame 3 -Mid base Gribskov value -48 0.929 -51 0.933 -54 0.930 -57 0.946 -60 0.940 -63 0.947 -66 0.947 -69 0.953 -72 0.968 -75 0.950 -78 0.949 -81 0.939 -84 0.929 -87 0.915 -90 0.910 -93 0.922 -96 0.921 -99 0.931 -102 0.925 -105 0.935 -108 0.945 -111 0.935 -114 0.930 -117 0.940 -120 0.949 -123 0.949 -126 0.960 -129 0.944 -132 0.947 -135 0.943 -138 0.946 -141 0.955 -144 0.949 -147 0.948 -150 0.953 -153 0.950 -156 0.960 -159 0.965 -162 0.958 -165 0.979 -168 0.987 -171 0.991 -174 1.003 -177 1.017 -180 1.018 -183 1.004 -186 0.994 -189 1.008 -192 1.010 -195 0.998 -198 1.002 -201 1.013 -204 1.021 -207 1.012 -210 1.002 -213 1.013 -216 1.001 -219 1.012 -222 1.024 -225 1.037 -228 1.035 -231 1.025 -234 1.028 -237 1.011 -240 1.007 -243 1.016 -246 1.006 -249 0.997 -252 0.999 -255 0.989 -258 0.971 -261 0.962 -264 0.950 -267 0.936 -270 0.931 -273 0.931 -276 0.928 -279 0.907 -282 0.897 -285 0.910 -288 0.915 -291 0.904 -294 0.902 -297 0.899 -300 0.905 -303 0.895 -306 0.905 -309 0.896 -312 0.887 -315 0.877 -318 0.879 -321 0.874 -324 0.875 -327 0.878 -330 0.880 -333 0.871 -336 0.871 -339 0.866 -342 0.853 -345 0.851 -348 0.861 -351 0.870 -354 0.874 -357 0.887 -360 0.892 -363 0.892 -366 0.897 -369 0.897 -372 0.903 -375 0.891 -378 0.881 -381 0.881 -384 0.879 -387 0.884 -390 0.875 -393 0.875 -396 0.866 -399 0.865 -402 0.861 -405 0.852 -408 0.852 -411 0.856 -414 0.852 -417 0.850 -420 0.859 -423 0.859 -426 0.867 -429 0.879 -432 0.893 -435 0.903 -438 0.912 -441 0.913 -444 0.910 -447 0.910 -450 0.908 -453 0.908 -456 0.906 -459 0.905 -462 0.918 -465 0.929 -468 0.939 -471 0.940 -474 0.940 -477 0.939 -480 0.943 -483 0.943 -486 0.942 -489 0.943 -492 0.948 -495 0.948 -498 0.948 -501 0.943 -504 0.958 -507 0.960 -510 0.954 -513 0.956 -516 0.947 diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_tranalign_out.fasta --- a/test-data/emboss_tranalign_out.fasta +++ /dev/null @@ -1,45 +0,0 @@ ->HSFAU1 -cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag -ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc -cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg -ctcctggcaggc---cccctggaggatgaggccactctgggccagtgcggggtggaggcc -ctgactaccctggaagtagcaggccgcatgcttgga---ggtaaagttcatggttccctg -gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag -aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg -cccacctttggcaagaagaagggccccaatgccaactct ->HSFAU2 -cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag -ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc -cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg -ctcctggcaggcgcgcccctggaggatgcactctgggccagtgcggggtggaggccc--- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------- ->HSFAU3 -cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag -ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc -cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg -ctcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggcc -ctgactaccctggaagtagcaggccgcatgcttgga---ggtaaagttcatggttccctg -gcccgtgctggaaaagtgagaggtcagactcctaagggggccaaacaggagaagaagaag -aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg -cccacctttggcaagaagaagggccccaatgccaactct ->HSFAU4 -cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag -ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc -cagatcaaggctcatgaaatagcctcactggagggcattgccccggaagatcaagtcgtg -ctcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggcc -ctgactaccctggaagtagcaggccgcatgcttgcccgaggtaaagttcatggttccctg -gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag -aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg -cccacctttggcaagaagaagggccccaatgccaactct ->HSFAU5 -cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag -ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc -cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg -ctcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggcc -ctgactaccctggaagtaggccgcatgctttttgga---ggtaaagttcatggttccctg -gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag -aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg -cccacctttggcaagaagaagggccccaatgccaactct \ No newline at end of file diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_transeq_out.fasta --- a/test-data/emboss_transeq_out.fasta +++ /dev/null @@ -1,5 +0,0 @@ ->Sequence_1 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -VRCLKYLLLSLHRPQFS*WLYTD*KFLCKH*LKAVGLECYRFV*LSASLALIKGSFSLLW -KTLWKNTTSTSLSPLVC*LLDTVVIPFATPRNYLYELFSLYYM**VRL*SSFSKSFTVFD -LNVHVLRLFWIICGQFNLRCFFLKYLFMV*FLVCTCSGASSLFTLFVYSSSFIFSMILI* -NNSNGQK diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_trimest_out.fasta --- a/test-data/emboss_trimest_out.fasta +++ /dev/null @@ -1,11 +0,0 @@ ->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; [poly-A tail removed] -gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt -tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac -cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg -aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg -gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt -tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac -ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt -ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt -tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa -aacaattctaatggtc diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_trimseq_out.fasta --- a/test-data/emboss_trimseq_out.fasta +++ /dev/null @@ -1,11 +0,0 @@ ->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt -tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac -cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg -aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg -gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt -tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac -ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt -ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt -tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa -aacaattctaatggtcaaaaa diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_union_out.fasta --- a/test-data/emboss_union_out.fasta +++ /dev/null @@ -1,11 +0,0 @@ ->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt -tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac -cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg -aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg -gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt -tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac -ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt -ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt -tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa -aacaattctaatggtcaaaaa diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_water_out.fasta --- a/test-data/emboss_water_out.fasta +++ /dev/null @@ -1,32 +0,0 @@ ->hg17 -GTTTGAAGTTGAGATGTGGGTACAATACCATAGCTTTATTC------CAGAGCAGGGTAT -TTGTTTCCAAATGCCATGTTCCCAGCAGCTGCCCTTGACTGGGAATTGGGGTGTGATTTG -GGCTTTT-----CCTTAAATCCTTGAGGAGCTGGAGGGGTGGGTGGCTCGCACTCCTGCT -TTctggatctgaatcctgactctgtcatggacctgtttgactttgggcaagttgactcct -attcctgagccccatatttttctcttctgtgaaattcagattaaaaAAACATGGCTTTGA -TCAAA----CATTATAAATAATATATAGACAGACTGCTTGTTTTTATTGTATTGCCAGAA -ATGAATCCTACTAATA-------------------TTGC-CATCTA-TGG--ACAGAAAA -TGTATTACCTGTCTTCATCAAGACCCAGACGAGGAAGAACACGAAAAGCGGA-------- ----GATTAATTTTACTGCC-------ATCTCCAGAA---CCGTCATCCTAATATTTACTT -A-CA----TTTTATTATTATTTCAGGCTC-ATGCACATATACTTAG-----CATGGATCA -T-TGGCCACAGACTCGCATACATTTAA-CTTTATTACCTTTTGCCTCATGTATCTCATTA -AAATTTTGCTGCTTAATCAAGGATCTGCATATTATTTTAATTTTAGAATTCACAGTTCCA -AGACTTTGAAAGTTTCAAGCGTTCTGGGTGaatgtgttatgctctctcccgcca--ccat -gtctttataccccctgatttct---cagccactatggcaaccactttctactcttagta- -gcccat----atttagtccaatccccagctcaggagacacttct ->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; -gttcga----------tgcctaaaatacctt--cttttgtccctacacagaccacagt-- ----tttcctaatggc---tttacacc----------gactagaaatt------------- ---cttgtgcaagcactaa----ttga-aagc---------ggttggc------------- ---ctaga--------------gtgt----taccggtttg--------------------t -atagctgagcgc-------gtctctt---------------------------gccctga -tcaaaggttcattttctctact---ttggaagac-----------gttgt-------gga -a-gaatacaacaagtacgagtctctcccccctggtttgctgat-tactggatacag---t -tgtaatacc---cttc-gcaacacc----------------------gcgtaactatcta -tatgaattatttt----ccctttattatatgtagtaggttcgtctt--taatcttccttt -agcaagtcttttactgt--tttcgacctcaatgttcatgttcttaggttgttttggataa -tatgcggtcag-----------tttaatcttcgt--------------tgtttcttctta -aaatat------ttattcatgg-------------tttaatttttggttt----gt---- ---actt--------------gttcaggg----------------------gccagttcat --tattta----ctctg-tttgtatacagc----------agttcttt-tatttttagtat -g---attttaattta-------------------aaacaattct diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_water_out.score --- a/test-data/emboss_water_out.score +++ /dev/null @@ -1,4 +0,0 @@ -Sequence hg17 884 (610.5) - -#--------------------------------------- -#--------------------------------------- diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_wobble_out.png Binary file test-data/emboss_wobble_out.png has changed diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_wobble_out.wobble --- a/test-data/emboss_wobble_out.wobble +++ /dev/null @@ -1,1 +0,0 @@ -Expected GC content in third position = 36.36 diff -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 -r 4dd1e50e78ef1c8e2f7bed547eaf3113efa55914 test-data/emboss_wordcount_out.wordcount --- a/test-data/emboss_wordcount_out.wordcount +++ /dev/null @@ -1,202 +0,0 @@ -ttta 13 -tttt 13 -tctt 11 -gttt 10 -ttgt 10 -taat 9 -ttct 8 -attt 8 -tttg 8 -gttc 8 -tgtt 8 -ggtt 8 -cttt 8 -aatt 6 -tatt 6 -ttaa 6 -ttat 6 -ttca 5 -ttcg 5 -tttc 5 -cagt 5 -gttg 5 -taca 5 -aata 5 -ccct 5 -agtt 5 -tgta 5 -tact 5 -cttc 5 -atac 5 -ttac 5 -aaaa 5 -atta 4 -tctc 4 -ctaa 4 -gtct 4 -ccta 4 -tata 4 -ctct 4 -cctt 4 -tatg 4 -ttgg 4 -acag 4 -tgga 4 -atat 4 -tcat 4 -tggt 4 -atct 3 -aaat 3 -ttcc 3 -taaa 3 -tcta 3 -attc 3 -tgat 3 -cggt 3 -agca 3 -aaca 3 -cccc 3 -agta 3 -tacc 3 -aatg 3 -caag 3 -cttg 3 -atgg 3 -atgt 3 -acaa 3 -acac 3 -tcaa 3 -aggt 3 -gcaa 3 -ttag 3 -ctga 3 -accg 3 -gtat 3 -acta 3 -tccc 3 -tgaa 2 -tcct 2 -actt 2 -ggaa 2 -gcct 2 -gtca 2 -ctac 2 -gaaa 2 -ctag 2 -gaag 2 -gctg 2 -ggat 2 -ctat 2 -gaat 2 -agcg 2 -tgcc 2 -agtc 2 -aatc 2 -cgac 2 -ggcc 2 -caaa 2 -caac 2 -gacc 2 -cctg 2 -tgtg 2 -caat 2 -ggtc 2 -ctta 2 -gata 2 -atga 2 -atgc 2 -tcga 2 -gatt 2 -gcgg 2 -tcgt 2 -ttgc 2 -gcgt 2 -cgcg 2 -caca 2 -cacc 2 -cgtc 2 -aaga 2 -catg 2 -aagc 2 -cgtt 2 -tcag 2 -catt 2 -aagt 2 -tggc 2 -taga 2 -tagc 2 -tagg 2 -gtaa 2 -ctgg 2 -gtac 2 -gtag 2 -tagt 2 -ctgt 2 -gagt 2 -agaa 2 -agac 2 -acct 2 -aaag 2 -actg 2 -gccc 1 -ccag 1 -tgag 1 -taac 1 -attg 1 -caga 1 -tctg 1 -cagc 1 -gtcc 1 -cagg 1 -gctt 1 -gtta 1 -agct 1 -tgca 1 -aact 1 -tgcg 1 -agtg 1 -tacg 1 -ctca 1 -cgag 1 -ctcc 1 -cctc 1 -tgct 1 -acga 1 -gacg 1 -tgtc 1 -cgat 1 -ggct 1 -tatc 1 -gact 1 -acgt 1 -gatc 1 -tcgc 1 -gatg 1 -gcgc 1 -ttga 1 -cgca 1 -gtgc 1 -gtgg 1 -cgta 1 -gtgt 1 -cact 1 -aggg 1 -ataa 1 -aagg 1 -atag 1 -ccga 1 -ccgc 1 -ccgg 1 -gcac 1 -gcag 1 -gggc 1 -gggg 1 -gagc 1 -acca 1 -accc 1 -atca 1 -agag 1 -aaac 1 -actc 1 -gcca 1 -ccac 1 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Tool shed masthead fixes due to new Galaxy styles.
by Bitbucket 21 Mar '12

21 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/10ffe462c024/ changeset: 10ffe462c024 user: greg date: 2012-03-21 20:50:48 summary: Tool shed masthead fixes due to new Galaxy styles. affected #: 1 file diff -r 243ad28621be905cdd09625520f3fe0ec0424f6d -r 10ffe462c0243fca53df78a3fdc83d8941dff9b4 templates/webapps/community/base_panels.mako --- a/templates/webapps/community/base_panels.mako +++ b/templates/webapps/community/base_panels.mako @@ -3,97 +3,127 @@ ## Default title <%def name="title()">Galaxy Tool Shed</%def> +<%def name="javascripts()"> + ${parent.javascripts()} + ${h.js( "jquery.tipsy" )} +</%def> + ## Masthead <%def name="masthead()"> ## Tab area, fills entire width - <div style="position: absolute; top: 0; left: 0; width: 100%; text-align: center"> + <div style="position: relative; right: -50%; float: left;"> + <div style="display: block; position: relative; right: 50%;"> + + <ul class="nav" border="0" cellspacing="0"> - <table class="tab-group" border="0" cellspacing="0" style="margin: auto;"> - <tr> - - <%def name="tab( id, display, href, target='_parent', visible=True, extra_class='' )"> - <% - cls = "tab" - if extra_class: - cls += " " + extra_class - if self.active_view == id: - cls += " active" - style = "" - if not visible: - style = "display: none;" - %> - <td class="${cls}" style="${style}"><a target="${target}" href="${href}">${display}</a></td> - </%def> + <%def name="tab( id, display, href, target='_parent', visible=True, extra_class='', menu_options=None )"> + <% + cls = "" + a_cls = "" + extra = "" + if extra_class: + cls += " " + extra_class + if self.active_view == id: + cls += " active" + if menu_options: + cls += " dropdown" + a_cls += " dropdown-toggle" + extra = "<b class='caret'></b>" + style = "" + if not visible: + style = "display: none;" + %> + <li class="${cls}" style="${style}"> + %if href: + <a class="${a_cls}" data-toggle="dropdown" target="${target}" href="${href}">${display}${extra}</a> + %else: + <a class="${a_cls}" data-toggle="dropdown">${display}${extra}</a> + %endif + %if menu_options: + <ul class="dropdown-menu"> + %for menu_item in menu_options: + %if not menu_item: + <li class="divider"></li> + %else: + <li> + %if len ( menu_item ) == 1: + ${menu_item[0]} + %elif len ( menu_item ) == 2: + <% name, link = menu_item %> + <a href="${link}">${name}</a> + %else: + <% name, link, target = menu_item %> + <a target="${target}" href="${link}">${name}</a> + %endif + </li> + %endif + %endfor + </ul> + %endif + </li> + </%def> - ${tab( "repositories", "Repositories", h.url_for( controller='/repository', action='index', webapp='community' ) )} - ${tab( "admin", "Admin", h.url_for( controller='/admin', action='index', webapp='community' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) )} - - <td class="tab"> - <a>Help</a> - <div class="submenu"> - <ul> - <li><a target="_blank" href="${app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" )}">Support</a></li> - <li><a target="_blank" href="${app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/Tool%20Shed" )}">Tool shed wiki</a></li> - <li><a target="_blank" href="${app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" )}">Galaxy wiki</a></li> - <li><a target="_blank" href="${app.config.get( "screencasts_url", "http://galaxycast.org" )}">Video tutorials (screencasts)</a></li> - <li><a target="_blank" href="${app.config.get( "citation_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" )}">How to Cite Galaxy</a></li> - </ul> + ## Repositories tab. + ${tab( "repositories", "Repositories", h.url_for( controller='/repository', action='index', webapp='community' ) )} + + ## Admin tab. + ${tab( "admin", "Admin", h.url_for( controller='/admin', action='index', webapp='community' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) )} + + ## Help tab. + <% + menu_options = [ + [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], + [_('Tool shed wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/Tool%20Shed" ), "_blank" ], + [_('Galaxy wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], + [_('Video tutorials (screencasts)'), app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ], + [_('How to Cite Galaxy'), app.config.get( "citation_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" ), "_blank" ] + ] + tab( "help", _("Help"), None, menu_options=menu_options) + %> + + ## User tabs. + <% + # Menu for user who is not logged in. + menu_options = [ [ _("Login"), h.url_for( controller='/user', action='login', webapp='community' ), "galaxy_main" ] ] + if app.config.allow_user_creation: + menu_options.append( [ _("Register"), h.url_for( controller='/user', action='create', cntrller='user', webapp='community' ), "galaxy_main" ] ) + extra_class = "loggedout-only" + visible = ( trans.user == None ) + tab( "user", _("User"), None, visible=visible, menu_options=menu_options ) + # Menu for user who is logged in. + if trans.user: + email = trans.user.email + else: + email = "" + menu_options = [ [ '<a>Logged in as <span id="user-email">%s</span></a>' % email ] ] + if app.config.use_remote_user: + if app.config.remote_user_logout_href: + menu_options.append( [ _('Logout'), app.config.remote_user_logout_href, "_top" ] ) + else: + menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user', webapp='community' ), "galaxy_main" ] ) + logout_url = h.url_for( controller='/user', action='logout', webapp='community' ) + menu_options.append( [ 'Logout', logout_url, "_top" ] ) + menu_options.append( None ) + if app.config.use_remote_user: + menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user', webapp='community' ), "galaxy_main" ] ) + + extra_class = "loggedin-only" + visible = ( trans.user != None ) + tab( "user", "User", None, visible=visible, menu_options=menu_options ) + %> + </ul></div> - </td> - - ## User tab. - <% - cls = "tab" - if self.active_view == 'user': - cls += " active" - %> - <td class="${cls}"> - <a>User</a> - <% - if trans.user: - user_email = trans.user.email - style1 = "display: none;" - style2 = ""; - else: - user_email = "" - style1 = "" - style2 = "display: none;" - %> - <div class="submenu"> - <ul class="loggedout-only" style="${style1}"> - <li><a target="galaxy_main" href="${h.url_for( controller='/user', action='login', webapp='community' )}">Login</a></li> - %if app.config.allow_user_creation: - <li><a target="galaxy_main" href="${h.url_for( controller='/user', action='create', cntrller='user', webapp='community' )}">Register</a></li> - %endif - </ul> - <ul class="loggedin-only" style="${style2}"> - %if app.config.use_remote_user: - %if app.config.remote_user_logout_href: - <li><a href="${app.config.remote_user_logout_href}" target="_top">Logout</a></li> - %endif - %else: - <li>Logged in as <span id="user-email">${user_email}</span></li> - <li><a target="galaxy_main" href="${h.url_for( controller='/user', action='index', cntrller='user', webapp='community' )}">Preferences</a></li> - <% logout_url = h.url_for( controller='/user', action='logout', webapp='community' ) %> - <li><a target="_top" href="${logout_url}">Logout</a></li> - %endif - </ul> - </div> - </td> - </tr> - </table></div> ## Logo, layered over tabs to be clickable - <div class="title" style="position: absolute; top: 0; left: 0;"> + <div class="title" style="position: absolute; top: 0; left: 0; white-space: nowrap;"><a href="${app.config.get( 'logo_url', '/' )}"> - <img border="0" src="${h.url_for('/static/images/galaxyIcon_noText.png')}" style="width: 26px; vertical-align: top;"> + <img border="0" src="${h.url_for('/static/images/galaxyIcon_noText.png')}" style="display: inline; width: 26px; vertical-align: top;"> Galaxy Tool Shed %if app.config.brand: <span class='brand'>/ ${app.config.brand}</span> %endif </a></div> - </%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 23 new changesets
by Bitbucket 21 Mar '12

21 Mar '12

23 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d0004f5eea59/ changeset: d0004f5eea59 user: james_taylor date: 2012-02-13 23:40:42 summary: style: allow stylesheets to be written in less instead of our custom approach, convert base and panel_layout, resulting CSS is equivalent affected #: 6 files diff -r 95876f2552d354bf88320521dcf5083f31147bf0 -r d0004f5eea59f83543349b161fdb4559d543b07c static/june_2007_style/Makefile --- a/static/june_2007_style/Makefile +++ b/static/june_2007_style/Makefile @@ -1,26 +1,26 @@ -menu_bg.png : - ./gradient.py 9 1000 DDDDFF 9999FF FFFFFF 0 0 FFFFFF 1 1 > $@ +OUT=blue +INI=$(OUT)_colors.ini -base_bg.png : - ./gradient.py 9 1000 EEEEFF - FFFFFF 0 0 FFFFFF 1 1 > $@ +# The catch-all rule is magic, it reruns make in the OUT directory with a VPATH +all: + @( cd blue; make -f ../Makefile VPATH=.. css ) -masthead_bg.png : - ./gradient.py 9 50 023858 000000 000000 0 0.5 000000 1 1 > $@ +ALL_CSS=base panel_layout masthead library history tool_menu iphone autocomplete_tagging trackster -footer_title_bg.png : - ./gradient.py 9 30 023858 000000 000000 0 0.5 000000 1 1 > $@ +css: $(foreach N,$(ALL_CSS),$N.css) -form_title_bg.png : - ./gradient.py 9 50 ebd9b2 b9a780 FFFFFF 0 0 FFFFFF 0.5 1 > $@ +# Convert variables from ini to less syntax +variables.less : $(INI) + ./variables_to_less.py < $< > $@ -ok_bg.png : - ./gradient.py 9 200 AAFFAA - CCFFCC 0 0.5 CCFFCC 1 1 > $@ +# Convert using less +%.css : %.less + lessc -x --include-path=$(OUT) $< > $@ -error_bg.png : - ./gradient.py 9 200 FFAAAA - FFCCCC 0 0.5 FFCCCC 1 1 > $@ +# Old style using process_css still works so we can move gradually +%.css : %.css.tmpl + ./process_css.py $(INI) shared_images:../images $(OUT) < $< > $@ -warn_bg.png : - ./gradient.py 9 200 FFFFAA - FFFFCC 0 0.5 FFFFCC 1 1 > $@ - -gray_bg.png : - ./gradient.py 9 200 AAAAAA - CCCCCC 0 0.5 CCCCCC 1 1 > $@ +# For building sprite images +%.less : %.less.tmpl + ./process_css.py $(INI) shared_images:../images $(OUT) < $< > $@ diff -r 95876f2552d354bf88320521dcf5083f31147bf0 -r d0004f5eea59f83543349b161fdb4559d543b07c static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -5,7 +5,7 @@ body{font-size:75%;} .unselectable{user-select:none;-moz-user-select:none;-webkit-user-select:none;} .shadow{-moz-box-shadow:0 3px 30px black;-webkit-box-shadow:0 3px 30px black;} -body{background:#FFFFFF;color:#303030;background-image:url(base_bg.png);background-repeat:repeat-x;background-position:top;margin:10px;} +body{background:#ffffff;color:#303030;background-image:url(base_bg.png);background-repeat:repeat-x;background-position:top;margin:10px;} img{border:0;} a:link,a:visited,a:active{color:#303030;} h1,h2,h3,h4{color:#023858;} @@ -17,10 +17,10 @@ div.toolFormTitle{font-weight:bold;padding:5px;padding-left:10px;padding-right:10px;background:#ebd9b2;background-repeat:repeat-x;background-position:top;border-bottom:solid #d8b365 1px;} div.toolParamHelp{color:#666;} div.toolParamHelp a{color:#666;} -div.toolFormBody{background:#FFFFFF;background-image:url(form_body_bg.png);background-repeat:repeat-x;background-position:top;padding:5px 0;} +div.toolFormBody{background:#ffffff;background-image:url(form_body_bg.png);background-repeat:repeat-x;background-position:top;padding:5px 0;} div.toolFormBody div.toolFormTitle{background:transparent;border:none;font-weight:bold;border-bottom:solid #d8b365 1px;margin-bottom:5px;} -div.toolFormDisabled div.toolFormTitle{background:#eee;border-color:#999;} -div.toolFormDisabled{border-color:#999;} +div.toolFormDisabled div.toolFormTitle{background:#eeeeee;border-color:#999999;} +div.toolFormDisabled{border-color:#999999;} div.toolHelp{margin-top:10px;} div.toolHelpBody{width:100%;} div.metadataForm{border:solid #aaaaaa 1px;} @@ -37,7 +37,7 @@ div.form-row{padding:5px 10px;} div.form-title-row{padding:5px 10px;} div.repeat-group-item{border-left:solid #d8b365 5px;margin-left:10px;margin-bottom:10px;} -div.form-row-error{background:#FFCCCC;} +div.form-row-error{background:#ffcccc;} div.form-row label{font-weight:bold;display:block;margin-bottom:.2em;} div.form-row label.inline{display:inline;} div.form-row-input{float:left;} @@ -46,15 +46,15 @@ .form-row .help{color:#666;} select,input,textarea{font:inherit;} select,textarea,input[type="text"],input[type="file"],input[type="password"]{-webkit-box-sizing:border-box;max-width:300px;} -.errormessagelarge,.warningmessagelarge,.donemessagelarge,.infomessagelarge{padding:10px;padding-left:52px;min-height:32px;border:1px solid #AA6666;background-color:#FFCCCC;background-image:url(error_message_icon.png);background-repeat:no-repeat;background-position:10px 10px;} -.warningmessagelarge{background-image:url(warn_message_icon.png);border-color:#AAAA66;background-color:#FFFFCC;} -.donemessagelarge{background-image:url(done_message_icon.png);border-color:#66AA66;background-color:#CCFFCC;} -.infomessagelarge{background-image:url(info_message_icon.png);border-color:#6666AA;background-color:#CCCCFF;} +.errormessagelarge,.warningmessagelarge,.donemessagelarge,.infomessagelarge{padding:10px;padding-left:52px;min-height:32px;border:1px solid #aa6666;background-color:#ffcccc;background-image:url(error_message_icon.png);background-repeat:no-repeat;background-position:10px 10px;} +.warningmessagelarge{background-image:url(warn_message_icon.png);border-color:#aaaa66;background-color:#ffffcc;} +.donemessagelarge{background-image:url(done_message_icon.png);border-color:#66aa66;background-color:#ccffcc;} +.infomessagelarge{background-image:url(info_message_icon.png);border-color:#6666aa;background-color:#ccccff;} .screencastBox{padding-left:10px;border-color:#AAAA66;background-color:#FFFFCC;background-image:none;} -.errormessage,.warningmessage,.donemessage,.infomessage,.errormessagesmall,.warningmessagesmall,.donemessagesmall,.infomessagesmall{padding:5px;padding-left:25px;min-height:15px;border:1px solid #AA6666;background-color:#FFCCCC;background-image:url(error_small.png);background-repeat:no-repeat;background-position:5px 5px;} -.warningmessage,.warningmessagesmall{background-image:url(warn_small.png);border-color:#AAAA66;background-color:#FFFFCC;} -.donemessage,.donemessagesmall{background-image:url(ok_small.png);border-color:#66AA66;background-color:#CCFFCC;} -.infomessage,.infomessagesmall{background-image:url(info_small.png);border-color:#6666AA;background-color:#CCCCFF;} +.errormessage,.warningmessage,.donemessage,.infomessage,.errormessagesmall,.warningmessagesmall,.donemessagesmall,.infomessagesmall{padding:5px;padding-left:25px;min-height:15px;border:1px solid #aa6666;background-color:#ffcccc;background-image:url(error_small.png);background-repeat:no-repeat;background-position:5px 5px;} +.warningmessage,.warningmessagesmall{background-image:url(warn_small.png);border-color:#aaaa66;background-color:#ffffcc;} +.donemessage,.donemessagesmall{background-image:url(ok_small.png);border-color:#66aa66;background-color:#ccffcc;} +.infomessage,.infomessagesmall{background-image:url(info_small.png);border-color:#6666aa;background-color:#ccccff;} .errormark,.warningmark,.donemark,.infomark,.ok_bgr,.err_bgr{padding-left:20px;min-height:15px;background:url(error_small.png) no-repeat;} .warningmark{background-image:url(warn_small.png);} .donemark{background-image:url(ok_small.png);} @@ -70,12 +70,12 @@ table.colored{border-top:solid #d8b365 1px;border-bottom:solid #d8b365 1px;} table.colored td,table.colored th{text-align:left;padding:5px;} table.colored tr.header{background:#ebd9b2;background-image:url(form_title_bg.png);background-repeat:repeat-x;background-position:top;border-bottom:solid #d8b365 1px;font-weight:bold;} -table.colored tr{background:white;} -table.colored tr.odd_row{background:#DADFEF;} +table.colored tr{background:#ffffff;} +table.colored tr.odd_row{background:#dadfef;} div.debug{margin:10px;padding:5px;background:#FFFF99;border:solid #FFFF33 1px;color:black;} -div.odd_row{background:#DADFEF;} +div.odd_row{background:#dadfef;} #footer{display:none;} -td.panel-body{background:white;color:#303030;background:#C1C9E5 url(menu_bg.png) top repeat-x;} +td.panel-body{background:white;color:#303030;background:#c1c9e5 url(menu_bg.png) top repeat-x;} div.toolSectionPad{margin:0;padding:0;height:5px;font-size:0px;} div.toolSectionDetailsInner{margin-left:5px;margin-right:5px;} div.toolSectionTitle{padding-bottom:0px;font-weight:bold;} @@ -84,14 +84,14 @@ ul.toolParameterExpandableCollapsable{list-style:none;} ul.manage-table-actions{float:right;margin-top:-2.5em;} ul.manage-table-actions li{display:block;float:left;margin-left:0.5em;} -.state-color-new{border-color:#A86030;background:#FFB030;} -.state-color-upload{border-color:#6666AA;background:#CCCCFF;} -.state-color-waiting{border-color:#A86030;background:#E8C060;} -.state-color-queued{border-color:#888888;background:#EEEEEE;} -.state-color-running{border-color:#AAAA66;background:#FFFFCC;} -.state-color-ok{border-color:#66AA66;background:#CCFFCC;} -.state-color-error{border-color:#AA6666;background:#FFCCCC;} -.state-color-deleted{border-color:#330066;background:#3399FF;} +.state-color-new{border-color:#a86030;background:#ffb030;} +.state-color-upload{border-color:#6666aa;background:#ccccff;} +.state-color-waiting{border-color:#a86030;background:#e8c060;} +.state-color-queued{border-color:#888888;background:#eeeeee;} +.state-color-running{border-color:#aaaa66;background:#ffffcc;} +.state-color-ok{border-color:#66aa66;background:#ccffcc;} +.state-color-error{border-color:#aa6666;background:#ffcccc;} +.state-color-deleted{border-color:#330066;background:#3399ff;} .state-fg-new{color:#FFB030;} .state-fg-upload{color:#D090D0;} .state-fg-waiting{color:#E8C060;} @@ -101,20 +101,17 @@ .state-fg-error{color:#AA6666;} .state-fg-deleted{color:#3399FF;} .action-button{background:transparent;line-height:16px;color:#333;text-decoration:none;font-size:100%;font-weight:bold;display:inline-block;cursor:pointer;padding:2px;border:solid #aaaaaa 1px;padding-right:0.5em;padding-left:0.5em;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;user-select:none;-moz-user-select:none;-webkit-user-select:none;} -.action-button > *{vertical-align:middle;} +.action-button>*{vertical-align:middle;} .action-button:hover{color:black;background:#dddddd;} .action-button:active{color:white;background:#aaaaaa;} -.menubutton{display:inline-block;cursor:pointer;position:relative;user-select:none;-moz-user-select:none;-webkit-user-select:none;border:solid transparent 1px;-moz-border-radius:0.25em;-webkit-border-radius:0.25em;border-radius:0.25em;padding:1px 0.25em;margin:-1px -0.25em;} -.menubutton .label{position:relative;display:block;border-right:none;} +.menubutton{display:inline-block;cursor:pointer;position:relative;user-select:none;-moz-user-select:none;-webkit-user-select:none;border:solid transparent 1px;-moz-border-radius:0.25em;-webkit-border-radius:0.25em;border-radius:0.25em;padding:1px 0.25em;margin:-1px -0.25em;}.menubutton .label{position:relative;display:block;border-right:none;} .menubutton.action-button{border-color:#aaaaaa;} .menubutton.popup,.action-button.popup{padding-right:20px;background-image:url(../images/dropdownarrow.png);background-repeat:no-repeat;background-position:right 7px;} .menubutton:hover{border-color:#aaaaaa;} .menubutton.popup.split{padding-right:2em;} .menubutton.popup.split:hover{background:url(../images/ddarrowsplit.png) no-repeat right -39px;} -.overlay-border{position:absolute;top:0;left:0;height:100%;width:100%;padding:1em;margin:-1em;background-color:rgba(0,0,0,0.5);-moz-border-radius:1em;-webkit-border-radius:1em;z-index:-1;} -div.popmenu-wrapper{position:absolute;top:100%;z-index:20000;} -div.popmenu-wrapper ul{display:block;margin:0;padding:0;background:white;color:#333;font-weight:bold;font-style:normal;white-space:nowrap;border:solid #aaaaaa 1px;padding:3px 0;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;user-select:none;-moz-user-select:none;-webkit-user-select:none;} -div.popmenu-wrapper ul li{display:block;padding:3px 1em;cursor:pointer;border-top:solid transparent 1px;border-bottom:solid transparent 1px;} +.overlay-border{position:absolute;top:0;left:0;height:100%;width:100%;padding:1em;margin:-1em;background-color:rgba(0, 0, 0, 0.5);-moz-border-radius:1em;-webkit-border-radius:1em;z-index:-1;} +div.popmenu-wrapper{position:absolute;top:100%;z-index:20000;}div.popmenu-wrapper ul{display:block;margin:0;padding:0;background:white;color:#333;font-weight:bold;font-style:normal;white-space:nowrap;border:solid #aaaaaa 1px;padding:3px 0;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;user-select:none;-moz-user-select:none;-webkit-user-select:none;}div.popmenu-wrapper ul li{display:block;padding:3px 1em;cursor:pointer;border-top:solid transparent 1px;border-bottom:solid transparent 1px;} div.popmenu-wrapper ul li.head{color:#999;font-style:italic;} div.popmenu-wrapper ul li:hover{background:#EEEEFF;border-color:#aaa;} div.popmenu-wrapper ul li.head:hover{background:inherit;border-color:transparent;} @@ -131,7 +128,6 @@ .grid thead th{background:#ebd9b2;background-repeat:repeat-x;background-position:top;border-top:solid #d8b365 1px;border-bottom:solid #d8b365 1px;padding:0.3em 0.5em;text-align:left;white-space:nowrap;} .grid tfoot td{background-color:#F8F8F8;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:0.3em 0.5em;} .grid .current{background-color:#EEEEFF;} -.text-content{} .text-content hr{display:block;background:black;color:black;width:100%;height:1px;border:none;background:#aaa;color:#aaa;} .text-content table{border-collapse:collapse;border-top:1px solid #ccc;border-left:1px solid #ccc;} .text-content blockquote{color:#666;} @@ -139,7 +135,7 @@ .text-content th,.text-content td{border-bottom:1px solid #ddd;border-right:1px solid #ccc;} .text-content th,.text-content td{padding:.8em;} .icon-button{width:16px;height:16px;display:block;float:left;margin-left:2px;text-indent:20px;background-repeat:no-repeat;background-position:0px 0px;padding:0;} -.icon-button.display{background:url(history-buttons.png) no-repeat 0px -0px;} +.icon-button.display{background:url(history-buttons.png) no-repeat 0px 0px;} .icon-button.display:hover{background:url(history-buttons.png) no-repeat 0px -26px;} .icon-button.display_disabled{background:url(history-buttons.png) no-repeat 0px -52px;} .icon-button.delete{background:url(history-buttons.png) no-repeat 0px -78px;} @@ -148,24 +144,22 @@ .icon-button.edit{background:url(history-buttons.png) no-repeat 0px -156px;} .icon-button.edit:hover{background:url(history-buttons.png) no-repeat 0px -182px;} .icon-button.edit_disabled{background:url(history-buttons.png) no-repeat 0px -208px;} -.icon-button.tag{background:url(fugue.png) no-repeat 0px -0px;} +.icon-button.tag{background:url(fugue.png) no-repeat 0px 0px;} .icon-button.tags{background:url(fugue.png) no-repeat 0px -26px;} .icon-button.tag--plus{background:url(fugue.png) no-repeat 0px -52px;} -.icon-button.toggle-expand{background:transparent url(../images/fugue/toggle-expand-bw.png) no-repeat;} -.icon-button.toggle-expand:hover{background:url(fugue.png) no-repeat 0px -78px;} -.icon-button.toggle{background:transparent url(../images/fugue/toggle-bw.png) no-repeat;} -.icon-button.toggle:hover{background:url(fugue.png) no-repeat 0px -104px;} +.icon-button.toggle-expand{background:url(fugue.png) no-repeat 0px -78px;} +.icon-button.toggle{background:url(fugue.png) no-repeat 0px -104px;} .icon-button.arrow-circle{background:url(fugue.png) no-repeat 0px -130px;} .icon-button.chevron{background:url(fugue.png) no-repeat 0px -156px;} .icon-button.bug{background:url(fugue.png) no-repeat 0px -182px;} .icon-button.disk{background:url(fugue.png) no-repeat 0px -208px;} .icon-button.information{background:url(fugue.png) no-repeat 0px -234px;} .icon-button.annotate{background:url(fugue.png) no-repeat 0px -260px;} -.icon-button.chart_curve{background:url(../images/silk/chart_curve.png) no-repeat;} -.icon-button.go-to-full-screen{background:url(fugue.png) no-repeat 0px -312px;} -.icon-button.import{background:url(fugue.png) no-repeat 0px -338px;} -.icon-button.plus-button{background:url(fugue.png) no-repeat 0px -364px;} -.icon-button.gear{background:url(fugue.png) no-repeat 0px -390px;} +.icon-button.go-to-full-screen{background:url(fugue.png) no-repeat 0px -286px;} +.icon-button.import{background:url(fugue.png) no-repeat 0px -312px;} +.icon-button.plus-button{background:url(fugue.png) no-repeat 0px -338px;} +.icon-button.gear{background:url(fugue.png) no-repeat 0px -364px;} +.text-and-autocomplete-select{background:url(fugue.png) no-repeat right -390px;} .tipsy{padding:5px;font-size:10px;filter:alpha(opacity=80);background-repeat:no-repeat;background-image:url(../images/tipsy.gif);} .tipsy-inner{padding:5px 8px 4px 8px;background-color:black;color:white;max-width:200px;text-align:center;} .tipsy-north{background-position:top center;} @@ -174,7 +168,6 @@ .tipsy-west{background-position:left center;} .editable-text{cursor:pointer;} .editable-text:hover{cursor:text;border:dotted #999999 1px;} -.text-and-autocomplete-select{background:url(fugue.png) no-repeat right -416px;} .icon-button.multiinput{background:url(../images/documents-stack.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;} .icon-button.multiinput.disabled{background:url(../images/documents-stack-faded.png) no-repeat;cursor:auto;} .workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;padding-left:5px;} diff -r 95876f2552d354bf88320521dcf5083f31147bf0 -r d0004f5eea59f83543349b161fdb4559d543b07c static/june_2007_style/blue/fugue.png Binary file static/june_2007_style/blue/fugue.png has changed diff -r 95876f2552d354bf88320521dcf5083f31147bf0 -r d0004f5eea59f83543349b161fdb4559d543b07c static/june_2007_style/blue/panel_layout.css --- a/static/june_2007_style/blue/panel_layout.css +++ b/static/june_2007_style/blue/panel_layout.css @@ -1,53 +1,340 @@ -body{font:75% "Lucida Grande",verdana,arial,helvetica,sans-serif;background:#eee;} -.unselectable{user-select:none;-moz-user-select:none;-webkit-user-select:none;} -#background{position:absolute;background:#eee;z-index:-1;top:0;left:0;margin:0;padding:0;width:100%;height:100%;} -#messagebox{position:absolute;top:33px;left:0;width:100%;height:24px !important;overflow:hidden;border-bottom:solid #999 1px;font-size:90%;} -#left,#left-border,#center,#right-border,#right{position:absolute;top:39px;bottom:0px;overflow:hidden;background:#fff;} -#left,#center,#right{border-top:solid #999 1px;} -#left-border,#right-border{background:#eeeeee;border-left:solid #999 1px;border-right:solid #999 1px;padding-right:1px;padding-left:1px;width:5px;z-index:10000;} -#left-border div,#right-border div{width:100%;height:100%;background-repeat:no-repeat;background-position:center center;position:absolute;width:5px;height:100%;} -#left-border div,#right-border.hidden div{background-image:url(tiny_arrow_left.png);cursor:w-resize;} -#left-border.hidden div,#right-border div{background-image:url(tiny_arrow_right.png);cursor:e-resize;} -#left-border.hover div,#right-border.hover div{background-color:#AAAAEE;} -#left{left:0px;width:250px;z-index:200;} -#left-border{left:250px;} -#center{left:259px;right:259px;overflow:hidden;z-index:1;} -#right-border{right:250px;} -#right{width:250px;right:0px;z-index:200;} -.unified-panel-header{height:2em;z-index:1000;background:#cccccc;background-image:url(panel_header_bg.png);background-position:top center;background-repeat:repeat-x;border-bottom:solid #999 1px;margin:0;padding:0;padding-right:10px;padding-left:10px;color:#333;font-weight:bold;} -.unified-panel-header-inner{padding-top:0.45em;} -.menu-bg{background:#C1C9E5 url(menu_bg.png) top repeat-x;} -div.unified-panel-body{position:absolute;top:2em;bottom:0;width:100%;margin-top:1px;} -.panel-header-button{color:#333;text-decoration:none;display:inline-block;cursor:pointer;margin:-1px;padding:1px;margin-top:-0.2em;border:solid #999 1px;padding-right:0.5em;padding-left:0.5em;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;} -.panel-header-button.popup{padding-right:1.75em;background:url(../images/dropdownarrow.png) no-repeat right 7px;} -.panel-header-button:hover{color:black;background-color:#ccc;} -.panel-header-button:active{color:white;background-color:#aaaaaa;} -#overlay{position:fixed;top:0;left:0;width:100%;height:100%;z-index:20000;} -#overlay.modal #overlay-background{background:rgba(0,0,0,0.5);} -.dialog-box-container{position:relative;margin-top:80px;margin-right:auto;margin-left:auto;} -.dialog-box-wrapper{position:relative;padding:1em;background-color:rgba(0,0,0,0.5);-moz-border-radius:1em;-webkit-border-radius:1em;} -.dialog-box{border:solid #999 1px;background:white;z-index:80000;} -#overlay.modal .dialog-box .body{min-width:600px;} -.dialog-box .body{padding:5px;overflow:auto;max-height:500px;min-width:300px;} -.dialog-box .buttons{padding:5px;} -.panel-error-message,.panel-warning-message,.panel-done-message,.panel-info-message{height:24px;line-height:24px;color:#303030;padding:0px;padding-left:26px;background-color:#FFCCCC;background-image:url(error_small.png);background-repeat:no-repeat;background-position:6px 50%;} -.panel-warning-message{background-image:url(warn_small.png);background-color:#FFFFCC;} -.panel-done-message{background-image:url(done_small.png);background-color:#CCFFCC;} -.panel-info-message{background-image:url(info_small.png);background-color:#CCCCFF;} -#masthead{position:absolute;top:0;left:0;width:100%;min-width:900px;height:32px;background:#2C3143;color:#fff;border-bottom:solid #444 1px;z-index:15000;padding:0;} -#masthead a{color:#eeeeee;text-decoration:none;} -#masthead .title{font-family:verdana;padding:3px 10px;font-size:175%;font-weight:bold;z-index:-1;} -#masthead a:hover{text-decoration:underline;} -.quota-meter-container{position:absolute;top:0;right:0;height:32px;} -.quota-meter{position:absolute;top:8px;right:8px;height:16px;width:100px;background-color:#C1C9E5;;} -.quota-meter-bar{position:absolute;top:0;left:0;height:16px;background-color:#969DB3;;} -.quota-meter-bar-warn{background-color:#FFB400;;} -.quota-meter-bar-error{background-color:#FF4343;;} -.quota-meter-text{position:absolute;top:50%;left:0;width:100px;height:16px;margin-top:-6px;text-align:center;z-index:9001;color:#000;;} -.tab-group{margin:0;padding:0 10px;height:100%;white-space:nowrap;cursor:default;background:transparent;} -.tab-group .tab{background:#2C3143;position:relative;float:left;margin:0;padding:0 1em;height:32px;line-height:32px;text-align:left;} -.tab-group .tab .submenu{display:none;position:absolute;z-index:16000;left:0;top:32px;padding:1em;margin:-1em;padding-top:0;margin-top:0;background-color:rgba(0,0,0,0.5);-moz-border-radius:0 0 1em 1em;-webkit-border-bottom-right-radius:1em;-webkit-border-bottom-left-radius:1em;} -.tab-group .tab .submenu ul{display:block;margin:0;padding:0;list-style-type:none;background:#2C3143;} -.tab-group .tab .submenu ul li{display:block;padding:0 1em;white-space:nowrap;} -.tab-group .tab:hover > a{color:gold !important;} -.tab-group .active{background:rgb(1,1,1);} +body { + font: 75% "Lucida Grande", verdana, arial, helvetica, sans-serif; + background: #eeeeee; +} +.unselectable { + user-select: none; + -moz-user-select: none; + -webkit-user-select: none; +} +#background { + position: absolute; + background: #eeeeee; + z-index: -1; + top: 0; + left: 0; + margin: 0; + padding: 0; + width: 100%; + height: 100%; +} +#messagebox { + position: absolute; + top: 33px; + left: 0; + width: 100%; + height: 24px !important; + overflow: hidden; + border-bottom: solid #999 1px; + font-size: 90%; +} +#left, +#left-border, +#center, +#right-border, +#right { + position: absolute; + top: 39px; + bottom: 0px; + overflow: hidden; + background: #fff; +} +#left, +#center, +#right { + border-top: solid #999999 1px; +} +#left-border, +#right-border { + background: #eeeeee; + border-left: solid #999999 1px; + border-right: solid #999999 1px; + padding-right: 1px; + padding-left: 1px; + width: 5px; + z-index: 10000; +} +#left-border div, +#right-border div { + width: 100%; + height: 100%; + background-repeat: no-repeat; + background-position: center center; + position: absolute; + width: 5px; + height: 100%; +} +#left-border div, +#right-border.hidden div { + background-image: url(tiny_arrow_left.png); + cursor: w-resize; +} +#left-border.hidden div, +#right-border div { + background-image: url(tiny_arrow_right.png); + cursor: e-resize; +} +#left-border.hover div, +#right-border.hover div { + background-color: #aaaaee; +} +#left { + left: 0px; + width: 250px; + z-index: 200; +} +#left-border { + left: 250px; +} +#center { + left: 259px; + right: 259px; + overflow: hidden; + z-index: 1; +} +#right-border { + right: 250px; +} +#right { + width: 250px; + right: 0px; + z-index: 200; +} +.unified-panel-header { + height: 2em; + z-index: 1000; + background: #cccccc; + background-image: url(panel_header_bg.png); + background-position: top center; + background-repeat: repeat-x; + border-bottom: solid #999999 1px; + margin: 0; + padding: 0; + padding-right: 10px; + padding-left: 10px; + color: #333; + font-weight: bold; +} +.unified-panel-header-inner { + padding-top: 0.45em; +} +.menu-bg { + background: #c1c9e5 url(menu_bg.png) top repeat-x; +} +div.unified-panel-body { + position: absolute; + top: 2em; + bottom: 0; + width: 100%; + margin-top: 1px; +} +.panel-header-button { + color: #333; + text-decoration: none; + display: inline-block; + cursor: pointer; + margin: -1px; + padding: 1px; + margin-top: -0.2em; + border: solid #999 1px; + padding-right: 0.5em; + padding-left: 0.5em; + -moz-border-radius: 0.5em; + -webkit-border-radius: 0.5em; + border-radius: 0.5em; +} +.panel-header-button.popup { + padding-right: 1.75em; + background: url(../images/dropdownarrow.png) no-repeat right 7px; +} +.panel-header-button:hover { + color: black; + background-color: #ccc; +} +.panel-header-button:active { + color: white; + background-color: #aaaaaa; +} +#overlay { + position: fixed; + top: 0; + left: 0; + width: 100%; + height: 100%; + z-index: 20000; +} +#overlay.modal #overlay-background { + background: rgba(0, 0, 0, 0.5); +} +.dialog-box-container { + position: relative; + margin-top: 80px; + margin-right: auto; + margin-left: auto; +} +.dialog-box-wrapper { + position: relative; + padding: 1em; + background-color: rgba(0, 0, 0, 0.5); + -moz-border-radius: 1em; + -webkit-border-radius: 1em; +} +.dialog-box { + border: solid #999 1px; + background: white; + z-index: 80000; +} +#overlay.modal .dialog-box .body { + min-width: 600px; +} +.dialog-box .body { + padding: 5px; + overflow: auto; + max-height: 500px; + min-width: 300px; +} +.dialog-box .buttons { + padding: 5px; +} +.panel-error-message, +.panel-warning-message, +.panel-done-message, +.panel-info-message { + height: 24px; + line-height: 24px; + color: #303030; + padding: 0px; + padding-left: 26px; + background-color: #ffcccc; + background-image: url(error_small.png); + background-repeat: no-repeat; + background-position: 6px 50%; +} +.panel-warning-message { + background-image: url(warn_small.png); + background-color: #ffffcc; +} +.panel-done-message { + background-image: url(done_small.png); + background-color: #ccffcc; +} +.panel-info-message { + background-image: url(info_small.png); + background-color: #ccccff; +} +#masthead { + position: absolute; + top: 0; + left: 0; + width: 100%; + min-width: 900px; + height: 32px; + background: #2c3143; + color: #fff; + border-bottom: solid #444444 1px; + z-index: 15000; + padding: 0; +} +#masthead a { + color: #eeeeee; + text-decoration: none; +} +#masthead .title { + font-family: verdana; + padding: 3px 10px; + font-size: 175%; + font-weight: bold; + z-index: -1; +} +#masthead a:hover { + text-decoration: underline; +} +.quota-meter-container { + position: absolute; + top: 0; + right: 0; + height: 32px; +} +.quota-meter { + position: absolute; + top: 8px; + right: 8px; + height: 16px; + width: 100px; + background-color: #c1c9e5; +} +.quota-meter-bar { + position: absolute; + top: 0; + left: 0; + height: 16px; + background-color: #969db3; +} +.quota-meter-bar-warn { + background-color: #ffb400; +} +.quota-meter-bar-error { + background-color: #ff4343; +} +.quota-meter-text { + position: absolute; + top: 50%; + left: 0; + width: 100px; + height: 16px; + margin-top: -6px; + text-align: center; + z-index: 9001; + color: #000000; +} +.tab-group { + margin: 0; + padding: 0 10px; + height: 100%; + white-space: nowrap; + cursor: default; + background: transparent; +} +.tab-group .tab { + background: #2c3143; + position: relative; + float: left; + margin: 0; + padding: 0 1em; + height: 32px; + line-height: 32px; + text-align: left; +} +.tab-group .tab .submenu { + display: none; + position: absolute; + z-index: 16000; + left: 0; + top: 32px; + padding: 1em; + margin: -1em; + padding-top: 0; + margin-top: 0; + background-color: rgba(0, 0, 0, 0.5); + -moz-border-radius: 0 0 1em 1em; + -webkit-border-bottom-right-radius: 1em; + -webkit-border-bottom-left-radius: 1em; +} +.tab-group .tab .submenu ul { + display: block; + margin: 0; + padding: 0; + list-style-type: none; + background: #2c3143; +} +.tab-group .tab .submenu ul li { + display: block; + padding: 0 1em; + white-space: nowrap; +} +.tab-group .tab:hover > a { + color: gold !important; +} +.tab-group .active { + background: #010101; +} diff -r 95876f2552d354bf88320521dcf5083f31147bf0 -r d0004f5eea59f83543349b161fdb4559d543b07c static/june_2007_style/blue_colors.ini --- a/static/june_2007_style/blue_colors.ini +++ b/static/june_2007_style/blue_colors.ini @@ -60,11 +60,11 @@ masthead_link=#eeeeee masthead_active_tab_bg=#222532 # Quota meter -quota_meter_bg=#C1C9E5; -quota_meter_bar=#969DB3; -quota_meter_warn_bar=#FFB400; -quota_meter_error_bar=#FF4343; -quota_meter_text=#000; +quota_meter_bg=#C1C9E5 +quota_meter_bar=#969DB3 +quota_meter_warn_bar=#FFB400 +quota_meter_error_bar=#FF4343 +quota_meter_text=#000 # ---- Layout ----------------------------------------------------------------- # Overall background color (including space between panels) layout_bg=#eee diff -r 95876f2552d354bf88320521dcf5083f31147bf0 -r d0004f5eea59f83543349b161fdb4559d543b07c static/june_2007_style/process_css.py --- a/static/june_2007_style/process_css.py +++ b/static/june_2007_style/process_css.py @@ -108,6 +108,9 @@ stylesheet_parser = build_stylesheet_parser() +class LessTemplate( string.Template ): + delimeter = "@" + class CSSProcessor( object ): def process( self, file, out, variables, image_dir, out_dir ): @@ -161,6 +164,8 @@ for selectors, properties in rules: for p in properties: p[1] = string.Template( p[1] ).substitute( context ).strip() + # Less style uses @ to prefix variables + p[1] = LessTemplate( p[1] ).substitute( context ).strip() def make_sprites( self, rules, image_dir, out_dir ): https://bitbucket.org/galaxy/galaxy-central/changeset/b1dac5a9b1d7/ changeset: b1dac5a9b1d7 user: james_taylor date: 2012-02-14 17:42:20 summary: style: adding (clean) bootstrap version 2 affected #: 35 files diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/accordion.less --- /dev/null +++ b/static/june_2007_style/bootstrap/accordion.less @@ -0,0 +1,28 @@ +// ACCORDION +// --------- + + +// Parent container +.accordion { + margin-bottom: @baseLineHeight; +} + +// Group == heading + body +.accordion-group { + margin-bottom: 2px; + border: 1px solid #e5e5e5; + .border-radius(4px); +} +.accordion-heading { + border-bottom: 0; +} +.accordion-heading .accordion-toggle { + display: block; + padding: 8px 15px; +} + +// Inner needs the styles because you can't animate properly with any styles on the element +.accordion-inner { + padding: 9px 15px; + border-top: 1px solid #e5e5e5; +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/alerts.less --- /dev/null +++ b/static/june_2007_style/bootstrap/alerts.less @@ -0,0 +1,70 @@ +// ALERT STYLES +// ------------ + +// Base alert styles +.alert { + padding: 8px 35px 8px 14px; + margin-bottom: @baseLineHeight; + text-shadow: 0 1px 0 rgba(255,255,255,.5); + background-color: @warningBackground; + border: 1px solid @warningBorder; + .border-radius(4px); +} +.alert, +.alert-heading { + color: @warningText; +} + +// Adjust close link position +.alert .close { + position: relative; + top: -2px; + right: -21px; + line-height: 18px; +} + +// Alternate styles +// ---------------- + +.alert-success { + background-color: @successBackground; + border-color: @successBorder; +} +.alert-success, +.alert-success .alert-heading { + color: @successText; +} +.alert-danger, +.alert-error { + background-color: @errorBackground; + border-color: @errorBorder; +} +.alert-danger, +.alert-error, +.alert-danger .alert-heading, +.alert-error .alert-heading { + color: @errorText; +} +.alert-info { + background-color: @infoBackground; + border-color: @infoBorder; +} +.alert-info, +.alert-info .alert-heading { + color: @infoText; +} + + +// Block alerts +// ------------------------ +.alert-block { + padding-top: 14px; + padding-bottom: 14px; +} +.alert-block > p, +.alert-block > ul { + margin-bottom: 0; +} +.alert-block p + p { + margin-top: 5px; +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/bootstrap.less --- /dev/null +++ b/static/june_2007_style/bootstrap/bootstrap.less @@ -0,0 +1,62 @@ +/*! + * Bootstrap v2.0.0 + * + * Copyright 2012 Twitter, Inc + * Licensed under the Apache License v2.0 + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Designed and built with all the love in the world @twitter by @mdo and @fat. + */ + +// CSS Reset +@import "reset.less"; + +// Core variables and mixins +@import "variables.less"; // Modify this for custom colors, font-sizes, etc +@import "mixins.less"; + +// Grid system and page structure +@import "scaffolding.less"; +@import "grid.less"; +@import "layouts.less"; + +// Base CSS +@import "type.less"; +@import "code.less"; +@import "forms.less"; +@import "tables.less"; + +// Components: common +@import "sprites.less"; +@import "dropdowns.less"; +@import "wells.less"; +@import "component-animations.less"; +@import "close.less"; + +// Components: Buttons & Alerts +@import "buttons.less"; +@import "button-groups.less"; +@import "alerts.less"; // Note: alerts share common CSS with buttons and thus have styles in buttons.less + +// Components: Nav +@import "navs.less"; +@import "navbar.less"; +@import "breadcrumbs.less"; +@import "pagination.less"; +@import "pager.less"; + +// Components: Popovers +@import "modals.less"; +@import "tooltip.less"; +@import "popovers.less"; + +// Components: Misc +@import "thumbnails.less"; +@import "labels.less"; +@import "progress-bars.less"; +@import "accordion.less"; +@import "carousel.less"; +@import "hero-unit.less"; + +// Utility classes +@import "utilities.less"; // Has to be last to override when necessary diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/breadcrumbs.less --- /dev/null +++ b/static/june_2007_style/bootstrap/breadcrumbs.less @@ -0,0 +1,22 @@ +// BREADCRUMBS +// ----------- + +.breadcrumb { + padding: 7px 14px; + margin: 0 0 @baseLineHeight; + #gradient > .vertical(@white, #f5f5f5); + border: 1px solid #ddd; + .border-radius(3px); + .box-shadow(inset 0 1px 0 @white); + li { + display: inline; + text-shadow: 0 1px 0 @white; + } + .divider { + padding: 0 5px; + color: @grayLight; + } + .active a { + color: @grayDark; + } +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/button-groups.less --- /dev/null +++ b/static/june_2007_style/bootstrap/button-groups.less @@ -0,0 +1,147 @@ +// BUTTON GROUPS +// ------------- + + +// Make the div behave like a button +.btn-group { + position: relative; + .clearfix(); // clears the floated buttons + .ie7-restore-left-whitespace(); +} + +// Space out series of button groups +.btn-group + .btn-group { + margin-left: 5px; +} + +// Optional: Group multiple button groups together for a toolbar +.btn-toolbar { + margin-top: @baseLineHeight / 2; + margin-bottom: @baseLineHeight / 2; + .btn-group { + display: inline-block; + .ie7-inline-block(); + } +} + +// Float them, remove border radius, then re-add to first and last elements +.btn-group .btn { + position: relative; + float: left; + margin-left: -1px; + .border-radius(0); +} +// Set corners individual because sometimes a single button can be in a .btn-group and we need :first-child and :last-child to both match +.btn-group .btn:first-child { + margin-left: 0; + -webkit-border-top-left-radius: 4px; + -moz-border-radius-topleft: 4px; + border-top-left-radius: 4px; + -webkit-border-bottom-left-radius: 4px; + -moz-border-radius-bottomleft: 4px; + border-bottom-left-radius: 4px; +} +.btn-group .btn:last-child, +.btn-group .dropdown-toggle { + -webkit-border-top-right-radius: 4px; + -moz-border-radius-topright: 4px; + border-top-right-radius: 4px; + -webkit-border-bottom-right-radius: 4px; + -moz-border-radius-bottomright: 4px; + border-bottom-right-radius: 4px; +} +// Reset corners for large buttons +.btn-group .btn.large:first-child { + margin-left: 0; + -webkit-border-top-left-radius: 6px; + -moz-border-radius-topleft: 6px; + border-top-left-radius: 6px; + -webkit-border-bottom-left-radius: 6px; + -moz-border-radius-bottomleft: 6px; + border-bottom-left-radius: 6px; +} +.btn-group .btn.large:last-child, +.btn-group .large.dropdown-toggle { + -webkit-border-top-right-radius: 6px; + -moz-border-radius-topright: 6px; + border-top-right-radius: 6px; + -webkit-border-bottom-right-radius: 6px; + -moz-border-radius-bottomright: 6px; + border-bottom-right-radius: 6px; +} + +// On hover/focus/active, bring the proper btn to front +.btn-group .btn:hover, +.btn-group .btn:focus, +.btn-group .btn:active, +.btn-group .btn.active { + z-index: 2; +} + +// On active and open, don't show outline +.btn-group .dropdown-toggle:active, +.btn-group.open .dropdown-toggle { + outline: 0; +} + + + +// Split button dropdowns +// ---------------------- + +// Give the line between buttons some depth +.btn-group .dropdown-toggle { + padding-left: 8px; + padding-right: 8px; + @shadow: inset 1px 0 0 rgba(255,255,255,.125), inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05); + .box-shadow(@shadow); + *padding-top: 5px; + *padding-bottom: 5px; +} + +.btn-group.open { + // IE7's z-index only goes to the nearest positioned ancestor, which would + // make the menu appear below buttons that appeared later on the page + *z-index: @zindexDropdown; + + // Reposition menu on open and round all corners + .dropdown-menu { + display: block; + margin-top: 1px; + .border-radius(5px); + } + + .dropdown-toggle { + background-image: none; + @shadow: inset 0 1px 6px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05); + .box-shadow(@shadow); + } +} + +// Reposition the caret +.btn .caret { + margin-top: 7px; + margin-left: 0; +} +.btn:hover .caret, +.open.btn-group .caret { + .opacity(100); +} + + +// Account for other colors +.btn-primary, +.btn-danger, +.btn-info, +.btn-success { + .caret { + border-top-color: @white; + .opacity(75); + } +} + +// Small button dropdowns +.btn-small .caret { + margin-top: 4px; +} + diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/buttons.less --- /dev/null +++ b/static/june_2007_style/bootstrap/buttons.less @@ -0,0 +1,165 @@ +// BUTTON STYLES +// ------------- + + +// Base styles +// -------------------------------------------------- + +// Core +.btn { + display: inline-block; + padding: 4px 10px 4px; + font-size: @baseFontSize; + line-height: @baseLineHeight; + color: @grayDark; + text-align: center; + text-shadow: 0 1px 1px rgba(255,255,255,.75); + #gradient > .vertical-three-colors(@white, @white, 25%, darken(@white, 10%)); // Don't use .gradientbar() here since it does a three-color gradient + border: 1px solid #ccc; + border-bottom-color: #bbb; + .border-radius(4px); + @shadow: inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05); + .box-shadow(@shadow); + cursor: pointer; + + // Give IE7 some love + .ie7-restore-left-whitespace(); +} + +// Hover state +.btn:hover { + color: @grayDark; + text-decoration: none; + background-color: darken(@white, 10%); + background-position: 0 -15px; + + // transition is only when going to hover, otherwise the background + // behind the gradient (there for IE<=9 fallback) gets mismatched + .transition(background-position .1s linear); +} + +// Focus state for keyboard and accessibility +.btn:focus { + .tab-focus(); +} + +// Active state +.btn.active, +.btn:active { + background-image: none; + @shadow: inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05); + .box-shadow(@shadow); + background-color: darken(@white, 10%); + background-color: darken(@white, 15%) e("\9"); + color: rgba(0,0,0,.5); + outline: 0; +} + +// Disabled state +.btn.disabled, +.btn[disabled] { + cursor: default; + background-image: none; + background-color: darken(@white, 10%); + .opacity(65); + .box-shadow(none); +} + + +// Button Sizes +// -------------------------------------------------- + +// Large +.btn-large { + padding: 9px 14px; + font-size: @baseFontSize + 2px; + line-height: normal; + .border-radius(5px); +} +.btn-large .icon { + margin-top: 1px; +} + +// Small +.btn-small { + padding: 5px 9px; + font-size: @baseFontSize - 2px; + line-height: @baseLineHeight - 2px; +} +.btn-small .icon { + margin-top: -1px; +} + + +// Alternate buttons +// -------------------------------------------------- + +// Set text color +// ------------------------- +.btn-primary, +.btn-primary:hover, +.btn-warning, +.btn-warning:hover, +.btn-danger, +.btn-danger:hover, +.btn-success, +.btn-success:hover, +.btn-info, +.btn-info:hover { + text-shadow: 0 -1px 0 rgba(0,0,0,.25); + color: @white; +} +// Provide *some* extra contrast for those who can get it +.btn-primary.active, +.btn-warning.active, +.btn-danger.active, +.btn-success.active, +.btn-info.active { + color: rgba(255,255,255,.75); +} + +// Set the backgrounds +// ------------------------- +.btn-primary { + .buttonBackground(@primaryButtonBackground, spin(@primaryButtonBackground, 20)); +} +// Warning appears are orange +.btn-warning { + .buttonBackground(lighten(@orange, 15%), @orange); +} +// Danger and error appear as red +.btn-danger { + .buttonBackground(#ee5f5b, #bd362f); +} +// Success appears as green +.btn-success { + .buttonBackground(#62c462, #51a351); +} +// Info appears as a neutral blue +.btn-info { + .buttonBackground(#5bc0de, #2f96b4); +} + + +// Cross-browser Jank +// -------------------------------------------------- + +button.btn, +input[type="submit"].btn { + &::-moz-focus-inner { + padding: 0; + border: 0; + } + + // IE7 has some default padding on button controls + *padding-top: 2px; + *padding-bottom: 2px; + &.large { + *padding-top: 7px; + *padding-bottom: 7px; + } + &.small { + *padding-top: 3px; + *padding-bottom: 3px; + } +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/carousel.less --- /dev/null +++ b/static/june_2007_style/bootstrap/carousel.less @@ -0,0 +1,121 @@ +// CAROUSEL +// -------- + +.carousel { + position: relative; + margin-bottom: @baseLineHeight; + line-height: 1; +} + +.carousel-inner { + overflow: hidden; + width: 100%; + position: relative; +} + +.carousel { + + .item { + display: none; + position: relative; + .transition(.6s ease-in-out left); + } + + // Account for jankitude on images + .item > img { + display: block; + line-height: 1; + } + + .active, + .next, + .prev { display: block; } + + .active { + left: 0; + } + + .next, + .prev { + position: absolute; + top: 0; + width: 100%; + } + + .next { + left: 100%; + } + .prev { + left: -100%; + } + .next.left, + .prev.right { + left: 0; + } + + .active.left { + left: -100%; + } + .active.right { + left: 100%; + } + +} + +// Left/right controls for nav +// --------------------------- + +.carousel-control { + position: absolute; + top: 40%; + left: 15px; + width: 40px; + height: 40px; + margin-top: -20px; + font-size: 60px; + font-weight: 100; + line-height: 30px; + color: @white; + text-align: center; + background: @grayDarker; + border: 3px solid @white; + .border-radius(23px); + .opacity(50); + + // we can't have this transition here + // because webkit cancels the carousel + // animation if you trip this while + // in the middle of another animation + // ;_; + // .transition(opacity .2s linear); + + // Reposition the right one + &.right { + left: auto; + right: 15px; + } + + // Hover state + &:hover { + color: @white; + text-decoration: none; + .opacity(90); + } +} + +// Caption for text below images +// ----------------------------- + +.carousel-caption { + position: absolute; + left: 0; + right: 0; + bottom: 0; + padding: 10px 15px 5px; + background: @grayDark; + background: rgba(0,0,0,.75); +} +.carousel-caption h4, +.carousel-caption p { + color: @white; +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/close.less --- /dev/null +++ b/static/june_2007_style/bootstrap/close.less @@ -0,0 +1,18 @@ +// CLOSE ICONS +// ----------- + +.close { + float: right; + font-size: 20px; + font-weight: bold; + line-height: @baseLineHeight; + color: @black; + text-shadow: 0 1px 0 rgba(255,255,255,1); + .opacity(20); + &:hover { + color: @black; + text-decoration: none; + .opacity(40); + cursor: pointer; + } +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/code.less --- /dev/null +++ b/static/june_2007_style/bootstrap/code.less @@ -0,0 +1,44 @@ +// Code.less +// Code typography styles for the <code> and <pre> elements +// -------------------------------------------------------- + +// Inline and block code styles +code, +pre { + padding: 0 3px 2px; + #font > #family > .monospace; + font-size: @baseFontSize - 1; + color: @grayDark; + .border-radius(3px); +} +code { + padding: 3px 4px; + color: #d14; + background-color: #f7f7f9; + border: 1px solid #e1e1e8; +} +pre { + display: block; + padding: (@baseLineHeight - 1) / 2; + margin: 0 0 @baseLineHeight / 2; + font-size: 12px; + line-height: @baseLineHeight; + background-color: #f5f5f5; + border: 1px solid #ccc; // fallback for IE7-8 + border: 1px solid rgba(0,0,0,.15); + .border-radius(4px); + white-space: pre; + white-space: pre-wrap; + word-break: break-all; + + // Make prettyprint styles more spaced out for readability + &.prettyprint { + margin-bottom: @baseLineHeight; + } + + // Account for some code outputs that place code tags in pre tags + code { + padding: 0; + background-color: transparent; + } +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/component-animations.less --- /dev/null +++ b/static/june_2007_style/bootstrap/component-animations.less @@ -0,0 +1,18 @@ +// COMPONENT ANIMATIONS +// -------------------- + +.fade { + .transition(opacity .15s linear); + opacity: 0; + &.in { + opacity: 1; + } +} + +.collapse { + .transition(height .35s ease); + position:relative; + overflow:hidden; + height: 0; + &.in { height: auto; } +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/dropdowns.less --- /dev/null +++ b/static/june_2007_style/bootstrap/dropdowns.less @@ -0,0 +1,131 @@ +// DROPDOWN MENUS +// -------------- + +// Use the .menu class on any <li> element within the topbar or ul.tabs and you'll get some superfancy dropdowns +.dropdown { + position: relative; +} +.dropdown-toggle { + // The caret makes the toggle a bit too tall in IE7 + *margin-bottom: -3px; +} +.dropdown-toggle:active, +.open .dropdown-toggle { + outline: 0; +} +// Dropdown arrow/caret +.caret { + display: inline-block; + width: 0; + height: 0; + text-indent: -99999px; + // IE7 won't do the border trick if there's a text indent, but it doesn't + // do the content that text-indent is hiding, either, so we're ok. + *text-indent: 0; + vertical-align: top; + border-left: 4px solid transparent; + border-right: 4px solid transparent; + border-top: 4px solid @black; + .opacity(30); + content: "\2193"; +} +.dropdown .caret { + margin-top: 8px; + margin-left: 2px; +} +.dropdown:hover .caret, +.open.dropdown .caret { + .opacity(100); +} +// The dropdown menu (ul) +.dropdown-menu { + position: absolute; + top: 100%; + left: 0; + z-index: @zindexDropdown; + float: left; + display: none; // none by default, but block on "open" of the menu + min-width: 160px; + max-width: 220px; + _width: 160px; + padding: 4px 0; + margin: 0; // override default ul + list-style: none; + background-color: @white; + border-color: #ccc; + border-color: rgba(0,0,0,.2); + border-style: solid; + border-width: 1px; + .border-radius(0 0 5px 5px); + .box-shadow(0 5px 10px rgba(0,0,0,.2)); + -webkit-background-clip: padding-box; + -moz-background-clip: padding; + background-clip: padding-box; + *border-right-width: 2px; + *border-bottom-width: 2px; + + // Allow for dropdowns to go bottom up (aka, dropup-menu) + &.bottom-up { + top: auto; + bottom: 100%; + margin-bottom: 2px; + } + + // Dividers (basically an hr) within the dropdown + .divider { + height: 1px; + margin: 5px 1px; + overflow: hidden; + background-color: #e5e5e5; + border-bottom: 1px solid @white; + + // IE7 needs a set width since we gave a height. Restricting just + // to IE7 to keep the 1px left/right space in other browsers. + // It is unclear where IE is getting the extra space that we need + // to negative-margin away, but so it goes. + *width: 100%; + *margin: -5px 0 5px; + } + + // Links within the dropdown menu + a { + display: block; + padding: 3px 15px; + clear: both; + font-weight: normal; + line-height: 18px; + color: @gray; + white-space: nowrap; + } +} + +// Hover state +.dropdown-menu li > a:hover, +.dropdown-menu .active > a, +.dropdown-menu .active > a:hover { + color: @white; + text-decoration: none; + background-color: @linkColor; +} + +// Open state for the dropdown +.dropdown.open { + // IE7's z-index only goes to the nearest positioned ancestor, which would + // make the menu appear below buttons that appeared later on the page + *z-index: @zindexDropdown; + + .dropdown-toggle { + color: @white; + background: #ccc; + background: rgba(0,0,0,.3); + } + .dropdown-menu { + display: block; + } +} + +// Typeahead +.typeahead { + margin-top: 2px; // give it some space to breathe + .border-radius(4px); +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/forms.less --- /dev/null +++ b/static/june_2007_style/bootstrap/forms.less @@ -0,0 +1,515 @@ +// Forms.less +// Base styles for various input types, form layouts, and states +// ------------------------------------------------------------- + + +// GENERAL STYLES +// -------------- + +// Make all forms have space below them +form { + margin: 0 0 @baseLineHeight; +} + +fieldset { + padding: 0; + margin: 0; + border: 0; +} + +// Groups of fields with labels on top (legends) +legend { + display: block; + width: 100%; + padding: 0; + margin-bottom: @baseLineHeight * 1.5; + font-size: @baseFontSize * 1.5; + line-height: @baseLineHeight * 2; + color: @grayDark; + border: 0; + border-bottom: 1px solid #eee; +} + +// Set font for forms +label, +input, +button, +select, +textarea { + #font > .sans-serif(@baseFontSize,normal,@baseLineHeight); +} + +// Identify controls by their labels +label { + display: block; + margin-bottom: 5px; + color: @grayDark; +} + +// Inputs, Textareas, Selects +input, +textarea, +select, +.uneditable-input { + display: inline-block; + width: 210px; + height: @baseLineHeight; + padding: 4px; + margin-bottom: 9px; + font-size: @baseFontSize; + line-height: @baseLineHeight; + color: @gray; + border: 1px solid #ccc; + .border-radius(3px); +} +.uneditable-textarea { + width: auto; + height: auto; +} + +// Inputs within a label +label input, +label textarea, +label select { + display: block; +} + +// Mini reset for unique input types +input[type="image"], +input[type="checkbox"], +input[type="radio"] { + width: auto; + height: auto; + padding: 0; + margin: 3px 0; + *margin-top: 0; /* IE7 */ + line-height: normal; + border: 0; + cursor: pointer; + .border-radius(0); +} + +// Reset the file input to browser defaults +input[type="file"] { + padding: initial; + line-height: initial; + border: initial; + background-color: @white; + background-color: initial; + .box-shadow(none); +} + +// Help out input buttons +input[type="button"], +input[type="reset"], +input[type="submit"] { + width: auto; + height: auto; +} + +// Set the height of select and file controls to match text inputs +select, +input[type="file"] { + height: 28px; /* In IE7, the height of the select element cannot be changed by height, only font-size */ + *margin-top: 4px; /* For IE7, add top margin to align select with labels */ + line-height: 28px; +} + +// Chrome on Linux and Mobile Safari need background-color +select { + width: 220px; // default input width + 10px of padding that doesn't get applied + background-color: @white; +} + +// Make multiple select elements height not fixed +select[multiple], +select[size] { + height: auto; +} + +// Remove shadow from image inputs +input[type="image"] { + .box-shadow(none); +} + +// Make textarea height behave +textarea { + height: auto; +} + +// Hidden inputs +input[type="hidden"] { + display: none; +} + + + +// CHECKBOXES & RADIOS +// ------------------- + +// Indent the labels to position radios/checkboxes as hanging +.radio, +.checkbox { + padding-left: 18px; +} +.radio input[type="radio"], +.checkbox input[type="checkbox"] { + float: left; + margin-left: -18px; +} + +// Move the options list down to align with labels +.controls > .radio:first-child, +.controls > .checkbox:first-child { + padding-top: 5px; // has to be padding because margin collaspes +} + +// Radios and checkboxes on same line +.radio.inline, +.checkbox.inline { + display: inline-block; + margin-bottom: 0; + vertical-align: middle; +} +.radio.inline + .radio.inline, +.checkbox.inline + .checkbox.inline { + margin-left: 10px; // space out consecutive inline controls +} +// But don't forget to remove their padding on first-child +.controls > .radio.inline:first-child, +.controls > .checkbox.inline:first-child { + padding-top: 0; +} + + + +// FOCUS STATE +// ----------- + +input, +textarea { + .box-shadow(inset 0 1px 1px rgba(0,0,0,.075)); + @transition: border linear .2s, box-shadow linear .2s; + .transition(@transition); +} +input:focus, +textarea:focus { + border-color: rgba(82,168,236,.8); + @shadow: inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(82,168,236,.6); + .box-shadow(@shadow); + outline: 0; + outline: thin dotted \9; /* IE6-8 */ +} +input[type="file"]:focus, +input[type="checkbox"]:focus, +select:focus { + .box-shadow(none); // override for file inputs + .tab-focus(); +} + + + +// INPUT SIZES +// ----------- + +// General classes for quick sizes +.input-mini { width: 60px; } +.input-small { width: 90px; } +.input-medium { width: 150px; } +.input-large { width: 210px; } +.input-xlarge { width: 270px; } +.input-xxlarge { width: 530px; } + +// Grid style input sizes +input[class*="span"], +select[class*="span"], +textarea[class*="span"], +.uneditable-input { + float: none; + margin-left: 0; +} + + + +// GRID SIZING FOR INPUTS +// ---------------------- + +#inputGridSystem > .generate(@gridColumns, @gridColumnWidth, @gridGutterWidth); + + + + +// DISABLED STATE +// -------------- + +// Disabled and read-only inputs +input[disabled], +select[disabled], +textarea[disabled], +input[readonly], +select[readonly], +textarea[readonly] { + background-color: #f5f5f5; + border-color: #ddd; + cursor: not-allowed; +} + + + + +// FORM FIELD FEEDBACK STATES +// -------------------------- + +// Mixin for form field states +.formFieldState(@textColor: #555, @borderColor: #ccc, @backgroundColor: #f5f5f5) { + // Set the text color + > label, + .help-block, + .help-inline { + color: @textColor; + } + // Style inputs accordingly + input, + select, + textarea { + color: @textColor; + border-color: @borderColor; + &:focus { + border-color: darken(@borderColor, 10%); + .box-shadow(0 0 6px lighten(@borderColor, 20%)); + } + } + // Give a small background color for input-prepend/-append + .input-prepend .add-on, + .input-append .add-on { + color: @textColor; + background-color: @backgroundColor; + border-color: @textColor; + } +} +// Warning +.control-group.warning { + .formFieldState(@warningText, @warningText, @warningBackground); +} +// Error +.control-group.error { + .formFieldState(@errorText, @errorText, @errorBackground); +} +// Success +.control-group.success { + .formFieldState(@successText, @successText, @successBackground); +} + +// HTML5 invalid states +// Shares styles with the .control-group.error above +input:focus:required:invalid, +textarea:focus:required:invalid, +select:focus:required:invalid { + color: #b94a48; + border-color: #ee5f5b; + &:focus { + border-color: darken(#ee5f5b, 10%); + .box-shadow(0 0 6px lighten(#ee5f5b, 20%)); + } +} + + + +// FORM ACTIONS +// ------------ + +.form-actions { + padding: (@baseLineHeight - 1) 20px @baseLineHeight; + margin-top: @baseLineHeight; + margin-bottom: @baseLineHeight; + background-color: #f5f5f5; + border-top: 1px solid #ddd; +} + +// For text that needs to appear as an input but should not be an input +.uneditable-input { + display: block; + background-color: @white; + border-color: #eee; + .box-shadow(inset 0 1px 2px rgba(0,0,0,.025)); + cursor: not-allowed; +} + +// Placeholder text gets special styles; can't be bundled together though for some reason +.placeholder(@grayLight); + + + +// HELP TEXT +// --------- + +.help-block { + margin-top: 5px; + margin-bottom: 0; + color: @grayLight; +} + +.help-inline { + display: inline-block; + .ie7-inline-block(); + margin-bottom: 9px; + vertical-align: middle; + padding-left: 5px; +} + + + +// INPUT GROUPS +// ------------ + +// Allow us to put symbols and text within the input field for a cleaner look +.input-prepend, +.input-append { + margin-bottom: 5px; + .clearfix(); // Clear the float to prevent wrapping + input, + .uneditable-input { + .border-radius(0 3px 3px 0); + &:focus { + position: relative; + z-index: 2; + } + } + .uneditable-input { + border-left-color: #ccc; + } + .add-on { + float: left; + display: block; + width: auto; + min-width: 16px; + height: @baseLineHeight; + margin-right: -1px; + padding: 4px 5px; + font-weight: normal; + line-height: @baseLineHeight; + color: @grayLight; + text-align: center; + text-shadow: 0 1px 0 @white; + background-color: #f5f5f5; + border: 1px solid #ccc; + .border-radius(3px 0 0 3px); + } + .active { + background-color: lighten(@green, 30); + border-color: @green; + } +} +.input-prepend { + .add-on { + *margin-top: 1px; /* IE6-7 */ + } +} +.input-append { + input, + .uneditable-input { + float: left; + .border-radius(3px 0 0 3px); + } + .uneditable-input { + border-right-color: #ccc; + } + .add-on { + margin-right: 0; + margin-left: -1px; + .border-radius(0 3px 3px 0); + } + input:first-child { + // In IE7, having a hasLayout container (from clearfix's zoom:1) can make the first input + // inherit the sum of its ancestors' margins. + *margin-left: -160px; + + &+.add-on { + *margin-left: -21px; + } + } +} + + + +// SEARCH FORM +// ----------- + +.search-query { + padding-left: 14px; + padding-right: 14px; + margin-bottom: 0; // remove the default margin on all inputs + .border-radius(14px); +} + + + +// HORIZONTAL & VERTICAL FORMS +// --------------------------- + +// Common properties +// ----------------- + +.form-search, +.form-inline, +.form-horizontal { + input, + textarea, + select, + .help-inline, + .uneditable-input { + display: inline-block; + margin-bottom: 0; + } +} +.form-search label, +.form-inline label, +.form-search .input-append, +.form-inline .input-append, +.form-search .input-prepend, +.form-inline .input-prepend { + display: inline-block; +} +// Make the prepend and append add-on vertical-align: middle; +.form-search .input-append .add-on, +.form-inline .input-prepend .add-on, +.form-search .input-append .add-on, +.form-inline .input-prepend .add-on { + vertical-align: middle; +} + +// Margin to space out fieldsets +.control-group { + margin-bottom: @baseLineHeight / 2; +} + +// Horizontal-specific styles +// -------------------------- + +.form-horizontal { + // Legend collapses margin, so we're relegated to padding + legend + .control-group { + margin-top: @baseLineHeight; + -webkit-margin-top-collapse: separate; + } + // Increase spacing between groups + .control-group { + margin-bottom: @baseLineHeight; + .clearfix(); + } + // Float the labels left + .control-group > label { + float: left; + width: 140px; + padding-top: 5px; + text-align: right; + } + // Move over all input controls and content + .controls { + margin-left: 160px; + } + // Move over buttons in .form-actions to align with .controls + .form-actions { + padding-left: 160px; + } +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/grid.less --- /dev/null +++ b/static/june_2007_style/bootstrap/grid.less @@ -0,0 +1,8 @@ +// GRID SYSTEM +// ----------- + +// Fixed (940px) +#gridSystem > .generate(@gridColumns, @gridColumnWidth, @gridGutterWidth); + +// Fluid (940px) +#fluidGridSystem > .generate(@gridColumns, @fluidGridColumnWidth, @fluidGridGutterWidth); diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/hero-unit.less --- /dev/null +++ b/static/june_2007_style/bootstrap/hero-unit.less @@ -0,0 +1,20 @@ +// HERO UNIT +// --------- + +.hero-unit { + padding: 60px; + margin-bottom: 30px; + background-color: #f5f5f5; + .border-radius(6px); + h1 { + margin-bottom: 0; + font-size: 60px; + line-height: 1; + letter-spacing: -1px; + } + p { + font-size: 18px; + font-weight: 200; + line-height: @baseLineHeight * 1.5; + } +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/labels.less --- /dev/null +++ b/static/june_2007_style/bootstrap/labels.less @@ -0,0 +1,16 @@ +// LABELS +// ------ + +.label { + padding: 1px 3px 2px; + font-size: @baseFontSize * .75; + font-weight: bold; + color: @white; + text-transform: uppercase; + background-color: @grayLight; + .border-radius(3px); +} +.label-important { background-color: @errorText; } +.label-warning { background-color: @orange; } +.label-success { background-color: @successText; } +.label-info { background-color: @infoText; } diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/layouts.less --- /dev/null +++ b/static/june_2007_style/bootstrap/layouts.less @@ -0,0 +1,17 @@ +// +// Layouts +// Fixed-width and fluid (with sidebar) layouts +// -------------------------------------------- + + +// Container (centered, fixed-width layouts) +.container { + .container-fixed(); +} + +// Fluid layouts (left aligned, with sidebar, min- & max-width content) +.container-fluid { + padding-left: @gridGutterWidth; + padding-right: @gridGutterWidth; + .clearfix(); +} \ No newline at end of file diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/mixins.less --- /dev/null +++ b/static/june_2007_style/bootstrap/mixins.less @@ -0,0 +1,537 @@ +// Mixins.less +// Snippets of reusable CSS to develop faster and keep code readable +// ----------------------------------------------------------------- + + +// UTILITY MIXINS +// -------------------------------------------------- + +// Clearfix +// -------- +// For clearing floats like a boss h5bp.com/q +.clearfix() { + *zoom: 1; + &:before, + &:after { + display: table; + content: ""; + } + &:after { + clear: both; + } +} + +// Webkit-style focus +// ------------------ +.tab-focus() { + // Default + outline: thin dotted; + // Webkit + outline: 5px auto -webkit-focus-ring-color; + outline-offset: -2px; +} + +// Center-align a block level element +// ---------------------------------- +.center-block() { + display: block; + margin-left: auto; + margin-right: auto; +} + +// IE7 inline-block +// ---------------- +.ie7-inline-block() { + *display: inline; /* IE7 inline-block hack */ + *zoom: 1; +} + +// IE7 likes to collapse whitespace on either side of the inline-block elements. +// Ems because we're attempting to match the width of a space character. Left +// version is for form buttons, which typically come after other elements, and +// right version is for icons, which come before. Applying both is ok, but it will +// mean that space between those elements will be .6em (~2 space characters) in IE7, +// instead of the 1 space in other browsers. +.ie7-restore-left-whitespace() { + *margin-left: .3em; + + &:first-child { + *margin-left: 0; + } +} + +.ie7-restore-right-whitespace() { + *margin-right: .3em; + + &:last-child { + *margin-left: 0; + } +} + +// Sizing shortcuts +// ------------------------- +.size(@height: 5px, @width: 5px) { + width: @width; + height: @height; +} +.square(@size: 5px) { + .size(@size, @size); +} + +// Placeholder text +// ------------------------- +.placeholder(@color: @placeholderText) { + :-moz-placeholder { + color: @color; + } + ::-webkit-input-placeholder { + color: @color; + } +} + + + +// FONTS +// -------------------------------------------------- + +#font { + #family { + .serif() { + font-family: Georgia, "Times New Roman", Times, serif; + } + .sans-serif() { + font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; + } + .monospace() { + font-family: Menlo, Monaco, "Courier New", monospace; + } + } + .shorthand(@size: @baseFontSize, @weight: normal, @lineHeight: @baseLineHeight) { + font-size: @size; + font-weight: @weight; + line-height: @lineHeight; + } + .serif(@size: @baseFontSize, @weight: normal, @lineHeight: @baseLineHeight) { + #font > #family > .serif; + #font > .shorthand(@size, @weight, @lineHeight); + } + .sans-serif(@size: @baseFontSize, @weight: normal, @lineHeight: @baseLineHeight) { + #font > #family > .sans-serif; + #font > .shorthand(@size, @weight, @lineHeight); + } + .monospace(@size: @baseFontSize, @weight: normal, @lineHeight: @baseLineHeight) { + #font > #family > .monospace; + #font > .shorthand(@size, @weight, @lineHeight); + } +} + + + +// GRID SYSTEM +// -------------------------------------------------- + +// Site container +// ------------------------- +.container-fixed() { + width: @gridRowWidth; + margin-left: auto; + margin-right: auto; + .clearfix(); +} + +// Le grid system +// ------------------------- +#gridSystem { + // Setup the mixins to be used + .columns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, @columns) { + width: (@gridColumnWidth * @columns) + (@gridGutterWidth * (@columns - 1)); + } + .offset(@gridColumnWidth, @gridGutterWidth, @columns) { + margin-left: (@gridColumnWidth * @columns) + (@gridGutterWidth * (@columns - 1)) + (@gridGutterWidth * 2); + } + .gridColumn(@gridGutterWidth) { + float: left; + margin-left: @gridGutterWidth; + } + // Take these values and mixins, and make 'em do their thang + .generate(@gridColumns, @gridColumnWidth, @gridGutterWidth) { + // Row surrounds the columns + .row { + margin-left: @gridGutterWidth * -1; + .clearfix(); + } + // Find all .span# classes within .row and give them the necessary properties for grid columns (supported by all browsers back to IE7, thanks @dhg) + [class*="span"] { + #gridSystem > .gridColumn(@gridGutterWidth); + } + // Default columns + .span1 { #gridSystem > .columns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, 1); } + .span2 { #gridSystem > .columns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, 2); } + .span3 { #gridSystem > .columns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, 3); } + .span4 { #gridSystem > .columns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, 4); } + .span5 { #gridSystem > .columns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, 5); } + .span6 { #gridSystem > .columns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, 6); } + .span7 { #gridSystem > .columns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, 7); } + .span8 { #gridSystem > .columns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, 8); } + .span9 { #gridSystem > .columns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, 9); } + .span10 { #gridSystem > .columns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, 10); } + .span11 { #gridSystem > .columns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, 11); } + .span12, + .container { #gridSystem > .columns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, 12); } + // Offset column options + .offset1 { #gridSystem > .offset(@gridColumnWidth, @gridGutterWidth, 1); } + .offset2 { #gridSystem > .offset(@gridColumnWidth, @gridGutterWidth, 2); } + .offset3 { #gridSystem > .offset(@gridColumnWidth, @gridGutterWidth, 3); } + .offset4 { #gridSystem > .offset(@gridColumnWidth, @gridGutterWidth, 4); } + .offset5 { #gridSystem > .offset(@gridColumnWidth, @gridGutterWidth, 5); } + .offset6 { #gridSystem > .offset(@gridColumnWidth, @gridGutterWidth, 6); } + .offset7 { #gridSystem > .offset(@gridColumnWidth, @gridGutterWidth, 7); } + .offset8 { #gridSystem > .offset(@gridColumnWidth, @gridGutterWidth, 8); } + .offset9 { #gridSystem > .offset(@gridColumnWidth, @gridGutterWidth, 9); } + .offset10 { #gridSystem > .offset(@gridColumnWidth, @gridGutterWidth, 10); } + .offset11 { #gridSystem > .offset(@gridColumnWidth, @gridGutterWidth, 11); } + } +} + +// Fluid grid system +// ------------------------- +#fluidGridSystem { + // Setup the mixins to be used + .columns(@fluidGridGutterWidth, @fluidGridColumnWidth, @columns) { + width: 1% * (@fluidGridColumnWidth * @columns) + (@fluidGridGutterWidth * (@columns - 1)); + } + .gridColumn(@fluidGridGutterWidth) { + float: left; + margin-left: @fluidGridGutterWidth; + } + // Take these values and mixins, and make 'em do their thang + .generate(@gridColumns, @fluidGridColumnWidth, @fluidGridGutterWidth) { + // Row surrounds the columns + .row-fluid { + width: 100%; + .clearfix(); + + // Find all .span# classes within .row and give them the necessary properties for grid columns (supported by all browsers back to IE7, thanks @dhg) + > [class*="span"] { + #fluidGridSystem > .gridColumn(@fluidGridGutterWidth); + } + > [class*="span"]:first-child { + margin-left: 0; + } + // Default columns + .span1 { #fluidGridSystem > .columns(@fluidGridGutterWidth, @fluidGridColumnWidth, 1); } + .span2 { #fluidGridSystem > .columns(@fluidGridGutterWidth, @fluidGridColumnWidth, 2); } + .span3 { #fluidGridSystem > .columns(@fluidGridGutterWidth, @fluidGridColumnWidth, 3); } + .span4 { #fluidGridSystem > .columns(@fluidGridGutterWidth, @fluidGridColumnWidth, 4); } + .span5 { #fluidGridSystem > .columns(@fluidGridGutterWidth, @fluidGridColumnWidth, 5); } + .span6 { #fluidGridSystem > .columns(@fluidGridGutterWidth, @fluidGridColumnWidth, 6); } + .span7 { #fluidGridSystem > .columns(@fluidGridGutterWidth, @fluidGridColumnWidth, 7); } + .span8 { #fluidGridSystem > .columns(@fluidGridGutterWidth, @fluidGridColumnWidth, 8); } + .span9 { #fluidGridSystem > .columns(@fluidGridGutterWidth, @fluidGridColumnWidth, 9); } + .span10 { #fluidGridSystem > .columns(@fluidGridGutterWidth, @fluidGridColumnWidth, 10); } + .span11 { #fluidGridSystem > .columns(@fluidGridGutterWidth, @fluidGridColumnWidth, 11); } + .span12 { #fluidGridSystem > .columns(@fluidGridGutterWidth, @fluidGridColumnWidth, 12); } + } + } +} + + + +// Input grid system +// ------------------------- +#inputGridSystem { + .inputColumns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, @columns) { + width: ((@gridColumnWidth) * @columns) + (@gridGutterWidth * (@columns - 1)) - 10; + } + .generate(@gridColumns, @gridColumnWidth, @gridGutterWidth) { + input, + textarea, + .uneditable-input { + &.span1 { #inputGridSystem > .inputColumns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, 1); } + &.span2 { #inputGridSystem > .inputColumns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, 2); } + &.span3 { #inputGridSystem > .inputColumns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, 3); } + &.span4 { #inputGridSystem > .inputColumns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, 4); } + &.span5 { #inputGridSystem > .inputColumns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, 5); } + &.span6 { #inputGridSystem > .inputColumns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, 6); } + &.span7 { #inputGridSystem > .inputColumns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, 7); } + &.span8 { #inputGridSystem > .inputColumns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, 8); } + &.span9 { #inputGridSystem > .inputColumns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, 9); } + &.span10 { #inputGridSystem > .inputColumns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, 10); } + &.span11 { #inputGridSystem > .inputColumns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, 11); } + &.span12 { #inputGridSystem > .inputColumns(@gridGutterWidth, @gridColumnWidth, @gridRowWidth, 12); } + } + } +} + + + +// CSS3 PROPERTIES +// -------------------------------------------------- + +// Border Radius +.border-radius(@radius: 5px) { + -webkit-border-radius: @radius; + -moz-border-radius: @radius; + border-radius: @radius; +} + +// Drop shadows +.box-shadow(@shadow: 0 1px 3px rgba(0,0,0,.25)) { + -webkit-box-shadow: @shadow; + -moz-box-shadow: @shadow; + box-shadow: @shadow; +} + +// Transitions +.transition(@transition) { + -webkit-transition: @transition; + -moz-transition: @transition; + -ms-transition: @transition; + -o-transition: @transition; + transition: @transition; +} + +// Transformations +.rotate(@degrees) { + -webkit-transform: rotate(@degrees); + -moz-transform: rotate(@degrees); + -ms-transform: rotate(@degrees); + -o-transform: rotate(@degrees); + transform: rotate(@degrees); +} +.scale(@ratio) { + -webkit-transform: scale(@ratio); + -moz-transform: scale(@ratio); + -ms-transform: scale(@ratio); + -o-transform: scale(@ratio); + transform: scale(@ratio); +} +.translate(@x: 0, @y: 0) { + -webkit-transform: translate(@x, @y); + -moz-transform: translate(@x, @y); + -ms-transform: translate(@x, @y); + -o-transform: translate(@x, @y); + transform: translate(@x, @y); +} +.skew(@x: 0, @y: 0) { + -webkit-transform: translate(@x, @y); + -moz-transform: translate(@x, @y); + -ms-transform: translate(@x, @y); + -o-transform: translate(@x, @y); + transform: translate(@x, @y); +} +.skew(@x: 0, @y: 0) { + -webkit-transform: skew(@x, @y); + -moz-transform: skew(@x, @y); + -ms-transform: skew(@x, @y); + -o-transform: skew(@x, @y); + transform: skew(@x, @y); +} + +// Background clipping +// Heads up: FF 3.6 and under need "padding" instead of "padding-box" +.background-clip(@clip) { + -webkit-background-clip: @clip; + -moz-background-clip: @clip; + background-clip: @clip; +} + +// Background sizing +.background-size(@size){ + -webkit-background-size: @size; + -moz-background-size: @size; + -o-background-size: @size; + background-size: @size; +} + + +// Box sizing +.box-sizing(@boxmodel) { + -webkit-box-sizing: @boxmodel; + -moz-box-sizing: @boxmodel; + box-sizing: @boxmodel; +} + +// User select +// For selecting text on the page +.user-select(@select) { + -webkit-user-select: @select; + -moz-user-select: @select; + -o-user-select: @select; + user-select: @select; +} + +// Resize anything +.resizable(@direction: both) { + resize: @direction; // Options: horizontal, vertical, both + overflow: auto; // Safari fix +} + +// CSS3 Content Columns +.content-columns(@columnCount, @columnGap: @gridColumnGutter) { + -webkit-column-count: @columnCount; + -moz-column-count: @columnCount; + column-count: @columnCount; + -webkit-column-gap: @columnGap; + -moz-column-gap: @columnGap; + column-gap: @columnGap; +} + +// Opacity +.opacity(@opacity: 100) { + opacity: @opacity / 100; + filter: e(%("alpha(opacity=%d)", @opacity)); +} + + + +// BACKGROUNDS +// -------------------------------------------------- + +// Add an alphatransparency value to any background or border color (via Elyse Holladay) +#translucent { + .background(@color: @white, @alpha: 1) { + background-color: hsla(hue(@color), saturation(@color), lightness(@color), @alpha); + } + .border(@color: @white, @alpha: 1) { + border-color: hsla(hue(@color), saturation(@color), lightness(@color), @alpha); + .background-clip(padding-box); + } +} + +// Gradient Bar Colors for buttons and alerts +.gradientBar(@primaryColor, @secondaryColor) { + #gradient > .vertical(@primaryColor, @secondaryColor); + border-color: @secondaryColor @secondaryColor darken(@secondaryColor, 15%); + border-color: rgba(0,0,0,.1) rgba(0,0,0,.1) fadein(rgba(0,0,0,.1), 15%); +} + +// Gradients +#gradient { + .horizontal(@startColor: #555, @endColor: #333) { + background-color: @endColor; + background-image: -moz-linear-gradient(left, @startColor, @endColor); // FF 3.6+ + background-image: -ms-linear-gradient(left, @startColor, @endColor); // IE10 + background-image: -webkit-gradient(linear, 0 0, 100% 0, from(@startColor), to(@endColor)); // Safari 4+, Chrome 2+ + background-image: -webkit-linear-gradient(left, @startColor, @endColor); // Safari 5.1+, Chrome 10+ + background-image: -o-linear-gradient(left, @startColor, @endColor); // Opera 11.10 + background-image: linear-gradient(left, @startColor, @endColor); // Le standard + background-repeat: repeat-x; + filter: e(%("progid:DXImageTransform.Microsoft.gradient(startColorstr='%d', endColorstr='%d', GradientType=1)",@startColor,@endColor)); // IE9 and down + } + .vertical(@startColor: #555, @endColor: #333) { + background-color: mix(@startColor, @endColor, 60%); + background-image: -moz-linear-gradient(top, @startColor, @endColor); // FF 3.6+ + background-image: -ms-linear-gradient(top, @startColor, @endColor); // IE10 + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(@startColor), to(@endColor)); // Safari 4+, Chrome 2+ + background-image: -webkit-linear-gradient(top, @startColor, @endColor); // Safari 5.1+, Chrome 10+ + background-image: -o-linear-gradient(top, @startColor, @endColor); // Opera 11.10 + background-image: linear-gradient(top, @startColor, @endColor); // The standard + background-repeat: repeat-x; + filter: e(%("progid:DXImageTransform.Microsoft.gradient(startColorstr='%d', endColorstr='%d', GradientType=0)",@startColor,@endColor)); // IE9 and down + } + .directional(@startColor: #555, @endColor: #333, @deg: 45deg) { + background-color: @endColor; + background-repeat: repeat-x; + background-image: -moz-linear-gradient(@deg, @startColor, @endColor); // FF 3.6+ + background-image: -ms-linear-gradient(@deg, @startColor, @endColor); // IE10 + background-image: -webkit-linear-gradient(@deg, @startColor, @endColor); // Safari 5.1+, Chrome 10+ + background-image: -o-linear-gradient(@deg, @startColor, @endColor); // Opera 11.10 + background-image: linear-gradient(@deg, @startColor, @endColor); // The standard + } + .vertical-three-colors(@startColor: #00b3ee, @midColor: #7a43b6, @colorStop: 50%, @endColor: #c3325f) { + background-color: mix(@midColor, @endColor, 80%); + background-image: -webkit-gradient(linear, 0 0, 0 100%, from(@startColor), color-stop(@colorStop, @midColor), to(@endColor)); + background-image: -webkit-linear-gradient(@startColor, @midColor @colorStop, @endColor); + background-image: -moz-linear-gradient(top, @startColor, @midColor @colorStop, @endColor); + background-image: -ms-linear-gradient(@startColor, @midColor @colorStop, @endColor); + background-image: -o-linear-gradient(@startColor, @midColor @colorStop, @endColor); + background-image: linear-gradient(@startColor, @midColor @colorStop, @endColor); + background-repeat: no-repeat; + filter: e(%("progid:DXImageTransform.Microsoft.gradient(startColorstr='%d', endColorstr='%d', GradientType=0)",@startColor,@endColor)); // IE9 and down, gets no color-stop at all for proper fallback + } + .radial(@innerColor: #555, @outerColor: #333) { + background-color: @outerColor; + background-image: -webkit-gradient(radial, center center, 0, center center, 460, from(@innerColor), to(@outerColor)); + background-image: -webkit-radial-gradient(circle, @innerColor, @outerColor); + background-image: -moz-radial-gradient(circle, @innerColor, @outerColor); + background-image: -ms-radial-gradient(circle, @innerColor, @outerColor); + background-repeat: no-repeat; + // Opera cannot do radial gradients yet + } + .striped(@color, @angle: -45deg) { + background-color: @color; + background-image: -webkit-gradient(linear, 0 100%, 100% 0, color-stop(.25, rgba(255,255,255,.15)), color-stop(.25, transparent), color-stop(.5, transparent), color-stop(.5, rgba(255,255,255,.15)), color-stop(.75, rgba(255,255,255,.15)), color-stop(.75, transparent), to(transparent)); + background-image: -webkit-linear-gradient(@angle, rgba(255,255,255,.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,.15) 50%, rgba(255,255,255,.15) 75%, transparent 75%, transparent); + background-image: -moz-linear-gradient(@angle, rgba(255,255,255,.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,.15) 50%, rgba(255,255,255,.15) 75%, transparent 75%, transparent); + background-image: -ms-linear-gradient(@angle, rgba(255,255,255,.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,.15) 50%, rgba(255,255,255,.15) 75%, transparent 75%, transparent); + background-image: -o-linear-gradient(@angle, rgba(255,255,255,.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,.15) 50%, rgba(255,255,255,.15) 75%, transparent 75%, transparent); + background-image: linear-gradient(@angle, rgba(255,255,255,.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,.15) 50%, rgba(255,255,255,.15) 75%, transparent 75%, transparent); + } +} +// Reset filters for IE +.reset-filter() { + filter: e(%("progid:DXImageTransform.Microsoft.gradient(enabled = false)")); +} + + +// Mixin for generating button backgrounds +// --------------------------------------- +.buttonBackground(@startColor, @endColor) { + // gradientBar will set the background to a pleasing blend of these, to support IE<=9 + .gradientBar(@startColor, @endColor); + .reset-filter(); + + // in these cases the gradient won't cover the background, so we override + &:hover, &:active, &.active, &.disabled, &[disabled] { + background-color: @endColor; + } + + // IE 7 + 8 can't handle box-shadow to show active, so we darken a bit ourselves + &:active, + &.active { + background-color: darken(@endColor, 10%) e("\9"); + } +} + + +// COMPONENT MIXINS +// -------------------------------------------------- + +// POPOVER ARROWS +// ------------------------- +// For tipsies and popovers +#popoverArrow { + .top(@arrowWidth: 5px) { + bottom: 0; + left: 50%; + margin-left: -@arrowWidth; + border-left: @arrowWidth solid transparent; + border-right: @arrowWidth solid transparent; + border-top: @arrowWidth solid @black; + } + .left(@arrowWidth: 5px) { + top: 50%; + right: 0; + margin-top: -@arrowWidth; + border-top: @arrowWidth solid transparent; + border-bottom: @arrowWidth solid transparent; + border-left: @arrowWidth solid @black; + } + .bottom(@arrowWidth: 5px) { + top: 0; + left: 50%; + margin-left: -@arrowWidth; + border-left: @arrowWidth solid transparent; + border-right: @arrowWidth solid transparent; + border-bottom: @arrowWidth solid @black; + } + .right(@arrowWidth: 5px) { + top: 50%; + left: 0; + margin-top: -@arrowWidth; + border-top: @arrowWidth solid transparent; + border-bottom: @arrowWidth solid transparent; + border-right: @arrowWidth solid @black; + } +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/modals.less --- /dev/null +++ b/static/june_2007_style/bootstrap/modals.less @@ -0,0 +1,72 @@ +// MODALS +// ------ + +.modal-open { + .dropdown-menu { z-index: @zindexDropdown + @zindexModal; } + .dropdown.open { *z-index: @zindexDropdown + @zindexModal; } + .popover { z-index: @zindexPopover + @zindexModal; } + .tooltip { z-index: @zindexTooltip + @zindexModal; } +} + +.modal-backdrop { + position: fixed; + top: 0; + right: 0; + bottom: 0; + left: 0; + z-index: @zindexModalBackdrop; + background-color: @black; + // Fade for backdrop + &.fade { opacity: 0; } +} + +.modal-backdrop, +.modal-backdrop.fade.in { + .opacity(80); +} + +.modal { + position: fixed; + top: 50%; + left: 50%; + z-index: @zindexModal; + max-height: 500px; + overflow: auto; + width: 560px; + margin: -250px 0 0 -280px; + background-color: @white; + border: 1px solid #999; + border: 1px solid rgba(0,0,0,.3); + *border: 1px solid #999; /* IE6-7 */ + .border-radius(6px); + .box-shadow(0 3px 7px rgba(0,0,0,0.3)); + .background-clip(padding-box); + &.fade { + .transition(e('opacity .3s linear, top .3s ease-out')); + top: -25%; + } + &.fade.in { top: 50%; } +} +.modal-header { + padding: 9px 15px; + border-bottom: 1px solid #eee; + // Close icon + .close { margin-top: 2px; } +} +.modal-body { + padding: 15px; +} +.modal-footer { + padding: 14px 15px 15px; + margin-bottom: 0; + background-color: #f5f5f5; + border-top: 1px solid #ddd; + .border-radius(0 0 6px 6px); + .box-shadow(inset 0 1px 0 @white); + .clearfix(); + .btn { + float: right; + margin-left: 5px; + margin-bottom: 0; // account for input[type="submit"] which gets the bottom margin like all other inputs + } +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/navbar.less --- /dev/null +++ b/static/june_2007_style/bootstrap/navbar.less @@ -0,0 +1,292 @@ +// NAVBAR (FIXED AND STATIC) +// ------------------------- + + +// COMMON STYLES +// ------------- + +.navbar { + overflow: visible; + margin-bottom: @baseLineHeight; +} + +// Gradient is applied to it's own element because overflow visible is not honored by IE when filter is present +.navbar-inner { + padding-left: 20px; + padding-right: 20px; + #gradient > .vertical(@navbarBackgroundHighlight, @navbarBackground); + .border-radius(4px); + @shadow: 0 1px 3px rgba(0,0,0,.25), inset 0 -1px 0 rgba(0,0,0,.1); + .box-shadow(@shadow); +} + +// Navbar button for toggling navbar items in responsive layouts +.btn-navbar { + display: none; + float: right; + padding: 7px 10px; + margin-left: 5px; + margin-right: 5px; + .buttonBackground(@navbarBackgroundHighlight, @navbarBackground); + @shadow: inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 rgba(255,255,255,.075); + .box-shadow(@shadow); +} +.btn-navbar .icon-bar { + display: block; + width: 18px; + height: 2px; + background-color: #f5f5f5; + .border-radius(1px); + .box-shadow(0 1px 0 rgba(0,0,0,.25)); +} +.btn-navbar .icon-bar + .icon-bar { + margin-top: 3px; +} +// Override the default collapsed state +.nav-collapse.collapse { + height: auto; +} + + +// Brand, links, text, and buttons +.navbar { + // Hover and active states + .brand:hover { + text-decoration: none; + } + // Website or project name + .brand { + float: left; + display: block; + padding: 8px 20px 12px; + margin-left: -20px; // negative indent to left-align the text down the page + font-size: 20px; + font-weight: 200; + line-height: 1; + color: @white; + } + // Plain text in topbar + .navbar-text { + margin-bottom: 0; + line-height: 40px; + color: @navbarText; + a:hover { + color: @white; + background-color: transparent; + } + } + // Buttons in navbar + .btn, + .btn-group { + margin-top: 5px; // make buttons vertically centered in navbar + } + .btn-group .btn { + margin-top: 0; + } +} + +// Navbar forms +.navbar-form { + margin-bottom: 0; // remove default bottom margin + .clearfix(); + input, + select { + display: inline-block; + margin-top: 5px; + margin-bottom: 0; + } + .radio, + .checkbox { + margin-top: 5px; + } + input[type="image"], + input[type="checkbox"], + input[type="radio"] { + margin-top: 3px; + } +} + +// Navbar search +.navbar-search { + position: relative; + float: left; + margin-top: 6px; + margin-bottom: 0; + .search-query { + padding: 4px 9px; + #font > .sans-serif(13px, normal, 1); + color: @white; + color: rgba(255,255,255,.75); + background: #666; + background: rgba(255,255,255,.3); + border: 1px solid #111; + @shadow: inset 0 1px 2px rgba(0,0,0,.1), 0 1px 0px rgba(255,255,255,.15); + .box-shadow(@shadow); + .transition(none); + + // Placeholder text gets special styles; can't be bundled together though for some reason + .placeholder(@grayLighter); + + // Hover states + &:hover { + color: @white; + background-color: @grayLight; + background-color: rgba(255,255,255,.5); + } + // Focus states (we use .focused since IE8 and down doesn't support :focus) + &:focus, + &.focused { + padding: 5px 10px; + color: @grayDark; + text-shadow: 0 1px 0 @white; + background-color: @white; + border: 0; + .box-shadow(0 0 3px rgba(0,0,0,.15)); + outline: 0; + } + } +} + + +// FIXED NAVBAR +// ------------ + +.navbar-fixed-top { + position: fixed; + top: 0; + right: 0; + left: 0; + z-index: @zindexFixedNavbar; +} +.navbar-fixed-top .navbar-inner { + padding-left: 0; + padding-right: 0; + .border-radius(0); +} + + +// NAVIGATION +// ---------- + +.navbar .nav { + position: relative; + left: 0; + display: block; + float: left; + margin: 0 10px 0 0; +} +.navbar .nav.pull-right { + float: right; // redeclare due to specificity +} +.navbar .nav > li { + display: block; + float: left; +} + +// Links +.navbar .nav > li > a { + float: none; + padding: 10px 10px 11px; + line-height: 19px; + color: @navbarLinkColor; + text-decoration: none; + text-shadow: 0 -1px 0 rgba(0,0,0,.25); +} +// Hover +.navbar .nav > li > a:hover { + background-color: transparent; + color: @navbarLinkColorHover; + text-decoration: none; +} + +// Active nav items +.navbar .nav .active > a, +.navbar .nav .active > a:hover { + color: @navbarLinkColorHover; + text-decoration: none; + background-color: @navbarBackground; + background-color: rgba(0,0,0,.5); +} + +// Dividers (basically a vertical hr) +.navbar .divider-vertical { + height: @navbarHeight; + width: 1px; + margin: 0 9px; + overflow: hidden; + background-color: @navbarBackground; + border-right: 1px solid @navbarBackgroundHighlight; +} + +// Secondary (floated right) nav in topbar +.navbar .nav.pull-right { + margin-left: 10px; + margin-right: 0; +} + + + +// Dropdown menus +// -------------- + +// Menu position and menu carets +.navbar .dropdown-menu { + margin-top: 1px; + .border-radius(4px); + &:before { + content: ''; + display: inline-block; + border-left: 7px solid transparent; + border-right: 7px solid transparent; + border-bottom: 7px solid #ccc; + border-bottom-color: rgba(0,0,0,.2); + position: absolute; + top: -7px; + left: 9px; + } + &:after { + content: ''; + display: inline-block; + border-left: 6px solid transparent; + border-right: 6px solid transparent; + border-bottom: 6px solid @white; + position: absolute; + top: -6px; + left: 10px; + } +} + +// Dropdown toggle caret +.navbar .nav .dropdown-toggle .caret, +.navbar .nav .open.dropdown .caret { + border-top-color: @white; +} +.navbar .nav .active .caret { + .opacity(100); +} + +// Remove background color from open dropdown +.navbar .nav .open > .dropdown-toggle, +.navbar .nav .active > .dropdown-toggle, +.navbar .nav .open.active > .dropdown-toggle { + background-color: transparent; +} + +// Dropdown link on hover +.navbar .nav .active > .dropdown-toggle:hover { + color: @white; +} + +// Right aligned menus need alt position +.navbar .nav.pull-right .dropdown-menu { + left: auto; + right: 0; + &:before { + left: auto; + right: 12px; + } + &:after { + left: auto; + right: 13px; + } +} \ No newline at end of file diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/navs.less --- /dev/null +++ b/static/june_2007_style/bootstrap/navs.less @@ -0,0 +1,344 @@ +// NAVIGATIONS +// ----------- + + + +// BASE CLASS +// ---------- + +.nav { + margin-left: 0; + margin-bottom: @baseLineHeight; + list-style: none; +} + +// Make links block level +.nav > li > a { + display: block; +} +.nav > li > a:hover { + text-decoration: none; + background-color: @grayLighter; +} + + + +// NAV LIST +// -------- + +.nav-list { + padding-left: 14px; + padding-right: 14px; + margin-bottom: 0; +} +.nav-list > li > a, +.nav-list .nav-header { + display: block; + padding: 3px 15px; + margin-left: -15px; + margin-right: -15px; + text-shadow: 0 1px 0 rgba(255,255,255,.5); +} +.nav-list .nav-header { + font-size: 11px; + font-weight: bold; + line-height: @baseLineHeight; + color: @grayLight; + text-transform: uppercase; +} +.nav-list > li + .nav-header { + margin-top: 9px; +} +.nav-list .active > a, +.nav-list .active > a:hover { + color: @white; + text-shadow: 0 -1px 0 rgba(0,0,0,.2); + background-color: @linkColor; +} +.nav-list [class^="icon-"] { + margin-right: 2px; +} + + + +// TABS AND PILLS +// ------------- + +// Common styles +.nav-tabs, +.nav-pills { + .clearfix(); +} +.nav-tabs > li, +.nav-pills > li { + float: left; +} +.nav-tabs > li > a, +.nav-pills > li > a { + padding-right: 12px; + padding-left: 12px; + margin-right: 2px; + line-height: 14px; // keeps the overall height an even number +} + +// TABS +// ---- + +// Give the tabs something to sit on +.nav-tabs { + border-bottom: 1px solid #ddd; +} + +// Make the list-items overlay the bottom border +.nav-tabs > li { + margin-bottom: -1px; +} + +// Actual tabs (as links) +.nav-tabs > li > a { + padding-top: 9px; + padding-bottom: 9px; + border: 1px solid transparent; + .border-radius(4px 4px 0 0); + &:hover { + border-color: @grayLighter @grayLighter #ddd; + } +} +// Active state, and it's :hover to override normal :hover +.nav-tabs > .active > a, +.nav-tabs > .active > a:hover { + color: @gray; + background-color: @white; + border: 1px solid #ddd; + border-bottom-color: transparent; + cursor: default; +} + +// PILLS +// ----- + +// Links rendered as pills +.nav-pills > li > a { + padding-top: 8px; + padding-bottom: 8px; + margin-top: 2px; + margin-bottom: 2px; + .border-radius(5px); +} + +// Active state +.nav-pills .active > a, +.nav-pills .active > a:hover { + color: @white; + background-color: @linkColor; +} + + + +// STACKED NAV +// ----------- + +// Stacked tabs and pills +.nav-stacked > li { + float: none; +} +.nav-stacked > li > a { + margin-right: 0; // no need for the gap between nav items +} + +// Tabs +.nav-tabs.nav-stacked { + border-bottom: 0; +} +.nav-tabs.nav-stacked > li > a { + border: 1px solid #ddd; + .border-radius(0); +} +.nav-tabs.nav-stacked > li:first-child > a { + .border-radius(4px 4px 0 0); +} +.nav-tabs.nav-stacked > li:last-child > a { + .border-radius(0 0 4px 4px); +} +.nav-tabs.nav-stacked > li > a:hover { + border-color: #ddd; + z-index: 2; +} + +// Pills +.nav-pills.nav-stacked > li > a { + margin-bottom: 3px; +} +.nav-pills.nav-stacked > li:last-child > a { + margin-bottom: 1px; // decrease margin to match sizing of stacked tabs +} + + + +// DROPDOWNS +// --------- + +// Position the menu +.nav-tabs .dropdown-menu, +.nav-pills .dropdown-menu { + margin-top: 1px; + border-width: 1px; +} +.nav-pills .dropdown-menu { + .border-radius(4px); +} + +// Default dropdown links +// ------------------------- +// Make carets use linkColor to start +.nav-tabs .dropdown-toggle .caret, +.nav-pills .dropdown-toggle .caret { + border-top-color: @linkColor; + margin-top: 6px; +} +.nav-tabs .dropdown-toggle:hover .caret, +.nav-pills .dropdown-toggle:hover .caret { + border-top-color: @linkColorHover; +} + +// Active dropdown links +// ------------------------- +.nav-tabs .active .dropdown-toggle .caret, +.nav-pills .active .dropdown-toggle .caret { + border-top-color: @grayDark; +} + +// Active:hover dropdown links +// ------------------------- +.nav > .dropdown.active > a:hover { + color: @black; + cursor: pointer; +} + +// Open dropdowns +// ------------------------- +.nav-tabs .open .dropdown-toggle, +.nav-pills .open .dropdown-toggle, +.nav > .open.active > a:hover { + color: @white; + background-color: @grayLight; + border-color: @grayLight; +} +.nav .open .caret, +.nav .open.active .caret, +.nav .open a:hover .caret { + border-top-color: @white; + .opacity(100); +} + +// Dropdowns in stacked tabs +.tabs-stacked .open > a:hover { + border-color: @grayLight; +} + + + +// TABBABLE +// -------- + + +// COMMON STYLES +// ------------- + +// Clear any floats +.tabbable { + .clearfix(); +} + +// Remove border on bottom, left, right +.tabs-below .nav-tabs, +.tabs-right .nav-tabs, +.tabs-left .nav-tabs { + border-bottom: 0; +} + +// Show/hide tabbable areas +.tab-content > .tab-pane, +.pill-content > .pill-pane { + display: none; +} +.tab-content > .active, +.pill-content > .active { + display: block; +} + + +// BOTTOM +// ------ + +.tabs-below .nav-tabs { + border-top: 1px solid #ddd; +} +.tabs-below .nav-tabs > li { + margin-top: -1px; + margin-bottom: 0; +} +.tabs-below .nav-tabs > li > a { + .border-radius(0 0 4px 4px); + &:hover { + border-bottom-color: transparent; + border-top-color: #ddd; + } +} +.tabs-below .nav-tabs .active > a, +.tabs-below .nav-tabs .active > a:hover { + border-color: transparent #ddd #ddd #ddd; +} + +// LEFT & RIGHT +// ------------ + +// Common styles +.tabs-left .nav-tabs > li, +.tabs-right .nav-tabs > li { + float: none; +} +.tabs-left .nav-tabs > li > a, +.tabs-right .nav-tabs > li > a { + min-width: 74px; + margin-right: 0; + margin-bottom: 3px; +} + +// Tabs on the left +.tabs-left .nav-tabs { + float: left; + margin-right: 19px; + border-right: 1px solid #ddd; +} +.tabs-left .nav-tabs > li > a { + margin-right: -1px; + .border-radius(4px 0 0 4px); +} +.tabs-left .nav-tabs > li > a:hover { + border-color: @grayLighter #ddd @grayLighter @grayLighter; +} +.tabs-left .nav-tabs .active > a, +.tabs-left .nav-tabs .active > a:hover { + border-color: #ddd transparent #ddd #ddd; + *border-right-color: @white; +} + +// Tabs on the right +.tabs-right .nav-tabs { + float: right; + margin-left: 19px; + border-left: 1px solid #ddd; +} +.tabs-right .nav-tabs > li > a { + margin-left: -1px; + .border-radius(0 4px 4px 0); +} +.tabs-right .nav-tabs > li > a:hover { + border-color: @grayLighter @grayLighter @grayLighter #ddd; +} +.tabs-right .nav-tabs .active > a, +.tabs-right .nav-tabs .active > a:hover { + border-color: #ddd #ddd #ddd transparent; + *border-left-color: @white; +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/pager.less --- /dev/null +++ b/static/june_2007_style/bootstrap/pager.less @@ -0,0 +1,30 @@ +// PAGER +// ----- + +.pager { + margin-left: 0; + margin-bottom: @baseLineHeight; + list-style: none; + text-align: center; + .clearfix(); +} +.pager li { + display: inline; +} +.pager a { + display: inline-block; + padding: 5px 14px; + background-color: #fff; + border: 1px solid #ddd; + .border-radius(15px); +} +.pager a:hover { + text-decoration: none; + background-color: #f5f5f5; +} +.pager .next a { + float: right; +} +.pager .previous a { + float: left; +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/pagination.less --- /dev/null +++ b/static/june_2007_style/bootstrap/pagination.less @@ -0,0 +1,55 @@ +// PAGINATION +// ---------- + +.pagination { + height: @baseLineHeight * 2; + margin: @baseLineHeight 0; + } +.pagination ul { + display: inline-block; + .ie7-inline-block(); + margin-left: 0; + margin-bottom: 0; + .border-radius(3px); + .box-shadow(0 1px 2px rgba(0,0,0,.05)); +} +.pagination li { + display: inline; + } +.pagination a { + float: left; + padding: 0 14px; + line-height: (@baseLineHeight * 2) - 2; + text-decoration: none; + border: 1px solid #ddd; + border-left-width: 0; +} +.pagination a:hover, +.pagination .active a { + background-color: #f5f5f5; +} +.pagination .active a { + color: @grayLight; + cursor: default; +} +.pagination .disabled a, +.pagination .disabled a:hover { + color: @grayLight; + background-color: transparent; + cursor: default; +} +.pagination li:first-child a { + border-left-width: 1px; + .border-radius(3px 0 0 3px); +} +.pagination li:last-child a { + .border-radius(0 3px 3px 0); +} + +// Centered +.pagination-centered { + text-align: center; +} +.pagination-right { + text-align: right; +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/popovers.less --- /dev/null +++ b/static/june_2007_style/bootstrap/popovers.less @@ -0,0 +1,49 @@ +// POPOVERS +// -------- + +.popover { + position: absolute; + top: 0; + left: 0; + z-index: @zindexPopover; + display: none; + padding: 5px; + &.top { margin-top: -5px; } + &.right { margin-left: 5px; } + &.bottom { margin-top: 5px; } + &.left { margin-left: -5px; } + &.top .arrow { #popoverArrow > .top(); } + &.right .arrow { #popoverArrow > .right(); } + &.bottom .arrow { #popoverArrow > .bottom(); } + &.left .arrow { #popoverArrow > .left(); } + .arrow { + position: absolute; + width: 0; + height: 0; + } +} +.popover-inner { + padding: 3px; + width: 280px; + overflow: hidden; + background: @black; // has to be full background declaration for IE fallback + background: rgba(0,0,0,.8); + .border-radius(6px); + .box-shadow(0 3px 7px rgba(0,0,0,0.3)); +} +.popover-title { + padding: 9px 15px; + line-height: 1; + background-color: #f5f5f5; + border-bottom:1px solid #eee; + .border-radius(3px 3px 0 0); +} +.popover-content { + padding: 14px; + background-color: @white; + .border-radius(0 0 3px 3px); + .background-clip(padding-box); + p, ul, ol { + margin-bottom: 0; + } +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/progress-bars.less --- /dev/null +++ b/static/june_2007_style/bootstrap/progress-bars.less @@ -0,0 +1,95 @@ +// PROGRESS BARS +// ------------- + + +// ANIMATIONS +// ---------- + +// Webkit +@-webkit-keyframes progress-bar-stripes { + from { background-position: 0 0; } + to { background-position: 40px 0; } +} + +// Firefox +@-moz-keyframes progress-bar-stripes { + from { background-position: 0 0; } + to { background-position: 40px 0; } +} + +// Spec +@keyframes progress-bar-stripes { + from { background-position: 0 0; } + to { background-position: 40px 0; } +} + + + +// THE BARS +// -------- + +// Outer container +.progress { + overflow: hidden; + height: 18px; + margin-bottom: 18px; + #gradient > .vertical(#f5f5f5, #f9f9f9); + .box-shadow(inset 0 1px 2px rgba(0,0,0,.1)); + .border-radius(4px); +} + +// Bar of progress +.progress .bar { + width: 0%; + height: 18px; + color: @white; + font-size: 12px; + text-align: center; + text-shadow: 0 -1px 0 rgba(0,0,0,.25); + #gradient > .vertical(#149bdf, #0480be); + .box-shadow(inset 0 -1px 0 rgba(0,0,0,.15)); + .box-sizing(border-box); + .transition(width .6s ease); +} + +// Striped bars +.progress-striped .bar { + #gradient > .striped(#62c462); + .background-size(40px 40px); +} + +// Call animation for the active one +.progress.active .bar { + -webkit-animation: progress-bar-stripes 2s linear infinite; + -moz-animation: progress-bar-stripes 2s linear infinite; + animation: progress-bar-stripes 2s linear infinite; +} + + + +// COLORS +// ------ + +// Danger (red) +.progress-danger .bar { + #gradient > .vertical(#ee5f5b, #c43c35); +} +.progress-danger.progress-striped .bar { + #gradient > .striped(#ee5f5b); +} + +// Success (green) +.progress-success .bar { + #gradient > .vertical(#62c462, #57a957); +} +.progress-success.progress-striped .bar { + #gradient > .striped(#62c462); +} + +// Info (teal) +.progress-info .bar { + #gradient > .vertical(#5bc0de, #339bb9); +} +.progress-info.progress-striped .bar { + #gradient > .striped(#5bc0de); +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/reset.less --- /dev/null +++ b/static/june_2007_style/bootstrap/reset.less @@ -0,0 +1,126 @@ +// Reset.less +// Adapted from Normalize.css http://github.com/necolas/normalize.css +// ------------------------------------------------------------------------ + +// Display in IE6-9 and FF3 +// ------------------------- + +article, +aside, +details, +figcaption, +figure, +footer, +header, +hgroup, +nav, +section { + display: block; +} + +// Display block in IE6-9 and FF3 +// ------------------------- + +audio, +canvas, +video { + display: inline-block; + *display: inline; + *zoom: 1; +} + +// Prevents modern browsers from displaying 'audio' without controls +// ------------------------- + +audio:not([controls]) { + display: none; +} + +// Base settings +// ------------------------- + +html { + font-size: 100%; + -webkit-text-size-adjust: 100%; + -ms-text-size-adjust: 100%; +} +// Focus states +a:focus { + .tab-focus(); +} +// Hover & Active +a:hover, +a:active { + outline: 0; +} + +// Prevents sub and sup affecting line-height in all browsers +// ------------------------- + +sub, +sup { + position: relative; + font-size: 75%; + line-height: 0; + vertical-align: baseline; +} +sup { + top: -0.5em; +} +sub { + bottom: -0.25em; +} + +// Img border in a's and image quality +// ------------------------- + +img { + max-width: 100%; + height: auto; + border: 0; + -ms-interpolation-mode: bicubic; +} + +// Forms +// ------------------------- + +// Font size in all browsers, margin changes, misc consistency +button, +input, +select, +textarea { + margin: 0; + font-size: 100%; + vertical-align: middle; +} +button, +input { + *overflow: visible; // Inner spacing ie IE6/7 + line-height: normal; // FF3/4 have !important on line-height in UA stylesheet +} +button::-moz-focus-inner, +input::-moz-focus-inner { // Inner padding and border oddities in FF3/4 + padding: 0; + border: 0; +} +button, +input[type="button"], +input[type="reset"], +input[type="submit"] { + cursor: pointer; // Cursors on all buttons applied consistently + -webkit-appearance: button; // Style clicable inputs in iOS +} +input[type="search"] { // Appearance in Safari/Chrome + -webkit-appearance: textfield; + -webkit-box-sizing: content-box; + -moz-box-sizing: content-box; + box-sizing: content-box; +} +input[type="search"]::-webkit-search-decoration, +input[type="search"]::-webkit-search-cancel-button { + -webkit-appearance: none; // Inner-padding issues in Chrome OSX, Safari 5 +} +textarea { + overflow: auto; // Remove vertical scrollbar in IE6-9 + vertical-align: top; // Readability and alignment cross-browser +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/responsive.less --- /dev/null +++ b/static/june_2007_style/bootstrap/responsive.less @@ -0,0 +1,323 @@ +/*! + * Bootstrap Responsive v2.0.0 + * + * Copyright 2012 Twitter, Inc + * Licensed under the Apache License v2.0 + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Designed and built with all the love in the world @twitter by @mdo and @fat. + */ + +// Responsive.less +// For phone and tablet devices +// ------------------------------------------------------------- + + +// REPEAT VARIABLES & MIXINS +// ------------------------- +// Required since we compile the responsive stuff separately + +@import "variables.less"; // Modify this for custom colors, font-sizes, etc +@import "mixins.less"; + + +// RESPONSIVE CLASSES +// ------------------ + +// Hide from screenreaders and browsers +// Credit: HTML5 Boilerplate +.hidden { + display: none; + visibility: hidden; +} + + + +// UP TO LANDSCAPE PHONE +// --------------------- + +@media (max-width: 480px) { + + // Smooth out the collapsing/expanding nav + .nav-collapse { + -webkit-transform: translate3d(0, 0, 0); // activate the GPU + } + + // Block level the page header small tag for readability + .page-header h1 small { + display: block; + line-height: @baseLineHeight; + } + + // Make span* classes full width + input[class*="span"], + select[class*="span"], + textarea[class*="span"], + .uneditable-input { + display: block; + width: 100%; + height: 28px; /* Make inputs at least the height of their button counterpart */ + /* Makes inputs behave like true block-level elements */ + -webkit-box-sizing: border-box; /* Older Webkit */ + -moz-box-sizing: border-box; /* Older FF */ + -ms-box-sizing: border-box; /* IE8 */ + box-sizing: border-box; /* CSS3 spec*/ + } + // But don't let it screw up prepend/append inputs + .input-prepend input[class*="span"], + .input-append input[class*="span"] { + width: auto; + } + + // Update checkboxes for iOS + input[type="checkbox"], + input[type="radio"] { + border: 1px solid #ccc; + } + + // Remove the horizontal form styles + .form-horizontal .control-group > label { + float: none; + width: auto; + padding-top: 0; + text-align: left; + } + // Move over all input controls and content + .form-horizontal .controls { + margin-left: 0; + } + // Move the options list down to align with labels + .form-horizontal .control-list { + padding-top: 0; // has to be padding because margin collaspes + } + // Move over buttons in .form-actions to align with .controls + .form-horizontal .form-actions { + padding-left: 10px; + padding-right: 10px; + } + + // Modals + .modal { + position: absolute; + top: 10px; + left: 10px; + right: 10px; + width: auto; + margin: 0; + &.fade.in { top: auto; } + } + .modal-header .close { + padding: 10px; + margin: -10px; + } + + // Carousel + .carousel-caption { + position: static; + } + +} + + + +// LANDSCAPE PHONE TO SMALL DESKTOP & PORTRAIT TABLET +// -------------------------------------------------- + +@media (max-width: 768px) { + // GRID & CONTAINERS + // ----------------- + // Remove width from containers + .container { + width: auto; + padding: 0 20px; + } + // Fluid rows + .row-fluid { + width: 100%; + } + // Undo negative margin on rows + .row { + margin-left: 0; + } + // Make all columns even + .row > [class*="span"], + .row-fluid > [class*="span"] { + float: none; + display: block; + width: auto; + margin: 0; + } +} + + + +// PORTRAIT TABLET TO DEFAULT DESKTOP +// ---------------------------------- + +@media (min-width: 768px) and (max-width: 980px) { + + // Fixed grid + #gridSystem > .generate(12, 42px, 20px); + + // Fluid grid + #fluidGridSystem > .generate(12, 5.801104972%, 2.762430939%); + + // Input grid + #inputGridSystem > .generate(12, 42px, 20px); + +} + + + +// TABLETS AND BELOW +// ----------------- +@media (max-width: 980px) { + + // UNFIX THE TOPBAR + // ---------------- + // Remove any padding from the body + body { + padding-top: 0; + } + // Unfix the navbar + .navbar-fixed-top { + position: static; + margin-bottom: @baseLineHeight; + } + .navbar-fixed-top .navbar-inner { + padding: 5px; + } + .navbar .container { + width: auto; + padding: 0; + } + // Account for brand name + .navbar .brand { + padding-left: 10px; + padding-right: 10px; + margin: 0 0 0 -5px; + } + // Nav collapse clears brand + .navbar .nav-collapse { + clear: left; + } + // Block-level the nav + .navbar .nav { + float: none; + margin: 0 0 (@baseLineHeight / 2); + } + .navbar .nav > li { + float: none; + } + .navbar .nav > li > a { + margin-bottom: 2px; + } + .navbar .nav > .divider-vertical { + display: none; + } + // Nav and dropdown links in navbar + .navbar .nav > li > a, + .navbar .dropdown-menu a { + padding: 6px 15px; + font-weight: bold; + color: @navbarLinkColor; + .border-radius(3px); + } + .navbar .dropdown-menu li + li a { + margin-bottom: 2px; + } + .navbar .nav > li > a:hover, + .navbar .dropdown-menu a:hover { + background-color: @navbarBackground; + } + // Dropdowns in the navbar + .navbar .dropdown-menu { + position: static; + top: auto; + left: auto; + float: none; + display: block; + max-width: none; + margin: 0 15px; + padding: 0; + background-color: transparent; + border: none; + .border-radius(0); + .box-shadow(none); + } + .navbar .dropdown-menu:before, + .navbar .dropdown-menu:after { + display: none; + } + .navbar .dropdown-menu .divider { + display: none; + } + // Forms in navbar + .navbar-form, + .navbar-search { + float: none; + padding: (@baseLineHeight / 2) 15px; + margin: (@baseLineHeight / 2) 0; + border-top: 1px solid @navbarBackground; + border-bottom: 1px solid @navbarBackground; + @shadow: inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 rgba(255,255,255,.1); + .box-shadow(@shadow); + } + // Pull right (secondary) nav content + .navbar .nav.pull-right { + float: none; + margin-left: 0; + } + // Static navbar + .navbar-static .navbar-inner { + padding-left: 10px; + padding-right: 10px; + } + // Navbar button + .btn-navbar { + display: block; + } + + // Hide everything in the navbar save .brand and toggle button */ + .nav-collapse { + overflow: hidden; + height: 0; + } +} + + + +// DEFAULT DESKTOP +// --------------- + +@media (min-width: 980px) { + .nav-collapse.collapse { + height: auto !important; + } +} + + + +// LARGE DESKTOP & UP +// ------------------ + +@media (min-width: 1200px) { + + // Fixed grid + #gridSystem > .generate(12, 70px, 30px); + + // Fluid grid + #fluidGridSystem > .generate(12, 5.982905983%, 2.564102564%); + + // Input grid + #inputGridSystem > .generate(12, 70px, 30px); + + // Thumbnails + .thumbnails { + margin-left: -30px; + } + .thumbnails > li { + margin-left: 30px; + } + +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/scaffolding.less --- /dev/null +++ b/static/june_2007_style/bootstrap/scaffolding.less @@ -0,0 +1,29 @@ +// Scaffolding +// Basic and global styles for generating a grid system, structural layout, and page templates +// ------------------------------------------------------------------------------------------- + + +// STRUCTURAL LAYOUT +// ----------------- + +body { + margin: 0; + font-family: @baseFontFamily; + font-size: @baseFontSize; + line-height: @baseLineHeight; + color: @textColor; + background-color: @white; +} + + +// LINKS +// ----- + +a { + color: @linkColor; + text-decoration: none; +} +a:hover { + color: @linkColorHover; + text-decoration: underline; +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/sprites.less --- /dev/null +++ b/static/june_2007_style/bootstrap/sprites.less @@ -0,0 +1,156 @@ +// SPRITES +// Glyphs and icons for buttons, nav, and more +// ------------------------------------------- + + +// ICONS +// ----- + +// All icons receive the styles of the <i> tag with a base class +// of .i and are then given a unique class to add width, height, +// and background-position. Your resulting HTML will look like +// <i class="i icon-inbox"></i>. + +// For the white version of the icons, just add the .icon-white class: +// <i class="i icon-inbox icon-white"></i> + +[class^="icon-"] { + display: inline-block; + width: 14px; + height: 14px; + vertical-align: text-top; + background-image: url(../img/glyphicons-halflings.png); + background-position: 14px 14px; + background-repeat: no-repeat; + + .ie7-restore-right-whitespace(); +} +.icon-white { + background-image: url(../img/glyphicons-halflings-white.png); +} + +.icon-glass { background-position: 0 0; } +.icon-music { background-position: -24px 0; } +.icon-search { background-position: -48px 0; } +.icon-envelope { background-position: -72px 0; } +.icon-heart { background-position: -96px 0; } +.icon-star { background-position: -120px 0; } +.icon-star-empty { background-position: -144px 0; } +.icon-user { background-position: -168px 0; } +.icon-film { background-position: -192px 0; } +.icon-th-large { background-position: -216px 0; } +.icon-th { background-position: -240px 0; } +.icon-th-list { background-position: -264px 0; } +.icon-ok { background-position: -288px 0; } +.icon-remove { background-position: -312px 0; } +.icon-zoom-in { background-position: -336px 0; } +.icon-zoom-out { background-position: -360px 0; } +.icon-off { background-position: -384px 0; } +.icon-signal { background-position: -408px 0; } +.icon-cog { background-position: -432px 0; } +.icon-trash { background-position: -456px 0; } + +.icon-home { background-position: 0 -24px; } +.icon-file { background-position: -24px -24px; } +.icon-time { background-position: -48px -24px; } +.icon-road { background-position: -72px -24px; } +.icon-download-alt { background-position: -96px -24px; } +.icon-download { background-position: -120px -24px; } +.icon-upload { background-position: -144px -24px; } +.icon-inbox { background-position: -168px -24px; } +.icon-play-circle { background-position: -192px -24px; } +.icon-repeat { background-position: -216px -24px; } +.icon-refresh { background-position: -240px -24px; } +.icon-list-alt { background-position: -264px -24px; } +.icon-lock { background-position: -287px -24px; } // 1px off +.icon-flag { background-position: -312px -24px; } +.icon-headphones { background-position: -336px -24px; } +.icon-volume-off { background-position: -360px -24px; } +.icon-volume-down { background-position: -384px -24px; } +.icon-volume-up { background-position: -408px -24px; } +.icon-qrcode { background-position: -432px -24px; } +.icon-barcode { background-position: -456px -24px; } + +.icon-tag { background-position: 0 -48px; } +.icon-tags { background-position: -25px -48px; } // 1px off +.icon-book { background-position: -48px -48px; } +.icon-bookmark { background-position: -72px -48px; } +.icon-print { background-position: -96px -48px; } +.icon-camera { background-position: -120px -48px; } +.icon-font { background-position: -144px -48px; } +.icon-bold { background-position: -167px -48px; } // 1px off +.icon-italic { background-position: -192px -48px; } +.icon-text-height { background-position: -216px -48px; } +.icon-text-width { background-position: -240px -48px; } +.icon-align-left { background-position: -264px -48px; } +.icon-align-center { background-position: -288px -48px; } +.icon-align-right { background-position: -312px -48px; } +.icon-align-justify { background-position: -336px -48px; } +.icon-list { background-position: -360px -48px; } +.icon-indent-left { background-position: -384px -48px; } +.icon-indent-right { background-position: -408px -48px; } +.icon-facetime-video { background-position: -432px -48px; } +.icon-picture { background-position: -456px -48px; } + +.icon-pencil { background-position: 0 -72px; } +.icon-map-marker { background-position: -24px -72px; } +.icon-adjust { background-position: -48px -72px; } +.icon-tint { background-position: -72px -72px; } +.icon-edit { background-position: -96px -72px; } +.icon-share { background-position: -120px -72px; } +.icon-check { background-position: -144px -72px; } +.icon-move { background-position: -168px -72px; } +.icon-step-backward { background-position: -192px -72px; } +.icon-fast-backward { background-position: -216px -72px; } +.icon-backward { background-position: -240px -72px; } +.icon-play { background-position: -264px -72px; } +.icon-pause { background-position: -288px -72px; } +.icon-stop { background-position: -312px -72px; } +.icon-forward { background-position: -336px -72px; } +.icon-fast-forward { background-position: -360px -72px; } +.icon-step-forward { background-position: -384px -72px; } +.icon-eject { background-position: -408px -72px; } +.icon-chevron-left { background-position: -432px -72px; } +.icon-chevron-right { background-position: -456px -72px; } + +.icon-plus-sign { background-position: 0 -96px; } +.icon-minus-sign { background-position: -24px -96px; } +.icon-remove-sign { background-position: -48px -96px; } +.icon-ok-sign { background-position: -72px -96px; } +.icon-question-sign { background-position: -96px -96px; } +.icon-info-sign { background-position: -120px -96px; } +.icon-screenshot { background-position: -144px -96px; } +.icon-remove-circle { background-position: -168px -96px; } +.icon-ok-circle { background-position: -192px -96px; } +.icon-ban-circle { background-position: -216px -96px; } +.icon-arrow-left { background-position: -240px -96px; } +.icon-arrow-right { background-position: -264px -96px; } +.icon-arrow-up { background-position: -289px -96px; } // 1px off +.icon-arrow-down { background-position: -312px -96px; } +.icon-share-alt { background-position: -336px -96px; } +.icon-resize-full { background-position: -360px -96px; } +.icon-resize-small { background-position: -384px -96px; } +.icon-plus { background-position: -408px -96px; } +.icon-minus { background-position: -433px -96px; } +.icon-asterisk { background-position: -456px -96px; } + +.icon-exclamation-sign { background-position: 0 -120px; } +.icon-gift { background-position: -24px -120px; } +.icon-leaf { background-position: -48px -120px; } +.icon-fire { background-position: -72px -120px; } +.icon-eye-open { background-position: -96px -120px; } +.icon-eye-close { background-position: -120px -120px; } +.icon-warning-sign { background-position: -144px -120px; } +.icon-plane { background-position: -168px -120px; } +.icon-calendar { background-position: -192px -120px; } +.icon-random { background-position: -216px -120px; } +.icon-comment { background-position: -240px -120px; } +.icon-magnet { background-position: -264px -120px; } +.icon-chevron-up { background-position: -288px -120px; } +.icon-chevron-down { background-position: -313px -119px; } // 1px off +.icon-retweet { background-position: -336px -120px; } +.icon-shopping-cart { background-position: -360px -120px; } +.icon-folder-close { background-position: -384px -120px; } +.icon-folder-open { background-position: -408px -120px; } +.icon-resize-vertical { background-position: -432px -119px; } +.icon-resize-horizontal { background-position: -456px -118px; } diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/tables.less --- /dev/null +++ b/static/june_2007_style/bootstrap/tables.less @@ -0,0 +1,139 @@ +// +// Tables.less +// Tables for, you guessed it, tabular data +// ---------------------------------------- + + +// BASE TABLES +// ----------------- + +table { + max-width: 100%; + border-collapse: collapse; + border-spacing: 0; +} + +// BASELINE STYLES +// --------------- + +.table { + width: 100%; + margin-bottom: @baseLineHeight; + // Cells + th, + td { + padding: 8px; + line-height: @baseLineHeight; + text-align: left; + border-top: 1px solid #ddd; + } + th { + font-weight: bold; + vertical-align: bottom; + } + td { + vertical-align: top; + } + // Remove top border from thead by default + thead:first-child tr th, + thead:first-child tr td { + border-top: 0; + } + // Account for multiple tbody instances + tbody + tbody { + border-top: 2px solid #ddd; + } +} + + + +// CONDENSED TABLE W/ HALF PADDING +// ------------------------------- + +.table-condensed { + th, + td { + padding: 4px 5px; + } +} + + +// BORDERED VERSION +// ---------------- + +.table-bordered { + border: 1px solid #ddd; + border-collapse: separate; // Done so we can round those corners! + *border-collapse: collapsed; // IE7 can't round corners anyway + .border-radius(4px); + th + th, + td + td, + th + td, + td + th { + border-left: 1px solid #ddd; + } + // Prevent a double border + thead:first-child tr:first-child th, + tbody:first-child tr:first-child th, + tbody:first-child tr:first-child td { + border-top: 0; + } + // For first th or td in the first row in the first thead or tbody + thead:first-child tr:first-child th:first-child, + tbody:first-child tr:first-child td:first-child { + .border-radius(4px 0 0 0); + } + thead:first-child tr:first-child th:last-child, + tbody:first-child tr:first-child td:last-child { + .border-radius(0 4px 0 0); + } + // For first th or td in the first row in the first thead or tbody + thead:last-child tr:last-child th:first-child, + tbody:last-child tr:last-child td:first-child { + .border-radius(0 0 0 4px); + } + thead:last-child tr:last-child th:last-child, + tbody:last-child tr:last-child td:last-child { + .border-radius(0 0 4px 0); + } +} + + +// ZEBRA-STRIPING +// -------------- + +// Default zebra-stripe styles (alternating gray and transparent backgrounds) +.table-striped { + tbody { + tr:nth-child(odd) td, + tr:nth-child(odd) th { + background-color: #f9f9f9; + } + } +} + + + +// TABLE CELL SIZING +// ----------------- + +// Change the columns +.tableColumns(@columnSpan: 1) { + float: none; + width: ((@gridColumnWidth) * @columnSpan) + (@gridGutterWidth * (@columnSpan - 1)) - 16; + margin-left: 0; +} +table { + .span1 { .tableColumns(1); } + .span2 { .tableColumns(2); } + .span3 { .tableColumns(3); } + .span4 { .tableColumns(4); } + .span5 { .tableColumns(5); } + .span6 { .tableColumns(6); } + .span7 { .tableColumns(7); } + .span8 { .tableColumns(8); } + .span9 { .tableColumns(9); } + .span10 { .tableColumns(10); } + .span11 { .tableColumns(11); } + .span12 { .tableColumns(12); } +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/thumbnails.less --- /dev/null +++ b/static/june_2007_style/bootstrap/thumbnails.less @@ -0,0 +1,35 @@ +// THUMBNAILS +// ---------- + +.thumbnails { + margin-left: -20px; + list-style: none; + .clearfix(); +} +.thumbnails > li { + float: left; + margin: 0 0 @baseLineHeight 20px; +} +.thumbnail { + display: block; + padding: 4px; + line-height: 1; + border: 1px solid #ddd; + .border-radius(4px); + .box-shadow(0 1px 1px rgba(0,0,0,.075)); +} +// Add a hover state for linked versions only +a.thumbnail:hover { + border-color: @linkColor; + .box-shadow(0 1px 4px rgba(0,105,214,.25)); +} +// Images and captions +.thumbnail > img { + display: block; + max-width: 100%; + margin-left: auto; + margin-right: auto; +} +.thumbnail .caption { + padding: 9px; +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/tooltip.less --- /dev/null +++ b/static/june_2007_style/bootstrap/tooltip.less @@ -0,0 +1,35 @@ +// TOOLTIP +// ------= + +.tooltip { + position: absolute; + z-index: @zindexTooltip; + display: block; + visibility: visible; + padding: 5px; + font-size: 11px; + .opacity(0); + &.in { .opacity(80); } + &.top { margin-top: -2px; } + &.right { margin-left: 2px; } + &.bottom { margin-top: 2px; } + &.left { margin-left: -2px; } + &.top .tooltip-arrow { #popoverArrow > .top(); } + &.left .tooltip-arrow { #popoverArrow > .left(); } + &.bottom .tooltip-arrow { #popoverArrow > .bottom(); } + &.right .tooltip-arrow { #popoverArrow > .right(); } +} +.tooltip-inner { + max-width: 200px; + padding: 3px 8px; + color: @white; + text-align: center; + text-decoration: none; + background-color: @black; + .border-radius(4px); +} +.tooltip-arrow { + position: absolute; + width: 0; + height: 0; +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/type.less --- /dev/null +++ b/static/june_2007_style/bootstrap/type.less @@ -0,0 +1,217 @@ +// Typography.less +// Headings, body text, lists, code, and more for a versatile and durable typography system +// ---------------------------------------------------------------------------------------- + + +// BODY TEXT +// --------- + +p { + margin: 0 0 @baseLineHeight / 2; + font-family: @baseFontFamily; + font-size: @baseFontSize; + line-height: @baseLineHeight; + small { + font-size: @baseFontSize - 2; + color: @grayLight; + } +} +.lead { + margin-bottom: @baseLineHeight; + font-size: 20px; + font-weight: 200; + line-height: @baseLineHeight * 1.5; +} + +// HEADINGS +// -------- + +h1, h2, h3, h4, h5, h6 { + margin: 0; + font-weight: bold; + color: @grayDark; + text-rendering: optimizelegibility; // Fix the character spacing for headings + small { + font-weight: normal; + color: @grayLight; + } +} +h1 { + font-size: 30px; + line-height: @baseLineHeight * 2; + small { + font-size: 18px; + } +} +h2 { + font-size: 24px; + line-height: @baseLineHeight * 2; + small { + font-size: 18px; + } +} +h3 { + line-height: @baseLineHeight * 1.5; + font-size: 18px; + small { + font-size: 14px; + } +} +h4, h5, h6 { + line-height: @baseLineHeight; +} +h4 { + font-size: 14px; + small { + font-size: 12px; + } +} +h5 { + font-size: 12px; +} +h6 { + font-size: 11px; + color: @grayLight; + text-transform: uppercase; +} + +// Page header +.page-header { + padding-bottom: @baseLineHeight - 1; + margin: @baseLineHeight 0; + border-bottom: 1px solid @grayLighter; +} +.page-header h1 { + line-height: 1; +} + + + +// LISTS +// ----- + +// Unordered and Ordered lists +ul, ol { + padding: 0; + margin: 0 0 @baseLineHeight / 2 25px; +} +ul ul, +ul ol, +ol ol, +ol ul { + margin-bottom: 0; +} +ul { + list-style: disc; +} +ol { + list-style: decimal; +} +li { + line-height: @baseLineHeight; +} +ul.unstyled { + margin-left: 0; + list-style: none; +} + +// Description Lists +dl { + margin-bottom: @baseLineHeight; +} +dt, +dd { + line-height: @baseLineHeight; +} +dt { + font-weight: bold; +} +dd { + margin-left: @baseLineHeight / 2; +} + +// MISC +// ---- + +// Horizontal rules +hr { + margin: @baseLineHeight 0; + border: 0; + border-top: 1px solid #e5e5e5; + border-bottom: 1px solid @white; +} + +// Emphasis +strong { + font-weight: bold; +} +em { + font-style: italic; +} +.muted { + color: @grayLight; +} + +// Abbreviations and acronyms +abbr { + font-size: 90%; + text-transform: uppercase; + border-bottom: 1px dotted #ddd; + cursor: help; +} + +// Blockquotes +blockquote { + padding: 0 0 0 15px; + margin: 0 0 @baseLineHeight; + border-left: 5px solid @grayLighter; + p { + margin-bottom: 0; + #font > .shorthand(16px,300,@baseLineHeight * 1.25); + } + small { + display: block; + line-height: @baseLineHeight; + color: @grayLight; + &:before { + content: '\2014 \00A0'; + } + } + + // Float right with text-align: right + &.pull-right { + float: right; + padding-left: 0; + padding-right: 15px; + border-left: 0; + border-right: 5px solid @grayLighter; + p, + small { + text-align: right; + } + } +} + +// Quotes +q:before, +q:after, +blockquote:before, +blockquote:after { + content: ""; +} + +// Addresses +address { + display: block; + margin-bottom: @baseLineHeight; + line-height: @baseLineHeight; + font-style: normal; +} + +// Misc +small { + font-size: 100%; +} +cite { + font-style: normal; +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/utilities.less --- /dev/null +++ b/static/june_2007_style/bootstrap/utilities.less @@ -0,0 +1,23 @@ +// UTILITY CLASSES +// --------------- + +// Quick floats +.pull-right { + float: right; +} +.pull-left { + float: left; +} + +// Toggling content +.hide { + display: none; +} +.show { + display: block; +} + +// Visibility +.invisible { + visibility: hidden; +} diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/variables.less --- /dev/null +++ b/static/june_2007_style/bootstrap/variables.less @@ -0,0 +1,99 @@ +// Variables.less +// Variables to customize the look and feel of Bootstrap +// ----------------------------------------------------- + + + +// GLOBAL VALUES +// -------------------------------------------------- + +// Links +@linkColor: #08c; +@linkColorHover: darken(@linkColor, 15%); + +// Grays +@black: #000; +@grayDarker: #222; +@grayDark: #333; +@gray: #555; +@grayLight: #999; +@grayLighter: #eee; +@white: #fff; + +// Accent colors +@blue: #049cdb; +@blueDark: #0064cd; +@green: #46a546; +@red: #9d261d; +@yellow: #ffc40d; +@orange: #f89406; +@pink: #c3325f; +@purple: #7a43b6; + +// Typography +@baseFontSize: 13px; +@baseFontFamily: "Helvetica Neue", Helvetica, Arial, sans-serif; +@baseLineHeight: 18px; +@textColor: @grayDark; + +// Buttons +@primaryButtonBackground: @linkColor; + + + +// COMPONENT VARIABLES +// -------------------------------------------------- + +// Z-index master list +// Used for a bird's eye view of components dependent on the z-axis +// Try to avoid customizing these :) +@zindexDropdown: 1000; +@zindexPopover: 1010; +@zindexTooltip: 1020; +@zindexFixedNavbar: 1030; +@zindexModalBackdrop: 1040; +@zindexModal: 1050; + +// Input placeholder text color +@placeholderText: @grayLight; + +// Navbar +@navbarHeight: 40px; +@navbarBackground: @grayDarker; +@navbarBackgroundHighlight: @grayDark; + +@navbarText: @grayLight; +@navbarLinkColor: @grayLight; +@navbarLinkColorHover: @white; + +// Form states and alerts +@warningText: #c09853; +@warningBackground: #fcf8e3; +@warningBorder: darken(spin(@warningBackground, -10), 3%); + +@errorText: #b94a48; +@errorBackground: #f2dede; +@errorBorder: darken(spin(@errorBackground, -10), 3%); + +@successText: #468847; +@successBackground: #dff0d8; +@successBorder: darken(spin(@successBackground, -10), 5%); + +@infoText: #3a87ad; +@infoBackground: #d9edf7; +@infoBorder: darken(spin(@infoBackground, -10), 7%); + + + +// GRID +// -------------------------------------------------- + +// Default 940px grid +@gridColumns: 12; +@gridColumnWidth: 60px; +@gridGutterWidth: 20px; +@gridRowWidth: (@gridColumns * @gridColumnWidth) + (@gridGutterWidth * (@gridColumns - 1)); + +// Fluid grid +@fluidGridColumnWidth: 6.382978723%; +@fluidGridGutterWidth: 2.127659574%; diff -r d0004f5eea59f83543349b161fdb4559d543b07c -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 static/june_2007_style/bootstrap/wells.less --- /dev/null +++ b/static/june_2007_style/bootstrap/wells.less @@ -0,0 +1,17 @@ +// WELLS +// ----- + +.well { + min-height: 20px; + padding: 19px; + margin-bottom: 20px; + background-color: #f5f5f5; + border: 1px solid #eee; + border: 1px solid rgba(0,0,0,.05); + .border-radius(4px); + .box-shadow(inset 0 1px 1px rgba(0,0,0,.05)); + blockquote { + border-color: #ddd; + border-color: rgba(0,0,0,.15); + } +} https://bitbucket.org/galaxy/galaxy-central/changeset/fca74f956202/ changeset: fca74f956202 user: james_taylor date: 2012-02-14 17:43:41 summary: style: move base and panel_layout over to less, experimenting with bootstrap mixins. affected #: 12 files diff -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 -r fca74f9562024605dd87a3a6ace02d28a1851f5e static/june_2007_style/Makefile --- a/static/june_2007_style/Makefile +++ b/static/june_2007_style/Makefile @@ -15,7 +15,7 @@ # Convert using less %.css : %.less - lessc -x --include-path=$(OUT) $< > $@ + lessc -x $< $@ # Old style using process_css still works so we can move gradually %.css : %.css.tmpl diff -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 -r fca74f9562024605dd87a3a6ace02d28a1851f5e static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl +++ /dev/null @@ -1,979 +0,0 @@ -## Lucida Grande for proper mac unicode characters, verdana/arial stack for others -body{font:13px/1.231 "Lucida Grande",verdana,arial,helvetica,sans-serif;*font-size:small;*font:x-small;}select,input,button,textarea,button{font:99% "Lucida Grande",verdana,arial,helvetica,sans-serif;}table{font-size:inherit;font:100%;}pre,code,kbd,samp,tt{font-family:monospace;*font-size:108%;line-height:100%;} -body{font-size:75%;} - -## Mixins - -.unselectable { - user-select: none; - -moz-user-select: none; - -webkit-user-select: none; -} - -.shadow { - -moz-box-shadow: 0 3px 30px black; - -webkit-box-shadow: 0 3px 30px black; -} - -## Real styles - -body { - background: $base_bg_bottom; - color: $base_text; - background-image: url(base_bg.png); - background-repeat: repeat-x; - background-position: top; - margin: 10px; -} - -img { - border: 0; -} - - -a:link, a:visited, a:active { - color: $link_text; -} - -h1, h2, h3, h4 { - color: $header_text; - /*text-shadow: #bbb 2px 2px 1px;*/ -} - -h1:first-child, h2:first-child, h3:first-child, h4:first-child { - margin-top: 0px; -} - -hr { - border: none; - height: 0px; - border-bottom: dotted $base_text 1px; -} - -table { - border-collapse: collapse; -} - -th { - text-align: left; -} - -div.toolForm { - border: solid $form_border 1px; -} - -div.toolFormTitle { - font-weight: bold; - padding: 5px; - padding-left: 10px; - padding-right: 10px; - background: $form_title_bg_bottom; - ## background-image: url(form_title_bg.png); - background-repeat: repeat-x; - background-position: top; - border-bottom: solid $form_border 1px; -} - -div.toolParamHelp { - color: #666; -} - -div.toolParamHelp a { - color: #666; -} - -div.toolFormBody { - background: $form_body_bg_bottom; - background-image: url(form_body_bg.png); - background-repeat: repeat-x; - background-position: top; - padding: 5px 0; -} - -div.toolFormBody div.toolFormTitle { - background: transparent; - border: none; - font-weight: bold; - border-bottom: solid $form_border 1px; - margin-bottom: 5px; -} - -div.toolFormDisabled div.toolFormTitle { - background: ${layout_bg}; - border-color: ${layout_border}; -} - -div.toolFormDisabled { - border-color: ${layout_border}; -} - -div.toolHelp { - margin-top: 10px; -} - -div.toolHelpBody { - width: 100%; -} - -div.metadataForm { - border:solid #aaaaaa 1px; -} - -div.metadataFormTitle { - font-weight:bold; - padding:5px; - padding-left:10px; - padding-right:10px; - background:#cccccc; - background-repeat:repeat-x; - background-position:top; - border-bottom:solid #aaaaaa 1px; -} - -div.metadataFormBody { - background:#FFFFFF; - background-image:url(form_body_bg.png); - background-repeat:repeat-x; - background-position:top; - padding:5px 0; -} - -div.metadataFormBody div.metadataFormTitle { - background:transparent; - border:none; - font-weight:bold; - border-bottom:solid #dcb790 1px; - margin-bottom:5px; -} - -div.metadataFormDisabled div.metadataFormTitle { - background:#eee; - border-color:#999; -} - -div.metadataFormDisabled { - border-color:#999; -} - -div.metadataHelpBody { - width:100%;overflow:auto; -} - -div.titleRow { - font-weight: bold; - border-bottom: dotted gray 1px; - margin-bottom: 0.5em; - padding-bottom: 0.25em; -} - -## Forms - -div.form { - border: solid $form_border 1px; -} - -div.form-title { - font-weight: bold; - padding: 5px 10px; - background: $form_title_bg_bottom; - background-image: url(form_title_bg.png); - background-repeat: repeat-x; - background-position: top; - border-bottom: solid $form_border 1px; -} - -div.form-body { - padding: 5px 0; -} - -div.form-row { - padding: 5px 10px; -} - -div.form-title-row { - padding: 5px 10px; -} - -div.repeat-group-item { - border-left: solid $form_border 5px; - margin-left: 10px; - margin-bottom: 10px; -} - -div.form-row-error { - background: $error_message_bg; -} - -div.form-row label { - font-weight: bold; - display: block; - margin-bottom: .2em; -} - -div.form-row label.inline { - display: inline; -} - -div.form-row-input { - float: left; -} - -div.form-row-input label { - font-weight: normal; - display: inline; -} - -div.form-row-error-message { - width: 300px; - float: left; - color: red; - font-weight: bold; - padding: 3px 0 0 1em; -} - -.form-row .help { - color: #666; -} - -select, input, textarea { - font: inherit; -} - -select, textarea, input[type="text"], input[type="file"], input[type="password"] { - -webkit-box-sizing: border-box; - max-width: 300px; -} - -## Messages - -.errormessagelarge, .warningmessagelarge, .donemessagelarge, .infomessagelarge { - padding: 10px; - padding-left: 52px; - min-height: 32px; - border: 1px solid $error_message_border; - background-color: $error_message_bg; - background-image: url(error_message_icon.png); - background-repeat: no-repeat; - background-position: 10px 10px; -} - -.warningmessagelarge { - background-image: url(warn_message_icon.png); - border-color: $warn_message_border; - background-color: $warn_message_bg; -} - -.donemessagelarge { - background-image: url(done_message_icon.png); - border-color: $done_message_border; - background-color: $done_message_bg; -} - -.infomessagelarge { - background-image: url(info_message_icon.png); - border-color: $info_message_border; - background-color: $info_message_bg; -} - -.screencastBox { - padding-left: 10px; - border-color: #AAAA66; - background-color: #FFFFCC; - background-image: none; -} - -.errormessage, .warningmessage, .donemessage, .infomessage, .errormessagesmall, .warningmessagesmall, .donemessagesmall, .infomessagesmall { - padding: 5px; - padding-left: 25px; - min-height: 15px; - border: 1px solid $error_message_border; - background-color: $error_message_bg; - background-image: url(error_small.png); - background-repeat: no-repeat; - background-position: 5px 5px; -} - -.warningmessage, .warningmessagesmall { - background-image: url(warn_small.png); - border-color: $warn_message_border; - background-color: $warn_message_bg; -} - -.donemessage, .donemessagesmall { - background-image: url(ok_small.png); - border-color: $done_message_border; - background-color: $done_message_bg; -} - -.infomessage, .infomessagesmall { - background-image: url(info_small.png); - border-color: $info_message_border; - background-color: $info_message_bg; -} - -.errormark, .warningmark, .donemark, .infomark, .ok_bgr, .err_bgr { - padding-left: 20px; - min-height: 15px; - background: url(error_small.png) no-repeat; -} - -.warningmark { - background-image: url(warn_small.png); -} - -.donemark { - background-image: url(ok_small.png); -} - -.infomark, .ok_bgr { - background-image: url(info_small.png); -} - -table.simple { - font-size: 12px; - background: #fff; - margin: 1em; - border-collapse: collapse; - text-align: left; -} -table.simple th { - font-size: 14px; - font-weight: normal; - padding: 10px 8px; - border-bottom: 2px solid #333; -} -table.simple td { - padding: 10px 8px 0px 8px; -} -table.simple tbody tr:hover td { - color: #333; -} - -table.tabletip { - width: 100%; - border-collapse: collapse; - text-align: left; -} -table.tabletip th { - white-space: nowrap; - border-bottom: 1px solid #444; - padding-right: 3px; -} -table.tabletip td { - border-bottom: 1px solid #ddd; -} -table.tabletip tbody tr:hover td { - background-color: #eee; -} - -table.colored { - border-top: solid $table_border 1px; - border-bottom: solid $table_border 1px; -} - -table.colored td, table.colored th { - text-align: left; - padding: 5px; -} - -table.colored tr.header { - background: $table_header_bg; - background-image: url(form_title_bg.png); - background-repeat: repeat-x; - background-position: top; - border-bottom: solid $table_border 1px; - font-weight: bold; -} - -table.colored tr { - background: $table_row_bg; -} - -table.colored tr.odd_row { - background: $odd_row_bg; -} - -div.debug { - margin: 10px; - padding: 5px; - background: #FFFF99; - border: solid #FFFF33 1px; - color: black; -} - -div.odd_row { - background: $odd_row_bg; -} - -#footer { - display: none; -} - -## Tool panel stuff - -td.panel-body { - background: white; - color: $base_text; - background: $menu_bg_over url(menu_bg.png) top repeat-x; -} - -div.toolSectionPad { - margin: 0; - padding: 0; - height: 5px; - font-size: 0px; -} - -div.toolSectionDetailsInner { - margin-left: 5px; - margin-right: 5px; -} - -div.toolSectionTitle { - padding-bottom: 0px; - font-weight: bold; -} - -div.toolTitle { - padding-top: 5px; - padding-bottom: 5px; - margin-left: 16px; - margin-right: 10px; - display: list-item; - list-style: square outside; -} - -span.toolParameterExpandableCollapsable { - font-weight: bold; - cursor: pointer; -} -ul.toolParameterExpandableCollapsable { - list-style: none; -} - -ul.manage-table-actions { - float: right; - margin-top: -2.5em; -} -ul.manage-table-actions li { - display: block; - float: left; - margin-left: 0.5em; -} - -## State colors - -.state-color-new { - border-color: $history_new_border; - background: $history_new_bg; -} - -.state-color-upload { - border-color: $history_upload_border; - background: $history_upload_bg; -} - -.state-color-waiting { - border-color: $history_waiting_border; - background: $history_waiting_bg; -} - -.state-color-queued { - border-color: $history_queued_border; - background: $history_queued_bg; -} - -.state-color-running { - border-color: $history_running_border; - background: $history_running_bg; -} - -.state-color-ok { - border-color: $history_ok_border; - background: $history_ok_bg; -} - -.state-color-error { - border-color: $history_error_border; - background: $history_error_bg; -} - -.state-color-deleted { - border-color: $history_deleted_border; - background: $history_deleted_bg; -} - -.state-fg-new { - color: #FFB030; -} - -.state-fg-upload { - color: #D090D0; -} - -.state-fg-waiting { - color: #E8C060; -} - -.state-fg-queued { - color: #888888; -} - -.state-fg-running { - color: #AAAA66; -} - -.state-fg-ok { - color: #66AA66; -} - -.state-fg-error { - color: #AA6666; -} - -.state-fg-deleted { - color: #3399FF; -} - -## Button styles - -.action-button { - background: transparent; - line-height: 16px; - color: #333; - text-decoration: none; - font-size: 100%; - font-weight: bold; - display: inline-block; - cursor: pointer; - padding: 2px; - border: solid #aaaaaa 1px; - padding-right: 0.5em; - padding-left: 0.5em; - -moz-border-radius: 0.5em; - -webkit-border-radius: 0.5em; - border-radius: 0.5em; - user-select: none; - -moz-user-select: none; - -webkit-user-select: none; -} - -.action-button > * { - vertical-align: middle; -} - -.action-button:hover { - color: black; - background: #dddddd; -} -.action-button:active { - color: white; - background: #aaaaaa; -} - -## A menu button is a button that has an attached popup menu - -.menubutton { - display: inline-block; - cursor: pointer; - position: relative; - .unselectable; - - border: solid transparent 1px; - -moz-border-radius: 0.25em; - -webkit-border-radius: 0.25em; - border-radius: 0.25em; - - padding: 1px 0.25em; - margin: -1px -0.25em; - - .label { - position: relative; - display: block; - border-right: none; - } -} - -.menubutton.action-button { - border-color: #aaaaaa; -} - -.menubutton.popup, .action-button.popup { - padding-right: 20px; - background-image: url(../images/dropdownarrow.png); - background-repeat: no-repeat; - background-position: right 7px; -} - -.menubutton:hover { - border-color: #aaaaaa; - ## background: #eeeeee; - ## color: #333; -} - -## A split menu button, the main button has an action, the arrow causes the -## popup menu to appear - -.menubutton.popup.split { - padding-right: 2em; -} - -.menubutton.popup.split:hover { - background: url(../images/ddarrowsplit.png) no-repeat right -39px; -} - -## Popup menu styles - -.overlay-border { - position: absolute; - top: 0; - left: 0; - height: 100%; - width: 100%; - padding: 1em; - margin: -1em; - background-color: rgba(0,0,0,0.5); - -moz-border-radius: 1em; - -webkit-border-radius: 1em; - z-index: -1; -} - -div.popmenu-wrapper { - - position: absolute; - top: 100%; - z-index: 20000; - - ul { - - display: block; - margin: 0; - padding: 0; - - background: white; - color: #333; - font-weight: bold; - font-style: normal; - white-space: nowrap; - border: solid #aaaaaa 1px; - padding: 3px 0; - -moz-border-radius: 0.5em; - -webkit-border-radius: 0.5em; - border-radius: 0.5em; - ## margin: -3px -0.5em; - ## min-width: 100%; - - .unselectable; - - li { - display: block; - padding: 3px 1em; - cursor: pointer; - border-top: solid transparent 1px; - border-bottom: solid transparent 1px; - } - - li.head { - color: #999; - font-style: italic; - } - } -} - -div.popmenu-wrapper ul li:hover { - background: #EEEEFF; - border-color: #aaa; -} - -div.popmenu-wrapper ul li.head:hover { - background: inherit; - border-color: transparent; -} - -.popup-arrow { - cursor: pointer; - text-decoration: none; - color: #555; -} - -.popup-arrow:hover { - color: black; -} - -div.permissionContainer { - padding-left: 20px; -} - -## Data grid style - -.grid-header { - padding-bottom: 1em; -} - -.grid-header h2 { - margin: 0; - margin-bottom: 0.5em; -} - -.grid-header .title { - font-weight: bold; -} - -.grid { - padding-top: 1em; - border-collapse: collapse; - width: 100%; -} -.grid tbody td { - border-top: solid #DDDDDD 1px; - border-bottom: solid #DDDDDD 1px; - padding: 0.3em 0.5em; -} -.grid tbody td:empty { - padding: 0; -} -.grid thead tr { - height: 2em; -} -.grid thead th { - background: $table_header_bg; - ## background-image: url(form_title_bg.png); - background-repeat: repeat-x; - background-position: top; - border-top: solid $table_border 1px; - border-bottom: solid $table_border 1px; - padding: 0.3em 0.5em; - text-align: left; - white-space: nowrap; -} -.grid tfoot td { - background-color: #F8F8F8; - border-top: solid #DDDDDD 1px; - border-bottom: solid #DDDDDD 1px; - padding: 0.3em 0.5em; -} -.grid .current { - background-color: #EEEEFF; -} - -## Styles for areas of text content - -.text-content { - - hr { - display:block; - background:black; - color:black; - width:100%; - height:1px; - border:none; - background:#aaa; - color:#aaa; - } - - table - { - border-collapse:collapse; - border-top:1px solid #ccc; - border-left:1px solid #ccc; - } - - blockquote { - color:#666; - } - - fieldset { - border-color:#ccc; - border:1px solid #ccc; - } - - th,td { - border-bottom:1px solid #ddd; - border-right:1px solid #ccc; - } - - th,td { - padding:.8em; - } - -} - -## Icon buttons. - -.icon-button { - width: 16px; - height: 16px; - display: block; - float: left; - margin-left: 2px; - ## Allow alt text for screen readers - text-indent: 20px; - background-repeat:no-repeat; - background-position: 0px 0px; - padding: 0; -} - -.icon-button.display { - -sprite-group: history-buttons; - -sprite-image: eye_icon.png; -} -.icon-button.display:hover { - -sprite-group: history-buttons; - -sprite-image: eye_icon_dark.png; -} -.icon-button.display_disabled { - -sprite-group: history-buttons; - -sprite-image: eye_icon_grey.png; -} -.icon-button.delete { - -sprite-group: history-buttons; - -sprite-image: delete_icon.png; -} -.icon-button.delete:hover { - -sprite-group: history-buttons; - -sprite-image: delete_icon_dark.png; -} -.icon-button.delete_disabled { - -sprite-group: history-buttons; - -sprite-image: delete_icon_grey.png; -} -.icon-button.edit { - -sprite-group: history-buttons; - -sprite-image: pencil_icon.png; -} -.icon-button.edit:hover { - -sprite-group: history-buttons; - -sprite-image: pencil_icon_dark.png; -} -.icon-button.edit_disabled { - -sprite-group: history-buttons; - -sprite-image: pencil_icon_grey.png; -} -.icon-button.tag { - -sprite-group: fugue; - -sprite-image: fugue/tag-label.png; -} -.icon-button.tags { - -sprite-group: fugue; - -sprite-image: fugue/tags.png; -} -.icon-button.tag--plus { - -sprite-group: fugue; - -sprite-image: fugue/tag--plus.png; -} -.icon-button.toggle-expand { - -sprite-group: fugue; - -sprite-image: fugue/toggle-expand.png; -} -.icon-button.toggle { - -sprite-group: fugue; - -sprite-image: fugue/toggle.png; -} -.icon-button.arrow-circle { - -sprite-group: fugue; - -sprite-image: fugue/arrow-circle.png; -} -.icon-button.chevron { - -sprite-group: fugue; - -sprite-image: fugue/chevron.png; -} -.icon-button.bug { - -sprite-group: fugue; - -sprite-image: fugue/bug.png; -} -.icon-button.disk { - -sprite-group: fugue; - -sprite-image: fugue/disk.png; -} -.icon-button.information { - -sprite-group: fugue; - -sprite-image: fugue/information-white.png; -} -.icon-button.annotate { - -sprite-group: fugue; - -sprite-image: fugue/sticky-note-text.png; -} -.icon-button.go-to-full-screen { - -sprite-group: fugue; - -sprite-image: fugue/external.png; -} -.icon-button.import { - -sprite-group: fugue; - -sprite-image: fugue/plus-circle.png; -} -.icon-button.plus-button { - -sprite-group: fugue; - -sprite-image: fugue/plus-button.png; -} -.icon-button.gear { - -sprite-group: fugue; - -sprite-image: fugue/gear.png; -} - -.icon-button.chart_curve { - background: url(../images/silk/chart_curve.png) no-repeat; -} - -.tipsy { - padding: 5px; - font-size: 10px; - filter: alpha(opacity=80); - background-repeat: no-repeat; - background-image: url(../images/tipsy.gif); -} -.tipsy-inner { - padding: 5px 8px 4px 8px; - background-color: black; - color: white; - max-width: 200px; - text-align: center; -} - -.tipsy-north { - background-position: top center; -} - -.tipsy-south { - background-position: bottom center; -} - -.tipsy-east { - background-position: right center; -} - -.tipsy-west { - background-position: left center; -} - -.editable-text { - cursor:pointer; -} - -.editable-text:hover { - cursor: text; - border: dotted #999999 1px; -} - -.text-and-autocomplete-select { - -sprite-group: fugue; - -sprite-image: fugue/control-270.png; - -sprite-horiz-position: right; -} -.icon-button.multiinput{ - background:url(../images/documents-stack.png) no-repeat; - cursor:pointer; - float:none; - display:inline-block; - margin-left:10px; -} -.icon-button.multiinput.disabled{ - background:url(../images/documents-stack-faded.png) no-repeat; - cursor:auto; -} -.workflow-invocation-complete{ - border:solid 1px #6A6; - border-left-width:5px; - margin:10px 0; - padding-left:5px; -} - diff -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 -r fca74f9562024605dd87a3a6ace02d28a1851f5e static/june_2007_style/base.less --- /dev/null +++ b/static/june_2007_style/base.less @@ -0,0 +1,886 @@ +@import "variables.less"; + +@import "galaxy_bootstrap.less"; + + +// Lucida Grande for proper mac unicode characters, verdana/arial stack for others +//body{font:13px/1.231 "Lucida Grande",verdana,arial,helvetica,sans-serif;*font-size:small;*font:x-small;}select,input,button,textarea,button{font:99% "Lucida Grande",verdana,arial,helvetica,sans-serif;}table{font-size:inherit;font:100%;}pre,code,kbd,samp,tt{font-family:monospace;*font-size:108%;line-height:100%;} +//body{font-size:75%;} + +// Mixins + +.unselectable { + user-select: none; + -moz-user-select: none; + -webkit-user-select: none; +} + +.shadow { + -moz-box-shadow: 0 3px 30px black; + -webkit-box-shadow: 0 3px 30px black; +} + +// Real styles + +body { + background: @base_bg_bottom; + color: @base_text; + background-image: url(base_bg.png); + background-repeat: repeat-x; + background-position: top; + margin: 10px; +} + +img { + border: 0; +} + + +a:link, a:visited, a:active { + color: @link_text; +} + +h1, h2, h3, h4 { + color: @header_text; + /*text-shadow: #bbb 2px 2px 1px;*/ +} + +h1:first-child, h2:first-child, h3:first-child, h4:first-child { + margin-top: 0px; +} + +hr { + border: none; + height: 0px; + border-bottom: dotted @base_text 1px; +} + +table { + border-collapse: collapse; +} + +th { + text-align: left; +} + +div.toolForm { + border: solid @form_border 1px; +} + +div.toolFormTitle { + font-weight: bold; + padding: 5px; + padding-left: 10px; + padding-right: 10px; + background: @form_title_bg_bottom; + // background-image: url(form_title_bg.png); + background-repeat: repeat-x; + background-position: top; + border-bottom: solid @form_border 1px; +} + +div.toolParamHelp { + color: #666; +} + +div.toolParamHelp a { + color: #666; +} + +div.toolFormBody { + background: @form_body_bg_bottom; + background-image: url(form_body_bg.png); + background-repeat: repeat-x; + background-position: top; + padding: 5px 0; +} + +div.toolFormBody div.toolFormTitle { + background: transparent; + border: none; + font-weight: bold; + border-bottom: solid @form_border 1px; + margin-bottom: 5px; +} + +div.toolFormDisabled div.toolFormTitle { + background: @layout_bg; + border-color: @layout_border; +} + +div.toolFormDisabled { + border-color: @layout_border; +} + +div.toolHelp { + margin-top: 10px; +} + +div.toolHelpBody { + width: 100%; +} + +div.metadataForm { + border:solid #aaaaaa 1px; +} + +div.metadataFormTitle { + font-weight:bold; + padding:5px; + padding-left:10px; + padding-right:10px; + background:#cccccc; + background-repeat:repeat-x; + background-position:top; + border-bottom:solid #aaaaaa 1px; +} + +div.metadataFormBody { + background:#FFFFFF; + background-image:url(form_body_bg.png); + background-repeat:repeat-x; + background-position:top; + padding:5px 0; +} + +div.metadataFormBody div.metadataFormTitle { + background:transparent; + border:none; + font-weight:bold; + border-bottom:solid #dcb790 1px; + margin-bottom:5px; +} + +div.metadataFormDisabled div.metadataFormTitle { + background:#eee; + border-color:#999; +} + +div.metadataFormDisabled { + border-color:#999; +} + +div.metadataHelpBody { + width:100%;overflow:auto; +} + +div.titleRow { + font-weight: bold; + border-bottom: dotted gray 1px; + margin-bottom: 0.5em; + padding-bottom: 0.25em; +} + +// Forms + +div.form { + border: solid @form_border 1px; +} + +div.form-title { + font-weight: bold; + padding: 5px 10px; + background: @form_title_bg_bottom; + background-image: url(form_title_bg.png); + background-repeat: repeat-x; + background-position: top; + border-bottom: solid @form_border 1px; +} + +div.form-body { + padding: 5px 0; +} + +div.form-row { + padding: 5px 10px; +} + +div.form-title-row { + padding: 5px 10px; +} + +div.repeat-group-item { + border-left: solid @form_border 5px; + margin-left: 10px; + margin-bottom: 10px; +} + +div.form-row-error { + background: @error_message_bg; +} + +div.form-row label { + font-weight: bold; + display: block; + margin-bottom: .2em; +} + +div.form-row label.inline { + display: inline; +} + +div.form-row-input { + float: left; +} + +div.form-row-input label { + font-weight: normal; + display: inline; +} + +div.form-row-error-message { + width: 300px; + float: left; + color: red; + font-weight: bold; + padding: 3px 0 0 1em; +} + +.form-row .help { + color: #666; +} + +select, input, textarea { + font: inherit; +} + +select, textarea, input[type="text"], input[type="file"], input[type="password"] { + // -webkit-box-sizing: border-box; + max-width: 300px; +} + +// Messages + +.errormessagelarge, .warningmessagelarge, .donemessagelarge, .infomessagelarge { + padding: 10px; + padding-left: 52px; + min-height: 32px; + border: 1px solid @error_message_border; + background-color: @error_message_bg; + background-image: url(error_message_icon.png); + background-repeat: no-repeat; + background-position: 10px 10px; +} + +.warningmessagelarge { + background-image: url(warn_message_icon.png); + border-color: @warn_message_border; + background-color: @warn_message_bg; +} + +.donemessagelarge { + background-image: url(done_message_icon.png); + border-color: @done_message_border; + background-color: @done_message_bg; +} + +.infomessagelarge { + background-image: url(info_message_icon.png); + border-color: @info_message_border; + background-color: @info_message_bg; +} + +.screencastBox { + padding-left: 10px; + border-color: #AAAA66; + background-color: #FFFFCC; + background-image: none; +} + +.errormessage, .warningmessage, .donemessage, .infomessage, .errormessagesmall, .warningmessagesmall, .donemessagesmall, .infomessagesmall { + padding: 5px; + padding-left: 25px; + min-height: 15px; + border: 1px solid @error_message_border; + background-color: @error_message_bg; + background-image: url(error_small.png); + background-repeat: no-repeat; + background-position: 5px 5px; +} + +.warningmessage, .warningmessagesmall { + background-image: url(warn_small.png); + border-color: @warn_message_border; + background-color: @warn_message_bg; +} + +.donemessage, .donemessagesmall { + background-image: url(ok_small.png); + border-color: @done_message_border; + background-color: @done_message_bg; +} + +.infomessage, .infomessagesmall { + background-image: url(info_small.png); + border-color: @info_message_border; + background-color: @info_message_bg; +} + +.errormark, .warningmark, .donemark, .infomark, .ok_bgr, .err_bgr { + padding-left: 20px; + min-height: 15px; + background: url(error_small.png) no-repeat; +} + +.warningmark { + background-image: url(warn_small.png); +} + +.donemark { + background-image: url(ok_small.png); +} + +.infomark, .ok_bgr { + background-image: url(info_small.png); +} + +table.simple { + font-size: 12px; + background: #fff; + margin: 1em; + border-collapse: collapse; + text-align: left; +} +table.simple th { + font-size: 14px; + font-weight: normal; + padding: 10px 8px; + border-bottom: 2px solid #333; +} +table.simple td { + padding: 10px 8px 0px 8px; +} +table.simple tbody tr:hover td { + color: #333; +} + +table.tabletip { + width: 100%; + border-collapse: collapse; + text-align: left; +} +table.tabletip th { + white-space: nowrap; + border-bottom: 1px solid #444; + padding-right: 3px; +} +table.tabletip td { + border-bottom: 1px solid #ddd; +} +table.tabletip tbody tr:hover td { + background-color: #eee; +} + +table.colored { + border-top: solid @table_border 1px; + border-bottom: solid @table_border 1px; +} + +table.colored td, table.colored th { + text-align: left; + padding: 5px; +} + +table.colored tr.header { + background: @table_header_bg; + background-image: url(form_title_bg.png); + background-repeat: repeat-x; + background-position: top; + border-bottom: solid @table_border 1px; + font-weight: bold; +} + +table.colored tr { + background: @table_row_bg; +} + +table.colored tr.odd_row { + background: @odd_row_bg; +} + +div.debug { + margin: 10px; + padding: 5px; + background: #FFFF99; + border: solid #FFFF33 1px; + color: black; +} + +div.odd_row { + background: @odd_row_bg; +} + +#footer { + display: none; +} + +// Tool panel stuff + +td.panel-body { + background: white; + color: @base_text; + background: @menu_bg_over url(menu_bg.png) top repeat-x; +} + +div.toolSectionPad { + margin: 0; + padding: 0; + height: 5px; + font-size: 0px; +} + +div.toolSectionDetailsInner { + margin-left: 5px; + margin-right: 5px; +} + +div.toolSectionTitle { + padding-bottom: 0px; + font-weight: bold; +} + +div.toolTitle { + padding-top: 5px; + padding-bottom: 5px; + margin-left: 16px; + margin-right: 10px; + display: list-item; + list-style: square outside; +} + +span.toolParameterExpandableCollapsable { + font-weight: bold; + cursor: pointer; +} +ul.toolParameterExpandableCollapsable { + list-style: none; +} + +ul.manage-table-actions { + float: right; + margin-top: -2.5em; +} +ul.manage-table-actions li { + display: block; + float: left; + margin-left: 0.5em; +} + +// State colors + +.state-color-new { + border-color: @history_new_border; + background: @history_new_bg; +} + +.state-color-upload { + border-color: @history_upload_border; + background: @history_upload_bg; +} + +.state-color-waiting { + border-color: @history_waiting_border; + background: @history_waiting_bg; +} + +.state-color-queued { + border-color: @history_queued_border; + background: @history_queued_bg; +} + +.state-color-running { + border-color: @history_running_border; + background: @history_running_bg; +} + +.state-color-ok { + border-color: @history_ok_border; + background: @history_ok_bg; +} + +.state-color-error { + border-color: @history_error_border; + background: @history_error_bg; +} + +.state-color-deleted { + border-color: @history_deleted_border; + background: @history_deleted_bg; +} + +.state-fg-new { + color: #FFB030; +} + +.state-fg-upload { + color: #D090D0; +} + +.state-fg-waiting { + color: #E8C060; +} + +.state-fg-queued { + color: #888888; +} + +.state-fg-running { + color: #AAAA66; +} + +.state-fg-ok { + color: #66AA66; +} + +.state-fg-error { + color: #AA6666; +} + +.state-fg-deleted { + color: #3399FF; +} + +// Button styles + +.action-button { + background: transparent; + line-height: 16px; + color: #333; + text-decoration: none; + font-size: 100%; + font-weight: bold; + display: inline-block; + cursor: pointer; + padding: 2px; + border: solid #aaaaaa 1px; + padding-right: 0.5em; + padding-left: 0.5em; + -moz-border-radius: 0.5em; + -webkit-border-radius: 0.5em; + border-radius: 0.5em; + user-select: none; + -moz-user-select: none; + -webkit-user-select: none; +} + +.action-button > * { + vertical-align: middle; +} + +.action-button:hover { + color: black; + background: #dddddd; +} +.action-button:active { + color: white; + background: #aaaaaa; +} + +// A menu button is a button that has an attached popup menu + +.menubutton { + display: inline-block; + cursor: pointer; + position: relative; + .unselectable; + + border: solid transparent 1px; + -moz-border-radius: 0.25em; + -webkit-border-radius: 0.25em; + border-radius: 0.25em; + + padding: 1px 0.25em; + margin: -1px -0.25em; + + .label { + position: relative; + display: block; + border-right: none; + } +} + +.menubutton.action-button { + border-color: #aaaaaa; +} + +.menubutton.popup, .action-button.popup { + padding-right: 20px; + background-image: url(../images/dropdownarrow.png); + background-repeat: no-repeat; + background-position: right 7px; +} + +.menubutton:hover { + border-color: #aaaaaa; + // background: #eeeeee; + // color: #333; +} + +// A split menu button, the main button has an action, the arrow causes the +// popup menu to appear + +.menubutton.popup.split { + padding-right: 2em; +} + +.menubutton.popup.split:hover { + background: url(../images/ddarrowsplit.png) no-repeat right -39px; +} + +// Popup menu styles + +.overlay-border { + position: absolute; + top: 0; + left: 0; + height: 100%; + width: 100%; + padding: 1em; + margin: -1em; + background-color: rgba(0,0,0,0.5); + -moz-border-radius: 1em; + -webkit-border-radius: 1em; + z-index: -1; +} + +div.popmenu-wrapper { + + position: absolute; + top: 100%; + z-index: 20000; + + ul { + + display: block; + margin: 0; + padding: 0; + + background: white; + color: #333; + font-weight: bold; + font-style: normal; + white-space: nowrap; + border: solid #aaaaaa 1px; + padding: 3px 0; + -moz-border-radius: 0.5em; + -webkit-border-radius: 0.5em; + border-radius: 0.5em; + // margin: -3px -0.5em; + // min-width: 100%; + + .unselectable; + + li { + display: block; + padding: 3px 1em; + cursor: pointer; + border-top: solid transparent 1px; + border-bottom: solid transparent 1px; + } + + li.head { + color: #999; + font-style: italic; + } + } +} + +div.popmenu-wrapper ul li:hover { + background: #EEEEFF; + border-color: #aaa; +} + +div.popmenu-wrapper ul li.head:hover { + background: inherit; + border-color: transparent; +} + +.popup-arrow { + cursor: pointer; + text-decoration: none; + color: #555; +} + +.popup-arrow:hover { + color: black; +} + +div.permissionContainer { + padding-left: 20px; +} + +// Data grid style + +.grid-header { + padding-bottom: 1em; +} + +.grid-header h2 { + margin: 0; + margin-bottom: 0.5em; +} + +.grid-header .title { + font-weight: bold; +} + +.grid { + padding-top: 1em; + border-collapse: collapse; + width: 100%; +} +.grid tbody td { + border-top: solid #DDDDDD 1px; + border-bottom: solid #DDDDDD 1px; + padding: 0.3em 0.5em; +} +.grid tbody td:empty { + padding: 0; +} +.grid thead tr { + height: 2em; +} +.grid thead th { + background: @table_header_bg; + // background-image: url(form_title_bg.png); + background-repeat: repeat-x; + background-position: top; + border-top: solid @table_border 1px; + border-bottom: solid @table_border 1px; + padding: 0.3em 0.5em; + text-align: left; + white-space: nowrap; +} +.grid tfoot td { + background-color: #F8F8F8; + border-top: solid #DDDDDD 1px; + border-bottom: solid #DDDDDD 1px; + padding: 0.3em 0.5em; +} +.grid .current { + background-color: #EEEEFF; +} + +// Styles for areas of text content + +.text-content { + + hr { + display:block; + background:black; + color:black; + width:100%; + height:1px; + border:none; + background:#aaa; + color:#aaa; + } + + table + { + border-collapse:collapse; + border-top:1px solid #ccc; + border-left:1px solid #ccc; + } + + blockquote { + color:#666; + } + + fieldset { + border-color:#ccc; + border:1px solid #ccc; + } + + th,td { + border-bottom:1px solid #ddd; + border-right:1px solid #ccc; + } + + th,td { + padding:.8em; + } + +} + +// Icon buttons. + +.icon-button { + width: 16px; + height: 16px; + display: block; + float: left; + margin-left: 2px; + // Allow alt text for screen readers + text-indent: 20px; + background-repeat:no-repeat; + background-position: 0px 0px; + padding: 0; +} + +@import "base_sprites"; + +.tipsy { + padding: 5px; + font-size: 10px; + filter: alpha(opacity=80); + background-repeat: no-repeat; + background-image: url(../images/tipsy.gif); +} +.tipsy-inner { + padding: 5px 8px 4px 8px; + background-color: black; + color: white; + max-width: 200px; + text-align: center; +} + +.tipsy-north { + background-position: top center; +} + +.tipsy-south { + background-position: bottom center; +} + +.tipsy-east { + background-position: right center; +} + +.tipsy-west { + background-position: left center; +} + +.editable-text { + cursor:pointer; +} + +.editable-text:hover { + cursor: text; + border: dotted #999999 1px; +} +/* +.text-and-autocomplete-select { + -sprite-group: fugue; + -sprite-image: fugue/control-270.png; + -sprite-horiz-position: right; +} +*/ +.icon-button.multiinput{ + background:url(../images/documents-stack.png) no-repeat; + cursor:pointer; + float:none; + display:inline-block; + margin-left:10px; +} +.icon-button.multiinput.disabled{ + background:url(../images/documents-stack-faded.png) no-repeat; + cursor:auto; +} +.workflow-invocation-complete{ + border:solid 1px #6A6; + border-left-width:5px; + margin:10px 0; + padding-left:5px; +} + diff -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 -r fca74f9562024605dd87a3a6ace02d28a1851f5e static/june_2007_style/base_sprites.less.tmpl --- /dev/null +++ b/static/june_2007_style/base_sprites.less.tmpl @@ -0,0 +1,102 @@ +.icon-button.display { + -sprite-group: history-buttons; + -sprite-image: eye_icon.png; +} +.icon-button.display:hover { + -sprite-group: history-buttons; + -sprite-image: eye_icon_dark.png; +} +.icon-button.display_disabled { + -sprite-group: history-buttons; + -sprite-image: eye_icon_grey.png; +} +.icon-button.delete { + -sprite-group: history-buttons; + -sprite-image: delete_icon.png; +} +.icon-button.delete:hover { + -sprite-group: history-buttons; + -sprite-image: delete_icon_dark.png; +} +.icon-button.delete_disabled { + -sprite-group: history-buttons; + -sprite-image: delete_icon_grey.png; +} +.icon-button.edit { + -sprite-group: history-buttons; + -sprite-image: pencil_icon.png; +} +.icon-button.edit:hover { + -sprite-group: history-buttons; + -sprite-image: pencil_icon_dark.png; +} +.icon-button.edit_disabled { + -sprite-group: history-buttons; + -sprite-image: pencil_icon_grey.png; +} +.icon-button.tag { + -sprite-group: fugue; + -sprite-image: fugue/tag-label.png; +} +.icon-button.tags { + -sprite-group: fugue; + -sprite-image: fugue/tags.png; +} +.icon-button.tag--plus { + -sprite-group: fugue; + -sprite-image: fugue/tag--plus.png; +} +.icon-button.toggle-expand { + -sprite-group: fugue; + -sprite-image: fugue/toggle-expand.png; +} +.icon-button.toggle { + -sprite-group: fugue; + -sprite-image: fugue/toggle.png; +} +.icon-button.arrow-circle { + -sprite-group: fugue; + -sprite-image: fugue/arrow-circle.png; +} +.icon-button.chevron { + -sprite-group: fugue; + -sprite-image: fugue/chevron.png; +} +.icon-button.bug { + -sprite-group: fugue; + -sprite-image: fugue/bug.png; +} +.icon-button.disk { + -sprite-group: fugue; + -sprite-image: fugue/disk.png; +} +.icon-button.information { + -sprite-group: fugue; + -sprite-image: fugue/information-white.png; +} +.icon-button.annotate { + -sprite-group: fugue; + -sprite-image: fugue/sticky-note-text.png; +} +.icon-button.go-to-full-screen { + -sprite-group: fugue; + -sprite-image: fugue/external.png; +} +.icon-button.import { + -sprite-group: fugue; + -sprite-image: fugue/plus-circle.png; +} +.icon-button.plus-button { + -sprite-group: fugue; + -sprite-image: fugue/plus-button.png; +} +.icon-button.gear { + -sprite-group: fugue; + -sprite-image: fugue/gear.png; +} + +.text-and-autocomplete-select { + -sprite-group: fugue; + -sprite-image: fugue/control-270.png; + -sprite-horiz-position: right; +} \ No newline at end of file diff -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 -r fca74f9562024605dd87a3a6ace02d28a1851f5e static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -1,8 +1,171 @@ -body{font:13px/1.231 "Lucida Grande",verdana,arial,helvetica,sans-serif;*font-size:small;*font:x-small;} -select,input,button,textarea,button{font:99% "Lucida Grande",verdana,arial,helvetica,sans-serif;} -table{font-size:inherit;font:100%;} -pre,code,kbd,samp,tt{font-family:monospace;*font-size:108%;line-height:100%;} -body{font-size:75%;} +article,aside,details,figcaption,figure,footer,header,hgroup,nav,section{display:block;} +audio,canvas,video{display:inline-block;*display:inline;*zoom:1;} +audio:not([controls]){display:none;} +html{font-size:100%;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%;} +a:focus{outline:thin dotted;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;} +a:hover,a:active{outline:0;} +sub,sup{position:relative;font-size:75%;line-height:0;vertical-align:baseline;} +sup{top:-0.5em;} +sub{bottom:-0.25em;} +img{max-width:100%;height:auto;border:0;-ms-interpolation-mode:bicubic;} +button,input,select,textarea{margin:0;font-size:100%;vertical-align:middle;} +button,input{*overflow:visible;line-height:normal;} +button::-moz-focus-inner,input::-moz-focus-inner{padding:0;border:0;} +button,input[type="button"],input[type="reset"],input[type="submit"]{cursor:pointer;-webkit-appearance:button;} +input[type="search"]{-webkit-appearance:textfield;-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box;} +input[type="search"]::-webkit-search-decoration,input[type="search"]::-webkit-search-cancel-button{-webkit-appearance:none;} +textarea{overflow:auto;vertical-align:top;} +body{margin:0;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:12px;line-height:16px;color:#333333;background-color:#ffffff;} +a{color:#0088cc;text-decoration:none;} +a:hover{color:#005580;text-decoration:underline;} +p{margin:0 0 8px;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:12px;line-height:16px;}p small{font-size:10px;color:#999999;} +.lead{margin-bottom:16px;font-size:20px;font-weight:200;line-height:24px;} +h1,h2,h3,h4,h5,h6{margin:0;font-weight:bold;color:#333333;text-rendering:optimizelegibility;}h1 small,h2 small,h3 small,h4 small,h5 small,h6 small{font-weight:normal;color:#999999;} +h1{font-size:30px;line-height:32px;}h1 small{font-size:18px;} +h2{font-size:24px;line-height:32px;}h2 small{font-size:18px;} +h3{line-height:24px;font-size:18px;}h3 small{font-size:14px;} +h4,h5,h6{line-height:16px;} +h4{font-size:14px;}h4 small{font-size:12px;} +h5{font-size:12px;} +h6{font-size:11px;color:#999999;text-transform:uppercase;} +.page-header{padding-bottom:15px;margin:16px 0;border-bottom:1px solid #eeeeee;} +.page-header h1{line-height:1;} +ul,ol{padding:0;margin:0 0 8px 25px;} +ul ul,ul ol,ol ol,ol ul{margin-bottom:0;} +ul{list-style:disc;} +ol{list-style:decimal;} +li{line-height:16px;} +ul.unstyled{margin-left:0;list-style:none;} +dl{margin-bottom:16px;} +dt,dd{line-height:16px;} +dt{font-weight:bold;} +dd{margin-left:8px;} +hr{margin:16px 0;border:0;border-top:1px solid #e5e5e5;border-bottom:1px solid #ffffff;} +strong{font-weight:bold;} +em{font-style:italic;} +.muted{color:#999999;} +abbr{font-size:90%;text-transform:uppercase;border-bottom:1px dotted #ddd;cursor:help;} +blockquote{padding:0 0 0 15px;margin:0 0 16px;border-left:5px solid #eeeeee;}blockquote p{margin-bottom:0;font-size:16px;font-weight:300;line-height:20px;} +blockquote small{display:block;line-height:16px;color:#999999;}blockquote small:before{content:'\2014 \00A0';} +blockquote.pull-right{float:right;padding-left:0;padding-right:15px;border-left:0;border-right:5px solid #eeeeee;}blockquote.pull-right p,blockquote.pull-right small{text-align:right;} +q:before,q:after,blockquote:before,blockquote:after{content:"";} +address{display:block;margin-bottom:16px;line-height:16px;font-style:normal;} +small{font-size:100%;} +cite{font-style:normal;} +code,pre{padding:0 3px 2px;font-family:Menlo,Monaco,"Courier New",monospace;font-size:11px;color:#333333;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;} +code{padding:3px 4px;color:#d14;background-color:#f7f7f9;border:1px solid #e1e1e8;} +pre{display:block;padding:7.5px;margin:0 0 8px;font-size:12px;line-height:16px;background-color:#f5f5f5;border:1px solid #ccc;border:1px solid rgba(0, 0, 0, 0.15);-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;white-space:pre;white-space:pre-wrap;word-break:break-all;}pre.prettyprint{margin-bottom:16px;} +pre code{padding:0;background-color:transparent;} +form{margin:0 0 16px;} +fieldset{padding:0;margin:0;border:0;} +legend{display:block;width:100%;padding:0;margin-bottom:24px;font-size:18px;line-height:32px;color:#333333;border:0;border-bottom:1px solid #eee;} +label,input,button,select,textarea{font-family:"Helvetica Neue",Helvetica,Arial,sans-serif;font-size:12px;font-weight:normal;line-height:16px;} +label{display:block;margin-bottom:5px;color:#333333;} +input,textarea,select,.uneditable-input{display:inline-block;width:210px;height:16px;padding:4px;margin-bottom:9px;font-size:12px;line-height:16px;color:#555555;border:1px solid #ccc;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;} +.uneditable-textarea{width:auto;height:auto;} +label input,label textarea,label select{display:block;} +input[type="image"],input[type="checkbox"],input[type="radio"]{width:auto;height:auto;padding:0;margin:3px 0;*margin-top:0;line-height:normal;border:0;cursor:pointer;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;} +input[type="file"]{padding:initial;line-height:initial;border:initial;background-color:#ffffff;background-color:initial;-webkit-box-shadow:none;-moz-box-shadow:none;box-shadow:none;} +input[type="button"],input[type="reset"],input[type="submit"]{width:auto;height:auto;} +select,input[type="file"]{height:28px;*margin-top:4px;line-height:28px;} +select{width:220px;background-color:#ffffff;} +select[multiple],select[size]{height:auto;} +input[type="image"]{-webkit-box-shadow:none;-moz-box-shadow:none;box-shadow:none;} +textarea{height:auto;} +input[type="hidden"]{display:none;} +.radio,.checkbox{padding-left:18px;} +.radio input[type="radio"],.checkbox input[type="checkbox"]{float:left;margin-left:-18px;} +.controls>.radio:first-child,.controls>.checkbox:first-child{padding-top:5px;} +.radio.inline,.checkbox.inline{display:inline-block;margin-bottom:0;vertical-align:middle;} +.radio.inline+.radio.inline,.checkbox.inline+.checkbox.inline{margin-left:10px;} +.controls>.radio.inline:first-child,.controls>.checkbox.inline:first-child{padding-top:0;} +input,textarea{-webkit-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075);-moz-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075);box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075);-webkit-transition:border linear 0.2s,box-shadow linear 0.2s;-moz-transition:border linear 0.2s,box-shadow linear 0.2s;-ms-transition:border linear 0.2s,box-shadow linear 0.2s;-o-transition:border linear 0.2s,box-shadow linear 0.2s;transition:border linear 0.2s,box-shadow linear 0.2s;} +input:focus,textarea:focus{border-color:rgba(82, 168, 236, 0.8);-webkit-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);-moz-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);outline:0;outline:thin dotted \9;} +input[type="file"]:focus,input[type="checkbox"]:focus,select:focus{-webkit-box-shadow:none;-moz-box-shadow:none;box-shadow:none;outline:thin dotted;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;} +.input-mini{width:60px;} +.input-small{width:90px;} +.input-medium{width:150px;} +.input-large{width:210px;} +.input-xlarge{width:270px;} +.input-xxlarge{width:530px;} +input[class*="span"],select[class*="span"],textarea[class*="span"],.uneditable-input{float:none;margin-left:0;} +input.span1,textarea.span1,.uneditable-input.span1{width:50px;} +input.span2,textarea.span2,.uneditable-input.span2{width:130px;} +input.span3,textarea.span3,.uneditable-input.span3{width:210px;} +input.span4,textarea.span4,.uneditable-input.span4{width:290px;} +input.span5,textarea.span5,.uneditable-input.span5{width:370px;} 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textarea:focus{border-color:#a47e3c;-webkit-box-shadow:0 0 6px #dbc59e;-moz-box-shadow:0 0 6px #dbc59e;box-shadow:0 0 6px #dbc59e;} +.control-group.warning .input-prepend .add-on,.control-group.warning .input-append .add-on{color:#c09853;background-color:#fcf8e3;border-color:#c09853;} +.control-group.error>label,.control-group.error .help-block,.control-group.error .help-inline{color:#b94a48;} +.control-group.error input,.control-group.error select,.control-group.error textarea{color:#b94a48;border-color:#b94a48;}.control-group.error input:focus,.control-group.error select:focus,.control-group.error textarea:focus{border-color:#953b39;-webkit-box-shadow:0 0 6px #d59392;-moz-box-shadow:0 0 6px #d59392;box-shadow:0 0 6px #d59392;} +.control-group.error .input-prepend .add-on,.control-group.error .input-append .add-on{color:#b94a48;background-color:#f2dede;border-color:#b94a48;} +.control-group.success>label,.control-group.success .help-block,.control-group.success .help-inline{color:#468847;} +.control-group.success input,.control-group.success select,.control-group.success textarea{color:#468847;border-color:#468847;}.control-group.success input:focus,.control-group.success select:focus,.control-group.success textarea:focus{border-color:#356635;-webkit-box-shadow:0 0 6px #7aba7b;-moz-box-shadow:0 0 6px #7aba7b;box-shadow:0 0 6px #7aba7b;} +.control-group.success .input-prepend .add-on,.control-group.success .input-append .add-on{color:#468847;background-color:#dff0d8;border-color:#468847;} +input:focus:required:invalid,textarea:focus:required:invalid,select:focus:required:invalid{color:#b94a48;border-color:#ee5f5b;}input:focus:required:invalid:focus,textarea:focus:required:invalid:focus,select:focus:required:invalid:focus{border-color:#e9322d;-webkit-box-shadow:0 0 6px #f8b9b7;-moz-box-shadow:0 0 6px #f8b9b7;box-shadow:0 0 6px #f8b9b7;} +.form-actions{padding:15px 20px 16px;margin-top:16px;margin-bottom:16px;background-color:#f5f5f5;border-top:1px solid #ddd;} +.uneditable-input{display:block;background-color:#ffffff;border-color:#eee;-webkit-box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.025);-moz-box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.025);box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.025);cursor:not-allowed;} +:-moz-placeholder{color:#999999;} +::-webkit-input-placeholder{color:#999999;} +.help-block{margin-top:5px;margin-bottom:0;color:#999999;} +.help-inline{display:inline-block;*display:inline;*zoom:1;margin-bottom:9px;vertical-align:middle;padding-left:5px;} +.input-prepend,.input-append{margin-bottom:5px;*zoom:1;}.input-prepend:before,.input-append:before,.input-prepend:after,.input-append:after{display:table;content:"";} +.input-prepend:after,.input-append:after{clear:both;} +.input-prepend input,.input-append input,.input-prepend .uneditable-input,.input-append .uneditable-input{-webkit-border-radius:0 3px 3px 0;-moz-border-radius:0 3px 3px 0;border-radius:0 3px 3px 0;}.input-prepend input:focus,.input-append input:focus,.input-prepend .uneditable-input:focus,.input-append .uneditable-input:focus{position:relative;z-index:2;} +.input-prepend .uneditable-input,.input-append .uneditable-input{border-left-color:#ccc;} +.input-prepend .add-on,.input-append .add-on{float:left;display:block;width:auto;min-width:16px;height:16px;margin-right:-1px;padding:4px 5px;font-weight:normal;line-height:16px;color:#999999;text-align:center;text-shadow:0 1px 0 #ffffff;background-color:#f5f5f5;border:1px solid #ccc;-webkit-border-radius:3px 0 0 3px;-moz-border-radius:3px 0 0 3px;border-radius:3px 0 0 3px;} +.input-prepend .active,.input-append .active{background-color:#a9dba9;border-color:#46a546;} +.input-prepend .add-on{*margin-top:1px;} +.input-append input,.input-append .uneditable-input{float:left;-webkit-border-radius:3px 0 0 3px;-moz-border-radius:3px 0 0 3px;border-radius:3px 0 0 3px;} +.input-append .uneditable-input{border-right-color:#ccc;} +.input-append .add-on{margin-right:0;margin-left:-1px;-webkit-border-radius:0 3px 3px 0;-moz-border-radius:0 3px 3px 0;border-radius:0 3px 3px 0;} +.input-append input:first-child{*margin-left:-160px;}.input-append input:first-child+.add-on{*margin-left:-21px;} +.search-query{padding-left:14px;padding-right:14px;margin-bottom:0;-webkit-border-radius:14px;-moz-border-radius:14px;border-radius:14px;} +.form-search input,.form-inline input,.form-horizontal input,.form-search textarea,.form-inline textarea,.form-horizontal textarea,.form-search select,.form-inline select,.form-horizontal select,.form-search .help-inline,.form-inline .help-inline,.form-horizontal .help-inline,.form-search .uneditable-input,.form-inline .uneditable-input,.form-horizontal .uneditable-input{display:inline-block;margin-bottom:0;} +.form-search label,.form-inline label,.form-search .input-append,.form-inline .input-append,.form-search .input-prepend,.form-inline .input-prepend{display:inline-block;} +.form-search .input-append .add-on,.form-inline .input-prepend .add-on,.form-search .input-append .add-on,.form-inline .input-prepend .add-on{vertical-align:middle;} +.control-group{margin-bottom:8px;} +.form-horizontal legend+.control-group{margin-top:16px;-webkit-margin-top-collapse:separate;} +.form-horizontal .control-group{margin-bottom:16px;*zoom:1;}.form-horizontal .control-group:before,.form-horizontal .control-group:after{display:table;content:"";} +.form-horizontal .control-group:after{clear:both;} +.form-horizontal .control-group>label{float:left;width:140px;padding-top:5px;text-align:right;} +.form-horizontal .controls{margin-left:160px;} +.form-horizontal .form-actions{padding-left:160px;} +table{max-width:100%;border-collapse:collapse;border-spacing:0;} +.table{width:100%;margin-bottom:16px;}.table th,.table td{padding:8px;line-height:16px;text-align:left;border-top:1px solid #ddd;} +.table th{font-weight:bold;vertical-align:bottom;} +.table td{vertical-align:top;} +.table thead:first-child tr th,.table thead:first-child tr td{border-top:0;} +.table tbody+tbody{border-top:2px solid #ddd;} +.table-condensed th,.table-condensed td{padding:4px 5px;} +.table-bordered{border:1px solid #ddd;border-collapse:separate;*border-collapse:collapsed;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;}.table-bordered th+th,.table-bordered td+td,.table-bordered th+td,.table-bordered td+th{border-left:1px solid #ddd;} +.table-bordered thead:first-child tr:first-child th,.table-bordered tbody:first-child tr:first-child th,.table-bordered tbody:first-child tr:first-child td{border-top:0;} +.table-bordered thead:first-child tr:first-child th:first-child,.table-bordered tbody:first-child tr:first-child td:first-child{-webkit-border-radius:4px 0 0 0;-moz-border-radius:4px 0 0 0;border-radius:4px 0 0 0;} +.table-bordered thead:first-child tr:first-child th:last-child,.table-bordered tbody:first-child tr:first-child td:last-child{-webkit-border-radius:0 4px 0 0;-moz-border-radius:0 4px 0 0;border-radius:0 4px 0 0;} +.table-bordered thead:last-child tr:last-child th:first-child,.table-bordered tbody:last-child tr:last-child td:first-child{-webkit-border-radius:0 0 0 4px;-moz-border-radius:0 0 0 4px;border-radius:0 0 0 4px;} +.table-bordered thead:last-child tr:last-child th:last-child,.table-bordered tbody:last-child tr:last-child td:last-child{-webkit-border-radius:0 0 4px 0;-moz-border-radius:0 0 4px 0;border-radius:0 0 4px 0;} +.table-striped tbody tr:nth-child(odd) td,.table-striped tbody tr:nth-child(odd) th{background-color:#f9f9f9;} +table .span1{float:none;width:44px;margin-left:0;} +table .span2{float:none;width:124px;margin-left:0;} +table .span3{float:none;width:204px;margin-left:0;} +table .span4{float:none;width:284px;margin-left:0;} +table .span5{float:none;width:364px;margin-left:0;} +table .span6{float:none;width:444px;margin-left:0;} +table .span7{float:none;width:524px;margin-left:0;} +table .span8{float:none;width:604px;margin-left:0;} +table .span9{float:none;width:684px;margin-left:0;} +table .span10{float:none;width:764px;margin-left:0;} +table .span11{float:none;width:844px;margin-left:0;} +table .span12{float:none;width:924px;margin-left:0;} .unselectable{user-select:none;-moz-user-select:none;-webkit-user-select:none;} .shadow{-moz-box-shadow:0 3px 30px black;-webkit-box-shadow:0 3px 30px black;} body{background:#ffffff;color:#303030;background-image:url(base_bg.png);background-repeat:repeat-x;background-position:top;margin:10px;} @@ -45,7 +208,7 @@ div.form-row-error-message{width:300px;float:left;color:red;font-weight:bold;padding:3px 0 0 1em;} .form-row .help{color:#666;} select,input,textarea{font:inherit;} -select,textarea,input[type="text"],input[type="file"],input[type="password"]{-webkit-box-sizing:border-box;max-width:300px;} +select,textarea,input[type="text"],input[type="file"],input[type="password"]{max-width:300px;} .errormessagelarge,.warningmessagelarge,.donemessagelarge,.infomessagelarge{padding:10px;padding-left:52px;min-height:32px;border:1px solid #aa6666;background-color:#ffcccc;background-image:url(error_message_icon.png);background-repeat:no-repeat;background-position:10px 10px;} .warningmessagelarge{background-image:url(warn_message_icon.png);border-color:#aaaa66;background-color:#ffffcc;} .donemessagelarge{background-image:url(done_message_icon.png);border-color:#66aa66;background-color:#ccffcc;} diff -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 -r fca74f9562024605dd87a3a6ace02d28a1851f5e static/june_2007_style/blue/panel_layout.css --- a/static/june_2007_style/blue/panel_layout.css +++ b/static/june_2007_style/blue/panel_layout.css @@ -1,340 +1,618 @@ -body { - font: 75% "Lucida Grande", verdana, arial, helvetica, sans-serif; - background: #eeeeee; -} -.unselectable { - user-select: none; - -moz-user-select: none; - -webkit-user-select: none; -} -#background { - position: absolute; - background: #eeeeee; - z-index: -1; - top: 0; - left: 0; - margin: 0; - padding: 0; - width: 100%; - height: 100%; -} -#messagebox { - position: absolute; - top: 33px; - left: 0; - width: 100%; - height: 24px !important; - overflow: hidden; - border-bottom: solid #999 1px; - font-size: 90%; -} -#left, -#left-border, -#center, -#right-border, -#right { - position: absolute; - top: 39px; - bottom: 0px; - overflow: hidden; - background: #fff; -} -#left, -#center, -#right { - border-top: solid #999999 1px; -} -#left-border, -#right-border { - background: #eeeeee; - border-left: solid #999999 1px; - border-right: solid #999999 1px; - padding-right: 1px; - padding-left: 1px; - width: 5px; - z-index: 10000; -} -#left-border div, -#right-border div { - width: 100%; - height: 100%; - background-repeat: no-repeat; - background-position: center center; - position: absolute; - width: 5px; - height: 100%; -} -#left-border div, -#right-border.hidden div { - background-image: url(tiny_arrow_left.png); - cursor: w-resize; -} -#left-border.hidden div, -#right-border div { - background-image: url(tiny_arrow_right.png); - cursor: e-resize; -} -#left-border.hover div, -#right-border.hover div { - background-color: #aaaaee; -} -#left { - left: 0px; - width: 250px; - z-index: 200; -} -#left-border { - left: 250px; -} -#center { - left: 259px; - right: 259px; - overflow: hidden; - z-index: 1; -} -#right-border { - right: 250px; -} -#right { - width: 250px; - right: 0px; - z-index: 200; -} -.unified-panel-header { - height: 2em; - z-index: 1000; - background: #cccccc; - background-image: url(panel_header_bg.png); - background-position: top center; - background-repeat: repeat-x; - border-bottom: solid #999999 1px; - margin: 0; - padding: 0; - padding-right: 10px; - padding-left: 10px; - color: #333; - font-weight: bold; -} -.unified-panel-header-inner { - padding-top: 0.45em; -} -.menu-bg { - background: #c1c9e5 url(menu_bg.png) top repeat-x; -} -div.unified-panel-body { - position: absolute; - top: 2em; - bottom: 0; - width: 100%; - margin-top: 1px; -} -.panel-header-button { - color: #333; - text-decoration: none; - display: inline-block; - cursor: pointer; - margin: -1px; - padding: 1px; - margin-top: -0.2em; - border: solid #999 1px; - padding-right: 0.5em; - padding-left: 0.5em; - -moz-border-radius: 0.5em; - -webkit-border-radius: 0.5em; - border-radius: 0.5em; -} -.panel-header-button.popup { - padding-right: 1.75em; - background: url(../images/dropdownarrow.png) no-repeat right 7px; -} -.panel-header-button:hover { - color: black; - background-color: #ccc; -} -.panel-header-button:active { - color: white; - background-color: #aaaaaa; -} -#overlay { - position: fixed; - top: 0; - left: 0; - width: 100%; - height: 100%; - z-index: 20000; -} -#overlay.modal #overlay-background { - background: rgba(0, 0, 0, 0.5); -} -.dialog-box-container { - position: relative; - margin-top: 80px; - margin-right: auto; - margin-left: auto; -} -.dialog-box-wrapper { - position: relative; - padding: 1em; - background-color: rgba(0, 0, 0, 0.5); - -moz-border-radius: 1em; - -webkit-border-radius: 1em; -} -.dialog-box { - border: solid #999 1px; - background: white; - z-index: 80000; -} -#overlay.modal .dialog-box .body { - min-width: 600px; -} -.dialog-box .body { - padding: 5px; - overflow: auto; - max-height: 500px; - min-width: 300px; -} -.dialog-box .buttons { - padding: 5px; -} -.panel-error-message, -.panel-warning-message, -.panel-done-message, -.panel-info-message { - height: 24px; - line-height: 24px; - color: #303030; - padding: 0px; - padding-left: 26px; - background-color: #ffcccc; - background-image: url(error_small.png); - background-repeat: no-repeat; - background-position: 6px 50%; -} -.panel-warning-message { - background-image: url(warn_small.png); - background-color: #ffffcc; -} -.panel-done-message { - background-image: url(done_small.png); - background-color: #ccffcc; -} -.panel-info-message { - background-image: url(info_small.png); - background-color: #ccccff; -} -#masthead { - position: absolute; - top: 0; - left: 0; - width: 100%; - min-width: 900px; - height: 32px; - background: #2c3143; - color: #fff; - border-bottom: solid #444444 1px; - z-index: 15000; - padding: 0; -} -#masthead a { - color: #eeeeee; - text-decoration: none; -} -#masthead .title { - font-family: verdana; - padding: 3px 10px; - font-size: 175%; - font-weight: bold; - z-index: -1; -} -#masthead a:hover { - text-decoration: underline; -} -.quota-meter-container { - position: absolute; - top: 0; - right: 0; - height: 32px; -} -.quota-meter { - position: absolute; - top: 8px; - right: 8px; - height: 16px; - width: 100px; - background-color: #c1c9e5; -} -.quota-meter-bar { - position: absolute; - top: 0; - left: 0; - height: 16px; - background-color: #969db3; -} -.quota-meter-bar-warn { - background-color: #ffb400; -} -.quota-meter-bar-error { - background-color: #ff4343; -} -.quota-meter-text { - position: absolute; - top: 50%; - left: 0; - width: 100px; - height: 16px; - margin-top: -6px; - text-align: center; - z-index: 9001; - color: #000000; -} -.tab-group { - margin: 0; - padding: 0 10px; - height: 100%; - white-space: nowrap; - cursor: default; - background: transparent; -} -.tab-group .tab { - background: #2c3143; - position: relative; - float: left; - margin: 0; - padding: 0 1em; - height: 32px; - line-height: 32px; - text-align: left; -} -.tab-group .tab .submenu { - display: none; - position: absolute; - z-index: 16000; - left: 0; - top: 32px; - padding: 1em; - margin: -1em; - padding-top: 0; - margin-top: 0; - background-color: rgba(0, 0, 0, 0.5); - -moz-border-radius: 0 0 1em 1em; - -webkit-border-bottom-right-radius: 1em; - -webkit-border-bottom-left-radius: 1em; -} -.tab-group .tab .submenu ul { - display: block; - margin: 0; - padding: 0; - list-style-type: none; - background: #2c3143; -} -.tab-group .tab .submenu ul li { - display: block; - padding: 0 1em; - white-space: nowrap; -} -.tab-group .tab:hover > a { - color: gold !important; -} -.tab-group .active { - background: #010101; -} +article,aside,details,figcaption,figure,footer,header,hgroup,nav,section{display:block;} +audio,canvas,video{display:inline-block;*display:inline;*zoom:1;} +audio:not([controls]){display:none;} +html{font-size:100%;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%;} +a:focus{outline:thin dotted;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;} +a:hover,a:active{outline:0;} +sub,sup{position:relative;font-size:75%;line-height:0;vertical-align:baseline;} +sup{top:-0.5em;} +sub{bottom:-0.25em;} +img{max-width:100%;height:auto;border:0;-ms-interpolation-mode:bicubic;} +button,input,select,textarea{margin:0;font-size:100%;vertical-align:middle;} +button,input{*overflow:visible;line-height:normal;} +button::-moz-focus-inner,input::-moz-focus-inner{padding:0;border:0;} 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+.btn-navbar:active,.btn-navbar.active{background-color:#181a24 \9;} +.btn-navbar .icon-bar{display:block;width:18px;height:2px;background-color:#f5f5f5;-webkit-border-radius:1px;-moz-border-radius:1px;border-radius:1px;-webkit-box-shadow:0 1px 0 rgba(0, 0, 0, 0.25);-moz-box-shadow:0 1px 0 rgba(0, 0, 0, 0.25);box-shadow:0 1px 0 rgba(0, 0, 0, 0.25);} +.btn-navbar .icon-bar+.icon-bar{margin-top:3px;} +.nav-collapse.collapse{height:auto;} +.navbar .brand:hover{text-decoration:none;} +.navbar .brand{float:left;display:block;padding:8px 20px 12px;margin-left:-20px;font-size:20px;font-weight:200;line-height:1;color:#ffffff;} +.navbar .navbar-text{margin-bottom:0;line-height:40px;color:#999999;}.navbar .navbar-text a:hover{color:#ffffff;background-color:transparent;} +.navbar .btn,.navbar .btn-group{margin-top:5px;} +.navbar .btn-group .btn{margin-top:0;} +.navbar-form{margin-bottom:0;*zoom:1;}.navbar-form:before,.navbar-form:after{display:table;content:"";} +.navbar-form:after{clear:both;} 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11px;line-height:19px;color:#999999;text-decoration:none;text-shadow:0 -1px 0 rgba(0, 0, 0, 0.25);} +.navbar .nav>li>a:hover{background-color:transparent;color:#ffffff;text-decoration:none;} +.navbar .nav .active>a,.navbar .nav .active>a:hover{color:#ffffff;text-decoration:none;background-color:#2c3143;background-color:rgba(0, 0, 0, 0.5);} +.navbar .divider-vertical{height:32px;width:1px;margin:0 9px;overflow:hidden;background-color:#2c3143;border-right:1px solid #333333;} +.navbar .nav.pull-right{margin-left:10px;margin-right:0;} +.navbar .dropdown-menu{margin-top:1px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;}.navbar .dropdown-menu:before{content:'';display:inline-block;border-left:7px solid transparent;border-right:7px solid transparent;border-bottom:7px solid #ccc;border-bottom-color:rgba(0, 0, 0, 0.2);position:absolute;top:-7px;left:9px;} +.navbar .dropdown-menu:after{content:'';display:inline-block;border-left:6px solid transparent;border-right:6px solid transparent;border-bottom:6px solid #ffffff;position:absolute;top:-6px;left:10px;} +.navbar .nav .dropdown-toggle .caret,.navbar .nav .open.dropdown .caret{border-top-color:#ffffff;} +.navbar .nav .active .caret{opacity:1;filter:alpha(opacity=100);} +.navbar .nav .open>.dropdown-toggle,.navbar .nav .active>.dropdown-toggle,.navbar .nav .open.active>.dropdown-toggle{background-color:transparent;} +.navbar .nav .active>.dropdown-toggle:hover{color:#ffffff;} +.navbar .nav.pull-right .dropdown-menu{left:auto;right:0;}.navbar .nav.pull-right .dropdown-menu:before{left:auto;right:12px;} +.navbar .nav.pull-right .dropdown-menu:after{left:auto;right:13px;} +.breadcrumb{padding:7px 14px;margin:0 0 16px;background-color:#fbfbfb;background-image:-moz-linear-gradient(top, #ffffff, #f5f5f5);background-image:-ms-linear-gradient(top, #ffffff, #f5f5f5);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#f5f5f5));background-image:-webkit-linear-gradient(top, #ffffff, 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a{float:left;padding:0 14px;line-height:30px;text-decoration:none;border:1px solid #ddd;border-left-width:0;} +.pagination a:hover,.pagination .active a{background-color:#f5f5f5;} +.pagination .active a{color:#999999;cursor:default;} +.pagination .disabled a,.pagination .disabled a:hover{color:#999999;background-color:transparent;cursor:default;} +.pagination li:first-child a{border-left-width:1px;-webkit-border-radius:3px 0 0 3px;-moz-border-radius:3px 0 0 3px;border-radius:3px 0 0 3px;} +.pagination li:last-child a{-webkit-border-radius:0 3px 3px 0;-moz-border-radius:0 3px 3px 0;border-radius:0 3px 3px 0;} +.pagination-centered{text-align:center;} +.pagination-right{text-align:right;} +.pager{margin-left:0;margin-bottom:16px;list-style:none;text-align:center;*zoom:1;}.pager:before,.pager:after{display:table;content:"";} +.pager:after{clear:both;} +.pager li{display:inline;} +.pager a{display:inline-block;padding:5px 14px;background-color:#fff;border:1px solid #ddd;-webkit-border-radius:15px;-moz-border-radius:15px;border-radius:15px;} +.pager a:hover{text-decoration:none;background-color:#f5f5f5;} +.pager .next a{float:right;} +.pager .previous a{float:left;} +.modal-open .dropdown-menu{z-index:2050;} +.modal-open .dropdown.open{*z-index:2050;} +.modal-open .popover{z-index:2060;} +.modal-open .tooltip{z-index:2070;} +.modal-backdrop{position:fixed;top:0;right:0;bottom:0;left:0;z-index:1040;background-color:#000000;}.modal-backdrop.fade{opacity:0;} +.modal-backdrop,.modal-backdrop.fade.in{opacity:0.8;filter:alpha(opacity=80);} +.modal{position:fixed;top:50%;left:50%;z-index:1050;max-height:500px;overflow:auto;width:560px;margin:-250px 0 0 -280px;background-color:#ffffff;border:1px solid #999;border:1px solid rgba(0, 0, 0, 0.3);*border:1px solid #999;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-moz-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);box-shadow:0 3px 7px rgba(0, 0, 0, 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.btn{float:right;margin-left:5px;margin-bottom:0;} +.tooltip{position:absolute;z-index:1020;display:block;visibility:visible;padding:5px;font-size:11px;opacity:0;filter:alpha(opacity=0);}.tooltip.in{opacity:0.8;filter:alpha(opacity=80);} +.tooltip.top{margin-top:-2px;} +.tooltip.right{margin-left:2px;} +.tooltip.bottom{margin-top:2px;} +.tooltip.left{margin-left:-2px;} +.tooltip.top .tooltip-arrow{bottom:0;left:50%;margin-left:-5px;border-left:5px solid transparent;border-right:5px solid transparent;border-top:5px solid #000000;} +.tooltip.left .tooltip-arrow{top:50%;right:0;margin-top:-5px;border-top:5px solid transparent;border-bottom:5px solid transparent;border-left:5px solid #000000;} +.tooltip.bottom .tooltip-arrow{top:0;left:50%;margin-left:-5px;border-left:5px solid transparent;border-right:5px solid transparent;border-bottom:5px solid #000000;} +.tooltip.right .tooltip-arrow{top:50%;left:0;margin-top:-5px;border-top:5px solid transparent;border-bottom:5px solid 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2px;font-size:9px;font-weight:bold;color:#ffffff;text-transform:uppercase;background-color:#999999;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;} +.label-important{background-color:#b94a48;} +.label-warning{background-color:#f89406;} +.label-success{background-color:#468847;} +.label-info{background-color:#3a87ad;} +@-webkit-keyframes progress-bar-stripes{from{background-position:0 0;} to{background-position:40px 0;}}@-moz-keyframes progress-bar-stripes{from{background-position:0 0;} to{background-position:40px 0;}}@keyframes progress-bar-stripes{from{background-position:0 0;} to{background-position:40px 0;}}.progress{overflow:hidden;height:18px;margin-bottom:18px;background-color:#f7f7f7;background-image:-moz-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-ms-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f5f5f5), to(#f9f9f9));background-image:-webkit-linear-gradient(top, #f5f5f5, 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#149bdf, #0480be);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#149bdf', endColorstr='#0480be', GradientType=0);-webkit-box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);-moz-box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;-webkit-transition:width 0.6s ease;-moz-transition:width 0.6s ease;-ms-transition:width 0.6s ease;-o-transition:width 0.6s ease;transition:width 0.6s ease;} +.progress-striped .bar{background-color:#62c462;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);-webkit-background-size:40px 40px;-moz-background-size:40px 40px;-o-background-size:40px 40px;background-size:40px 40px;} +.progress.active .bar{-webkit-animation:progress-bar-stripes 2s linear infinite;-moz-animation:progress-bar-stripes 2s linear infinite;animation:progress-bar-stripes 2s linear infinite;} +.progress-danger .bar{background-color:#dd514c;background-image:-moz-linear-gradient(top, #ee5f5b, #c43c35);background-image:-ms-linear-gradient(top, #ee5f5b, #c43c35);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#c43c35));background-image:-webkit-linear-gradient(top, #ee5f5b, #c43c35);background-image:-o-linear-gradient(top, #ee5f5b, #c43c35);background-image:linear-gradient(top, #ee5f5b, #c43c35);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ee5f5b', endColorstr='#c43c35', GradientType=0);} +.progress-danger.progress-striped .bar{background-color:#ee5f5b;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} +.progress-success .bar{background-color:#5eb95e;background-image:-moz-linear-gradient(top, #62c462, #57a957);background-image:-ms-linear-gradient(top, #62c462, #57a957);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#62c462), to(#57a957));background-image:-webkit-linear-gradient(top, #62c462, #57a957);background-image:-o-linear-gradient(top, #62c462, #57a957);background-image:linear-gradient(top, #62c462, #57a957);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#62c462', endColorstr='#57a957', GradientType=0);} +.progress-success.progress-striped .bar{background-color:#62c462;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} +.progress-info .bar{background-color:#4bb1cf;background-image:-moz-linear-gradient(top, #5bc0de, #339bb9);background-image:-ms-linear-gradient(top, #5bc0de, #339bb9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#5bc0de), to(#339bb9));background-image:-webkit-linear-gradient(top, #5bc0de, #339bb9);background-image:-o-linear-gradient(top, #5bc0de, #339bb9);background-image:linear-gradient(top, #5bc0de, #339bb9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#5bc0de', endColorstr='#339bb9', GradientType=0);} +.progress-info.progress-striped .bar{background-color:#5bc0de;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} +.accordion{margin-bottom:16px;} +.accordion-group{margin-bottom:2px;border:1px solid #e5e5e5;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;} +.accordion-heading{border-bottom:0;} +.accordion-heading .accordion-toggle{display:block;padding:8px 15px;} +.accordion-inner{padding:9px 15px;border-top:1px solid #e5e5e5;} +.carousel{position:relative;margin-bottom:16px;line-height:1;} +.carousel-inner{overflow:hidden;width:100%;position:relative;} +.carousel .item{display:none;position:relative;-webkit-transition:0.6s ease-in-out left;-moz-transition:0.6s ease-in-out left;-ms-transition:0.6s ease-in-out left;-o-transition:0.6s ease-in-out left;transition:0.6s ease-in-out left;} +.carousel .item>img{display:block;line-height:1;} +.carousel .active,.carousel .next,.carousel .prev{display:block;} +.carousel .active{left:0;} +.carousel .next,.carousel .prev{position:absolute;top:0;width:100%;} +.carousel .next{left:100%;} +.carousel .prev{left:-100%;} +.carousel .next.left,.carousel .prev.right{left:0;} +.carousel .active.left{left:-100%;} +.carousel .active.right{left:100%;} +.carousel-control{position:absolute;top:40%;left:15px;width:40px;height:40px;margin-top:-20px;font-size:60px;font-weight:100;line-height:30px;color:#ffffff;text-align:center;background:#222222;border:3px solid #ffffff;-webkit-border-radius:23px;-moz-border-radius:23px;border-radius:23px;opacity:0.5;filter:alpha(opacity=50);}.carousel-control.right{left:auto;right:15px;} +.carousel-control:hover{color:#ffffff;text-decoration:none;opacity:0.9;filter:alpha(opacity=90);} +.carousel-caption{position:absolute;left:0;right:0;bottom:0;padding:10px 15px 5px;background:#333333;background:rgba(0, 0, 0, 0.75);} +.carousel-caption h4,.carousel-caption p{color:#ffffff;} +.hero-unit{padding:60px;margin-bottom:30px;background-color:#f5f5f5;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;}.hero-unit h1{margin-bottom:0;font-size:60px;line-height:1;letter-spacing:-1px;} +.hero-unit p{font-size:18px;font-weight:200;line-height:24px;} +.pull-right{float:right;} +.pull-left{float:left;} +.hide{display:none;} +.show{display:block;} +.invisible{visibility:hidden;} +body{background:#eeeeee;} +.unselectable{user-select:none;-moz-user-select:none;-webkit-user-select:none;} +#background{position:absolute;background:#eeeeee;z-index:-1;top:0;left:0;margin:0;padding:0;width:100%;height:100%;} +#messagebox{position:absolute;top:33px;left:0;width:100%;height:24px !important;overflow:hidden;border-bottom:solid #999 1px;font-size:90%;} +#left,#left-border,#center,#right-border,#right{position:absolute;top:39px;bottom:0px;overflow:hidden;background:#fff;} +#left,#center,#right{border-top:solid #999999 1px;} +#left-border,#right-border{background:#eeeeee;border-left:solid #999999 1px;border-right:solid #999999 1px;padding-right:1px;padding-left:1px;width:5px;z-index:10000;} +#left-border div,#right-border div{width:100%;height:100%;background-repeat:no-repeat;background-position:center center;position:absolute;width:5px;height:100%;} +#left-border div,#right-border.hidden div{background-image:url(tiny_arrow_left.png);cursor:w-resize;} +#left-border.hidden div,#right-border div{background-image:url(tiny_arrow_right.png);cursor:e-resize;} +#left-border.hover div,#right-border.hover div{background-color:#aaaaee;} +#left{left:0px;width:250px;z-index:200;} +#left-border{left:250px;} +#center{left:259px;right:259px;overflow:hidden;z-index:1;} +#right-border{right:250px;} +#right{width:250px;right:0px;z-index:200;} +.unified-panel-header{height:2em;z-index:1000;background:#cccccc;background-image:url(panel_header_bg.png);background-position:top center;background-repeat:repeat-x;border-bottom:solid #999999 1px;margin:0;padding:0;padding-right:10px;padding-left:10px;color:#333;font-weight:bold;} +.unified-panel-header-inner{padding-top:0.45em;} +.menu-bg{background:#c1c9e5 url(menu_bg.png) top repeat-x;} +div.unified-panel-body{position:absolute;top:2em;bottom:0;width:100%;margin-top:1px;} +.panel-header-button{color:#333;text-decoration:none;display:inline-block;cursor:pointer;margin:-1px;padding:1px;margin-top:-0.2em;border:solid #999 1px;padding-right:0.5em;padding-left:0.5em;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;} +.panel-header-button.popup{padding-right:1.75em;background:url(../images/dropdownarrow.png) no-repeat right 7px;} +.panel-header-button:hover{color:black;background-color:#ccc;} +.panel-header-button:active{color:white;background-color:#aaaaaa;} +#overlay{position:fixed;top:0;left:0;width:100%;height:100%;z-index:20000;} +#overlay.modal #overlay-background{background:rgba(0, 0, 0, 0.5);} +.dialog-box-container{position:relative;margin-top:80px;margin-right:auto;margin-left:auto;} +.dialog-box-wrapper{position:relative;padding:1em;background-color:rgba(0, 0, 0, 0.5);-moz-border-radius:1em;-webkit-border-radius:1em;} +.dialog-box{border:solid #999 1px;background:white;z-index:80000;} +#overlay.modal .dialog-box .body{min-width:600px;} +.dialog-box .body{padding:5px;overflow:auto;max-height:500px;min-width:300px;} +.dialog-box .buttons{padding:5px;} +.panel-error-message,.panel-warning-message,.panel-done-message,.panel-info-message{height:24px;line-height:24px;color:#303030;padding:0px;padding-left:26px;background-color:#ffcccc;background-image:url(error_small.png);background-repeat:no-repeat;background-position:6px 50%;} +.panel-warning-message{background-image:url(warn_small.png);background-color:#ffffcc;} +.panel-done-message{background-image:url(done_small.png);background-color:#ccffcc;} +.panel-info-message{background-image:url(info_small.png);background-color:#ccccff;} +#masthead{-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;overflow:visible;margin-bottom:16px;position:absolute;top:0;left:0;width:100%;min-width:900px;height:32px;border-bottom:solid #444444 1px;z-index:15000;padding:0;}#masthead .brand:hover{text-decoration:none;} +#masthead .brand{float:left;display:block;padding:8px 20px 12px;margin-left:-20px;font-size:20px;font-weight:200;line-height:1;color:#ffffff;} +#masthead .navbar-text{margin-bottom:0;line-height:40px;color:#999999;}#masthead .navbar-text a:hover{color:#ffffff;background-color:transparent;} +#masthead .btn,#masthead .btn-group{margin-top:5px;} +#masthead .btn-group .btn{margin-top:0;} +#masthead a{color:#eeeeee;text-decoration:none;} +#masthead .title{float:left;display:block;padding:8px 20px 12px;margin-left:-20px;font-size:20px;font-weight:200;line-height:1;color:#ffffff;font-family:verdana;z-index:2000;} +#masthead .masthead-inner{padding-left:20px;padding-right:20px;background-color:#303239;background-image:-moz-linear-gradient(top, #333333, #2c3143);background-image:-ms-linear-gradient(top, #333333, #2c3143);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#333333), to(#2c3143));background-image:-webkit-linear-gradient(top, #333333, #2c3143);background-image:-o-linear-gradient(top, #333333, #2c3143);background-image:linear-gradient(top, #333333, #2c3143);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#333333', endColorstr='#2c3143', GradientType=0);-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:0 1px 3px rgba(0, 0, 0, 0.25),inset 0 -1px 0 rgba(0, 0, 0, 0.1);-moz-box-shadow:0 1px 3px rgba(0, 0, 0, 0.25),inset 0 -1px 0 rgba(0, 0, 0, 0.1);box-shadow:0 1px 3px rgba(0, 0, 0, 0.25),inset 0 -1px 0 rgba(0, 0, 0, 0.1);height:32px;} +#masthead .tab-group{margin:0;padding:0 10px;height:100%;white-space:nowrap;cursor:default;background:transparent;}#masthead .tab-group .tab{position:relative;float:left;margin:0;padding:0 1em;height:32px;line-height:32px;text-align:left;}#masthead .tab-group .tab .submenu{display:none;position:absolute;z-index:16000;left:0;top:32px;padding:1em;margin:-1em;padding-top:0;margin-top:0;background-color:rgba(0, 0, 0, 0.5);-moz-border-radius:0 0 1em 1em;-webkit-border-bottom-right-radius:1em;-webkit-border-bottom-left-radius:1em;}#masthead .tab-group .tab .submenu ul{display:block;margin:0;padding:0;list-style-type:none;background:#2c3143;}#masthead .tab-group .tab .submenu ul li{display:block;padding:0 1em;white-space:nowrap;} +#masthead .tab-group .tab:hover>a{color:gold !important;} +#masthead .tab-group .active{background:#010101;} +#masthead a:hover{text-decoration:underline;} +.quota-meter-container{position:absolute;top:0;right:0;height:32px;} +.quota-meter{position:absolute;top:8px;right:8px;height:16px;width:100px;background-color:#c1c9e5;} +.quota-meter-bar{position:absolute;top:0;left:0;height:16px;background-color:#969db3;} +.quota-meter-bar-warn{background-color:#ffb400;} +.quota-meter-bar-error{background-color:#ff4343;} +.quota-meter-text{position:absolute;top:50%;left:0;width:100px;height:16px;margin-top:-6px;text-align:center;z-index:9001;color:#000000;} diff -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 -r fca74f9562024605dd87a3a6ace02d28a1851f5e static/june_2007_style/galaxy_bootstrap.less --- /dev/null +++ b/static/june_2007_style/galaxy_bootstrap.less @@ -0,0 +1,146 @@ +// Variables.less +// Variables to customize the look and feel of Bootstrap +// ----------------------------------------------------- + +// GLOBAL VALUES +// -------------------------------------------------- + +// Links +@linkColor: #08c; +@linkColorHover: darken(@linkColor, 15%); + +// Grays +@black: #000; +@grayDarker: #222; +@grayDark: #333; +@gray: #555; +@grayLight: #999; +@grayLighter: #eee; +@white: #fff; + +// Accent colors +@blue: #049cdb; +@blueDark: #0064cd; +@green: #46a546; +@red: #9d261d; +@yellow: #ffc40d; +@orange: #f89406; +@pink: #c3325f; +@purple: #7a43b6; + +// Typography +@baseFontSize: 12px; +@baseFontFamily: "Lucida Grande",verdana,arial,helvetica,sans-serif; +@baseLineHeight: 16px; +@textColor: @grayDark; + +// Buttons +@primaryButtonBackground: @linkColor; + + + +// COMPONENT VARIABLES +// -------------------------------------------------- + +// Z-index master list +// Used for a bird's eye view of components dependent on the z-axis +// Try to avoid customizing these :) +@zindexDropdown: 1000; +@zindexPopover: 1010; +@zindexTooltip: 1020; +@zindexFixedNavbar: 1030; +@zindexModalBackdrop: 1040; +@zindexModal: 1050; + +// Input placeholder text color +@placeholderText: @grayLight; + +// Navbar +@navbarHeight: 32px; +@navbarBackground: @masthead_bg; +@navbarBackgroundHighlight: @grayDark; + +@navbarText: @grayLight; +@navbarLinkColor: @grayLight; +@navbarLinkColorHover: @white; + +// Form states and alerts +@warningText: #c09853; +@warningBackground: #fcf8e3; +@warningBorder: darken(spin(@warningBackground, -10), 3%); + +@errorText: #b94a48; +@errorBackground: #f2dede; +@errorBorder: darken(spin(@errorBackground, -10), 3%); + +@successText: #468847; +@successBackground: #dff0d8; +@successBorder: darken(spin(@successBackground, -10), 5%); + +@infoText: #3a87ad; +@infoBackground: #d9edf7; +@infoBorder: darken(spin(@infoBackground, -10), 7%); + + + +// GRID +// -------------------------------------------------- + +// Default 940px grid +@gridColumns: 12; +@gridColumnWidth: 60px; +@gridGutterWidth: 20px; +@gridRowWidth: (@gridColumns * @gridColumnWidth) + (@gridGutterWidth * (@gridColumns - 1)); + +// Fluid grid +@fluidGridColumnWidth: 6.382978723%; +@fluidGridGutterWidth: 2.127659574%; + +// ---- Imports ---- + +@import "bootstrap/reset.less"; +@import "bootstrap/mixins.less"; + +// Grid system and page structure +@import "bootstrap/scaffolding.less"; + +// Base CSS +@import "bootstrap/type.less"; +@import "bootstrap/code.less"; +@import "bootstrap/forms.less"; +@import "bootstrap/tables.less"; + +// Components: common +@import "bootstrap/sprites.less"; +@import "bootstrap/dropdowns.less"; +@import "bootstrap/wells.less"; +@import "bootstrap/component-animations.less"; +@import "bootstrap/close.less"; + +// Components: Buttons & Alerts +@import "bootstrap/buttons.less"; +@import "bootstrap/button-groups.less"; +@import "bootstrap/alerts.less"; // Note: alerts share common CSS with buttons and thus have styles in buttons.less + +// Components: Nav +@import "bootstrap/navs.less"; +@import "bootstrap/navbar.less"; +@import "bootstrap/breadcrumbs.less"; +@import "bootstrap/pagination.less"; +@import "bootstrap/pager.less"; + +// Components: Popovers +@import "bootstrap/modals.less"; +@import "bootstrap/tooltip.less"; +@import "bootstrap/popovers.less"; + +// Components: Misc +@import "bootstrap/thumbnails.less"; +@import "bootstrap/labels.less"; +@import "bootstrap/progress-bars.less"; +@import "bootstrap/accordion.less"; +@import "bootstrap/carousel.less"; +@import "bootstrap/hero-unit.less"; + +// Utility classes +@import "bootstrap/utilities.less"; \ No newline at end of file diff -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 -r fca74f9562024605dd87a3a6ace02d28a1851f5e static/june_2007_style/make_style.py --- a/static/june_2007_style/make_style.py +++ b/static/june_2007_style/make_style.py @@ -18,16 +18,6 @@ def run( cmd ): return Popen( cmd, stdout=PIPE).communicate()[0] -templates = [ ( "base.css.tmpl", "base.css" ), - ( "panel_layout.css.tmpl", "panel_layout.css" ), - ( "masthead.css.tmpl", "masthead.css" ), - ( "library.css.tmpl", "library.css" ), - ( "history.css.tmpl", "history.css" ), - ( "tool_menu.css.tmpl", "tool_menu.css" ), - ( "iphone.css.tmpl", "iphone.css" ), - ( "autocomplete_tagging.css.tmpl", "autocomplete_tagging.css" ), - ( "trackster.css.tmpl", "trackster.css" ) ] - # TODO: Are these images still being used? If not, clean this code up! images = [ ( "./gradient.py 9 30 $panel_header_bg_top - $panel_header_bg_bottom 0 0 $panel_header_bg_bottom 1 1", "panel_header_bg.png" ), @@ -62,6 +52,10 @@ ] if __name__ == "__main__": + print "This script is no longer used for generating stylesheets. Please use the Makefile instead" + + # Old code for processing stylesheets + """ if len(sys.argv) > 1: # has params ini_file, out_dir = sys.argv[1:] else: @@ -71,8 +65,9 @@ for in_file, out_file in templates: print in_file ,"->", out_file subprocess.call( "./process_css.py %s shared_images:../images %s < %s > %s" % ( ini_file, out_dir, in_file, os.path.join( out_dir, out_file ) ), shell=True ) - + """ +# Old code for processing images, long disabled, though images are still used. """ for rule, output in images: t = string.Template( rule ).substitute( context ) diff -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 -r fca74f9562024605dd87a3a6ace02d28a1851f5e static/june_2007_style/panel_layout.css.tmpl --- a/static/june_2007_style/panel_layout.css.tmpl +++ /dev/null @@ -1,383 +0,0 @@ -body { - font: 75% "Lucida Grande",verdana,arial,helvetica,sans-serif; - background: ${layout_bg}; -} - -.unselectable { - user-select: none; - -moz-user-select: none; - -webkit-user-select: none; -} - -#background { - position: absolute; - background: ${layout_bg}; - z-index: -1; - top: 0; - left: 0; - margin: 0; - padding: 0; - width: 100%; - height: 100%; -} - -#messagebox { - position:absolute; - top:33px; - left:0; - width:100%; - height:24px !important; - overflow: hidden; - border-bottom: solid #999 1px; - font-size: 90%; -} - -#left, #left-border, #center, #right-border, #right { - position: absolute; - top: 39px; - bottom: 0px; - overflow: hidden; - background: #fff; -} -#left, #center, #right { - border-top: solid ${layout_border} 1px; -} -#left-border, #right-border { - background: #eeeeee; - border-left: solid ${layout_border} 1px; - border-right: solid ${layout_border} 1px; - padding-right: 1px; - padding-left: 1px; - width: 5px; - z-index: 10000; } -#left-border div, #right-border div { - width: 100%; - height: 100%; - background-repeat: no-repeat; - background-position: center center; - position: absolute; - width: 5px; - height: 100%; -} -#left-border div, #right-border.hidden div { - background-image: url(tiny_arrow_left.png); - cursor: w-resize; -} -#left-border.hidden div, #right-border div { - background-image: url(tiny_arrow_right.png); - cursor: e-resize; -} -#left-border.hover div, #right-border.hover div { - background-color: ${layout_hover}; -} -#left { - left: 0px; - width: 250px; - z-index: 200; -} -#left-border { - left: 250px; -} -#center { - left:259px; - right: 259px; - overflow: hidden; - z-index: 1; -} -#right-border { - right: 250px; -} -#right { - width: 250px; - right: 0px; - z-index: 200; -} - -.unified-panel-header { - height: 2em; - z-index: 1000; - background: ${panel_header_bg_bottom}; - background-image: url(panel_header_bg.png); - background-position: top center; - background-repeat: repeat-x; - border-bottom: solid ${layout_border} 1px; - margin: 0; - padding: 0; - padding-right: 10px; - padding-left: 10px; - color: #333; - font-weight: bold; -} - -.unified-panel-header-inner { - padding-top: 0.45em; -} - -.menu-bg { - background: $menu_bg_over url(menu_bg.png) top repeat-x; -} - -div.unified-panel-body { - position: absolute; - top: 2em; - bottom: 0; - width: 100%; - margin-top: 1px; -} - -.panel-header-button { - color: #333; - text-decoration: none; - display: inline-block; - cursor: pointer; - margin: -1px; padding: 1px; - margin-top: -0.2em; - border: solid #999 1px; - padding-right: 0.5em; - padding-left: 0.5em; - -moz-border-radius: 0.5em; - -webkit-border-radius: 0.5em; - border-radius: 0.5em; -} - -.panel-header-button.popup { - padding-right: 1.75em; - background: url(../images/dropdownarrow.png) no-repeat right 7px; -} - -.panel-header-button:hover { - color: black; - background-color: #ccc; -} - -.panel-header-button:active { - color: white; - background-color: #aaaaaa; -} - -#overlay { - position: fixed; - top: 0; left: 0; width: 100%; height: 100%; - z-index: 20000; -} - -#overlay.modal #overlay-background { - background: rgba(0,0,0,0.5); -} - -.dialog-box-container { - position: relative; - margin-top: 80px; - margin-right: auto; - margin-left: auto; -} - -.dialog-box-wrapper { - position: relative; - padding: 1em; - background-color: rgba(0,0,0,0.5); - -moz-border-radius: 1em; - -webkit-border-radius: 1em; -} - -.dialog-box { - border: solid #999 1px; - background: white; - z-index: 80000; -} - -#overlay.modal .dialog-box .body { - min-width: 600px; -} - -.dialog-box .body { - padding: 5px; - overflow: auto; - max-height: 500px; - min-width: 300px; -} - -.dialog-box .buttons { - padding: 5px; -} - -## Messages for message box, slightly different style - -.panel-error-message, .panel-warning-message, .panel-done-message, .panel-info-message -{ - height: 24px; - line-height: 24px; - color: $base_text; - padding: 0px; - padding-left: 26px; - background-color: $error_message_bg; - background-image: url(error_small.png); - background-repeat: no-repeat; - background-position: 6px 50%; -} - -.panel-warning-message -{ - background-image: url(warn_small.png); - background-color: $warn_message_bg; -} - -.panel-done-message -{ - background-image: url(done_small.png); - background-color: $done_message_bg; -} - -.panel-info-message -{ - background-image: url(info_small.png); - background-color: $info_message_bg; -} - -## Masthead - -#masthead { - position:absolute; - top:0; - left:0; - width:100%; - min-width:900px; - height:32px; - background: ${masthead_bg}; - color:#fff; - border-bottom: solid ${layout_masthead_border} 1px; - z-index: 15000; - padding: 0; - - a { - color: ${masthead_link}; - text-decoration: none; - } - - .title { - font-family: verdana; - padding: 3px 10px; - font-size: 175%; - font-weight: bold; - z-index: -1; - } -} - -#masthead a:hover { - text-decoration: underline; -} - -.quota-meter-container -{ - position: absolute; - top: 0; - right: 0; - height: 32px; -} - -.quota-meter -{ - position: absolute; - top: 8px; - right: 8px; - height: 16px; - width: 100px; - background-color: $quota_meter_bg; -} - -.quota-meter-bar -{ - position: absolute; - top: 0; - left: 0; - height: 16px; - background-color: $quota_meter_bar; -} - -.quota-meter-bar-warn -{ - background-color: $quota_meter_warn_bar; -} - -.quota-meter-bar-error -{ - background-color: $quota_meter_error_bar; -} - -.quota-meter-text -{ - position: absolute; - top: 50%; - left: 0; - width: 100px; - height: 16px; - margin-top: -6px; - text-align: center; - z-index: 9001; - color: $quota_meter_text; -} - -## Tabs - -.tab-group { - - margin: 0; - padding: 0 10px; - height: 100%; - white-space: nowrap; - cursor: default; - background: transparent; - - .tab { - - background: ${masthead_bg}; - position: relative; - float: left; - margin: 0; - padding: 0 1em; - height: 32px; - line-height: 32px; - text-align: left; - - .submenu { - - display: none; - position: absolute; - z-index: 16000; - left: 0; - top: 32px; - padding: 1em; - margin: -1em; - padding-top: 0; - margin-top: 0; - background-color: rgba(0,0,0,0.5); - -moz-border-radius: 0 0 1em 1em; - -webkit-border-bottom-right-radius: 1em; - -webkit-border-bottom-left-radius: 1em; - - ul { - - display: block; - margin: 0; - padding: 0; - list-style-type: none; - background: ${masthead_bg}; - - li { - - display: block; - padding: 0 1em; - white-space: nowrap; - } - } - } - } - - .tab:hover > a { - color: gold !important; - } - - .active { - background: rgb(1,1,1); - } -} diff -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 -r fca74f9562024605dd87a3a6ace02d28a1851f5e static/june_2007_style/panel_layout.less --- /dev/null +++ b/static/june_2007_style/panel_layout.less @@ -0,0 +1,395 @@ +@import "variables"; + +@import "galaxy_bootstrap.less"; + +body { + // font: 75% "Lucida Grande",verdana,arial,helvetica,sans-serif; + background: @layout_bg; +} + +.unselectable { + user-select: none; + -moz-user-select: none; + -webkit-user-select: none; +} + +#background { + position: absolute; + background: @layout_bg; + z-index: -1; + top: 0; + left: 0; + margin: 0; + padding: 0; + width: 100%; + height: 100%; +} + +#messagebox { + position:absolute; + top:33px; + left:0; + width:100%; + height:24px !important; + overflow: hidden; + border-bottom: solid #999 1px; + font-size: 90%; +} + +#left, #left-border, #center, #right-border, #right { + position: absolute; + top: 39px; + bottom: 0px; + overflow: hidden; + background: #fff; +} +#left, #center, #right { + border-top: solid @layout_border 1px; +} +#left-border, #right-border { + background: #eeeeee; + border-left: solid @layout_border 1px; + border-right: solid @layout_border 1px; + padding-right: 1px; + padding-left: 1px; + width: 5px; + z-index: 10000; } +#left-border div, #right-border div { + width: 100%; + height: 100%; + background-repeat: no-repeat; + background-position: center center; + position: absolute; + width: 5px; + height: 100%; +} +#left-border div, #right-border.hidden div { + background-image: url(tiny_arrow_left.png); + cursor: w-resize; +} +#left-border.hidden div, #right-border div { + background-image: url(tiny_arrow_right.png); + cursor: e-resize; +} +#left-border.hover div, #right-border.hover div { + background-color: @layout_hover; +} +#left { + left: 0px; + width: 250px; + z-index: 200; +} +#left-border { + left: 250px; +} +#center { + left:259px; + right: 259px; + overflow: hidden; + z-index: 1; +} +#right-border { + right: 250px; +} +#right { + width: 250px; + right: 0px; + z-index: 200; +} + +.unified-panel-header { + height: 2em; + z-index: 1000; + background: @panel_header_bg_bottom; + background-image: url(panel_header_bg.png); + background-position: top center; + background-repeat: repeat-x; + border-bottom: solid @layout_border 1px; + margin: 0; + padding: 0; + padding-right: 10px; + padding-left: 10px; + color: #333; + font-weight: bold; +} + +.unified-panel-header-inner { + padding-top: 0.45em; +} + +.menu-bg { + background: @menu_bg_over url(menu_bg.png) top repeat-x; +} + +div.unified-panel-body { + position: absolute; + top: 2em; + bottom: 0; + width: 100%; + margin-top: 1px; +} + +.panel-header-button { + color: #333; + text-decoration: none; + display: inline-block; + cursor: pointer; + margin: -1px; padding: 1px; + margin-top: -0.2em; + border: solid #999 1px; + padding-right: 0.5em; + padding-left: 0.5em; + -moz-border-radius: 0.5em; + -webkit-border-radius: 0.5em; + border-radius: 0.5em; +} + +.panel-header-button.popup { + padding-right: 1.75em; + background: url(../images/dropdownarrow.png) no-repeat right 7px; +} + +.panel-header-button:hover { + color: black; + background-color: #ccc; +} + +.panel-header-button:active { + color: white; + background-color: #aaaaaa; +} + +#overlay { + position: fixed; + top: 0; left: 0; width: 100%; height: 100%; + z-index: 20000; +} + +#overlay.modal #overlay-background { + background: rgba(0,0,0,0.5); +} + +.dialog-box-container { + position: relative; + margin-top: 80px; + margin-right: auto; + margin-left: auto; +} + +.dialog-box-wrapper { + position: relative; + padding: 1em; + background-color: rgba(0,0,0,0.5); + -moz-border-radius: 1em; + -webkit-border-radius: 1em; +} + +.dialog-box { + border: solid #999 1px; + background: white; + z-index: 80000; +} + +#overlay.modal .dialog-box .body { + min-width: 600px; +} + +.dialog-box .body { + padding: 5px; + overflow: auto; + max-height: 500px; + min-width: 300px; +} + +.dialog-box .buttons { + padding: 5px; +} + +// Messages for message box, slightly different style + +.panel-error-message, .panel-warning-message, .panel-done-message, .panel-info-message +{ + height: 24px; + line-height: 24px; + color: @base_text; + padding: 0px; + padding-left: 26px; + background-color: @error_message_bg; + background-image: url(error_small.png); + background-repeat: no-repeat; + background-position: 6px 50%; +} + +.panel-warning-message +{ + background-image: url(warn_small.png); + background-color: @warn_message_bg; +} + +.panel-done-message +{ + background-image: url(done_small.png); + background-color: @done_message_bg; +} + +.panel-info-message +{ + background-image: url(info_small.png); + background-color: @info_message_bg; +} + +// Masthead + +#masthead { + .border-radius(0); + .navbar(); + position:absolute; + top:0; + left:0; + width:100%; + min-width:900px; + height:32px; + // background: @masthead_bg; + // color:#fff; + border-bottom: solid @layout_masthead_border 1px; + z-index: 15000; + padding: 0; + + a { + color: @masthead_link; + text-decoration: none; + } + + .title { + .navbar.brand(); + font-family: verdana; + //padding: 3px 10px; + //font-size: 175%; + //font-weight: bold; + z-index: 2000; + } + + .masthead-inner { + .navbar-inner(); + height: 32px; + } + + // Tabs + + .tab-group { + + margin: 0; + padding: 0 10px; + height: 100%; + white-space: nowrap; + cursor: default; + background: transparent; + + .tab { + + // background: @masthead_bg; + position: relative; + float: left; + margin: 0; + padding: 0 1em; + height: 32px; + line-height: 32px; + text-align: left; + + .submenu { + + display: none; + position: absolute; + z-index: 16000; + left: 0; + top: 32px; + padding: 1em; + margin: -1em; + padding-top: 0; + margin-top: 0; + background-color: rgba(0,0,0,0.5); + -moz-border-radius: 0 0 1em 1em; + -webkit-border-bottom-right-radius: 1em; + -webkit-border-bottom-left-radius: 1em; + + ul { + + display: block; + margin: 0; + padding: 0; + list-style-type: none; + background: @masthead_bg; + + li { + + display: block; + padding: 0 1em; + white-space: nowrap; + } + } + } + } + + .tab:hover > a { + color: gold !important; + } + + .active { + background: rgb(1,1,1); + } + } +} + +#masthead a:hover { + text-decoration: underline; +} + +.quota-meter-container +{ + position: absolute; + top: 0; + right: 0; + height: 32px; +} + +.quota-meter +{ + position: absolute; + top: 8px; + right: 8px; + height: 16px; + width: 100px; + background-color: @quota_meter_bg; +} + +.quota-meter-bar +{ + position: absolute; + top: 0; + left: 0; + height: 16px; + background-color: @quota_meter_bar; +} + +.quota-meter-bar-warn +{ + background-color: @quota_meter_warn_bar; +} + +.quota-meter-bar-error +{ + background-color: @quota_meter_error_bar; +} + +.quota-meter-text +{ + position: absolute; + top: 50%; + left: 0; + width: 100px; + height: 16px; + margin-top: -6px; + text-align: center; + z-index: 9001; + color: @quota_meter_text; +} diff -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 -r fca74f9562024605dd87a3a6ace02d28a1851f5e static/june_2007_style/variables_to_less.py --- /dev/null +++ b/static/june_2007_style/variables_to_less.py @@ -0,0 +1,23 @@ +#!/usr/bin/env python + +""" +Read ini-like variable definition and output in less format. +""" + +import sys + +def main(): + # Read variable definitions from a (sorta) ini file + context = dict() + for line in sys.stdin: + if line.startswith( '#' ): + continue + key, value = line.rstrip("\r\n").split( '=' ) + if value.startswith( '"' ) and value.endswith( '"' ): + value = value[1:-1] + if value == "-": + continue + print "@%s: %s;" % ( key, value ) + +if __name__ == "__main__": + main() diff -r b1dac5a9b1d7d01a9e55940a4546fc5ed6f79bd0 -r fca74f9562024605dd87a3a6ace02d28a1851f5e templates/base_panels.mako --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -217,8 +217,10 @@ ## Background displays first <div id="background"></div> ## Layer iframes over backgrounds - <div id="masthead"> - ${self.masthead()} + <div id="masthead" class="navbar nabbar-fixed-top"> + <div class="masthead-inner navbar-inner"> + <div class="container">${self.masthead()}</div> + </div></div><div id="messagebox" class="panel-${self.message_box_class}-message"> %if self.message_box_visible: https://bitbucket.org/galaxy/galaxy-central/changeset/691da36cb16e/ changeset: 691da36cb16e user: james_taylor date: 2012-02-23 17:41:36 summary: style: new styles for panels, rewrite panel javascript. normalizing styles for popups. add iconic icon font. various other style tweaks. affected #: 25 files Diff too large to display. https://bitbucket.org/galaxy/galaxy-central/changeset/31b3f926d928/ changeset: 31b3f926d928 user: james_taylor date: 2012-02-23 19:16:54 summary: style: don't import bootstrap tooltips, conflicts with our use of that class. fix panels for viz view. affected #: 6 files diff -r 691da36cb16e533af00dfaf72c69bd878c58384d -r 31b3f926d9284eee0331245b3be5299c0f7d9dd1 static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -16,6 +16,10 @@ // ==== Real (basic) styles ==== +.clear { + .clearfix(); +} + body { background: @base_bg_bottom; color: @base_text; @@ -236,11 +240,15 @@ div.unified-panel-body { position: absolute; top: @panel_header_height; - bottom: @panel_footer_height; + bottom: 0; width: 100%; margin-top: 1px; } +#left > div.unified-panel-body, #right > div.unified-panel-body { + bottom: @panel_footer_height; +} + .panel-header-button { color: #333; text-decoration: none; @@ -251,27 +259,20 @@ // border: solid #999 1px; padding-right: 0.5em; padding-left: 0.5em; - // -moz-border-radius: 0.5em; - // -webkit-border-radius: 0.5em; - // border-radius: 0.5em; + // Fade to maroon on hover + &:hover { + color: maroon; + .transition(color .25s linear); + } + // Bootstrap style span caret needs positioning .caret { margin-top: 7px; } -} - -.panel-header-button.popup { - padding-right: 1.75em; - background: url(../images/dropdownarrow.png) no-repeat right 7px; -} - -.panel-header-button:hover { - // color: black; - // background-color: #ccc; -} - -.panel-header-button:active { - // color: white; - // background-color: #aaaaaa; + // Another way to get a caret + &.popup { + padding-right: 1.75em; + background: url(../images/dropdownarrow.png) no-repeat right 7px; + } } #overlay { @@ -695,6 +696,8 @@ } .infomessagelarge { + .alert(); + .alert-info(); background-image: url(info_message_icon.png); border-color: @info_message_border; background-color: @info_message_bg; @@ -1327,7 +1330,7 @@ // Default history item appearance div.historyItem { - margin: 5px -5px 5px 0px; + margin: -5px -5px 5px 0px; padding: 5px 11px 5px 5px; border: solid @history_queued_border 1px; border-left: solid @history_queued_border 5px; diff -r 691da36cb16e533af00dfaf72c69bd878c58384d -r 31b3f926d9284eee0331245b3be5299c0f7d9dd1 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -279,17 +279,6 @@ .modal-footer{padding:14px 15px 15px;margin-bottom:0;background-color:#f5f5f5;border-top:1px solid #ddd;-webkit-border-radius:0 0 6px 6px;-moz-border-radius:0 0 6px 6px;border-radius:0 0 6px 6px;-webkit-box-shadow:inset 0 1px 0 #ffffff;-moz-box-shadow:inset 0 1px 0 #ffffff;box-shadow:inset 0 1px 0 #ffffff;*zoom:1;}.modal-footer:before,.modal-footer:after{display:table;content:"";} .modal-footer:after{clear:both;} .modal-footer .btn{float:right;margin-left:5px;margin-bottom:0;} -.tooltip{position:absolute;z-index:1020;display:block;visibility:visible;padding:5px;font-size:11px;opacity:0;filter:alpha(opacity=0);}.tooltip.in{opacity:0.8;filter:alpha(opacity=80);} -.tooltip.top{margin-top:-2px;} -.tooltip.right{margin-left:2px;} -.tooltip.bottom{margin-top:2px;} -.tooltip.left{margin-left:-2px;} -.tooltip.top .tooltip-arrow{bottom:0;left:50%;margin-left:-5px;border-left:5px solid transparent;border-right:5px solid transparent;border-top:5px solid #000000;} -.tooltip.left .tooltip-arrow{top:50%;right:0;margin-top:-5px;border-top:5px solid transparent;border-bottom:5px solid transparent;border-left:5px solid #000000;} -.tooltip.bottom .tooltip-arrow{top:0;left:50%;margin-left:-5px;border-left:5px solid transparent;border-right:5px solid transparent;border-bottom:5px solid #000000;} -.tooltip.right .tooltip-arrow{top:50%;left:0;margin-top:-5px;border-top:5px solid transparent;border-bottom:5px solid transparent;border-right:5px solid #000000;} -.tooltip-inner{max-width:200px;padding:3px 8px;color:#ffffff;text-align:center;text-decoration:none;background-color:#000000;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;} -.tooltip-arrow{position:absolute;width:0;height:0;} .popover{position:absolute;top:0;left:0;z-index:1010;display:none;padding:5px;}.popover.top{margin-top:-5px;} .popover.right{margin-left:5px;} .popover.bottom{margin-top:5px;} @@ -341,158 +330,160 @@ .show{display:block;} .invisible{visibility:hidden;} @font-face{font-family:'IconicStroke';src:url('../images/fonts/iconic_stroke.eot');src:url('../images/fonts/iconic_stroke.eot?#iefix') format('embedded-opentype'),url('../images/fonts/iconic_stroke.ttf') format('truetype'),url('../images/fonts/iconic_stroke.svg#iconic') format('svg');font-weight:normal;font-style:normal;}.iconic{display:inline-block;font-family:'IconicStroke';} -.lightbulb:before{content:'\e063';} -.equalizer:before{content:'\e052';} -.map_pin_stroke:before{content:'\e068';} -.brush_alt:before{content:'\e01c';} -.move:before{content:'\e03e';} -.pen_alt_stroke:before{content:'\e005';} -.move_vertical:before{content:'\e03b';} -.book_alt2:before{content:'\e06a';} -.layers:before{content:'\e01f';} -.pause:before{content:'\e049';} -.layers_alt:before{content:'\e020';} -.cloud_upload:before{content:'\e045';} -.chart_alt:before{content:'\e029';} -.fullscreen_exit_alt:before{content:'\e051';} -.cloud_download:before{content:'\e044';} -.comment_alt2_stroke:before{content:'\e004';} -.mail:before{content:'\2709';} -.check_alt:before{content:'\2718';} -.document_stroke:before{content:'\e066';} -.battery_charging:before{content:'\e05d';} -.stop:before{content:'\e04a';} -.arrow_up:before{content:'\2191';} -.move_horizontal:before{content:'\e038';} -.compass:before{content:'\e021';} -.minus_alt:before{content:'\e009';} -.battery_empty:before{content:'\e05c';} -.map_pin_alt:before{content:'\e002';} -.unlock_stroke:before{content:'\e076';} -.lock_stroke:before{content:'\e075';} -.question_mark:before{content:'\003f';} -.list:before{content:'\e055';} -.upload:before{content:'\e043';} -.reload:before{content:'\e030';} -.loop_alt4:before{content:'\e035';} -.loop_alt3:before{content:'\e034';} -.loop_alt2:before{content:'\e033';} -.loop_alt1:before{content:'\e032';} -.left_quote:before{content:'\275d';} -.x:before{content:'\2713';} -.last:before{content:'\e04d';} -.document_alt_stroke:before{content:'\e000';} -.bars:before{content:'\e06f';} -.arrow_left:before{content:'\2190';} -.arrow_down:before{content:'\2193';} -.download:before{content:'\e042';} -.home:before{content:'\2302';} -.calendar:before{content:'\e001';} -.right_quote_alt:before{content:'\e012';} -.fullscreen:before{content:'\e04e';} -.dial:before{content:'\e058';} -.plus_alt:before{content:'\e008';} -.clock:before{content:'\e079';} -.movie:before{content:'\e060';} -.steering_wheel:before{content:'\e024';} -.pen:before{content:'\270e';} -.tag_stroke:before{content:'\e02b';} -.pin:before{content:'\e067';} -.denied:before{content:'\26d4';} -.left_quote_alt:before{content:'\e011';} -.volume_mute:before{content:'\e071';} -.arrow_up_alt2:before{content:'\e018';} -.list_nested:before{content:'\e056';} -.arrow_up_alt1:before{content:'\e014';} -.comment_stroke:before{content:'\e06d';} -.undo:before{content:'\e02f';} -.umbrella:before{content:'\2602';} -.bolt:before{content:'\26a1';} -.article:before{content:'\e053';} -.read_more:before{content:'\e054';} -.beaker:before{content:'\e023';} -.beaker_alt:before{content:'\e010';} -.battery_full:before{content:'\e073';} -.arrow_right:before{content:'\2192';} -.new_window:before{content:'\e059';} -.plus:before{content:'\2795';} -.cog:before{content:'\2699';} -.key_stroke:before{content:'\26bf';} -.first:before{content:'\e04c';} -.comment_alt1_stroke:before{content:'\e003';} -.trash_stroke:before{content:'\e05a';} -.image:before{content:'\e027';} -.chat_alt_stroke:before{content:'\e007';} -.cd:before{content:'\e064';} -.right_quote:before{content:'\275e';} -.brush:before{content:'\e01b';} -.cloud:before{content:'\2601';} -.eye:before{content:'\e025';} -.play_alt:before{content:'\e048';} -.transfer:before{content:'\e041';} -.pen_alt2:before{content:'\e006';} -.camera:before{content:'\e070';} -.move_horizontal_alt2:before{content:'\e03a';} -.curved_arrow:before{content:'\2935';} -.move_horizontal_alt1:before{content:'\e039';} -.aperture:before{content:'\e026';} -.reload_alt:before{content:'\e031';} -.magnifying_glass:before{content:'\e074';} -.iphone:before{content:'\e06e';} -.fork:before{content:'\e046';} -.box:before{content:'\e06b';} -.bars_alt:before{content:'\e00a';} -.heart_stroke:before{content:'\2764';} -.volume:before{content:'\e072';} -.x_alt:before{content:'\2714';} -.link:before{content:'\e077';} -.moon_stroke:before{content:'\263e';} -.eyedropper:before{content:'\e01e';} -.spin:before{content:'\e036';} -.rss:before{content:'\e02c';} -.info:before{content:'\2139';} -.target:before{content:'\e02a';} -.cursor:before{content:'\e057';} -.minus:before{content:'\2796';} -.book_alt:before{content:'\e00b';} -.headphones:before{content:'\e061';} -.hash:before{content:'\0023';} -.arrow_left_alt1:before{content:'\e013';} -.arrow_left_alt2:before{content:'\e017';} -.fullscreen_exit:before{content:'\e050';} -.share:before{content:'\e02e';} -.fullscreen_alt:before{content:'\e04f';} -.at:before{content:'\0040';} -.chat:before{content:'\e05e';} -.move_vertical_alt2:before{content:'\e03d';} -.move_vertical_alt1:before{content:'\e03c';} -.check:before{content:'\2717';} -.mic:before{content:'\e05f';} -.calendar_alt_stroke:before{content:'\e06c';} -.book:before{content:'\e069';} -.move_alt1:before{content:'\e03f';} -.move_alt2:before{content:'\e040';} -.award_stroke:before{content:'\e022';} -.wrench:before{content:'\e078';} -.play:before{content:'\e047';} -.star:before{content:'\2605';} -.chart:before{content:'\e028';} -.rain:before{content:'\26c6';} -.folder_stroke:before{content:'\e065';} -.sun_stroke:before{content:'\2600';} -.user:before{content:'\e062';} -.battery_half:before{content:'\e05b';} -.aperture_alt:before{content:'\e00c';} -.eject:before{content:'\e04b';} -.arrow_down_alt1:before{content:'\e016';} -.pilcrow:before{content:'\00b6';} -.arrow_down_alt2:before{content:'\e01a';} -.arrow_right_alt1:before{content:'\e015';} -.arrow_right_alt2:before{content:'\e019';} -.rss_alt:before{content:'\e02d';} -.spin_alt:before{content:'\e037';} +.iconic.lightbulb:before{content:'\e063';} +.iconic.equalizer:before{content:'\e052';} +.iconic.map_pin_stroke:before{content:'\e068';} +.iconic.brush_alt:before{content:'\e01c';} +.iconic.move:before{content:'\e03e';} +.iconic.pen_alt_stroke:before{content:'\e005';} +.iconic.move_vertical:before{content:'\e03b';} +.iconic.book_alt2:before{content:'\e06a';} +.iconic.layers:before{content:'\e01f';} +.iconic.pause:before{content:'\e049';} +.iconic.layers_alt:before{content:'\e020';} +.iconic.cloud_upload:before{content:'\e045';} +.iconic.chart_alt:before{content:'\e029';} +.iconic.fullscreen_exit_alt:before{content:'\e051';} +.iconic.cloud_download:before{content:'\e044';} +.iconic.comment_alt2_stroke:before{content:'\e004';} +.iconic.mail:before{content:'\2709';} +.iconic.check_alt:before{content:'\2718';} +.iconic.document_stroke:before{content:'\e066';} +.iconic.battery_charging:before{content:'\e05d';} +.iconic.stop:before{content:'\e04a';} +.iconic.arrow_up:before{content:'\2191';} +.iconic.move_horizontal:before{content:'\e038';} +.iconic.compass:before{content:'\e021';} +.iconic.minus_alt:before{content:'\e009';} +.iconic.battery_empty:before{content:'\e05c';} +.iconic.map_pin_alt:before{content:'\e002';} +.iconic.unlock_stroke:before{content:'\e076';} +.iconic.lock_stroke:before{content:'\e075';} +.iconic.question_mark:before{content:'\003f';} +.iconic.list:before{content:'\e055';} +.iconic.upload:before{content:'\e043';} +.iconic.reload:before{content:'\e030';} +.iconic.loop_alt4:before{content:'\e035';} +.iconic.loop_alt3:before{content:'\e034';} +.iconic.loop_alt2:before{content:'\e033';} +.iconic.loop_alt1:before{content:'\e032';} +.iconic.left_quote:before{content:'\275d';} +.iconic.x:before{content:'\2713';} +.iconic.last:before{content:'\e04d';} +.iconic.document_alt_stroke:before{content:'\e000';} +.iconic.bars:before{content:'\e06f';} +.iconic.arrow_left:before{content:'\2190';} +.iconic.arrow_down:before{content:'\2193';} +.iconic.download:before{content:'\e042';} +.iconic.home:before{content:'\2302';} +.iconic.calendar:before{content:'\e001';} +.iconic.right_quote_alt:before{content:'\e012';} +.iconic.fullscreen:before{content:'\e04e';} +.iconic.dial:before{content:'\e058';} +.iconic.plus_alt:before{content:'\e008';} +.iconic.clock:before{content:'\e079';} +.iconic.movie:before{content:'\e060';} +.iconic.steering_wheel:before{content:'\e024';} +.iconic.pen:before{content:'\270e';} +.iconic.tag_stroke:before{content:'\e02b';} +.iconic.pin:before{content:'\e067';} +.iconic.denied:before{content:'\26d4';} +.iconic.left_quote_alt:before{content:'\e011';} +.iconic.volume_mute:before{content:'\e071';} +.iconic.arrow_up_alt2:before{content:'\e018';} +.iconic.list_nested:before{content:'\e056';} +.iconic.arrow_up_alt1:before{content:'\e014';} +.iconic.comment_stroke:before{content:'\e06d';} +.iconic.undo:before{content:'\e02f';} +.iconic.umbrella:before{content:'\2602';} +.iconic.bolt:before{content:'\26a1';} +.iconic.article:before{content:'\e053';} +.iconic.read_more:before{content:'\e054';} +.iconic.beaker:before{content:'\e023';} +.iconic.beaker_alt:before{content:'\e010';} +.iconic.battery_full:before{content:'\e073';} +.iconic.arrow_right:before{content:'\2192';} +.iconic.new_window:before{content:'\e059';} +.iconic.plus:before{content:'\2795';} +.iconic.cog:before{content:'\2699';} +.iconic.key_stroke:before{content:'\26bf';} +.iconic.first:before{content:'\e04c';} +.iconic.comment_alt1_stroke:before{content:'\e003';} +.iconic.trash_stroke:before{content:'\e05a';} +.iconic.image:before{content:'\e027';} +.iconic.chat_alt_stroke:before{content:'\e007';} +.iconic.cd:before{content:'\e064';} +.iconic.right_quote:before{content:'\275e';} +.iconic.brush:before{content:'\e01b';} +.iconic.cloud:before{content:'\2601';} +.iconic.eye:before{content:'\e025';} +.iconic.play_alt:before{content:'\e048';} +.iconic.transfer:before{content:'\e041';} +.iconic.pen_alt2:before{content:'\e006';} +.iconic.camera:before{content:'\e070';} +.iconic.move_horizontal_alt2:before{content:'\e03a';} +.iconic.curved_arrow:before{content:'\2935';} +.iconic.move_horizontal_alt1:before{content:'\e039';} +.iconic.aperture:before{content:'\e026';} +.iconic.reload_alt:before{content:'\e031';} +.iconic.magnifying_glass:before{content:'\e074';} +.iconic.iphone:before{content:'\e06e';} +.iconic.fork:before{content:'\e046';} +.iconic.box:before{content:'\e06b';} +.iconic.bars_alt:before{content:'\e00a';} +.iconic.heart_stroke:before{content:'\2764';} +.iconic.volume:before{content:'\e072';} +.iconic.x_alt:before{content:'\2714';} +.iconic.link:before{content:'\e077';} +.iconic.moon_stroke:before{content:'\263e';} +.iconic.eyedropper:before{content:'\e01e';} +.iconic.spin:before{content:'\e036';} +.iconic.rss:before{content:'\e02c';} +.iconic.info:before{content:'\2139';} +.iconic.target:before{content:'\e02a';} +.iconic.cursor:before{content:'\e057';} +.iconic.minus:before{content:'\2796';} +.iconic.book_alt:before{content:'\e00b';} +.iconic.headphones:before{content:'\e061';} +.iconic.hash:before{content:'\0023';} +.iconic.arrow_left_alt1:before{content:'\e013';} +.iconic.arrow_left_alt2:before{content:'\e017';} +.iconic.fullscreen_exit:before{content:'\e050';} +.iconic.share:before{content:'\e02e';} +.iconic.fullscreen_alt:before{content:'\e04f';} +.iconic.at:before{content:'\0040';} +.iconic.chat:before{content:'\e05e';} +.iconic.move_vertical_alt2:before{content:'\e03d';} +.iconic.move_vertical_alt1:before{content:'\e03c';} +.iconic.check:before{content:'\2717';} +.iconic.mic:before{content:'\e05f';} +.iconic.calendar_alt_stroke:before{content:'\e06c';} +.iconic.book:before{content:'\e069';} +.iconic.move_alt1:before{content:'\e03f';} +.iconic.move_alt2:before{content:'\e040';} +.iconic.award_stroke:before{content:'\e022';} +.iconic.wrench:before{content:'\e078';} +.iconic.play:before{content:'\e047';} +.iconic.star:before{content:'\2605';} +.iconic.chart:before{content:'\e028';} +.iconic.rain:before{content:'\26c6';} +.iconic.folder_stroke:before{content:'\e065';} +.iconic.sun_stroke:before{content:'\2600';} +.iconic.user:before{content:'\e062';} +.iconic.battery_half:before{content:'\e05b';} +.iconic.aperture_alt:before{content:'\e00c';} +.iconic.eject:before{content:'\e04b';} +.iconic.arrow_down_alt1:before{content:'\e016';} +.iconic.pilcrow:before{content:'\00b6';} +.iconic.arrow_down_alt2:before{content:'\e01a';} +.iconic.arrow_right_alt1:before{content:'\e015';} +.iconic.arrow_right_alt2:before{content:'\e019';} +.iconic.rss_alt:before{content:'\e02d';} +.iconic.spin_alt:before{content:'\e037';} .unselectable{-webkit-user-select:none;-moz-user-select:none;-o-user-select:none;user-select:none;} .shadow{-webkit-box-shadow:0 1px 3px rgba(0, 0, 0, 0.25);-moz-box-shadow:0 1px 3px rgba(0, 0, 0, 0.25);box-shadow:0 1px 3px rgba(0, 0, 0, 0.25);} +.clear{*zoom:1;}.clear:before,.clear:after{display:table;content:"";} +.clear:after{clear:both;} body{background:#ffffff;color:#303030;background-image:url(base_bg.png);background-repeat:repeat-x;background-position:top;margin:10px;} img{border:0;} a:link,a:visited,a:active{text-decoration:underline;color:#303030;} @@ -522,8 +513,10 @@ #right>.unified-panel-footer .collapse:before{content:'\2192';} #right>.unified-panel-footer .collapse.hidden:before{content:'\2190';} .menu-bg{background:whiteSmoke top repeat-x;} -div.unified-panel-body{position:absolute;top:30px;bottom:25px;width:100%;margin-top:1px;} -.panel-header-button{color:#333;text-decoration:none;display:inline-block;cursor:pointer;margin:-1px;padding:1px;margin-top:-0.2em;padding-right:0.5em;padding-left:0.5em;}.panel-header-button .caret{margin-top:7px;} +div.unified-panel-body{position:absolute;top:30px;bottom:0;width:100%;margin-top:1px;} +#left>div.unified-panel-body,#right>div.unified-panel-body{bottom:25px;} +.panel-header-button{color:#333;text-decoration:none;display:inline-block;cursor:pointer;margin:-1px;padding:1px;margin-top:-0.2em;padding-right:0.5em;padding-left:0.5em;}.panel-header-button:hover{color:maroon;-webkit-transition:color 0.25s linear;-moz-transition:color 0.25s linear;-ms-transition:color 0.25s linear;-o-transition:color 0.25s linear;transition:color 0.25s linear;} +.panel-header-button .caret{margin-top:7px;} .panel-header-button.popup{padding-right:1.75em;background:url(../images/dropdownarrow.png) no-repeat right 7px;} #overlay{position:fixed;top:0;left:0;width:100%;height:100%;z-index:20000;} #overlay.modal #overlay-background{background:rgba(0, 0, 0, 0.5);} @@ -591,7 +584,7 @@ .errormessagelarge{background-color:#f2dede;border-color:#eed3d7;color:#b94a48;padding-left:52px;} .warningmessagelarge{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#fcf8e3;border:1px solid #fbeed5;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#c09853;background-image:url(warn_message_icon.png);border-color:#aaaa66;background-color:#ffffcc;} .donemessagelarge{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#fcf8e3;border:1px solid #fbeed5;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#c09853;background-color:#ccffcc;border-color:#1a9900;color:#006600;padding-left:52px;background-image:url(done_message_icon.png);} -.infomessagelarge{background-image:url(info_message_icon.png);border-color:#6666aa;background-color:#ccccff;} +.infomessagelarge{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#fcf8e3;border:1px solid #fbeed5;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#c09853;background-color:#d9edf7;border-color:#bce8f1;color:#3a87ad;background-image:url(info_message_icon.png);border-color:#6666aa;background-color:#ccccff;} .screencastBox{padding-left:10px;border-color:#AAAA66;background-color:#FFFFCC;background-image:none;} .errormessage,.warningmessage,.donemessage,.infomessage,.errormessagesmall,.warningmessagesmall,.donemessagesmall,.infomessagesmall{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#fcf8e3;border:1px solid #fbeed5;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#c09853;padding:5px;padding-left:25px;min-height:15px;background-image:url(error_small.png);background-repeat:no-repeat;background-position:5px 5px;} .errormessage{background-color:#f2dede;border-color:#eed3d7;color:#b94a48;} diff -r 691da36cb16e533af00dfaf72c69bd878c58384d -r 31b3f926d9284eee0331245b3be5299c0f7d9dd1 static/june_2007_style/galaxy_bootstrap.less --- a/static/june_2007_style/galaxy_bootstrap.less +++ b/static/june_2007_style/galaxy_bootstrap.less @@ -134,7 +134,7 @@ // Components: Popovers @import "bootstrap/modals.less"; -@import "bootstrap/tooltip.less"; +// @import "bootstrap/tooltip.less"; @import "bootstrap/popovers.less"; // Components: Misc diff -r 691da36cb16e533af00dfaf72c69bd878c58384d -r 31b3f926d9284eee0331245b3be5299c0f7d9dd1 templates/base_panels.mako --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -236,15 +236,11 @@ <div class="drag"></div></div></div> - <div id="left-border"> - <div id="left-border-inner" style="display: none;"></div> - </div> %endif <div id="center"> ${self.center_panel()} </div> %if self.has_right_panel: - <div id="right-border"><div id="right-border-inner" style="display: none;"></div></div><div id="right"> ${self.right_panel()} <div class="unified-panel-footer"> diff -r 691da36cb16e533af00dfaf72c69bd878c58384d -r 31b3f926d9284eee0331245b3be5299c0f7d9dd1 templates/root/history.mako --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -1,7 +1,7 @@ <%namespace file="/message.mako" import="render_msg" /><% _=n_ %> -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> +<!DOCTYPE HTML><html> @@ -467,6 +467,7 @@ </head><body class="historyPage"> + <div id="top-links" class="historyLinks"><a title="${_('refresh')}" class="icon-button arrow-circle tooltip" href="${h.url_for('history', show_deleted=show_deleted)}"></a> @@ -478,10 +479,9 @@ <a id="history-annotate" title="Edit history annotation" class="icon-button annotate tooltip" target="galaxy_main" href="${h.url_for( controller='history', action='annotate' )}"></a></div> %endif - </div> -<div style="clear: both;"></div> +<div class="clear"></div> %if show_deleted: <div class="historyLinks"> diff -r 691da36cb16e533af00dfaf72c69bd878c58384d -r 31b3f926d9284eee0331245b3be5299c0f7d9dd1 templates/workflow/editor.mako --- a/templates/workflow/editor.mako +++ b/templates/workflow/editor.mako @@ -7,15 +7,15 @@ %></%def> -<%def name="late_javascripts()"> - <script type='text/javascript' src="${h.url_for('/static/scripts/galaxy.panels.js')}"></script> - <script type="text/javascript"> - ensure_dd_helper(); - make_left_panel( $("#left"), $("#center"), $("#left-border" ) ); - make_right_panel( $("#right"), $("#center"), $("#right-border" ) ); - ## handle_minwidth_hint = rp.handle_minwidth_hint; - </script> -</%def> +## <%def name="late_javascripts()"> +## <script type='text/javascript' src="${h.url_for('/static/scripts/galaxy.panels.js')}"></script> +## <script type="text/javascript"> +## ensure_dd_helper(); +## make_left_panel( $("#left"), $("#center"), $("#left-border" ) ); +## make_right_panel( $("#right"), $("#center"), $("#right-border" ) ); +## ## handle_minwidth_hint = rp.handle_minwidth_hint; +## </script> +## </%def><%def name="javascripts()"> @@ -727,9 +727,9 @@ body { margin: 0; padding: 0; overflow: hidden; } /* Wider right panel */ - #center { right: 309px; } - #right-border { right: 300px; } - #right { width: 300px; } + ## #center { right: 309px; } + ## #right-border { right: 300px; } + ## #right { width: 300px; } ## /* Relative masthead size */ ## #masthead { height: 2.5em; } ## #masthead div.title { font-size: 1.8em; } https://bitbucket.org/galaxy/galaxy-central/changeset/3e01fd6ea098/ changeset: 3e01fd6ea098 user: james_taylor date: 2012-02-23 21:44:09 summary: style: fix dialog boxes affected #: 11 files diff -r 31b3f926d9284eee0331245b3be5299c0f7d9dd1 -r 3e01fd6ea098bb5fc6d1225784c568c399f330cd static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -130,6 +130,14 @@ border-left: solid @layout_border 1px; } +.subnavbar { + #gradient > .vertical-three-colors(@white, @white, 25%, darken(@white, 10%)); + border-bottom: solid @layout_border 1px; + border-top: solid @layout_border 1px; + padding: 5px; + color: #555; +} + .unified-panel-header { .unselectable(); height: @panel_header_height; @@ -166,7 +174,7 @@ width: 100%; z-index: 1000; border-top: solid @layout_border 1px; - #gradient > .vertical-three-colors(@white, @white, 25%, darken(@white, 10%)); + #gradient > .vertical-three-colors(darken(@white, 5%), darken(@white, 5%), 25%, darken(@white, 10%)); color: #555; a { @@ -200,7 +208,7 @@ background: none; border-right: solid @layout_border 1px; border-top: solid @layout_border 1px; - #gradient > .vertical-three-colors(@white, @white, 25%, darken(@white, 10%)); + #gradient > .vertical-three-colors(darken(@white, 5%), darken(@white, 5%), 25%, darken(@white, 10%)); .iconic(); } @@ -281,7 +289,7 @@ z-index: 20000; } -#overlay.modal #overlay-background { +#overlay.is_modal #overlay-background { background: rgba(0,0,0,0.5); } @@ -306,7 +314,7 @@ z-index: 80000; } -#overlay.modal .dialog-box .body { +#overlay.is_modal .dialog-box .body { min-width: 600px; } @@ -630,6 +638,7 @@ } div.form-row-input { + width: 300px; float: left; } @@ -643,7 +652,7 @@ float: left; color: red; font-weight: bold; - padding: 3px 0 0 1em; + padding: 3px 0; } .form-row .help { @@ -659,6 +668,24 @@ max-width: 300px; } +/* +.search-query { + display: inline-block; + width: 210px; + height: @baseLineHeight; + padding: 4px; + margin-bottom: 9px; + font-size: @baseFontSize; + line-height: @baseLineHeight; + color: @gray; + border: 1px solid @formElementBorder; + padding-left: 14px; + padding-right: 14px; + margin-bottom: 0; // remove the default margin on all inputs + .border-radius(14px); +} +*/ + // Messages .errormessagelarge, .warningmessagelarge, .donemessagelarge, .infomessagelarge { @@ -668,6 +695,8 @@ border: 1px solid @error_message_border; background-color: @error_message_bg; */ + .alert(); + min-height: 32px; padding-left: 52px; background-image: url(error_message_icon.png); background-repeat: no-repeat; @@ -680,14 +709,12 @@ } .warningmessagelarge { - .alert(); background-image: url(warn_message_icon.png); border-color: @warn_message_border; background-color: @warn_message_bg; } .donemessagelarge { - .alert(); .alert-success(); padding-left: 52px; background-image: url(done_message_icon.png); @@ -696,7 +723,6 @@ } .infomessagelarge { - .alert(); .alert-info(); background-image: url(info_message_icon.png); border-color: @info_message_border; @@ -974,6 +1000,10 @@ // Button styles +button { + .btn(); +} + .action-button { .btn(); } @@ -1284,13 +1314,7 @@ cursor: text; border: dotted #999999 1px; } -/* -.text-and-autocomplete-select { - -sprite-group: fugue; - -sprite-image: fugue/control-270.png; - -sprite-horiz-position: right; -} -*/ + .icon-button.multiinput{ background:url(../images/documents-stack.png) no-repeat; cursor:pointer; @@ -1330,10 +1354,10 @@ // Default history item appearance div.historyItem { - margin: -5px -5px 5px 0px; - padding: 5px 11px 5px 5px; - border: solid @history_queued_border 1px; - border-left: solid @history_queued_border 5px; + margin: 0px -5px; + padding: 8px 10px; + border-top: solid @layout_border 1px; + // border-left: solid @history_queued_border 5px; border-right: none; word-wrap: break-word; background: @history_queued_bg; @@ -1351,6 +1375,10 @@ } } +.historyItemContainer:last-child div.historyItem { + border-bottom: solid @layout_border 1px; +} + // Nested history items div.historyItem div.historyItem { margin-right: -11px; @@ -1359,7 +1387,7 @@ // Change background/border color depending on state div.historyItem-ok, div.historyItem-failed_metadata { - border-color: @history_ok_border; + // border-color: @history_ok_border; background: @history_ok_bg; .state-icon { display: none; @@ -1367,7 +1395,7 @@ } div.historyItem-error { - border-color: @history_error_border; + // border-color: @history_error_border; background: @history_error_bg; .state-icon { -sprite-group: history-states; @@ -1376,7 +1404,7 @@ } div.historyItem-empty { - border-color: @history_error_border; + // border-color: @history_error_border; background: @history_error_bg; .state-icon { -sprite-group: history-states; @@ -1385,7 +1413,7 @@ } div.historyItem-running { - border-color: @history_running_border; + // border-color: @history_running_border; background: @history_running_bg; .state-icon { background-image: url(data_running.gif); @@ -1393,7 +1421,7 @@ } div.historyItem-setting_metadata { - border-color: @history_running_border; + // border-color: @history_running_border; background: @history_running_bg; .state-icon { background-image: url(data_running.gif); @@ -1401,7 +1429,7 @@ } div.historyItem-upload { - border-color: @history_upload_border; + // border-color: @history_upload_border; background: @history_upload_bg; .state-icon { background-image: url(data_upload.gif); @@ -1409,7 +1437,7 @@ } div.historyItem-queued { - background: @history_queued_bg; + // background: @history_queued_bg; .state-icon { -sprite-group: history-states; -sprite-image: data_queued.png; diff -r 31b3f926d9284eee0331245b3be5299c0f7d9dd1 -r 3e01fd6ea098bb5fc6d1225784c568c399f330cd static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -21,9 +21,9 @@ p{margin:0 0 8px;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:12px;line-height:16px;}p small{font-size:10px;color:#999999;} .lead{margin-bottom:16px;font-size:20px;font-weight:200;line-height:24px;} h1,h2,h3,h4,h5,h6{margin:0;font-weight:bold;color:#333333;text-rendering:optimizelegibility;}h1 small,h2 small,h3 small,h4 small,h5 small,h6 small{font-weight:normal;color:#999999;} -h1{font-size:30px;line-height:32px;}h1 small{font-size:18px;} -h2{font-size:24px;line-height:32px;}h2 small{font-size:18px;} -h3{line-height:24px;font-size:18px;}h3 small{font-size:14px;} +h1{font-size:24px;line-height:32px;}h1 small{font-size:18px;} +h2{font-size:18px;line-height:24px;}h2 small{font-size:14px;} +h3{line-height:16px;font-size:14px;}h3 small{font-size:12px;} h4,h5,h6{line-height:16px;} h4{font-size:14px;}h4 small{font-size:12px;} h5{font-size:12px;} @@ -138,15 +138,15 @@ .btn:hover .caret,.open.btn-group .caret{opacity:1;filter:alpha(opacity=100);} .btn-primary .caret,.btn-danger .caret,.btn-info .caret,.btn-success .caret{border-top-color:#ffffff;opacity:0.75;filter:alpha(opacity=75);} .btn-small .caret{margin-top:4px;} -.alert{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#fcf8e3;border:1px solid #fbeed5;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;} -.alert,.alert-heading{color:#c09853;} +.alert{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#ffffcc;border:1px solid #ffdd33;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;} +.alert,.alert-heading{color:#666600;} .alert .close{position:relative;top:-2px;right:-21px;line-height:18px;} .alert-success{background-color:#ccffcc;border-color:#1a9900;} .alert-success,.alert-success .alert-heading{color:#006600;} -.alert-danger,.alert-error{background-color:#f2dede;border-color:#eed3d7;} -.alert-danger,.alert-error,.alert-danger .alert-heading,.alert-error .alert-heading{color:#b94a48;} -.alert-info{background-color:#d9edf7;border-color:#bce8f1;} -.alert-info,.alert-info .alert-heading{color:#3a87ad;} +.alert-danger,.alert-error{background-color:#ffcccc;border-color:#ff3355;} +.alert-danger,.alert-error,.alert-danger .alert-heading,.alert-error .alert-heading{color:#660000;} +.alert-info{background-color:#d9edf7;border-color:#1b7183;} +.alert-info,.alert-info .alert-heading{color:#134158;} .alert-block{padding-top:14px;padding-bottom:14px;} .alert-block>p,.alert-block>ul{margin-bottom:0;} .alert-block p+p{margin-top:5px;} @@ -500,12 +500,13 @@ #center{left:250px;right:250px;overflow:hidden;z-index:1;} #right-border{right:250px;} #right{width:250px;right:0px;z-index:200;border-left:solid #999999 1px;} +.subnavbar{background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border-bottom:solid #999999 1px;border-top:solid #999999 1px;padding:5px;color:#555;} .unified-panel-header{-webkit-user-select:none;-moz-user-select:none;-o-user-select:none;user-select:none;height:30px;z-index:1000;text-shadow:rgba(255, 255, 255, 0.8) 0 1px 0;background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border-bottom:solid #999999 1px;margin:0;padding:0;padding-right:10px;padding-left:10px;font-weight:bold;color:#555;}.unified-panel-header a{color:#555;} .unified-panel-header-inner{padding-top:8px;} -.unified-panel-footer{-webkit-user-select:none;-moz-user-select:none;-o-user-select:none;user-select:none;position:absolute;bottom:0;height:25px;line-height:25px;width:100%;z-index:1000;border-top:solid #999999 1px;background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);color:#555;}.unified-panel-footer a{color:#555;} +.unified-panel-footer{-webkit-user-select:none;-moz-user-select:none;-o-user-select:none;user-select:none;position:absolute;bottom:0;height:25px;line-height:25px;width:100%;z-index:1000;border-top:solid #999999 1px;background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-ms-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#f2f2f2', endColorstr='#e6e6e6', GradientType=0);color:#555;}.unified-panel-footer a{color:#555;} .unified-panel-footer .drag,.unified-panel-footer .collapse{position:absolute;top:0;right:0;padding:0 5px;text-align:center;height:25px;width:20px;background-image:url(../images/visualization/draggable_horizontal.png);background-repeat:no-repeat;background-position:50% 50%;} .unified-panel-footer .drag{cursor:w-resize;} -.unified-panel-footer .collapse{position:fixed;left:0;top:inherit;bottom:0;background:none;border-right:solid #999999 1px;border-top:solid #999999 1px;background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);display:inline-block;font-family:'IconicStroke';} +.unified-panel-footer .collapse{position:fixed;left:0;top:inherit;bottom:0;background:none;border-right:solid #999999 1px;border-top:solid #999999 1px;background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-ms-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#f2f2f2', endColorstr='#e6e6e6', GradientType=0);display:inline-block;font-family:'IconicStroke';} .unified-panel-footer .collapse:before{content:'\2190';} .unified-panel-footer .collapse.hidden:before{content:'\2192';} #right>.unified-panel-footer .drag{left:0;} @@ -519,17 +520,17 @@ .panel-header-button .caret{margin-top:7px;} .panel-header-button.popup{padding-right:1.75em;background:url(../images/dropdownarrow.png) no-repeat right 7px;} #overlay{position:fixed;top:0;left:0;width:100%;height:100%;z-index:20000;} -#overlay.modal #overlay-background{background:rgba(0, 0, 0, 0.5);} +#overlay.is_modal #overlay-background{background:rgba(0, 0, 0, 0.5);} .dialog-box-container{position:relative;margin-top:80px;margin-right:auto;margin-left:auto;} .dialog-box-wrapper{position:relative;padding:1em;background-color:rgba(0, 0, 0, 0.5);-moz-border-radius:1em;-webkit-border-radius:1em;} .dialog-box{border:solid #999 1px;background:white;z-index:80000;} -#overlay.modal .dialog-box .body{min-width:600px;} +#overlay.is_modal .dialog-box .body{min-width:600px;} .dialog-box .body{padding:5px;overflow:auto;max-height:500px;min-width:300px;} .dialog-box .buttons{padding:5px;} .panel-error-message,.panel-warning-message,.panel-done-message,.panel-info-message{height:24px;line-height:24px;color:#303030;padding:0px;padding-left:26px;background-color:#ffcccc;background-image:url(error_small.png);background-repeat:no-repeat;background-position:6px 50%;} .panel-warning-message{background-image:url(warn_small.png);background-color:#ffffcc;} .panel-done-message{background-image:url(done_small.png);background-color:#ccffcc;} -.panel-info-message{background-image:url(info_small.png);background-color:#ccccff;} +.panel-info-message{background-image:url(info_small.png);background-color:#d9edf7;} #masthead{-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;overflow:visible;margin-bottom:16px;position:absolute;top:0;left:0;width:100%;min-width:900px;height:32px;border-bottom:solid #444444 1px;z-index:15000;padding:0;}#masthead .brand:hover{text-decoration:none;} #masthead .brand{float:left;display:block;padding:8px 20px 12px;margin-left:-20px;font-size:20px;font-weight:200;line-height:1;color:#ffffff;} #masthead .navbar-text{margin-bottom:0;line-height:40px;color:#999999;}#masthead .navbar-text a:hover{color:#ffffff;background-color:transparent;} @@ -574,23 +575,23 @@ div.form-row-error{background:#ffcccc;} div.form-row label{font-weight:bold;display:block;margin-bottom:.2em;} div.form-row label.inline{display:inline;} -div.form-row-input{float:left;} +div.form-row-input{width:300px;float:left;} div.form-row-input label{font-weight:normal;display:inline;} -div.form-row-error-message{width:300px;float:left;color:red;font-weight:bold;padding:3px 0 0 1em;} +div.form-row-error-message{width:300px;float:left;color:red;font-weight:bold;padding:3px 0;} .form-row .help{color:#666;} select,input,textarea{font:inherit;} select,textarea,input[type="text"],input[type="file"],input[type="password"]{max-width:300px;} -.errormessagelarge,.warningmessagelarge,.donemessagelarge,.infomessagelarge{padding-left:52px;background-image:url(error_message_icon.png);background-repeat:no-repeat;background-position:10px 10px;} -.errormessagelarge{background-color:#f2dede;border-color:#eed3d7;color:#b94a48;padding-left:52px;} -.warningmessagelarge{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#fcf8e3;border:1px solid #fbeed5;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#c09853;background-image:url(warn_message_icon.png);border-color:#aaaa66;background-color:#ffffcc;} -.donemessagelarge{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#fcf8e3;border:1px solid #fbeed5;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#c09853;background-color:#ccffcc;border-color:#1a9900;color:#006600;padding-left:52px;background-image:url(done_message_icon.png);} -.infomessagelarge{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#fcf8e3;border:1px solid #fbeed5;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#c09853;background-color:#d9edf7;border-color:#bce8f1;color:#3a87ad;background-image:url(info_message_icon.png);border-color:#6666aa;background-color:#ccccff;} +.errormessagelarge,.warningmessagelarge,.donemessagelarge,.infomessagelarge{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#ffffcc;border:1px solid #ffdd33;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#666600;min-height:32px;padding-left:52px;background-image:url(error_message_icon.png);background-repeat:no-repeat;background-position:10px 10px;} +.errormessagelarge{background-color:#ffcccc;border-color:#ff3355;color:#660000;padding-left:52px;} +.warningmessagelarge{background-image:url(warn_message_icon.png);border-color:#aaaa66;background-color:#ffffcc;} +.donemessagelarge{background-color:#ccffcc;border-color:#1a9900;color:#006600;padding-left:52px;background-image:url(done_message_icon.png);} +.infomessagelarge{background-color:#d9edf7;border-color:#1b7183;color:#134158;background-image:url(info_message_icon.png);border-color:#6666aa;background-color:#d9edf7;} .screencastBox{padding-left:10px;border-color:#AAAA66;background-color:#FFFFCC;background-image:none;} -.errormessage,.warningmessage,.donemessage,.infomessage,.errormessagesmall,.warningmessagesmall,.donemessagesmall,.infomessagesmall{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#fcf8e3;border:1px solid #fbeed5;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#c09853;padding:5px;padding-left:25px;min-height:15px;background-image:url(error_small.png);background-repeat:no-repeat;background-position:5px 5px;} -.errormessage{background-color:#f2dede;border-color:#eed3d7;color:#b94a48;} +.errormessage,.warningmessage,.donemessage,.infomessage,.errormessagesmall,.warningmessagesmall,.donemessagesmall,.infomessagesmall{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#ffffcc;border:1px solid #ffdd33;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#666600;padding:5px;padding-left:25px;min-height:15px;background-image:url(error_small.png);background-repeat:no-repeat;background-position:5px 5px;} +.errormessage{background-color:#ffcccc;border-color:#ff3355;color:#660000;} .warningmessage,.warningmessagesmall{background-image:url(warn_small.png);} .donemessage,.donemessagesmall{background-color:#ccffcc;border-color:#1a9900;color:#006600;background-image:url(ok_small.png);} -.infomessage,.infomessagesmall{background-color:#d9edf7;border-color:#bce8f1;color:#3a87ad;background-image:url(info_small.png);} +.infomessage,.infomessagesmall{background-color:#d9edf7;border-color:#1b7183;color:#134158;background-image:url(info_small.png);} .errormark,.warningmark,.donemark,.infomark,.ok_bgr,.err_bgr{padding-left:20px;min-height:15px;background:url(error_small.png) no-repeat;} .warningmark{background-image:url(warn_small.png);} .donemark{background-image:url(ok_small.png);} @@ -631,6 +632,7 @@ .state-fg-ok{color:#66AA66;} .state-fg-error{color:#AA6666;} .state-fg-deleted{color:#3399FF;} +button{display:inline-block;padding:4px 10px 4px;font-size:12px;line-height:16px;color:#333333;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border:1px solid #ccc;border-bottom-color:#bbb;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);cursor:pointer;*margin-left:.3em;}button:first-child{*margin-left:0;} .action-button{display:inline-block;padding:4px 10px 4px;font-size:12px;line-height:16px;color:#333333;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border:1px solid #ccc;border-bottom-color:#bbb;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);cursor:pointer;*margin-left:.3em;}.action-button:first-child{*margin-left:0;} a.action-button{text-decoration:none;} .action-button>img{vertical-align:middle;} @@ -706,16 +708,17 @@ body.historyPage{background:#c1c9e5;color:#303030;margin:5px;border:0;padding:0;} a{color:#303030;} div.historyLinks{margin:5px 5px;} -div.historyItem{margin:5px -5px 5px 0px;padding:5px 11px 5px 5px;border:solid #888888 1px;border-left:solid #888888 5px;border-right:none;word-wrap:break-word;background:#eeeeee;}div.historyItem .state-icon{display:inline-block;vertical-align:middle;width:16px;height:16px;background-position:0 1px;background-repeat:no-repeat;} +div.historyItem{margin:0px -5px;padding:8px 10px;border-top:solid #999999 1px;border-right:none;word-wrap:break-word;background:#eeeeee;}div.historyItem .state-icon{display:inline-block;vertical-align:middle;width:16px;height:16px;background-position:0 1px;background-repeat:no-repeat;} div.historyItem .historyItemTitle{font-weight:bold;line-height:16px;} +.historyItemContainer:last-child div.historyItem{border-bottom:solid #999999 1px;} div.historyItem div.historyItem{margin-right:-11px;} -div.historyItem-ok,div.historyItem-failed_metadata{border-color:#66aa66;background:#ccffcc;}div.historyItem-ok .state-icon,div.historyItem-failed_metadata .state-icon{display:none;} -div.historyItem-error{border-color:#aa6666;background:#ffcccc;}div.historyItem-error .state-icon{-sprite-group:history-states;-sprite-image:data_error.png;} -div.historyItem-empty{border-color:#aa6666;background:#ffcccc;}div.historyItem-empty .state-icon{-sprite-group:history-states;-sprite-image:data_empty.png;} -div.historyItem-running{border-color:#aaaa66;background:#ffffcc;}div.historyItem-running .state-icon{background-image:url(data_running.gif);} -div.historyItem-setting_metadata{border-color:#aaaa66;background:#ffffcc;}div.historyItem-setting_metadata .state-icon{background-image:url(data_running.gif);} -div.historyItem-upload{border-color:#6666aa;background:#ccccff;}div.historyItem-upload .state-icon{background-image:url(data_upload.gif);} -div.historyItem-queued{background:#eeeeee;}div.historyItem-queued .state-icon{-sprite-group:history-states;-sprite-image:data_queued.png;} +div.historyItem-ok,div.historyItem-failed_metadata{background:#ccffcc;}div.historyItem-ok .state-icon,div.historyItem-failed_metadata .state-icon{display:none;} +div.historyItem-error{background:#ffcccc;}div.historyItem-error .state-icon{-sprite-group:history-states;-sprite-image:data_error.png;} +div.historyItem-empty{background:#ffcccc;}div.historyItem-empty .state-icon{-sprite-group:history-states;-sprite-image:data_empty.png;} +div.historyItem-running{background:#ffffcc;}div.historyItem-running .state-icon{background-image:url(data_running.gif);} +div.historyItem-setting_metadata{background:#ffffcc;}div.historyItem-setting_metadata .state-icon{background-image:url(data_running.gif);} +div.historyItem-upload{background:#ccccff;}div.historyItem-upload .state-icon{background-image:url(data_upload.gif);} +div.historyItem-queued .state-icon{-sprite-group:history-states;-sprite-image:data_queued.png;} div.historyItem-noPermission{filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60;} div.historyItemTitleBar.spinner .state-icon{background:url(data_running.gif) 0 1px no-repeat !important;} div.historyItemButtons{float:right;} diff -r 31b3f926d9284eee0331245b3be5299c0f7d9dd1 -r 3e01fd6ea098bb5fc6d1225784c568c399f330cd static/june_2007_style/blue_colors.ini --- a/static/june_2007_style/blue_colors.ini +++ b/static/june_2007_style/blue_colors.ini @@ -24,7 +24,7 @@ done_message_border=#66AA66 done_message_bg=#CCFFCC info_message_border=#6666AA -info_message_bg=#CCCCFF +info_message_bg=#d9edf7 # Tables table_header_bg=#ebd9b2 table_row_bg=white diff -r 31b3f926d9284eee0331245b3be5299c0f7d9dd1 -r 3e01fd6ea098bb5fc6d1225784c568c399f330cd static/june_2007_style/bootstrap/forms.less --- a/static/june_2007_style/bootstrap/forms.less +++ b/static/june_2007_style/bootstrap/forms.less @@ -59,7 +59,7 @@ font-size: @baseFontSize; line-height: @baseLineHeight; color: @gray; - border: 1px solid #ccc; + border: 1px solid @formElementBorder; .border-radius(3px); } .uneditable-textarea { @@ -261,7 +261,7 @@ // -------------------------- // Mixin for form field states -.formFieldState(@textColor: #555, @borderColor: #ccc, @backgroundColor: #f5f5f5) { +.formFieldState(@textColor: #555, @borderColor: @formElementBorder, @backgroundColor: #f5f5f5) { // Set the text color > label, .help-block, @@ -392,7 +392,7 @@ text-align: center; text-shadow: 0 1px 0 @white; background-color: #f5f5f5; - border: 1px solid #ccc; + border: 1px solid @formElementBorder; .border-radius(3px 0 0 3px); } .active { @@ -412,7 +412,7 @@ .border-radius(3px 0 0 3px); } .uneditable-input { - border-right-color: #ccc; + border-right-color: @formElementBorder; } .add-on { margin-right: 0; diff -r 31b3f926d9284eee0331245b3be5299c0f7d9dd1 -r 3e01fd6ea098bb5fc6d1225784c568c399f330cd static/june_2007_style/bootstrap/type.less --- a/static/june_2007_style/bootstrap/type.less +++ b/static/june_2007_style/bootstrap/type.less @@ -37,24 +37,24 @@ } } h1 { - font-size: 30px; + font-size: 24px; line-height: @baseLineHeight * 2; small { font-size: 18px; } } h2 { - font-size: 24px; - line-height: @baseLineHeight * 2; + font-size: 18px; + line-height: @baseLineHeight * 1.5; small { - font-size: 18px; + font-size: 14px; } } h3 { - line-height: @baseLineHeight * 1.5; - font-size: 18px; + line-height: @baseLineHeight; + font-size: 14px; small { - font-size: 14px; + font-size: 12px; } } h4, h5, h6 { diff -r 31b3f926d9284eee0331245b3be5299c0f7d9dd1 -r 3e01fd6ea098bb5fc6d1225784c568c399f330cd static/june_2007_style/galaxy_bootstrap.less --- a/static/june_2007_style/galaxy_bootstrap.less +++ b/static/june_2007_style/galaxy_bootstrap.less @@ -40,6 +40,9 @@ // Buttons @primaryButtonBackground: @linkColor; +// Forms +@formElementBorder: @grayLight; + // COMPONENT VARIABLES @@ -68,21 +71,21 @@ @navbarLinkColorHover: @white; // Form states and alerts -@warningText: #c09853; -@warningBackground: #fcf8e3; -@warningBorder: darken(spin(@warningBackground, -10), 3%); +@warningText: darken(@warn_message_bg,70%); +@warningBackground: @warn_message_bg; +@warningBorder: darken(spin(@warningBackground, -10), 30%); -@errorText: #b94a48; -@errorBackground: #f2dede; -@errorBorder: darken(spin(@errorBackground, -10), 3%); +@errorText: darken(@error_message_bg,70%); +@errorBackground: @error_message_bg; +@errorBorder: darken(spin(@errorBackground, -10), 30%); @successText: darken(@done_message_bg,70%); @successBackground: @done_message_bg; @successBorder: darken(spin(@successBackground, -10), 60%); -@infoText: #3a87ad; -@infoBackground: #d9edf7; -@infoBorder: darken(spin(@infoBackground, -10), 7%); +@infoText: darken(@info_message_bg,70%); +@infoBackground: @info_message_bg; +@infoBorder: darken(spin(@info_message_bg, -10), 60%); diff -r 31b3f926d9284eee0331245b3be5299c0f7d9dd1 -r 3e01fd6ea098bb5fc6d1225784c568c399f330cd static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js +++ b/static/scripts/galaxy.panels.js @@ -126,15 +126,15 @@ // Modal dialog boxes function hide_modal() { - $(".dialog-box-container" ).hide( 0, function() { + $("#overlay .modal" ).hide( 0, function() { $("#overlay").hide(); - $("#overlay").removeClass( "modal" ); + $("#overlay-background").removeClass( "in" ); $( ".dialog-box" ).find( ".body" ).children().remove(); } ); }; function show_modal() { - $("#overlay").addClass( "modal" ); + $("#overlay-background").addClass( "in" ); _show_modal.apply( this, arguments ); } @@ -144,41 +144,40 @@ function _show_modal( title, body, buttons, extra_buttons, init_fn ) { if ( title ) { - $( ".dialog-box" ).find( ".title" ).html( title ); - $( ".dialog-box" ).find( ".unified-panel-header" ).show(); + $( "#dialog-box .modal-header .title" ).html( title ); + $( "#dialog-box .modal-header" ).show(); } else { - $( ".dialog-box" ).find( ".unified-panel-header" ).hide(); + $( "#dialog-box .modal-header" ).hide(); } - var b = $( ".dialog-box" ).find( ".buttons" ).html( "" ); + var b = $( "#dialog-box" ).find( ".buttons" ).html( "" ); if ( buttons ) { $.each( buttons, function( name, value ) { b.append( $( '<button/>' ).text( name ).click( value ) ); b.append( " " ); }); - b.show(); - } else { - b.hide(); } - var b = $( ".dialog-box" ).find( ".extra_buttons" ).html( "" ); + var b = $( "#dialog-box" ).find( ".extra_buttons" ).html( "" ); if ( extra_buttons ) { $.each( extra_buttons, function( name, value ) { b.append( $( '<button/>' ).text( name ).click( value ) ); b.append( " " ); }); - b.show(); + } + if ( buttons || extra_buttons ) { + $( "#dialog-box .modal-footer" ).show(); } else { - b.hide(); + $( "#dialog-box .modal-footer" ).hide(); } if ( body == "progress" ) { - body = $("<img/>").attr("src", image_path + "/yui/rel_interstitial_loading.gif"); + body = $("<div class='progress progress-striped active'><div class='bar'></div></div>"); } var body_elt = $( ".dialog-box" ).find( ".body" ); // Clear min-width to allow for modal to take size of new body. body_elt.css("min-width", "0px"); - $( ".dialog-box" ).find( ".body" ).html( body ); - if ( ! $(".dialog-box-container").is( ":visible" ) ) { + $( "#dialog-box" ).find( ".modal-body" ).html( body ); + if ( ! $("#dialog-box").is( ":visible" ) ) { $("#overlay").show(); - $(".dialog-box-container").show(); + $("#dialog-box").show(); } // Fix min-width so that modal cannot shrink considerably if // new content is loaded. diff -r 31b3f926d9284eee0331245b3be5299c0f7d9dd1 -r 3e01fd6ea098bb5fc6d1225784c568c399f330cd templates/base_panels.mako --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -172,28 +172,26 @@ %endif > ## - <div id="overlay-background" style="position: absolute; width: 100%; height: 100%;"></div> + <div id="overlay-background" class="modal-backdrop fade"></div> ## Need a table here for centering in IE6 - <table class="dialog-box-container" border="0" cellpadding="0" cellspacing="0" + <div id="dialog-box" class="modal" border="0" %if not visible: style="display: none;" %endif - ><tr><td> - <div class="dialog-box-wrapper"> - <div class="dialog-box"> - <div class="unified-panel-header"> - <div class="unified-panel-header-inner"><span class='title'>${title}</span></div> + > + <div class="modal-header"> + <span><h3 class='title'>${title}</h3></span></div> - <div class="body">${content}</div> - <div> - <div class="buttons" style="display: none; float: right;"></div> - <div class="extra_buttons" style="display: none; padding: 5px;"></div> + <div class="modal-body">${content}</div> + <div class="modal-footer"> + <div class="buttons" style="float: right;"></div> + <div class="extra_buttons" style=""></div><div style="clear: both;"></div></div> - </div> + </div> - </td></tr></table> + </div></%def> diff -r 31b3f926d9284eee0331245b3be5299c0f7d9dd1 -r 3e01fd6ea098bb5fc6d1225784c568c399f330cd templates/root/history.mako --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -568,6 +568,7 @@ %else: ## Render requested datasets, ordered from newest to oldest + <div> %for data in reversed( datasets ): %if data.visible or show_hidden: <div class="historyItemContainer" id="historyItemContainer-${trans.app.security.encode_id(data.id)}"> @@ -575,6 +576,7 @@ </div> %endif %endfor + </div><div class="infomessagesmall" id="emptyHistoryMessage" style="display:none;"> %endif diff -r 31b3f926d9284eee0331245b3be5299c0f7d9dd1 -r 3e01fd6ea098bb5fc6d1225784c568c399f330cd templates/root/tool_menu.mako --- a/templates/root/tool_menu.mako +++ b/templates/root/tool_menu.mako @@ -321,12 +321,12 @@ else: display = "none" %> - <div id="tool-search" style="padding-bottom: 5px; position: relative; display: ${display}; width: 100%"> + <div id="tool-search" class="bar" style="margin: -6px -10px 10px -10px; padding: 5px 10px; position: relative; display: ${display};"> %if trans.app.config.get_bool( 'enable_tool_tags', False ): <b>Tags:</b> ${render_tool_tagging_elements()} %endif - <input type="text" name="query" value="search tools" id="tool-search-query" autocomplete="off" style="width: 100%; font-style:italic; font-size: inherit"/> + <input type="text" name="query" value="search tools" id="tool-search-query" autocomplete="off" class="search-query" style="width: 90%"/><img src="${h.url_for('/static/images/loading_small_white_bg.gif')}" id="search-spinner" style="display: none; position: absolute; right: 0; top: 5px;"/></div> diff -r 31b3f926d9284eee0331245b3be5299c0f7d9dd1 -r 3e01fd6ea098bb5fc6d1225784c568c399f330cd templates/workflow/editor.mako --- a/templates/workflow/editor.mako +++ b/templates/workflow/editor.mako @@ -926,7 +926,7 @@ <%def name="overlay(visible=False)"> ${parent.overlay( "Loading workflow editor...", - "<img src='" + h.url_for('/static/images/yui/rel_interstitial_loading.gif') + "'/>", self.overlay_visible )} + "<div class='progress progress-striped progress-info active'><div class='bar' style='width: 100%;'></div></div>", self.overlay_visible )} </%def><%def name="left_panel()"> https://bitbucket.org/galaxy/galaxy-central/changeset/dce46e57a70b/ changeset: dce46e57a70b user: james_taylor date: 2012-02-24 18:57:25 summary: style: fixing header spacing affected #: 2 files diff -r 3e01fd6ea098bb5fc6d1225784c568c399f330cd -r dce46e57a70b85cb8b34751551e2c92001a3aa2e static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -41,6 +41,7 @@ h1, h2, h3, h4 { color: @header_text; + margin: 0.5em 0; /*text-shadow: #bbb 2px 2px 1px;*/ } @@ -391,10 +392,9 @@ padding: 6px 10px 8px; // Force cursor to be pointer since tabs are either a link of a button cursor: pointer; - } - - .nav > li > a:hover { - color: gold; + &:hover { + color: gold; + } } .dropdown-menu a, .dropdown-menu a:hover { @@ -1516,7 +1516,7 @@ div.toolSectionTitle { - // font-weight: bold; + font-weight: bold; } div.toolPanelLabel diff -r 3e01fd6ea098bb5fc6d1225784c568c399f330cd -r dce46e57a70b85cb8b34751551e2c92001a3aa2e static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -487,7 +487,7 @@ body{background:#ffffff;color:#303030;background-image:url(base_bg.png);background-repeat:repeat-x;background-position:top;margin:10px;} img{border:0;} a:link,a:visited,a:active{text-decoration:underline;color:#303030;} -h1,h2,h3,h4{color:#023858;} +h1,h2,h3,h4{color:#023858;margin:0.5em 0;} h1:first-child,h2:first-child,h3:first-child,h4:first-child{margin-top:0px;} hr{border:none;height:0px;border-bottom:dotted #303030 1px;} table{border-collapse:collapse;} @@ -536,8 +536,7 @@ #masthead .navbar-text{margin-bottom:0;line-height:40px;color:#999999;}#masthead .navbar-text a:hover{color:#ffffff;background-color:transparent;} #masthead .btn,#masthead .btn-group{margin-top:5px;} #masthead .btn-group .btn{margin-top:0;} -#masthead .nav>li>a{padding:6px 10px 8px;cursor:pointer;} -#masthead .nav>li>a:hover{color:gold;} +#masthead .nav>li>a{padding:6px 10px 8px;cursor:pointer;}#masthead .nav>li>a:hover{color:gold;} #masthead .dropdown-menu a,#masthead .dropdown-menu a:hover{text-decoration:none;} #masthead .title{float:left;display:block;padding:8px 20px 12px;margin-left:-20px;font-size:20px;font-weight:200;line-height:1;color:#ffffff;font-family:verdana;font-weight:bold;color:white;padding:5px 20px 12px;margin-left:-15px;z-index:2000;}#masthead .title a{color:white;text-decoration:none;} #masthead .masthead-inner{padding-left:20px;padding-right:20px;background-color:#303239;background-image:-moz-linear-gradient(top, #333333, #2c3143);background-image:-ms-linear-gradient(top, #333333, #2c3143);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#333333), to(#2c3143));background-image:-webkit-linear-gradient(top, #333333, #2c3143);background-image:-o-linear-gradient(top, #333333, #2c3143);background-image:linear-gradient(top, #333333, #2c3143);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#333333', endColorstr='#2c3143', GradientType=0);-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:0 1px 3px rgba(0, 0, 0, 0.25),inset 0 -1px 0 rgba(0, 0, 0, 0.1);-moz-box-shadow:0 1px 3px rgba(0, 0, 0, 0.25),inset 0 -1px 0 rgba(0, 0, 0, 0.1);box-shadow:0 1px 3px rgba(0, 0, 0, 0.25),inset 0 -1px 0 rgba(0, 0, 0, 0.1);padding-left:0;padding-right:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;height:32px;} @@ -728,6 +727,7 @@ hr{border:none;height:0px;margin-top:0px;} div.toolSectionWrapper{margin-bottom:5px;} div.toolSectionDetailsInner{margin-left:5px;margin-right:5px;} +div.toolSectionTitle{font-weight:bold;} div.toolPanelLabel{font-weight:bold;color:gray;text-transform:uppercase;} div.toolTitle{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:square outside;} div.toolSectionBody div.toolPanelLabel{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:none outside;} https://bitbucket.org/galaxy/galaxy-central/changeset/e5460d5fa71f/ changeset: e5460d5fa71f user: james_taylor date: 2012-02-24 18:57:41 summary: Automated merge with https://bitbucket.org/galaxy/galaxy-central affected #: 65 files Diff too large to display. https://bitbucket.org/galaxy/galaxy-central/changeset/65e36ccf037c/ changeset: 65e36ccf037c user: james_taylor date: 2012-02-24 23:56:40 summary: style: rewrite modal dialog script affected #: 9 files diff -r e5460d5fa71f873ed72dd10cfa0ff8ffa3001dda -r 65e36ccf037c427a053f3331e7e3aca08befe5e5 static/june_2007_style/Makefile --- a/static/june_2007_style/Makefile +++ b/static/june_2007_style/Makefile @@ -19,7 +19,7 @@ # Old style using process_css still works so we can move gradually %.css : %.css.tmpl - ../process_css.py $(INI) shared_images:../images $(OUT) < $< > $@ + ../process_css.py ../$(INI) shared_images:../images $(OUT) < $< > $@ # For building sprite images %.less : %.less.tmpl diff -r e5460d5fa71f873ed72dd10cfa0ff8ffa3001dda -r 65e36ccf037c427a053f3331e7e3aca08befe5e5 static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -79,10 +79,10 @@ #messagebox { position:absolute; - top:33px; + top: @navbarHeight + @layout_top_padding + 1; left:0; width:100%; - height:24px !important; + height: @panel_header_height !important; overflow: hidden; border-bottom: solid #999 1px; font-size: 90%; diff -r e5460d5fa71f873ed72dd10cfa0ff8ffa3001dda -r 65e36ccf037c427a053f3331e7e3aca08befe5e5 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -493,7 +493,7 @@ table{border-collapse:collapse;} th{text-align:left;} #background{position:absolute;background:#eeeeee;z-index:-1;top:0;left:0;margin:0;padding:0;width:100%;height:100%;} -#messagebox{position:absolute;top:33px;left:0;width:100%;height:24px !important;overflow:hidden;border-bottom:solid #999 1px;font-size:90%;} +#messagebox{position:absolute;top:33px;left:0;width:100%;height:30px !important;overflow:hidden;border-bottom:solid #999 1px;font-size:90%;} #left,#left-border,#center,#right-border,#right{position:absolute;top:33px;bottom:0px;overflow:hidden;background:#fff;} #left{left:0px;width:250px;z-index:200;border-right:solid #999999 1px;} #left-border{left:250px;} diff -r e5460d5fa71f873ed72dd10cfa0ff8ffa3001dda -r 65e36ccf037c427a053f3331e7e3aca08befe5e5 static/june_2007_style/blue/trackster.css --- a/static/june_2007_style/blue/trackster.css +++ b/static/june_2007_style/blue/trackster.css @@ -1,6 +1,6 @@ .viewport-container{overflow-x:hidden;overflow-y:auto;} -.nav-container{width:100%;} -.nav{padding:0 0;color:#333;font-weight:bold;background:#cccccc;background-image:url(panel_header_bg.png);background-position:middle center;background-repeat:repeat-x;border-bottom:solid #333 1px;} +.trackster-nav-container{width:100%;} +.trackster-nav{padding:0 0;color:#333;font-weight:bold;background:#cccccc;background-image:url(panel_header_bg.png);background-position:middle center;background-repeat:repeat-x;border-bottom:solid #333 1px;} .content{font:10px verdana;} .nav-controls{text-align:center;padding:1px 0;} .nav-controls input{margin:0 5px;} @@ -57,11 +57,11 @@ .param-row{margin-top:0.2em;margin-left:1em;} .param-label{float:left;font-weight:bold;padding-top:0.2em;width:50%;} .menu-button{margin:0px 4px 0px 4px;} +.exclamation{background:transparent url(../images/fugue/exclamation.png) no-repeat;margin-left:5em;} .layer-transparent{background:transparent url(../images/fugue/layer-transparent-bw.png) no-repeat;} .layer-transparent.active{background:transparent url(../images/fugue/layer-transparent.png) no-repeat;} .arrow-resize-090{background:transparent url(../images/fugue/arrow-resize-090-bw.png) no-repeat;} .arrow-resize-090.active{background:transparent url(../images/fugue/arrow-resize-090.png) no-repeat;} -.exclamation{background:transparent url(../images/fugue/exclamation.png) no-repeat;margin-left:5em;} .layers-stack{background:transparent url(../images/fugue/layers-stack-bw.png) no-repeat;} .layers-stack:hover{background:transparent url(../images/fugue/layers-stack.png) no-repeat;} .chevron-expand{background:transparent url(../images/fugue/chevron-expand-bw.png) no-repeat;} @@ -94,6 +94,6 @@ .icon{display:inline-block;width:16px;height:16px;} .icon.more-down{background:url('../images/fugue/arrow-transition-270-bw.png') no-repeat 0px 0px;} .icon.more-across{background:url('../images/fugue/arrow-transition-bw.png') no-repeat 0px 0px;} -.intro > .action-button{margin:1em;padding:1em;text-decoration:underline;} +.intro > .action-button{background-color:#CCC;margin-top:10px;padding:1em;text-decoration:underline;} .feature-popup{position:absolute;z-index:1000;padding:5px;font-size:10px;filter:alpha(opacity=80);background-repeat:no-repeat;background-image:url(../images/tipsy.gif);background-position:top center;} -.feature-popup-inner{padding:5px 8px 4px 8px;background-color:black;color:white;} \ No newline at end of file +.feature-popup-inner{padding:5px 8px 4px 8px;background-color:black;color:white;} diff -r e5460d5fa71f873ed72dd10cfa0ff8ffa3001dda -r 65e36ccf037c427a053f3331e7e3aca08befe5e5 static/june_2007_style/trackster.css.tmpl --- a/static/june_2007_style/trackster.css.tmpl +++ b/static/june_2007_style/trackster.css.tmpl @@ -2,10 +2,10 @@ overflow-x: hidden; overflow-y: auto; } -.nav-container { +.trackster-nav-container { width: 100%; } -.nav { +.trackster-nav { padding: 0 0; color:#333; font-weight:bold; @@ -447,6 +447,7 @@ } .intro > .action-button { background-color: #CCC; + margin-top: 10px; padding: 1em; text-decoration:underline; } diff -r e5460d5fa71f873ed72dd10cfa0ff8ffa3001dda -r 65e36ccf037c427a053f3331e7e3aca08befe5e5 static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js +++ b/static/scripts/galaxy.panels.js @@ -121,72 +121,97 @@ $(self.toggle).on( "click", function() { self.do_toggle(); } ); } }); - // Modal dialog boxes +var Modal = function( options ) { + this.$overlay = options.overlay; + this.$dialog = options.dialog; + this.$header = this.$dialog.find( ".modal-header" ); + this.$body = this.$dialog.find( ".modal-body" ); + this.$footer = this.$dialog.find( ".modal-footer" ); + this.$backdrop = options.backdrop; +} +$.extend( Modal.prototype, { + setContent: function( options ) { + // Title + if ( options.title ) { + this.$header.find( ".title" ).html( options.title ); + this.$header.show(); + } else { + this.$header.hide(); + } + // Buttons + this.$footer.hide(); + console.log( this.$footer, options.buttons ); + var $buttons = this.$footer.find( ".buttons" ).html( "" ); + if ( options.buttons ) { + $.each( options.buttons, function( name, value ) { + $buttons.append( $( '<button>' ).text( name ).click( value ) ); + }); + this.$footer.show(); + } + var $extraButtons = this.$footer.find( ".extra_buttons" ).html( "" ); + if ( options.extra_buttons ) { + $.each( options.extra_buttons, function( name, value ) { + $extraButtons.append( $( '<button>' ).text( name ).click( value ) ); + }); + this.$footer.show(); + } + // Body + var body = options.body; + if ( body == "progress" ) { + body = $("<div class='progress progress-striped active'><div class='bar' style='width: 100%'></div></div>"); + } + this.$body.html( body ); + }, + show: function( options, callback ) { + if ( ! this.$dialog.is( ":visible" ) ) { + if ( options.backdrop) { + this.$backdrop.addClass( "in" ); + } else { + this.$backdrop.removeClass( "in" ); + } + this.$overlay.show(); + this.$dialog.show(); + // Fix min-width so that modal cannot shrink considerably if + // new content is loaded. + this.$body.css( "min-width", this.$body.width() ); + } + // Callback on init + if ( callback ) { + callback(); + } + }, + hide: function() { + var modal = this; + modal.$dialog.fadeOut( function() { + modal.$overlay.hide(); + modal.$backdrop.removeClass( "in" ); + modal.$body.children().remove(); + // Clear min-width to allow for modal to take size of new body. + modal.$body.css( "min-width", undefined ); + }); + } +}); +var modal; + +$(function(){ + modal = new Modal( { overlay: $("#overlay"), dialog: $("#dialog-box"), backdrop: $("#overlay-background") } ); +}); + +// Backward compatibility function hide_modal() { - $("#overlay .modal" ).hide( 0, function() { - $("#overlay").hide(); - $("#overlay-background").removeClass( "in" ); - $( ".dialog-box" ).find( ".body" ).children().remove(); - } ); -}; - -function show_modal() { - $("#overlay-background").addClass( "in" ); - _show_modal.apply( this, arguments ); + modal.hide(); } - -function show_message() { - _show_modal.apply( this, arguments ); +function show_modal( title, body, buttons, extra_buttons, init_fn ) { + modal.setContent( { title: title, body: body, buttons: buttons, extra_buttons: extra_buttons } ); + modal.show( { backdrop: true }, init_fn ); } - -function _show_modal( title, body, buttons, extra_buttons, init_fn ) { - if ( title ) { - $( "#dialog-box .modal-header .title" ).html( title ); - $( "#dialog-box .modal-header" ).show(); - } else { - $( "#dialog-box .modal-header" ).hide(); - } - var b = $( "#dialog-box" ).find( ".buttons" ).html( "" ); - if ( buttons ) { - $.each( buttons, function( name, value ) { - b.append( $( '<button/>' ).text( name ).click( value ) ); - b.append( " " ); - }); - } - var b = $( "#dialog-box" ).find( ".extra_buttons" ).html( "" ); - if ( extra_buttons ) { - $.each( extra_buttons, function( name, value ) { - b.append( $( '<button/>' ).text( name ).click( value ) ); - b.append( " " ); - }); - } - if ( buttons || extra_buttons ) { - $( "#dialog-box .modal-footer" ).show(); - } else { - $( "#dialog-box .modal-footer" ).hide(); - } - if ( body == "progress" ) { - body = $("<div class='progress progress-striped active'><div class='bar'></div></div>"); - } - var body_elt = $( ".dialog-box" ).find( ".body" ); - // Clear min-width to allow for modal to take size of new body. - body_elt.css("min-width", "0px"); - $( "#dialog-box" ).find( ".modal-body" ).html( body ); - if ( ! $("#dialog-box").is( ":visible" ) ) { - $("#overlay").show(); - $("#dialog-box").show(); - } - // Fix min-width so that modal cannot shrink considerably if - // new content is loaded. - body_elt.css("min-width", body_elt.width()); - if ( init_fn ) { - init_fn(); - } -}; - +function show_message( title, body, buttons, extra_buttons, init_fn ) { + modal.setContent( { title: title, body: body, buttons: buttons, extra_buttons: extra_buttons } ); + modal.show( { backdrop: false }, init_fn ); +} function show_in_overlay( options ) { var width = options.width || '600'; var height = options.height || '400'; @@ -237,6 +262,7 @@ // Exports exports.ensure_dd_helper = ensure_dd_helper; exports.Panel = Panel; +exports.Modal = Modal; exports.hide_modal = hide_modal; exports.show_modal = show_modal; exports.show_message = show_message; diff -r e5460d5fa71f873ed72dd10cfa0ff8ffa3001dda -r 65e36ccf037c427a053f3331e7e3aca08befe5e5 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -1339,8 +1339,8 @@ // Another label track at bottom this.nav_labeltrack = $("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container); // Navigation at top - this.nav_container = $("<div/>").addClass("nav-container").prependTo(this.top_container); - this.nav = $("<div/>").addClass("nav").appendTo(this.nav_container); + this.nav_container = $("<div/>").addClass("trackster-nav-container").prependTo(this.top_container); + this.nav = $("<div/>").addClass("trackster-nav").appendTo(this.nav_container); // Overview (scrollbar and overview plot) at bottom this.overview = $("<div/>").addClass("overview").appendTo(this.bottom_container); this.overview_viewport = $("<div/>").addClass("overview-viewport").appendTo(this.overview); diff -r e5460d5fa71f873ed72dd10cfa0ff8ffa3001dda -r 65e36ccf037c427a053f3331e7e3aca08befe5e5 templates/base_panels.mako --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -166,31 +166,30 @@ <%def name="title()"></%def><%def name="content()"></%def> - <div id="overlay" - %if not visible: - style="display: none;" - %endif - > - ## - <div id="overlay-background" class="modal-backdrop fade"></div> - - ## Need a table here for centering in IE6 - <div id="dialog-box" class="modal" border="0" - %if not visible: - style="display: none;" - %endif - > - <div class="modal-header"> - <span><h3 class='title'>${title}</h3></span> - </div> - <div class="modal-body">${content}</div> - <div class="modal-footer"> - <div class="buttons" style="float: right;"></div> - <div class="extra_buttons" style=""></div> - <div style="clear: both;"></div> - </div> + <% + if visible: + display = "" + overlay_class = "in" + else: + display = "style='display: none;'" + overlay_class = "" + %> - </div> + <div id="overlay" ${display}> + + <div id="overlay-background" class="modal-backdrop fade $overlay_class"></div> + + <div id="dialog-box" class="modal" border="0" ${display}> + <div class="modal-header"> + <span><h3 class='title'>${title}</h3></span> + </div> + <div class="modal-body">${content}</div> + <div class="modal-footer"> + <div class="buttons" style="float: right;"></div> + <div class="extra_buttons" style=""></div> + <div style="clear: both;"></div> + </div> + </div></div></%def> diff -r e5460d5fa71f873ed72dd10cfa0ff8ffa3001dda -r 65e36ccf037c427a053f3331e7e3aca08befe5e5 templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -18,13 +18,13 @@ #browser-container { overflow: none; } - .nav-container { + .trackster-nav-container { width: 100%; ## Overriding styles from trackster.css to push nav up into title bar height: 0; text-align: center; } - .nav { + .trackster-nav { ## Overriding styles from trackster.css to push nav up into title bar position: relative; display: inline-block; https://bitbucket.org/galaxy/galaxy-central/changeset/93a4eeb167d9/ changeset: 93a4eeb167d9 user: james_taylor date: 2012-02-27 20:42:39 summary: style: making menubuttons look like other buttons, buttons in grids now look like buttons affected #: 5 files diff -r 65e36ccf037c427a053f3331e7e3aca08befe5e5 -r 93a4eeb167d9f9c355ef5372c5a07f1c6ece8494 static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -34,10 +34,12 @@ } +/* a:link, a:visited, a:active { text-decoration: underline; color: @link_text; } +*/ h1, h2, h3, h4 { color: @header_text; @@ -790,6 +792,7 @@ background-image: url(info_small.png); } +/* I think this is only used in view details */ table.simple { font-size: 12px; background: #fff; @@ -809,7 +812,6 @@ table.simple tbody tr:hover td { color: #333; } - table.tabletip { width: 100%; border-collapse: collapse; @@ -827,6 +829,7 @@ background-color: #eee; } + table.colored { border-top: solid @table_border 1px; border-bottom: solid @table_border 1px; @@ -835,6 +838,7 @@ table.colored td, table.colored th { text-align: left; padding: 5px; + line-height: @baseLineHeight; } table.colored tr.header { @@ -862,6 +866,63 @@ color: black; } +// Data grid style + +.grid-header { + padding-bottom: 1em; +} + +.grid-header h2 { + margin: 0; + margin-bottom: 0.5em; +} + +.grid-header .title { + font-weight: bold; +} + +.grid { + padding-top: 1em; + border-collapse: collapse; + width: 100%; +} +.grid tbody td { + line-height: @baseLineHeight; + border-top: solid #DDDDDD 1px; + border-bottom: solid #DDDDDD 1px; + padding: 0.3em 0.5em; +} +.grid tbody td:empty { + padding: 0; +} +.grid thead tr { + height: 2em; +} +.grid thead th { + line-height: @baseLineHeight; + background: @table_header_bg; + // background-image: url(form_title_bg.png); + background-repeat: repeat-x; + background-position: top; + border-top: solid @table_border 1px; + border-bottom: solid @table_border 1px; + padding: 0.3em 0.5em; + text-align: left; + white-space: nowrap; +} +.grid tfoot td { + background-color: #F8F8F8; + border-top: solid #DDDDDD 1px; + border-bottom: solid #DDDDDD 1px; + padding: 0.3em 0.5em; +} +.grid .current { + background-color: #EEEEFF; +} + + + + div.odd_row { background: @odd_row_bg; } @@ -1040,47 +1101,52 @@ position: relative; .unselectable; - border: solid transparent 1px; - -moz-border-radius: 0.25em; - -webkit-border-radius: 0.25em; - border-radius: 0.25em; + // border: solid transparent 1px; + // -moz-border-radius: 0.25em; + // -webkit-border-radius: 0.25em; + // border-radius: 0.25em; - padding: 1px 0.25em; - margin: -1px -0.25em; + // padding: 1px 0.25em; + // margin: -1px -0.25em; .label { position: relative; - display: block; + // display: block; border-right: none; + text-decoration: none; } -} -.menubutton.action-button { - border-color: #aaaaaa; -} + &.popup .label { + border-right: solid @buttonBorder 1px; + padding-right: 6px; + } -.menubutton.popup, .action-button.popup { - padding-right: 20px; - background-image: url(../images/dropdownarrow.png); - background-repeat: no-repeat; - background-position: right 7px; -} + &.popup { + &:after { + margin-top: 6px; + .caret(); + } + } -.menubutton:hover { - border-color: #aaaaaa; - // background: #eeeeee; - // color: #333; + &.popup.split { + &:after { + margin-top: 6px; + margin-left: 0px; + .caret(); + } + } + } // A split menu button, the main button has an action, the arrow causes the // popup menu to appear .menubutton.popup.split { - padding-right: 2em; + // padding-right: 2em; } .menubutton.popup.split:hover { - background: url(../images/ddarrowsplit.png) no-repeat right -39px; + //background: url(../images/ddarrowsplit.png) no-repeat right -39px; } // Popup menu styles @@ -1164,58 +1230,6 @@ padding-left: 20px; } -// Data grid style - -.grid-header { - padding-bottom: 1em; -} - -.grid-header h2 { - margin: 0; - margin-bottom: 0.5em; -} - -.grid-header .title { - font-weight: bold; -} - -.grid { - padding-top: 1em; - border-collapse: collapse; - width: 100%; -} -.grid tbody td { - border-top: solid #DDDDDD 1px; - border-bottom: solid #DDDDDD 1px; - padding: 0.3em 0.5em; -} -.grid tbody td:empty { - padding: 0; -} -.grid thead tr { - height: 2em; -} -.grid thead th { - background: @table_header_bg; - // background-image: url(form_title_bg.png); - background-repeat: repeat-x; - background-position: top; - border-top: solid @table_border 1px; - border-bottom: solid @table_border 1px; - padding: 0.3em 0.5em; - text-align: left; - white-space: nowrap; -} -.grid tfoot td { - background-color: #F8F8F8; - border-top: solid #DDDDDD 1px; - border-bottom: solid #DDDDDD 1px; - padding: 0.3em 0.5em; -} -.grid .current { - background-color: #EEEEFF; -} - // Styles for areas of text content .text-content { @@ -1343,10 +1357,6 @@ padding: 0; } -a { - color: @base_text; -} - // Control links at top of history div.historyLinks { margin: 5px 5px; diff -r 65e36ccf037c427a053f3331e7e3aca08befe5e5 -r 93a4eeb167d9f9c355ef5372c5a07f1c6ece8494 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -95,10 +95,10 @@ .fade{-webkit-transition:opacity 0.15s linear;-moz-transition:opacity 0.15s linear;-ms-transition:opacity 0.15s linear;-o-transition:opacity 0.15s linear;transition:opacity 0.15s linear;opacity:0;}.fade.in{opacity:1;} .collapse{-webkit-transition:height 0.35s ease;-moz-transition:height 0.35s ease;-ms-transition:height 0.35s ease;-o-transition:height 0.35s ease;transition:height 0.35s ease;position:relative;overflow:hidden;height:0;}.collapse.in{height:auto;} .close{float:right;font-size:20px;font-weight:bold;line-height:16px;color:#000000;text-shadow:0 1px 0 #ffffff;opacity:0.2;filter:alpha(opacity=20);}.close:hover{color:#000000;text-decoration:none;opacity:0.4;filter:alpha(opacity=40);cursor:pointer;} -.btn{display:inline-block;padding:4px 10px 4px;font-size:12px;line-height:16px;color:#333333;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border:1px solid #ccc;border-bottom-color:#bbb;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);cursor:pointer;*margin-left:.3em;}.btn:first-child{*margin-left:0;} +.btn{display:inline-block;padding:4px 10px 4px;font-size:12px;line-height:16px;color:#333333;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border:1px solid #999999;border-bottom-color:#888888;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);cursor:pointer;*margin-left:.3em;}.btn:first-child{*margin-left:0;} .btn.hover,.btn:hover{color:#333333;text-decoration:none;background-color:#e6e6e6;background-position:0 -15px;-webkit-transition:background-position 0.1s linear;-moz-transition:background-position 0.1s linear;-ms-transition:background-position 0.1s linear;-o-transition:background-position 0.1s linear;transition:background-position 0.1s linear;} .btn:focus{outline:thin dotted;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;} -.btn.active,.btn:active{background-image:none;-webkit-box-shadow:inset 0 2px 4px rgba(0, 0, 0, 0.15),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 2px 4px rgba(0, 0, 0, 0.15),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 2px 4px rgba(0, 0, 0, 0.15),0 1px 2px rgba(0, 0, 0, 0.05);background-color:#e6e6e6;background-color:#d9d9d9 \9;color:rgba(0, 0, 0, 0.5);outline:0;} +.btn.active,.btn:active{background-image:none;-webkit-box-shadow:inset 0 2px 4px rgba(0, 0, 0, 0.15),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 2px 4px rgba(0, 0, 0, 0.15),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 2px 4px rgba(0, 0, 0, 0.15),0 1px 2px rgba(0, 0, 0, 0.05);background-color:#e6e6e6;background-color:#d9d9d9 \9;outline:0;} .btn.disabled,.btn[disabled]{cursor:default;background-image:none;background-color:#e6e6e6;opacity:0.65;filter:alpha(opacity=65);-webkit-box-shadow:none;-moz-box-shadow:none;box-shadow:none;} .btn-large{padding:9px 14px;font-size:14px;line-height:normal;-webkit-border-radius:5px;-moz-border-radius:5px;border-radius:5px;} .btn-large .icon{margin-top:1px;} @@ -486,7 +486,6 @@ .clear:after{clear:both;} body{background:#ffffff;color:#303030;background-image:url(base_bg.png);background-repeat:repeat-x;background-position:top;margin:10px;} img{border:0;} -a:link,a:visited,a:active{text-decoration:underline;color:#303030;} h1,h2,h3,h4{color:#023858;margin:0.5em 0;} h1:first-child,h2:first-child,h3:first-child,h4:first-child{margin-top:0px;} hr{border:none;height:0px;border-bottom:dotted #303030 1px;} @@ -604,11 +603,21 @@ table.tabletip td{border-bottom:1px solid #ddd;} table.tabletip tbody tr:hover td{background-color:#eee;} table.colored{border-top:solid #d8b365 1px;border-bottom:solid #d8b365 1px;} -table.colored td,table.colored th{text-align:left;padding:5px;} +table.colored td,table.colored th{text-align:left;padding:5px;line-height:16px;} table.colored tr.header{background:#ebd9b2;background-image:url(form_title_bg.png);background-repeat:repeat-x;background-position:top;border-bottom:solid #d8b365 1px;font-weight:bold;} table.colored tr{background:#ffffff;} table.colored tr.odd_row{background:#dadfef;} div.debug{margin:10px;padding:5px;background:#FFFF99;border:solid #FFFF33 1px;color:black;} +.grid-header{padding-bottom:1em;} +.grid-header h2{margin:0;margin-bottom:0.5em;} +.grid-header .title{font-weight:bold;} +.grid{padding-top:1em;border-collapse:collapse;width:100%;} +.grid tbody td{line-height:16px;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:0.3em 0.5em;} +.grid tbody td:empty{padding:0;} +.grid thead tr{height:2em;} +.grid thead th{line-height:16px;background:#ebd9b2;background-repeat:repeat-x;background-position:top;border-top:solid #d8b365 1px;border-bottom:solid #d8b365 1px;padding:0.3em 0.5em;text-align:left;white-space:nowrap;} +.grid tfoot td{background-color:#F8F8F8;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:0.3em 0.5em;} +.grid .current{background-color:#EEEEFF;} div.odd_row{background:#dadfef;} #footer{display:none;} span.toolParameterExpandableCollapsable{font-weight:bold;cursor:pointer;} @@ -631,19 +640,17 @@ .state-fg-ok{color:#66AA66;} .state-fg-error{color:#AA6666;} .state-fg-deleted{color:#3399FF;} -button{display:inline-block;padding:4px 10px 4px;font-size:12px;line-height:16px;color:#333333;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border:1px solid #ccc;border-bottom-color:#bbb;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);cursor:pointer;*margin-left:.3em;}button:first-child{*margin-left:0;} -.action-button{display:inline-block;padding:4px 10px 4px;font-size:12px;line-height:16px;color:#333333;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border:1px solid #ccc;border-bottom-color:#bbb;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);cursor:pointer;*margin-left:.3em;}.action-button:first-child{*margin-left:0;} +button{display:inline-block;padding:4px 10px 4px;font-size:12px;line-height:16px;color:#333333;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border:1px solid #999999;border-bottom-color:#888888;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);cursor:pointer;*margin-left:.3em;}button:first-child{*margin-left:0;} +.action-button{display:inline-block;padding:4px 10px 4px;font-size:12px;line-height:16px;color:#333333;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border:1px solid #999999;border-bottom-color:#888888;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);cursor:pointer;*margin-left:.3em;}.action-button:first-child{*margin-left:0;} a.action-button{text-decoration:none;} .action-button>img{vertical-align:middle;} .action-button:hover{color:#333333;text-decoration:none;background-color:#e6e6e6;background-position:0 -15px;-webkit-transition:background-position 0.1s linear;-moz-transition:background-position 0.1s linear;-ms-transition:background-position 0.1s linear;-o-transition:background-position 0.1s linear;transition:background-position 0.1s linear;} -.action-button:active{background-image:none;-webkit-box-shadow:inset 0 2px 4px rgba(0, 0, 0, 0.15),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 2px 4px rgba(0, 0, 0, 0.15),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 2px 4px rgba(0, 0, 0, 0.15),0 1px 2px rgba(0, 0, 0, 0.05);background-color:#e6e6e6;background-color:#d9d9d9 \9;color:rgba(0, 0, 0, 0.5);outline:0;} -.menubutton{display:inline-block;padding:4px 10px 4px;font-size:12px;line-height:16px;color:#333333;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border:1px solid #ccc;border-bottom-color:#bbb;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);cursor:pointer;*margin-left:.3em;display:inline-block;cursor:pointer;position:relative;-webkit-user-select:none;-moz-user-select:none;-o-user-select:none;user-select:none;border:solid transparent 1px;-moz-border-radius:0.25em;-webkit-border-radius:0.25em;border-radius:0.25em;padding:1px 0.25em;margin:-1px -0.25em;}.menubutton:first-child{*margin-left:0;} -.menubutton .label{position:relative;display:block;border-right:none;} -.menubutton.action-button{border-color:#aaaaaa;} -.menubutton.popup,.action-button.popup{padding-right:20px;background-image:url(../images/dropdownarrow.png);background-repeat:no-repeat;background-position:right 7px;} -.menubutton:hover{border-color:#aaaaaa;} -.menubutton.popup.split{padding-right:2em;} -.menubutton.popup.split:hover{background:url(../images/ddarrowsplit.png) no-repeat right -39px;} +.action-button:active{background-image:none;-webkit-box-shadow:inset 0 2px 4px rgba(0, 0, 0, 0.15),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 2px 4px rgba(0, 0, 0, 0.15),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 2px 4px rgba(0, 0, 0, 0.15),0 1px 2px rgba(0, 0, 0, 0.05);background-color:#e6e6e6;background-color:#d9d9d9 \9;outline:0;} +.menubutton{display:inline-block;padding:4px 10px 4px;font-size:12px;line-height:16px;color:#333333;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border:1px solid #999999;border-bottom-color:#888888;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);cursor:pointer;*margin-left:.3em;display:inline-block;cursor:pointer;position:relative;-webkit-user-select:none;-moz-user-select:none;-o-user-select:none;user-select:none;}.menubutton:first-child{*margin-left:0;} +.menubutton .label{position:relative;border-right:none;text-decoration:none;} +.menubutton.popup .label{border-right:solid #999999 1px;padding-right:6px;} +.menubutton.popup:after{margin-top:6px;display:inline-block;width:0;height:0;text-indent:-99999px;*text-indent:0;vertical-align:top;border-left:4px solid transparent;border-right:4px solid transparent;border-top:4px solid #000000;opacity:0.3;filter:alpha(opacity=30);content:"\2193";} +.menubutton.popup.split:after{margin-top:6px;margin-left:0px;display:inline-block;width:0;height:0;text-indent:-99999px;*text-indent:0;vertical-align:top;border-left:4px solid transparent;border-right:4px solid transparent;border-top:4px solid #000000;opacity:0.3;filter:alpha(opacity=30);content:"\2193";} div.popmenu-wrapper{position:absolute;top:100%;z-index:20000;}div.popmenu-wrapper ul.dropdown-menu{display:block;position:relative;float:none;} ul.dropdown-menu a{text-decoration:none;} ul.dropdown-menu li.head>a{text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);font-size:11px;font-weight:bold;line-height:16px;color:#999999;text-transform:uppercase;} @@ -651,16 +658,6 @@ .popup-arrow{cursor:pointer;text-decoration:none;color:#555;} .popup-arrow:hover{color:black;} div.permissionContainer{padding-left:20px;} -.grid-header{padding-bottom:1em;} -.grid-header h2{margin:0;margin-bottom:0.5em;} -.grid-header .title{font-weight:bold;} -.grid{padding-top:1em;border-collapse:collapse;width:100%;} -.grid tbody td{border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:0.3em 0.5em;} -.grid tbody td:empty{padding:0;} -.grid thead tr{height:2em;} -.grid thead th{background:#ebd9b2;background-repeat:repeat-x;background-position:top;border-top:solid #d8b365 1px;border-bottom:solid #d8b365 1px;padding:0.3em 0.5em;text-align:left;white-space:nowrap;} -.grid tfoot td{background-color:#F8F8F8;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:0.3em 0.5em;} -.grid .current{background-color:#EEEEFF;} .text-content hr{display:block;background:black;color:black;width:100%;height:1px;border:none;background:#aaa;color:#aaa;} .text-content table{border-collapse:collapse;border-top:1px solid #ccc;border-left:1px solid #ccc;} .text-content blockquote{color:#666;} @@ -704,8 +701,7 @@ .icon-button.multiinput{background:url(../images/documents-stack.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;} .icon-button.multiinput.disabled{background:url(../images/documents-stack-faded.png) no-repeat;cursor:auto;} .workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;padding-left:5px;} -body.historyPage{background:#c1c9e5;color:#303030;margin:5px;border:0;padding:0;} -a{color:#303030;} +body.historyPage{background:#dfe5f9;color:#303030;margin:5px;border:0;padding:0;} div.historyLinks{margin:5px 5px;} div.historyItem{margin:0px -5px;padding:8px 10px;border-top:solid #999999 1px;border-right:none;word-wrap:break-word;background:#eeeeee;}div.historyItem .state-icon{display:inline-block;vertical-align:middle;width:16px;height:16px;background-position:0 1px;background-repeat:no-repeat;} div.historyItem .historyItemTitle{font-weight:bold;line-height:16px;} @@ -723,7 +719,7 @@ div.historyItemButtons{float:right;} div.historyItemBody div{padding-top:2px;} pre.peek{background:white;color:black;width:100%;overflow:auto;}pre.peek th{color:white;background:#023858;} -body.toolMenuPage{background:white;color:#303030;background:#c1c9e5;margin:5px;margin-right:10px;margin-left:10px;} +body.toolMenuPage{background:white;color:#303030;background:#dfe5f9;margin:5px;margin-right:10px;margin-left:10px;} hr{border:none;height:0px;margin-top:0px;} div.toolSectionWrapper{margin-bottom:5px;} div.toolSectionDetailsInner{margin-left:5px;margin-right:5px;} diff -r 65e36ccf037c427a053f3331e7e3aca08befe5e5 -r 93a4eeb167d9f9c355ef5372c5a07f1c6ece8494 static/june_2007_style/blue_colors.ini --- a/static/june_2007_style/blue_colors.ini +++ b/static/june_2007_style/blue_colors.ini @@ -4,7 +4,7 @@ link_text=#303030 header_text=#023858 #menu_bg_top=#DADFEF -menu_bg_over=#C1C9E5 +menu_bg_over=#DFE5F9 menu_bg_hatch=- #menu_bg_hatch=#AAAAFF # Forms diff -r 65e36ccf037c427a053f3331e7e3aca08befe5e5 -r 93a4eeb167d9f9c355ef5372c5a07f1c6ece8494 static/june_2007_style/bootstrap/buttons.less --- a/static/june_2007_style/bootstrap/buttons.less +++ b/static/june_2007_style/bootstrap/buttons.less @@ -15,8 +15,8 @@ text-align: center; text-shadow: 0 1px 1px rgba(255,255,255,.75); #gradient > .vertical-three-colors(@white, @white, 25%, darken(@white, 10%)); // Don't use .gradientbar() here since it does a three-color gradient - border: 1px solid #ccc; - border-bottom-color: #bbb; + border: 1px solid @buttonBorder; + border-bottom-color: @buttonBorderBottom; .border-radius(4px); @shadow: inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05); .box-shadow(@shadow); @@ -52,7 +52,7 @@ .box-shadow(@shadow); background-color: darken(@white, 10%); background-color: darken(@white, 15%) e("\9"); - color: rgba(0,0,0,.5); + // color: rgba(0,0,0,.5); outline: 0; } diff -r 65e36ccf037c427a053f3331e7e3aca08befe5e5 -r 93a4eeb167d9f9c355ef5372c5a07f1c6ece8494 static/june_2007_style/galaxy_bootstrap.less --- a/static/june_2007_style/galaxy_bootstrap.less +++ b/static/june_2007_style/galaxy_bootstrap.less @@ -40,6 +40,9 @@ // Buttons @primaryButtonBackground: @linkColor; +@buttonBorder: #999; +@buttonBorderBottom: #888; + // Forms @formElementBorder: @grayLight; https://bitbucket.org/galaxy/galaxy-central/changeset/874b3006e35f/ changeset: 874b3006e35f user: james_taylor date: 2012-02-27 20:44:56 summary: style: restore underlined links affected #: 2 files diff -r 93a4eeb167d9f9c355ef5372c5a07f1c6ece8494 -r 874b3006e35f60e9ff4f47c1fc4fd8ad7136d7da static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -34,12 +34,11 @@ } -/* -a:link, a:visited, a:active { +a, a:link, a:visited, a:active { text-decoration: underline; color: @link_text; } -*/ + h1, h2, h3, h4 { color: @header_text; diff -r 93a4eeb167d9f9c355ef5372c5a07f1c6ece8494 -r 874b3006e35f60e9ff4f47c1fc4fd8ad7136d7da static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -486,6 +486,7 @@ .clear:after{clear:both;} body{background:#ffffff;color:#303030;background-image:url(base_bg.png);background-repeat:repeat-x;background-position:top;margin:10px;} img{border:0;} +a,a:link,a:visited,a:active{text-decoration:underline;color:#303030;} h1,h2,h3,h4{color:#023858;margin:0.5em 0;} h1:first-child,h2:first-child,h3:first-child,h4:first-child{margin-top:0px;} hr{border:none;height:0px;border-bottom:dotted #303030 1px;} https://bitbucket.org/galaxy/galaxy-central/changeset/09daefc0ccba/ changeset: 09daefc0ccba user: james_taylor date: 2012-02-28 00:09:16 summary: style: fix panels in firefox, pretty search box affected #: 6 files diff -r 874b3006e35f60e9ff4f47c1fc4fd8ad7136d7da -r 09daefc0ccba2088234c8bfbd95fdcc20c0054b5 static/june_2007_style/Makefile --- a/static/june_2007_style/Makefile +++ b/static/june_2007_style/Makefile @@ -19,12 +19,12 @@ # Old style using process_css still works so we can move gradually %.css : %.css.tmpl - ../process_css.py ../$(INI) shared_images:../images $(OUT) < $< > $@ + ../process_css.py ../$(INI) ..:../shared_images:../../images . < $< > $@ # For building sprite images %.less : %.less.tmpl - ../process_css.py $(INI) shared_images:../images $(OUT) < $< > $@ + ../process_css.py ../$(INI) ..:../shared_images:../../images . < $< > $@ # Some dependencies -base.css: variables.less galaxy_bootstrap.less iconic_stroke.less +base.css: variables.less galaxy_bootstrap.less iconic_stroke.less base_sprites.less diff -r 874b3006e35f60e9ff4f47c1fc4fd8ad7136d7da -r 09daefc0ccba2088234c8bfbd95fdcc20c0054b5 static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -14,6 +14,11 @@ .box-shadow(); } +.parent-width { + .box-sizing(border-box); + width: 100%; +} + // ==== Real (basic) styles ==== .clear { @@ -183,7 +188,7 @@ color: #555; } - .drag, .collapse { + .drag { position: absolute; top: 0; right: 0; @@ -194,52 +199,49 @@ background-image: url(../images/visualization/draggable_horizontal.png); background-repeat: no-repeat; background-position: 50% 50%; - - // .ie7-restore-right-whitespace(); - } - - .drag { cursor: w-resize; } - - .collapse { - position: fixed; - left: 0; - top: inherit; - bottom: 0; - background: none; - border-right: solid @layout_border 1px; - border-top: solid @layout_border 1px; - #gradient > .vertical-three-colors(darken(@white, 5%), darken(@white, 5%), 25%, darken(@white, 10%)); - .iconic(); - - } - .collapse.hidden { - // .opacity(50); - } - .collapse:before { - content:'\2190'; - } - .collapse.hidden:before { - content:'\2192'; - } } #right > .unified-panel-footer { .drag { left: 0; } - .collapse { +} + +// Needs to be outside panel to show when hidden +.panel-collapse { + .unified-panel-footer(); + z-index: 10000; + position: fixed; + left: 0; + top: inherit; + bottom: 0; + padding: 0 5px; + text-align: center; + width: @panel_footer_height - 5; + background: none; + border-right: solid @layout_border 1px; + border-top: solid @layout_border 1px; + #gradient > .vertical-three-colors(darken(@white, 5%), darken(@white, 5%), 25%, darken(@white, 10%)); + .iconic(); + &:before { + content:'\2190'; + } + &.hidden:before { + content:'\2192'; + } + &.right { left: inherit; right: 0; border-right: none; border-left: solid @layout_border 1px; - } - .collapse:before{ - content:'\2192'; - } - .collapse.hidden:before { - content:'\2190'; + &.right:before{ + content:'\2192'; + } + &.right.hidden:before { + content:'\2190'; + } } } @@ -669,11 +671,8 @@ max-width: 300px; } -/* .search-query { display: inline-block; - width: 210px; - height: @baseLineHeight; padding: 4px; margin-bottom: 9px; font-size: @baseFontSize; @@ -684,8 +683,22 @@ padding-right: 14px; margin-bottom: 0; // remove the default margin on all inputs .border-radius(14px); + max-width: auto; } -*/ +.search-query:focus { + border-color: rgba(82,168,236,.8); + @shadow: inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(82,168,236,.6); + .box-shadow(@shadow); + outline: 0; + outline: thin dotted \9; /* IE6-8 */ +} + +.search-spinner { + position: absolute; + display: none; + right: 8px; + top: 10px; +} // Messages @@ -889,7 +902,7 @@ line-height: @baseLineHeight; border-top: solid #DDDDDD 1px; border-bottom: solid #DDDDDD 1px; - padding: 0.3em 0.5em; + padding: 5px; } .grid tbody td:empty { padding: 0; @@ -905,7 +918,7 @@ background-position: top; border-top: solid @table_border 1px; border-bottom: solid @table_border 1px; - padding: 0.3em 0.5em; + padding: 5px; text-align: left; white-space: nowrap; } @@ -913,7 +926,7 @@ background-color: #F8F8F8; border-top: solid #DDDDDD 1px; border-bottom: solid #DDDDDD 1px; - padding: 0.3em 0.5em; + padding: 5px; } .grid .current { background-color: #EEEEFF; @@ -1503,7 +1516,6 @@ margin-top: 0px; } -/* div.toolSectionPad { margin: 0; @@ -1511,10 +1523,9 @@ height: 5px; font-size: 0px; } -*/ div.toolSectionWrapper { - margin-bottom: 5px; + // margin-bottom: 5px; } div.toolSectionDetailsInner diff -r 874b3006e35f60e9ff4f47c1fc4fd8ad7136d7da -r 09daefc0ccba2088234c8bfbd95fdcc20c0054b5 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -482,6 +482,7 @@ .iconic.spin_alt:before{content:'\e037';} .unselectable{-webkit-user-select:none;-moz-user-select:none;-o-user-select:none;user-select:none;} .shadow{-webkit-box-shadow:0 1px 3px rgba(0, 0, 0, 0.25);-moz-box-shadow:0 1px 3px rgba(0, 0, 0, 0.25);box-shadow:0 1px 3px rgba(0, 0, 0, 0.25);} +.parent-width{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;width:100%;} .clear{*zoom:1;}.clear:before,.clear:after{display:table;content:"";} .clear:after{clear:both;} body{background:#ffffff;color:#303030;background-image:url(base_bg.png);background-repeat:repeat-x;background-position:top;margin:10px;} @@ -504,15 +505,14 @@ .unified-panel-header{-webkit-user-select:none;-moz-user-select:none;-o-user-select:none;user-select:none;height:30px;z-index:1000;text-shadow:rgba(255, 255, 255, 0.8) 0 1px 0;background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border-bottom:solid #999999 1px;margin:0;padding:0;padding-right:10px;padding-left:10px;font-weight:bold;color:#555;}.unified-panel-header a{color:#555;} .unified-panel-header-inner{padding-top:8px;} .unified-panel-footer{-webkit-user-select:none;-moz-user-select:none;-o-user-select:none;user-select:none;position:absolute;bottom:0;height:25px;line-height:25px;width:100%;z-index:1000;border-top:solid #999999 1px;background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-ms-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#f2f2f2', endColorstr='#e6e6e6', GradientType=0);color:#555;}.unified-panel-footer a{color:#555;} -.unified-panel-footer .drag,.unified-panel-footer .collapse{position:absolute;top:0;right:0;padding:0 5px;text-align:center;height:25px;width:20px;background-image:url(../images/visualization/draggable_horizontal.png);background-repeat:no-repeat;background-position:50% 50%;} -.unified-panel-footer .drag{cursor:w-resize;} -.unified-panel-footer .collapse{position:fixed;left:0;top:inherit;bottom:0;background:none;border-right:solid #999999 1px;border-top:solid #999999 1px;background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-ms-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#f2f2f2', endColorstr='#e6e6e6', GradientType=0);display:inline-block;font-family:'IconicStroke';} -.unified-panel-footer .collapse:before{content:'\2190';} -.unified-panel-footer .collapse.hidden:before{content:'\2192';} +.unified-panel-footer .drag{position:absolute;top:0;right:0;padding:0 5px;text-align:center;height:25px;width:20px;background-image:url(../images/visualization/draggable_horizontal.png);background-repeat:no-repeat;background-position:50% 50%;cursor:w-resize;} #right>.unified-panel-footer .drag{left:0;} -#right>.unified-panel-footer .collapse{left:inherit;right:0;border-right:none;border-left:solid #999999 1px;} -#right>.unified-panel-footer .collapse:before{content:'\2192';} -#right>.unified-panel-footer .collapse.hidden:before{content:'\2190';} +.panel-collapse{-webkit-user-select:none;-moz-user-select:none;-o-user-select:none;user-select:none;position:absolute;bottom:0;height:25px;line-height:25px;width:100%;z-index:1000;border-top:solid #999999 1px;background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-ms-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#f2f2f2', endColorstr='#e6e6e6', GradientType=0);color:#555;z-index:10000;position:fixed;left:0;top:inherit;bottom:0;padding:0 5px;text-align:center;width:20px;background:none;border-right:solid #999999 1px;border-top:solid #999999 1px;background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-ms-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#f2f2f2', endColorstr='#e6e6e6', GradientType=0);display:inline-block;font-family:'IconicStroke';}.panel-collapse a{color:#555;} +.panel-collapse .drag{position:absolute;top:0;right:0;padding:0 5px;text-align:center;height:25px;width:20px;background-image:url(../images/visualization/draggable_horizontal.png);background-repeat:no-repeat;background-position:50% 50%;cursor:w-resize;} +.panel-collapse:before{content:'\2190';} +.panel-collapse.hidden:before{content:'\2192';} +.panel-collapse.right{left:inherit;right:0;border-right:none;border-left:solid #999999 1px;}.panel-collapse.right.right:before{content:'\2192';} +.panel-collapse.right.right.hidden:before{content:'\2190';} .menu-bg{background:whiteSmoke top repeat-x;} div.unified-panel-body{position:absolute;top:30px;bottom:0;width:100%;margin-top:1px;} #left>div.unified-panel-body,#right>div.unified-panel-body{bottom:25px;} @@ -580,6 +580,9 @@ .form-row .help{color:#666;} select,input,textarea{font:inherit;} select,textarea,input[type="text"],input[type="file"],input[type="password"]{max-width:300px;} +.search-query{display:inline-block;padding:4px;margin-bottom:9px;font-size:12px;line-height:16px;color:#555555;border:1px solid #999999;padding-left:14px;padding-right:14px;margin-bottom:0;-webkit-border-radius:14px;-moz-border-radius:14px;border-radius:14px;max-width:auto;} +.search-query:focus{border-color:rgba(82, 168, 236, 0.8);-webkit-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);-moz-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);outline:0;outline:thin dotted \9;} +.search-spinner{position:absolute;display:none;right:8px;top:10px;} .errormessagelarge,.warningmessagelarge,.donemessagelarge,.infomessagelarge{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#ffffcc;border:1px solid #ffdd33;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#666600;min-height:32px;padding-left:52px;background-image:url(error_message_icon.png);background-repeat:no-repeat;background-position:10px 10px;} .errormessagelarge{background-color:#ffcccc;border-color:#ff3355;color:#660000;padding-left:52px;} .warningmessagelarge{background-image:url(warn_message_icon.png);border-color:#aaaa66;background-color:#ffffcc;} @@ -613,11 +616,11 @@ .grid-header h2{margin:0;margin-bottom:0.5em;} .grid-header .title{font-weight:bold;} .grid{padding-top:1em;border-collapse:collapse;width:100%;} -.grid tbody td{line-height:16px;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:0.3em 0.5em;} +.grid tbody td{line-height:16px;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:5px;} .grid tbody td:empty{padding:0;} .grid thead tr{height:2em;} -.grid thead th{line-height:16px;background:#ebd9b2;background-repeat:repeat-x;background-position:top;border-top:solid #d8b365 1px;border-bottom:solid #d8b365 1px;padding:0.3em 0.5em;text-align:left;white-space:nowrap;} -.grid tfoot td{background-color:#F8F8F8;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:0.3em 0.5em;} +.grid thead th{line-height:16px;background:#ebd9b2;background-repeat:repeat-x;background-position:top;border-top:solid #d8b365 1px;border-bottom:solid #d8b365 1px;padding:5px;text-align:left;white-space:nowrap;} +.grid tfoot td{background-color:#F8F8F8;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:5px;} .grid .current{background-color:#EEEEFF;} div.odd_row{background:#dadfef;} #footer{display:none;} @@ -722,7 +725,7 @@ pre.peek{background:white;color:black;width:100%;overflow:auto;}pre.peek th{color:white;background:#023858;} body.toolMenuPage{background:white;color:#303030;background:#dfe5f9;margin:5px;margin-right:10px;margin-left:10px;} hr{border:none;height:0px;margin-top:0px;} -div.toolSectionWrapper{margin-bottom:5px;} +div.toolSectionPad{margin:0;padding:0;height:5px;font-size:0px;} div.toolSectionDetailsInner{margin-left:5px;margin-right:5px;} div.toolSectionTitle{font-weight:bold;} div.toolPanelLabel{font-weight:bold;color:gray;text-transform:uppercase;} diff -r 874b3006e35f60e9ff4f47c1fc4fd8ad7136d7da -r 09daefc0ccba2088234c8bfbd95fdcc20c0054b5 static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js +++ b/static/scripts/galaxy.panels.js @@ -18,10 +18,10 @@ MAX_PANEL_WIDTH = 800; var Panel = function( options ) { - this.panel = options.panel; - this.center = options.center; - this.drag = options.drag; - this.toggle = options.toggle; + this.$panel = options.panel; + this.$center = options.center; + this.$drag = options.drag; + this.$toggle = options.toggle; this.left = !options.right; this.hidden = false; this.hidden_by_tool = false; @@ -30,11 +30,11 @@ } $.extend( Panel.prototype, { resize: function( x ) { - $(this.panel).css( "width", x ); + this.$panel.css( "width", x ); if ( this.left ) { - $(center).css( "left", x ); + this.$center.css( "left", x ); } else { - $(center).css( "right", x ); + this.$center.css( "right", x ); } // ie7-recalc.js if ( document.recalc ) { document.recalc(); } @@ -42,44 +42,40 @@ do_toggle: function() { var self = this; if ( this.hidden ) { - $(this.toggle).removeClass( "hidden" ); + this.$toggle.removeClass( "hidden" ); if ( this.left ) { - $(this.panel).css( "left", - this.saved_size ).show().animate( { "left": 0 }, "fast", function () { + this.$panel.css( "left", - this.saved_size ).show().animate( { "left": 0 }, "fast", function () { self.resize( self.saved_size ); }); } else { - $(this.panel).css( "right", - this.saved_size ).show().animate( { "right": 0 }, "fast", function () { + this.$panel.css( "right", - this.saved_size ).show().animate( { "right": 0 }, "fast", function () { self.resize( self.saved_size ); }); } self.hidden = false; } else { - self.saved_size = $(this.panel).width(); - // Move center - - // $( center_el ).css( "right", $(border_el).innerWidth() + 1 ); - + self.saved_size = this.$panel.width(); if ( document.recalc ) { document.recalc(); } // Hide border if ( this.left ) { - $(this.panel).animate( { left: - this.saved_size }, "fast" ); + this.$panel.animate( { left: - this.saved_size }, "fast" ); } else { - $(this.panel).animate( { right: - this.saved_size }, "fast" ); + this.$panel.animate( { right: - this.saved_size }, "fast" ); } // self.resize(0); if ( this.left ) { - $(center).css( "left", 0 ); + this.$center.css( "left", 0 ); } else { - $(center).css( "right", 0 ); + this.$center.css( "right", 0 ); } self.hidden = true; - $(self.toggle).addClass( "hidden" ); + self.$toggle.addClass( "hidden" ); } this.hidden_by_tool = false; }, handle_minwidth_hint: function( x ) { - var space = $(this.center).width() - ( this.hidden ? this.saved_size : 0 ); + var space = this.$center.width() - ( this.hidden ? this.saved_size : 0 ); if ( space < x ) { if ( ! this.hidden ) { @@ -100,10 +96,12 @@ }, init: function() { var self = this; + // Pull the collapse element out to body level so it is visible when panel is hidden + this.$toggle.remove().appendTo( "body" ); // Resizing using drag element - $(this.drag).on( "dragstart", function( e, d ) { + this.$drag.on( "dragstart", function( e, d ) { $( '#DD-helper' ).show(); - d.width = $(self.panel).width(); + d.width = self.$panel.width(); }).on( "dragend", function() { $( '#DD-helper' ).hide(); }).on( "drag", function( e, d ) { @@ -118,7 +116,7 @@ self.resize( x ); }); // Hide/show using toggle element - $(self.toggle).on( "click", function() { self.do_toggle(); } ); + self.$toggle.on( "click", function() { self.do_toggle(); } ); } }); diff -r 874b3006e35f60e9ff4f47c1fc4fd8ad7136d7da -r 09daefc0ccba2088234c8bfbd95fdcc20c0054b5 templates/base_panels.mako --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -64,12 +64,12 @@ ensure_dd_helper(); %if self.has_left_panel: - var lp = new Panel( { panel: $("#left"), center: $("#center"), drag: $("#left > .unified-panel-footer > .drag" ), toggle: $("#left > .unified-panel-footer > .collapse" ) } ); + var lp = new Panel( { panel: $("#left"), center: $("#center"), drag: $("#left > .unified-panel-footer > .drag" ), toggle: $("#left > .unified-panel-footer > .panel-collapse" ) } ); force_left_panel = lp.force_panel; %endif %if self.has_right_panel: - var rp = new Panel( { panel: $("#right"), center: $("#center"), drag: $("#right > .unified-panel-footer > .drag" ), toggle: $("#right > .unified-panel-footer > .collapse" ), right: true } ); + var rp = new Panel( { panel: $("#right"), center: $("#center"), drag: $("#right > .unified-panel-footer > .drag" ), toggle: $("#right > .unified-panel-footer > .panel-collapse" ), right: true } ); window.handle_minwidth_hint = function( x ) { console.log( "hint", x ); rp.handle_minwidth_hint( x ) }; force_right_panel = function( x ) { rp.force_panel( x ) }; %endif @@ -168,7 +168,7 @@ <% if visible: - display = "" + display = "style='display: block;'" overlay_class = "in" else: display = "style='display: none;'" @@ -177,7 +177,7 @@ <div id="overlay" ${display}> - <div id="overlay-background" class="modal-backdrop fade $overlay_class"></div> + <div id="overlay-background" class="modal-backdrop fade ${overlay_class}"></div><div id="dialog-box" class="modal" border="0" ${display}><div class="modal-header"> @@ -229,7 +229,7 @@ <div id="left"> ${self.left_panel()} <div class="unified-panel-footer"> - <div class="collapse"></span></div> + <div class="panel-collapse"></span></div><div class="drag"></div></div></div> @@ -241,7 +241,7 @@ <div id="right"> ${self.right_panel()} <div class="unified-panel-footer"> - <div class="collapse"></span></div> + <div class="panel-collapse right"></span></div><div class="drag"></div></div></div> diff -r 874b3006e35f60e9ff4f47c1fc4fd8ad7136d7da -r 09daefc0ccba2088234c8bfbd95fdcc20c0054b5 templates/root/tool_menu.mako --- a/templates/root/tool_menu.mako +++ b/templates/root/tool_menu.mako @@ -321,13 +321,13 @@ else: display = "none" %> - <div id="tool-search" class="bar" style="margin: -6px -10px 10px -10px; padding: 5px 10px; position: relative; display: ${display};"> + <div id="tool-search" class="bar" style="padding-top: 5px; padding-bottom: 10px;position: relative; display: ${display};"> %if trans.app.config.get_bool( 'enable_tool_tags', False ): <b>Tags:</b> ${render_tool_tagging_elements()} %endif - <input type="text" name="query" value="search tools" id="tool-search-query" autocomplete="off" class="search-query" style="width: 90%"/> - <img src="${h.url_for('/static/images/loading_small_white_bg.gif')}" id="search-spinner" style="display: none; position: absolute; right: 0; top: 5px;"/> + <input type="text" name="query" value="search tools" id="tool-search-query" autocomplete="off" class="search-query parent-width" /> + <img src="${h.url_for('/static/images/loading_small_white_bg.gif')}" id="search-spinner" class="search-spinner"/></div> ## Recently used tools. https://bitbucket.org/galaxy/galaxy-central/changeset/31937c331c4d/ changeset: 31937c331c4d user: james_taylor date: 2012-03-05 19:48:46 summary: style: less file for iconic font affected #: 1 file diff -r 09daefc0ccba2088234c8bfbd95fdcc20c0054b5 -r 31937c331c4d4fc04e1d4436906411e458228d9e static/june_2007_style/iconic_stroke.less --- /dev/null +++ b/static/june_2007_style/iconic_stroke.less @@ -0,0 +1,461 @@ +@font-face { + font-family: 'IconicStroke'; + src: url('../images/fonts/iconic_stroke.eot'); + src: url('../images/fonts/iconic_stroke.eot?#iefix') format('embedded-opentype'), url('../images/fonts/iconic_stroke.ttf') format('truetype'), url('../images/fonts/iconic_stroke.svg#iconic') format('svg'); + font-weight: normal; + font-style: normal; +} +.iconic { + display: inline-block; + font-family: 'IconicStroke'; +} +.iconic.lightbulb:before { + content: '\e063'; +} +.iconic.equalizer:before { + content: '\e052'; +} +.iconic.map_pin_stroke:before { + content: '\e068'; +} +.iconic.brush_alt:before { + content: '\e01c'; +} +.iconic.move:before { + content: '\e03e'; +} +.iconic.pen_alt_stroke:before { + content: '\e005'; +} +.iconic.move_vertical:before { + content: '\e03b'; +} +.iconic.book_alt2:before { + content: '\e06a'; +} +.iconic.layers:before { + content: '\e01f'; +} +.iconic.pause:before { + content: '\e049'; +} +.iconic.layers_alt:before { + content: '\e020'; +} +.iconic.cloud_upload:before { + content: '\e045'; +} +.iconic.chart_alt:before { + content: '\e029'; +} +.iconic.fullscreen_exit_alt:before { + content: '\e051'; +} +.iconic.cloud_download:before { + content: '\e044'; +} +.iconic.comment_alt2_stroke:before { + content: '\e004'; +} +.iconic.mail:before { + content: '\2709'; +} +.iconic.check_alt:before { + content: '\2718'; +} +.iconic.document_stroke:before { + content: '\e066'; +} +.iconic.battery_charging:before { + content: '\e05d'; +} +.iconic.stop:before { + content: '\e04a'; +} +.iconic.arrow_up:before { + content: '\2191'; +} +.iconic.move_horizontal:before { + content: '\e038'; +} +.iconic.compass:before { + content: '\e021'; +} +.iconic.minus_alt:before { + content: '\e009'; +} +.iconic.battery_empty:before { + content: '\e05c'; +} +.iconic.map_pin_alt:before { + content: '\e002'; +} +.iconic.unlock_stroke:before { + content: '\e076'; +} +.iconic.lock_stroke:before { + content: '\e075'; +} +.iconic.question_mark:before { + content: '\003f'; +} +.iconic.list:before { + content: '\e055'; +} +.iconic.upload:before { + content: '\e043'; +} +.iconic.reload:before { + content: '\e030'; +} +.iconic.loop_alt4:before { + content: '\e035'; +} +.iconic.loop_alt3:before { + content: '\e034'; +} +.iconic.loop_alt2:before { + content: '\e033'; +} +.iconic.loop_alt1:before { + content: '\e032'; +} +.iconic.left_quote:before { + content: '\275d'; +} +.iconic.x:before { + content: '\2713'; +} +.iconic.last:before { + content: '\e04d'; +} +.iconic.document_alt_stroke:before { + content: '\e000'; +} +.iconic.bars:before { + content: '\e06f'; +} +.iconic.arrow_left:before { + content: '\2190'; +} +.iconic.arrow_down:before { + content: '\2193'; +} +.iconic.download:before { + content: '\e042'; +} +.iconic.home:before { + content: '\2302'; +} +.iconic.calendar:before { + content: '\e001'; +} +.iconic.right_quote_alt:before { + content: '\e012'; +} +.iconic.fullscreen:before { + content: '\e04e'; +} +.iconic.dial:before { + content: '\e058'; +} +.iconic.plus_alt:before { + content: '\e008'; +} +.iconic.clock:before { + content: '\e079'; +} +.iconic.movie:before { + content: '\e060'; +} +.iconic.steering_wheel:before { + content: '\e024'; +} +.iconic.pen:before { + content: '\270e'; +} +.iconic.tag_stroke:before { + content: '\e02b'; +} +.iconic.pin:before { + content: '\e067'; +} +.iconic.denied:before { + content: '\26d4'; +} +.iconic.left_quote_alt:before { + content: '\e011'; +} +.iconic.volume_mute:before { + content: '\e071'; +} +.iconic.arrow_up_alt2:before { + content: '\e018'; +} +.iconic.list_nested:before { + content: '\e056'; +} +.iconic.arrow_up_alt1:before { + content: '\e014'; +} +.iconic.comment_stroke:before { + content: '\e06d'; +} +.iconic.undo:before { + content: '\e02f'; +} +.iconic.umbrella:before { + content: '\2602'; +} +.iconic.bolt:before { + content: '\26a1'; +} +.iconic.article:before { + content: '\e053'; +} +.iconic.read_more:before { + content: '\e054'; +} +.iconic.beaker:before { + content: '\e023'; +} +.iconic.beaker_alt:before { + content: '\e010'; +} +.iconic.battery_full:before { + content: '\e073'; +} +.iconic.arrow_right:before { + content: '\2192'; +} +.iconic.new_window:before { + content: '\e059'; +} +.iconic.plus:before { + content: '\2795'; +} +.iconic.cog:before { + content: '\2699'; +} +.iconic.key_stroke:before { + content: '\26bf'; +} +.iconic.first:before { + content: '\e04c'; +} +.iconic.comment_alt1_stroke:before { + content: '\e003'; +} +.iconic.trash_stroke:before { + content: '\e05a'; +} +.iconic.image:before { + content: '\e027'; +} +.iconic.chat_alt_stroke:before { + content: '\e007'; +} +.iconic.cd:before { + content: '\e064'; +} +.iconic.right_quote:before { + content: '\275e'; +} +.iconic.brush:before { + content: '\e01b'; +} +.iconic.cloud:before { + content: '\2601'; +} +.iconic.eye:before { + content: '\e025'; +} +.iconic.play_alt:before { + content: '\e048'; +} +.iconic.transfer:before { + content: '\e041'; +} +.iconic.pen_alt2:before { + content: '\e006'; +} +.iconic.camera:before { + content: '\e070'; +} +.iconic.move_horizontal_alt2:before { + content: '\e03a'; +} +.iconic.curved_arrow:before { + content: '\2935'; +} +.iconic.move_horizontal_alt1:before { + content: '\e039'; +} +.iconic.aperture:before { + content: '\e026'; +} +.iconic.reload_alt:before { + content: '\e031'; +} +.iconic.magnifying_glass:before { + content: '\e074'; +} +.iconic.iphone:before { + content: '\e06e'; +} +.iconic.fork:before { + content: '\e046'; +} +.iconic.box:before { + content: '\e06b'; +} +.iconic.bars_alt:before { + content: '\e00a'; +} +.iconic.heart_stroke:before { + content: '\2764'; +} +.iconic.volume:before { + content: '\e072'; +} +.iconic.x_alt:before { + content: '\2714'; +} +.iconic.link:before { + content: '\e077'; +} +.iconic.moon_stroke:before { + content: '\263e'; +} +.iconic.eyedropper:before { + content: '\e01e'; +} +.iconic.spin:before { + content: '\e036'; +} +.iconic.rss:before { + content: '\e02c'; +} +.iconic.info:before { + content: '\2139'; +} +.iconic.target:before { + content: '\e02a'; +} +.iconic.cursor:before { + content: '\e057'; +} +.iconic.minus:before { + content: '\2796'; +} +.iconic.book_alt:before { + content: '\e00b'; +} +.iconic.headphones:before { + content: '\e061'; +} +.iconic.hash:before { + content: '\0023'; +} +.iconic.arrow_left_alt1:before { + content: '\e013'; +} +.iconic.arrow_left_alt2:before { + content: '\e017'; +} +.iconic.fullscreen_exit:before { + content: '\e050'; +} +.iconic.share:before { + content: '\e02e'; +} +.iconic.fullscreen_alt:before { + content: '\e04f'; +} +.iconic.at:before { + content: '\0040'; +} +.iconic.chat:before { + content: '\e05e'; +} +.iconic.move_vertical_alt2:before { + content: '\e03d'; +} +.iconic.move_vertical_alt1:before { + content: '\e03c'; +} +.iconic.check:before { + content: '\2717'; +} +.iconic.mic:before { + content: '\e05f'; +} +.iconic.calendar_alt_stroke:before { + content: '\e06c'; +} +.iconic.book:before { + content: '\e069'; +} +.iconic.move_alt1:before { + content: '\e03f'; +} +.iconic.move_alt2:before { + content: '\e040'; +} +.iconic.award_stroke:before { + content: '\e022'; +} +.iconic.wrench:before { + content: '\e078'; +} +.iconic.play:before { + content: '\e047'; +} +.iconic.star:before { + content: '\2605'; +} +.iconic.chart:before { + content: '\e028'; +} +.iconic.rain:before { + content: '\26c6'; +} +.iconic.folder_stroke:before { + content: '\e065'; +} +.iconic.sun_stroke:before { + content: '\2600'; +} +.iconic.user:before { + content: '\e062'; +} +.iconic.battery_half:before { + content: '\e05b'; +} +.iconic.aperture_alt:before { + content: '\e00c'; +} +.iconic.eject:before { + content: '\e04b'; +} +.iconic.arrow_down_alt1:before { + content: '\e016'; +} +.iconic.pilcrow:before { + content: '\00b6'; +} +.iconic.arrow_down_alt2:before { + content: '\e01a'; +} +.iconic.arrow_right_alt1:before { + content: '\e015'; +} +.iconic.arrow_right_alt2:before { + content: '\e019'; +} +.iconic.rss_alt:before { + content: '\e02d'; +} +.iconic.spin_alt:before { + content: '\e037'; +} https://bitbucket.org/galaxy/galaxy-central/changeset/78bf0820161f/ changeset: 78bf0820161f user: james_taylor date: 2012-03-05 19:57:30 summary: style: updating make_style.py to call make, removing scripts that are no longer used affected #: 4 files diff -r 31937c331c4d4fc04e1d4436906411e458228d9e -r 78bf0820161fdf30cd65fc54a804b778a08f032e static/june_2007_style/callout_top.py --- a/static/june_2007_style/callout_top.py +++ /dev/null @@ -1,55 +0,0 @@ -#!/usr/bin/env python - -""" -usage: %prog width height bg_color hatch_color [color alpha stop_pos] + -""" - -from __future__ import division - -import sys -import cairo - -assert sys.version_info[:2] >= ( 2, 4 ) - -def parse_css_color( color ): - if color.startswith( '#' ): - color = color[1:] - if len( color ) == 3: - r = int( color[0]*2, 16 ) - g = int( color[1]*2, 16 ) - b = int( color[2]*2, 16 ) - elif len( color ) == 6: - r = int( color[0:2], 16 ) - g = int( color[2:4], 16 ) - b = int( color[4:6], 16 ) - else: - raise Exception( "Color should be 3 hex numbers" ) - return r/256, g/256, b/256 - -width = int( sys.argv[1] ) -height = int( sys.argv[2] ) - -surface = cairo.ImageSurface( cairo.FORMAT_ARGB32, width, height ) -c = cairo.Context( surface ) - -height -= 1 -width -= 1 - -hw = width / 2 - -c.set_line_width( 1 ) - -def t( x ): return x + 0.5 - -c.move_to( t( 0 ), t( height+2 ) ) -c.line_to( t( hw ), t( 0 ) ) -c.line_to( t( width ), t( height+2 ) ) -c.close_path() - -c.set_source_rgb( *parse_css_color( sys.argv[3] ) ) -c.fill_preserve() - -c.set_source_rgb( *parse_css_color( sys.argv[4] ) ) -c.stroke() - -surface.write_to_png( "/dev/stdout" ) diff -r 31937c331c4d4fc04e1d4436906411e458228d9e -r 78bf0820161fdf30cd65fc54a804b778a08f032e static/june_2007_style/gradient.py --- a/static/june_2007_style/gradient.py +++ /dev/null @@ -1,74 +0,0 @@ -#!/usr/bin/env python - -""" -usage: %prog width height bg_color hatch_color [color alpha stop_pos] + -""" - -from __future__ import division - -import sys -import cairo - -assert sys.version_info[:2] >= ( 2, 4 ) - -def parse_css_color( color ): - if color.startswith( '#' ): - color = color[1:] - if len( color ) == 3: - r = int( color[0], 16 ) - g = int( color[1], 16 ) - b = int( color[2], 16 ) - elif len( color ) == 6: - r = int( color[0:2], 16 ) - g = int( color[2:4], 16 ) - b = int( color[4:6], 16 ) - else: - raise Exception( "Color should be 3 hex numbers" ) - return r/256, g/256, b/256 - -def gradient( width, height, args ): - pat = cairo.LinearGradient(0.0, 0.0, 0.0, height) - while len( args ) > 2: - col = parse_css_color( args[0] ) - alpha = float( args[1]) - pos = float( args[2] ) - pat.add_color_stop_rgba( pos, col[0], col[1], col[2], alpha ) - args = args[3:] - return pat - -def hatch( width, height, color ): - im_surf = cairo.ImageSurface( cairo.FORMAT_ARGB32, width, width ) - c = cairo.Context( im_surf ) - c.set_source_rgb ( *color ) - c.set_line_width( 0.75 ) - for i in range( 0, 2*max(height,width), 3 ): - c.move_to ( 0-10, i+10 ) - c.line_to ( width+10, i - width - 10 ) - c.stroke() - pat = cairo.SurfacePattern( im_surf ) - pat.set_extend (cairo.EXTEND_REPEAT) - return pat - -width = int( sys.argv[1] ) -height = int( sys.argv[2] ) - -surface = cairo.ImageSurface( cairo.FORMAT_ARGB32, width, height ) -c = cairo.Context( surface ) - -c.rectangle(0,0,width,height) -c.set_source_rgb( *parse_css_color( sys.argv[3] ) ) -c.fill() - -if sys.argv[4] != "-": - c.rectangle (0, 0, width, height) - c.set_source( hatch( width, height, parse_css_color( sys.argv[4] ) ) ) - c.fill() - -pat = cairo.LinearGradient(0.0, 0.0, 0.0, height) -pat.add_color_stop_rgba( 0, 1, 1, 1, 0 ) -pat.add_color_stop_rgba( 1, 1, 1, 1, 1 ) -c.rectangle (0, 0, width, height) -c.set_source( gradient( width, height, sys.argv[5:] ) ) -c.fill() - -surface.write_to_png( "/dev/stdout" ) diff -r 31937c331c4d4fc04e1d4436906411e458228d9e -r 78bf0820161fdf30cd65fc54a804b778a08f032e static/june_2007_style/make_style.py --- a/static/june_2007_style/make_style.py +++ b/static/june_2007_style/make_style.py @@ -1,83 +1,17 @@ #!/usr/bin/env python -import sys, string, os, tempfile, subprocess +import sys, os -# from Cheetah.Template import Template -from subprocess import Popen, PIPE +ini_file, out_dir = "blue_colors.ini", "blue" +if len(sys.argv) > 1: + ini_file, out_dir = sys.argv[1:] -assert sys.version_info[:2] >= ( 2, 4 ) +cmd = "make INI=%s OUT=%s" % ( ini_file, out_dir ) -# To create a new style ( this is an example ): -# In case you have not yet installed required packages: -# % sudo easy_install pyparsing -# % sudo easy_install http://effbot.org/downloads/Imaging-1.1.7.tar.gz -# When you have the above installed, add whatever new style you want to /static/june_2007_style/blue_colors.ini and then: -# % cd ~/static/june_2007_style/ -# % python make_style.py blue_colors.ini blue +print """NOTE: This script is no longer used for generating stylesheets. +Invoking '%s' instead""" % cmd -def run( cmd ): - return Popen( cmd, stdout=PIPE).communicate()[0] +os.system( cmd ) -# TODO: Are these images still being used? If not, clean this code up! -images = [ - ( "./gradient.py 9 30 $panel_header_bg_top - $panel_header_bg_bottom 0 0 $panel_header_bg_bottom 1 1", "panel_header_bg.png" ), - ( "./gradient.py 9 30 $panel_header_bg_bottom - $panel_header_bg_top 0 0 $panel_header_bg_top 1 1", "panel_header_bg_pressed.png" ), - ( "./gradient.py 9 1000 $menu_bg_top $menu_bg_hatch $menu_bg_over 0 0 $menu_bg_over 1 1", "menu_bg.png" ), - ( "./gradient.py 9 1000 $base_bg_top - $base_bg_bottom 0 0 $base_bg_bottom 1 1", "base_bg.png" ), - ( "./gradient.py 9 500 $form_body_bg_top - $form_body_bg_bottom 0 0 $form_body_bg_bottom 1 1", "form_body_bg.png" ), - ( "./gradient.py 9 50 $masthead_bg $masthead_bg_hatch", "masthead_bg.png" ), - ( "./gradient.py 9 30 $footer_title_bg $footer_title_hatch 000000 0 0.5 000000 1 1", "footer_title_bg.png" ), - ( "./gradient.py 9 50 $form_title_bg_top $form_title_bg_hatch $form_title_bg_bottom 0 0 $form_title_bg_bottom 1 1", "form_title_bg.png" ), - ( "./gradient.py 9 200 $history_ok_bg - FFFFFF 0 0.5 FFFFFF 0.5 1", "ok_bg.png" ), - ( "./gradient.py 9 200 $history_error_bg - FFFFFF 0 0.5 FFFFFF 0.5 1", "error_bg.png" ), - ( "./gradient.py 9 200 $history_running_bg - FFFFFF 0 0.5 FFFFFF 0.5 1", "warn_bg.png" ), - ( "./gradient.py 9 200 $history_queued_bg - FFFFFF 0 0.5 FFFFFF 0.5 1", "gray_bg.png" ), - ( "./callout_top.py 20 10 $panel_header_bg_top $layout_border", "popupmenu_callout_top.png" ), - ( "./circle.py 12 #FFFFFF #D8B365 right > workflow_circle_open.png" ), - ( "./circle.py 12 #BBFFBB #D8B365 right > workflow_circle_green.png" ), - ( "./circle.py 12 #FFFFFF #D8B365 none> workflow_circle_drag.png" ), - ] -# TODO: Are these shared_images still being used? If not, clean this code up! -shared_images = [ - # Dialog boxes - ( "ok_large.png", "done_message_bg", "done_message_icon.png" ), - ( "info_large.png", "info_message_bg", "info_message_icon.png" ), - ( "warn_large.png", "warn_message_bg", "warn_message_icon.png" ), - ( "error_large.png", "error_message_bg", "error_message_icon.png" ), - # History icons - ( "ok_small.png", "history_ok_bg", "data_ok.png" ), - ( "error_small.png", "history_error_bg", "data_error.png" ), - ( "wait_small.png", "history_queued_bg", "data_queued.png" ), -] -if __name__ == "__main__": - print "This script is no longer used for generating stylesheets. Please use the Makefile instead" - - # Old code for processing stylesheets - """ - if len(sys.argv) > 1: # has params - ini_file, out_dir = sys.argv[1:] - else: - cwd = os.getcwd() # default settings - ini_file, out_dir = cwd + "/blue_colors.ini", cwd + "/blue" - - for in_file, out_file in templates: - print in_file ,"->", out_file - subprocess.call( "./process_css.py %s shared_images:../images %s < %s > %s" % ( ini_file, out_dir, in_file, os.path.join( out_dir, out_file ) ), shell=True ) - """ - -# Old code for processing images, long disabled, though images are still used. -""" -for rule, output in images: - t = string.Template( rule ).substitute( context ) - print t, "->", output - open( os.path.join( out_dir, output ), "w" ).write( run( t.split() ) ) - -for src, bg, out in shared_images: - t = "./png_over_color.py shared_images/%s %s %s" % ( src, context[bg], os.path.join( out_dir, out ) ) - print t - run( t.split() ) -""" - - diff -r 31937c331c4d4fc04e1d4436906411e458228d9e -r 78bf0820161fdf30cd65fc54a804b778a08f032e static/june_2007_style/png_over_color.py --- a/static/june_2007_style/png_over_color.py +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env python - -import sys -import Image -import ImageColor - -assert sys.version_info[:2] >= ( 2, 4 ) - -over = Image.open( sys.argv[1] ) -color = ImageColor.getrgb( sys.argv[2] ) - -new = Image.new( 'RGBA', over.size, color ) - -# 'Over' is passed twice since it has an alpha channel -- it is it's own mask -new.paste( over, over ) - -new.save( sys.argv[3] ) \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/changeset/484c3bfb7f3e/ changeset: 484c3bfb7f3e user: james_taylor date: 2012-03-05 20:21:46 summary: merge affected #: 73 files Diff too large to display. https://bitbucket.org/galaxy/galaxy-central/changeset/551adce80d00/ changeset: 551adce80d00 user: james_taylor date: 2012-03-09 19:37:49 summary: style: use fontawesome instead of iconic, many fixes for IE8 compatibility affected #: 18 files 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b/static/june_2007_style/base.less @@ -2,7 +2,7 @@ @import "galaxy_bootstrap.less"; -@import "iconic_stroke.less"; +@import "fontawesome/font-awesome.less"; // Mixins @@ -17,6 +17,7 @@ .parent-width { .box-sizing(border-box); width: 100%; + *width: 90%; } // ==== Real (basic) styles ==== @@ -224,12 +225,13 @@ border-right: solid @layout_border 1px; border-top: solid @layout_border 1px; #gradient > .vertical-three-colors(darken(@white, 5%), darken(@white, 5%), 25%, darken(@white, 10%)); - .iconic(); + .ficon(); + font-size: 4/3em; &:before { - content:'\2190'; + content:'\f053'; } &.hidden:before { - content:'\2192'; + content:'\f054'; } &.right { left: inherit; @@ -237,10 +239,10 @@ border-right: none; border-left: solid @layout_border 1px; &.right:before{ - content:'\2192'; + content:'\f054'; } &.right.hidden:before { - content:'\2190'; + content:'\f053'; } } } @@ -484,63 +486,6 @@ // ==== Tool form styles ==== -div.toolForm { - border: solid @form_border 1px; -} - -div.toolFormTitle { - font-weight: bold; - padding: 5px; - padding-left: 10px; - padding-right: 10px; - background: @form_title_bg_bottom; - // background-image: url(form_title_bg.png); - background-repeat: repeat-x; - background-position: top; - border-bottom: solid @form_border 1px; -} - -div.toolParamHelp { - color: #666; -} - -div.toolParamHelp a { - color: #666; -} - -div.toolFormBody { - background: @form_body_bg_bottom; - background-image: url(form_body_bg.png); - background-repeat: repeat-x; - background-position: top; - padding: 5px 0; -} - -div.toolFormBody div.toolFormTitle { - background: transparent; - border: none; - font-weight: bold; - border-bottom: solid @form_border 1px; - margin-bottom: 5px; -} - -div.toolFormDisabled div.toolFormTitle { - background: @layout_bg; - border-color: @layout_border; -} - -div.toolFormDisabled { - border-color: @layout_border; -} - -div.toolHelp { - margin-top: 10px; -} - -div.toolHelpBody { - width: 100%; -} - div.metadataForm { border:solid #aaaaaa 1px; } @@ -594,17 +539,54 @@ // Forms -div.form { - border: solid @form_border 1px; +div.toolFormBody { + background: @form_body_bg_bottom; + background-image: url(form_body_bg.png); + background-repeat: repeat-x; + background-position: top; + padding: 5px 0; } -div.form-title { +div.toolFormBody div.toolFormTitle { + background: transparent; + border: none; font-weight: bold; + border-bottom: solid @form_border 1px; + margin-bottom: 5px; +} + +div.toolFormDisabled div.toolFormTitle { + background: @layout_bg; + border-color: @layout_border; +} + +div.toolFormDisabled { + border-color: @layout_border; +} + +div.toolHelp { + margin-top: 15px; + padding: 5px; +} + +div.toolHelpBody { + width: 100%; +} + + + +div.form, div.toolForm { + // border: solid @form_border 1px; +} + +div.form-title, div.toolFormTitle { + font-size: @baseFontSize * 1.25; + line-height: @baseLineHeight * 1.5; padding: 5px 10px; background: @form_title_bg_bottom; - background-image: url(form_title_bg.png); - background-repeat: repeat-x; - background-position: top; + // background-image: url(form_title_bg.png); + // background-repeat: repeat-x; + // background-position: top; border-bottom: solid @form_border 1px; } @@ -658,8 +640,27 @@ padding: 3px 0; } -.form-row .help { +.form-row .help, .toolParamHelp { color: #666; + a { + color: #666; + } +} + +.form-row.form-actions { + background: whiteSmoke; + border-top: solid #ddd 1px; + padding-top: 10px; + padding-bottom: 10px; + margin-top: 5px; +} + +// Selects +select { + //border: 1px solid @formElementBorder; + padding: 4px; + font-size: @baseFontSize; + line-height: @baseLineHeight; } select, input, textarea { @@ -671,22 +672,28 @@ max-width: 300px; } +textarea, input[type="text"], input[type="password"] { + font-size: @baseFontSize; + line-height: @baseLineHeight; + border: 1px solid @formElementBorder; + padding: 3px; +} + .search-query { display: inline-block; padding: 4px; - margin-bottom: 9px; font-size: @baseFontSize; line-height: @baseLineHeight; color: @gray; border: 1px solid @formElementBorder; - padding-left: 14px; - padding-right: 14px; + padding-left: 14px !important; + padding-right: 14px !important; margin-bottom: 0; // remove the default margin on all inputs .border-radius(14px); max-width: auto; } .search-query:focus { - border-color: rgba(82,168,236,.8); + border-color: darken(rgba(82,168,236,.8),15%); @shadow: inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(82,168,236,.6); .box-shadow(@shadow); outline: 0; @@ -710,7 +717,7 @@ background-color: @error_message_bg; */ .alert(); - min-height: 32px; + min-height: 36px; padding-left: 52px; background-image: url(error_message_icon.png); background-repeat: no-repeat; @@ -932,6 +939,91 @@ background-color: #EEEEFF; } +// Pulled out of grid base +.count-box { + min-width: 1.1em; + padding: 5px; + border-width: 1px; + border-style: solid; + text-align: center; + display: inline-block; +} +.text-filter-val { + border: solid 1px #AAAAAA; + padding: 1px 2px 1px 3px; + margin-right: 5px; + -moz-border-radius: .5em; + -webkit-border-radius: .5em; + font-style: italic; +} +.page-link a, .inactive-link { + padding: 0px 7px 0px 7px; + color: #555; +} +.inactive-link, .current-filter { + font-weight: bold; + color: #000; +} +.submit-image { + background: url(../images/fugue/magnifier-left.png) no-repeat center transparent; + background-color: #eee; + width: @baseLineHeight + 8; + height: @baseLineHeight + 8; + cursor: pointer; + margin: 0; + padding: 0; + display: block; + //float: right; + border: 1px solid #aaa; + border-left: none; +} +#advanced-search td { + padding: 3px; +} +#advanced-search table { + border-collapse: separate; +} +.delete-search-icon { + background: url(../images/delete_tag_icon_gray.png) center no-repeat; + display: inline-block; + width: 10px; + cursor: pointer; + height: 18px; + vertical-align: middle; + margin-left: 2px; + +} +.search-box-input { + border: 0; + float: left; + outline: medium none; + font-style: italic; + font-size: inherit; +} +.search-box { + vertical-align: bottom; + display: inline-block; + padding: 0; + // border: 1px solid #aaa; +} +.gray-background { + background-color: #DDDDDD; +} +.loading-elt-overlay { + background-color : white; + opacity : 0.5; + width : 100%; + height : 100%; + z-index : 14000; + position : fixed; + display: none; +} + + + + + + @@ -1073,9 +1165,9 @@ // Button styles -button { - .btn(); -} +//button { +// .btn(); +//} .action-button { .btn(); diff -r 484c3bfb7f3e24213447ea45ed273c328e599eb8 -r 551adce80d002272ce47a850834c26b8b63028a7 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -15,7 +15,7 @@ input[type="search"]{-webkit-appearance:textfield;-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box;} input[type="search"]::-webkit-search-decoration,input[type="search"]::-webkit-search-cancel-button{-webkit-appearance:none;} textarea{overflow:auto;vertical-align:top;} -body{margin:0;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:12px;line-height:16px;color:#333333;background-color:#ffffff;} +body{margin:0;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:12px;line-height:16px;color:#111111;background-color:#ffffff;} a{color:#303030;text-decoration:none;} a:hover{color:#0a0a0a;text-decoration:underline;} p{margin:0 0 8px;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:12px;line-height:16px;}p small{font-size:10px;color:#999999;} @@ -95,8 +95,8 @@ .fade{-webkit-transition:opacity 0.15s linear;-moz-transition:opacity 0.15s linear;-ms-transition:opacity 0.15s linear;-o-transition:opacity 0.15s linear;transition:opacity 0.15s linear;opacity:0;}.fade.in{opacity:1;} .collapse{-webkit-transition:height 0.35s ease;-moz-transition:height 0.35s ease;-ms-transition:height 0.35s ease;-o-transition:height 0.35s ease;transition:height 0.35s ease;position:relative;overflow:hidden;height:0;}.collapse.in{height:auto;} .close{float:right;font-size:20px;font-weight:bold;line-height:16px;color:#000000;text-shadow:0 1px 0 #ffffff;opacity:0.2;filter:alpha(opacity=20);}.close:hover{color:#000000;text-decoration:none;opacity:0.4;filter:alpha(opacity=40);cursor:pointer;} -.btn{display:inline-block;padding:4px 10px 4px;font-size:12px;line-height:16px;color:#333333;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border:1px solid #999999;border-bottom-color:#888888;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);cursor:pointer;*margin-left:.3em;}.btn:first-child{*margin-left:0;} -.btn.hover,.btn:hover{color:#333333;text-decoration:none;background-color:#e6e6e6;background-position:0 -15px;-webkit-transition:background-position 0.1s linear;-moz-transition:background-position 0.1s linear;-ms-transition:background-position 0.1s linear;-o-transition:background-position 0.1s linear;transition:background-position 0.1s linear;} +.btn{display:inline-block;padding:4px 10px 4px;font-size:12px;line-height:16px;color:#111111;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border:1px solid #999999;border-bottom-color:#888888;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);cursor:pointer;*margin-left:.3em;}.btn:first-child{*margin-left:0;} +.btn.hover,.btn:hover{color:#111111;text-decoration:none;background-color:#e6e6e6;background-position:0 -15px;-webkit-transition:background-position 0.1s linear;-moz-transition:background-position 0.1s linear;-ms-transition:background-position 0.1s linear;-o-transition:background-position 0.1s linear;transition:background-position 0.1s linear;} .btn:focus{outline:thin dotted;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;} .btn.active,.btn:active{background-image:none;-webkit-box-shadow:inset 0 2px 4px rgba(0, 0, 0, 0.15),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 2px 4px rgba(0, 0, 0, 0.15),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 2px 4px rgba(0, 0, 0, 0.15),0 1px 2px rgba(0, 0, 0, 0.05);background-color:#e6e6e6;background-color:#d9d9d9 \9;outline:0;} .btn.disabled,.btn[disabled]{cursor:default;background-image:none;background-color:#e6e6e6;opacity:0.65;filter:alpha(opacity=65);-webkit-box-shadow:none;-moz-box-shadow:none;box-shadow:none;} @@ -106,8 +106,8 @@ .btn-small .icon{margin-top:-1px;} .btn-primary,.btn-primary:hover,.btn-warning,.btn-warning:hover,.btn-danger,.btn-danger:hover,.btn-success,.btn-success:hover,.btn-info,.btn-info:hover{text-shadow:0 -1px 0 rgba(0, 0, 0, 0.25);color:#ffffff;} .btn-primary.active,.btn-warning.active,.btn-danger.active,.btn-success.active,.btn-info.active{color:rgba(255, 255, 255, 0.75);} -.btn-primary{background-color:#303030;background-image:-moz-linear-gradient(top, #303030, #303030);background-image:-ms-linear-gradient(top, #303030, #303030);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#303030), to(#303030));background-image:-webkit-linear-gradient(top, #303030, #303030);background-image:-o-linear-gradient(top, #303030, #303030);background-image:linear-gradient(top, #303030, #303030);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#303030', endColorstr='#303030', GradientType=0);border-color:#303030 #303030 #0a0a0a;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);}.btn-primary:hover,.btn-primary:active,.btn-primary.active,.btn-primary.disabled,.btn-primary[disabled]{background-color:#303030;} -.btn-primary:active,.btn-primary.active{background-color:#161616 \9;} +.btn-primary{background-color:#0049cd;background-image:-moz-linear-gradient(top, #0064cd, #0020cd);background-image:-ms-linear-gradient(top, #0064cd, #0020cd);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#0064cd), to(#0020cd));background-image:-webkit-linear-gradient(top, #0064cd, #0020cd);background-image:-o-linear-gradient(top, #0064cd, #0020cd);background-image:linear-gradient(top, #0064cd, #0020cd);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#0064cd', endColorstr='#0020cd', GradientType=0);border-color:#0020cd #0020cd #001481;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);}.btn-primary:hover,.btn-primary:active,.btn-primary.active,.btn-primary.disabled,.btn-primary[disabled]{background-color:#0020cd;} +.btn-primary:active,.btn-primary.active{background-color:#00189a \9;} .btn-warning{background-color:#faa732;background-image:-moz-linear-gradient(top, #fbb450, #f89406);background-image:-ms-linear-gradient(top, #fbb450, #f89406);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#fbb450), to(#f89406));background-image:-webkit-linear-gradient(top, #fbb450, #f89406);background-image:-o-linear-gradient(top, #fbb450, #f89406);background-image:linear-gradient(top, #fbb450, #f89406);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fbb450', endColorstr='#f89406', GradientType=0);border-color:#f89406 #f89406 #ad6704;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);}.btn-warning:hover,.btn-warning:active,.btn-warning.active,.btn-warning.disabled,.btn-warning[disabled]{background-color:#f89406;} .btn-warning:active,.btn-warning.active{background-color:#c67605 \9;} .btn-danger{background-color:#da4f49;background-image:-moz-linear-gradient(top, #ee5f5b, #bd362f);background-image:-ms-linear-gradient(top, #ee5f5b, #bd362f);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#bd362f));background-image:-webkit-linear-gradient(top, #ee5f5b, #bd362f);background-image:-o-linear-gradient(top, #ee5f5b, #bd362f);background-image:linear-gradient(top, #ee5f5b, #bd362f);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ee5f5b', endColorstr='#bd362f', GradientType=0);border-color:#bd362f #bd362f #802420;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);}.btn-danger:hover,.btn-danger:active,.btn-danger.active,.btn-danger.disabled,.btn-danger[disabled]{background-color:#bd362f;} @@ -329,7 +329,7 @@ .hide{display:none;} .show{display:block;} .invisible{visibility:hidden;} -@font-face{font-family:'IconicStroke';src:url('../images/fonts/iconic_stroke.eot');src:url('../images/fonts/iconic_stroke.eot?#iefix') format('embedded-opentype'),url('../images/fonts/iconic_stroke.ttf') format('truetype'),url('../images/fonts/iconic_stroke.svg#iconic') format('svg');font-weight:normal;font-style:normal;}.iconic{display:inline-block;font-family:'IconicStroke';} +@font-face{font-family:'IconicStroke';src:url('/static/images/fonts/iconic_stroke.eot');src:url('/static/images/fonts/iconic_stroke.eot?#iefix') format('embedded-opentype'),url('../images/fonts/iconic_stroke.ttf') format('truetype'),url('../images/fonts/iconic_stroke.svg#iconic') format('svg');font-weight:normal;font-style:normal;}.iconic{display:inline-block;font-family:'IconicStroke';} .iconic.lightbulb:before{content:'\e063';} .iconic.equalizer:before{content:'\e052';} .iconic.map_pin_stroke:before{content:'\e068';} @@ -480,9 +480,156 @@ .iconic.arrow_right_alt2:before{content:'\e019';} .iconic.rss_alt:before{content:'\e02d';} .iconic.spin_alt:before{content:'\e037';} +@font-face{font-family:'FontAwesome';src:url('../images/fonts/fontawesome-webfont.eot');src:url('../images/fonts/fontawesome-webfont.eot?#iefix') format('embedded-opentype'),url('../images/fonts/fontawesome-webfont.woff') format('woff'),url('../images/fonts/fontawesome-webfont.ttf') format('truetype'),url('../images/fonts/fontawesome-webfont.svgz#FontAwesomeRegular') format('svg'),url('../images/fonts/fontawesome-webfont.svg#FontAwesomeRegular') format('svg');font-weight:normal;font-style:normal;}.ficon,[class^="ficon"]:before,[class*=" ficon"]:before{font-family:FontAwesome;font-weight:normal;font-style:normal;display:inline-block;} +.ficon.large:before{font-size:1.3333333333333333em;} +.btn [class^="ficon"],.btn [class*=" ficon"]{line-height:.9em;} +li [class^="ficon"],li [class*=" ficon"]{display:inline-block;width:1.25em;text-align:center;} +li .ficon.large[class^="ficon"],li .ficon.large[class*=" ficon"]{width:1.875em;} +li[class^="ficon"],li[class*=" ficon"]{margin-left:0;list-style-type:none;}li[class^="ficon"]:before,li[class*=" ficon"]:before{text-indent:-2em;text-align:center;} +li[class^="ficon"].ficon.large:before,li[class*=" ficon"].ficon.large:before{text-indent:-1.3333333333333333em;} +.ficon.glass:before{content:"\f000";} +.ficon.music:before{content:"\f001";} +.ficon.search:before{content:"\f002";} +.ficon.envelope:before{content:"\f003";} +.ficon.heart:before{content:"\f004";} +.ficon.star:before{content:"\f005";} +.ficon.star-empty:before{content:"\f006";} +.ficon.user:before{content:"\f007";} +.ficon.film:before{content:"\f008";} +.ficon.th-large:before{content:"\f009";} +.ficon.th:before{content:"\f00a";} +.ficon.th-list:before{content:"\f00b";} +.ficon.ok:before{content:"\f00c";} +.ficon.remove:before{content:"\f00d";} +.ficon.zoom-in:before{content:"\f00e";} +.ficon.zoom-out:before{content:"\f010";} +.ficon.off:before{content:"\f011";} +.ficon.signal:before{content:"\f012";} +.ficon.cog:before{content:"\f013";} +.ficon.trash:before{content:"\f014";} +.ficon.home:before{content:"\f015";} +.ficon.file:before{content:"\f016";} +.ficon.time:before{content:"\f017";} +.ficon.road:before{content:"\f018";} +.ficon.download-alt:before{content:"\f019";} +.ficon.download:before{content:"\f01a";} +.ficon.upload:before{content:"\f01b";} +.ficon.inbox:before{content:"\f01c";} +.ficon.play-circle:before{content:"\f01d";} +.ficon.repeat:before{content:"\f01e";} +.ficon.refresh:before{content:"\f021";} +.ficon.list-alt:before{content:"\f022";} +.ficon.lock:before{content:"\f023";} +.ficon.flag:before{content:"\f024";} +.ficon.headphones:before{content:"\f025";} +.ficon.volume-off:before{content:"\f026";} +.ficon.volume-down:before{content:"\f027";} +.ficon.volume-up:before{content:"\f028";} +.ficon.qrcode:before{content:"\f029";} +.ficon.barcode:before{content:"\f02a";} +.ficon.tag:before{content:"\f02b";} +.ficon.tags:before{content:"\f02c";} +.ficon.book:before{content:"\f02d";} +.ficon.bookmark:before{content:"\f02e";} +.ficon.print:before{content:"\f02f";} +.ficon.camera:before{content:"\f030";} +.ficon.font:before{content:"\f031";} +.ficon.bold:before{content:"\f032";} +.ficon.italic:before{content:"\f033";} +.ficon.text-height:before{content:"\f034";} +.ficon.text-width:before{content:"\f035";} +.ficon.align-left:before{content:"\f036";} +.ficon.align-center:before{content:"\f037";} +.ficon.align-right:before{content:"\f038";} +.ficon.align-justify:before{content:"\f039";} +.ficon.list:before{content:"\f03a";} +.ficon.indent-left:before{content:"\f03b";} +.ficon.indent-right:before{content:"\f03c";} +.ficon.facetime-video:before{content:"\f03d";} +.ficon.picture:before{content:"\f03e";} +.ficon.pencil:before{content:"\f040";} +.ficon.map-marker:before{content:"\f041";} +.ficon.adjust:before{content:"\f042";} +.ficon.tint:before{content:"\f043";} +.ficon.edit:before{content:"\f044";} +.ficon.share:before{content:"\f045";} +.ficon.check:before{content:"\f046";} +.ficon.move:before{content:"\f047";} +.ficon.step-backward:before{content:"\f048";} +.ficon.fast-backward:before{content:"\f049";} +.ficon.backward:before{content:"\f04a";} +.ficon.play:before{content:"\f04b";} +.ficon.pause:before{content:"\f04c";} +.ficon.stop:before{content:"\f04d";} +.ficon.forward:before{content:"\f04e";} +.ficon.fast-forward:before{content:"\f050";} +.ficon.step-forward:before{content:"\f051";} +.ficon.eject:before{content:"\f052";} +.ficon.chevron-left:before{content:"\f053";} +.ficon.chevron-right:before{content:"\f054";} +.ficon.plus-sign:before{content:"\f055";} +.ficon.minus-sign:before{content:"\f056";} +.ficon.remove-sign:before{content:"\f057";} +.ficon.ok-sign:before{content:"\f058";} +.ficon.question-sign:before{content:"\f059";} +.ficon.info-sign:before{content:"\f05a";} +.ficon.screenshot:before{content:"\f05b";} +.ficon.remove-circle:before{content:"\f05c";} +.ficon.ok-circle:before{content:"\f05d";} +.ficon.ban-circle:before{content:"\f05e";} +.ficon.arrow-left:before{content:"\f060";} +.ficon.arrow-right:before{content:"\f061";} +.ficon.arrow-up:before{content:"\f062";} +.ficon.arrow-down:before{content:"\f063";} +.ficon.share-alt:before{content:"\f064";} +.ficon.resize-full:before{content:"\f065";} +.ficon.resize-small:before{content:"\f066";} +.ficon.plus:before{content:"\f067";} +.ficon.minus:before{content:"\f068";} +.ficon.asterisk:before{content:"\f069";} +.ficon.exclamation-sign:before{content:"\f06a";} +.ficon.gift:before{content:"\f06b";} +.ficon.leaf:before{content:"\f06c";} +.ficon.fire:before{content:"\f06d";} +.ficon.eye-open:before{content:"\f06e";} +.ficon.eye-close:before{content:"\f070";} +.ficon.warning-sign:before{content:"\f071";} +.ficon.plane:before{content:"\f072";} +.ficon.calendar:before{content:"\f073";} +.ficon.random:before{content:"\f074";} +.ficon.comment:before{content:"\f075";} +.ficon.magnet:before{content:"\f076";} +.ficon.chevron-up:before{content:"\f077";} +.ficon.chevron-down:before{content:"\f078";} +.ficon.retweet:before{content:"\f079";} +.ficon.shopping-cart:before{content:"\f07a";} +.ficon.folder-close:before{content:"\f07b";} +.ficon.folder-open:before{content:"\f07c";} +.ficon.resize-vertical:before{content:"\f07d";} +.ficon.resize-horizontal:before{content:"\f07e";} +.ficon.bar-chart:before{content:"\f080";} +.ficon.twitter-sign:before{content:"\f081";} +.ficon.facebook-sign:before{content:"\f082";} +.ficon.camera-retro:before{content:"\f083";} +.ficon.key:before{content:"\f084";} +.ficon.cogs:before{content:"\f085";} +.ficon.comments:before{content:"\f086";} +.ficon.thumbs-up:before{content:"\f087";} +.ficon.thumbs-down:before{content:"\f088";} +.ficon.star-half:before{content:"\f089";} +.ficon.heart-empty:before{content:"\f08a";} +.ficon.signout:before{content:"\f08b";} +.ficon.linkedin-sign:before{content:"\f08c";} +.ficon.pushpin:before{content:"\f08d";} +.ficon.external-link:before{content:"\f08e";} +.ficon.signin:before{content:"\f090";} +.ficon.trophy:before{content:"\f091";} +.ficon.github-sign:before{content:"\f092";} +.ficon.upload-alt:before{content:"\f093";} +.ficon.lemon:before{content:"\f094";} .unselectable{-webkit-user-select:none;-moz-user-select:none;-o-user-select:none;user-select:none;} .shadow{-webkit-box-shadow:0 1px 3px rgba(0, 0, 0, 0.25);-moz-box-shadow:0 1px 3px rgba(0, 0, 0, 0.25);box-shadow:0 1px 3px rgba(0, 0, 0, 0.25);} -.parent-width{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;width:100%;} +.parent-width{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;width:100%;*width:90%;} .clear{*zoom:1;}.clear:before,.clear:after{display:table;content:"";} .clear:after{clear:both;} body{background:#ffffff;color:#303030;background-image:url(base_bg.png);background-repeat:repeat-x;background-position:top;margin:10px;} @@ -507,12 +654,12 @@ .unified-panel-footer{-webkit-user-select:none;-moz-user-select:none;-o-user-select:none;user-select:none;position:absolute;bottom:0;height:25px;line-height:25px;width:100%;z-index:1000;border-top:solid #999999 1px;background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-ms-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#f2f2f2', endColorstr='#e6e6e6', GradientType=0);color:#555;}.unified-panel-footer a{color:#555;} .unified-panel-footer .drag{position:absolute;top:0;right:0;padding:0 5px;text-align:center;height:25px;width:20px;background-image:url(../images/visualization/draggable_horizontal.png);background-repeat:no-repeat;background-position:50% 50%;cursor:w-resize;} #right>.unified-panel-footer .drag{left:0;} -.panel-collapse{-webkit-user-select:none;-moz-user-select:none;-o-user-select:none;user-select:none;position:absolute;bottom:0;height:25px;line-height:25px;width:100%;z-index:1000;border-top:solid #999999 1px;background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-ms-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#f2f2f2', endColorstr='#e6e6e6', GradientType=0);color:#555;z-index:10000;position:fixed;left:0;top:inherit;bottom:0;padding:0 5px;text-align:center;width:20px;background:none;border-right:solid #999999 1px;border-top:solid #999999 1px;background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-ms-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#f2f2f2', endColorstr='#e6e6e6', GradientType=0);display:inline-block;font-family:'IconicStroke';}.panel-collapse a{color:#555;} +.panel-collapse{-webkit-user-select:none;-moz-user-select:none;-o-user-select:none;user-select:none;position:absolute;bottom:0;height:25px;line-height:25px;width:100%;z-index:1000;border-top:solid #999999 1px;background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-ms-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#f2f2f2', endColorstr='#e6e6e6', GradientType=0);color:#555;z-index:10000;position:fixed;left:0;top:inherit;bottom:0;padding:0 5px;text-align:center;width:20px;background:none;border-right:solid #999999 1px;border-top:solid #999999 1px;background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-ms-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#f2f2f2', endColorstr='#e6e6e6', GradientType=0);font-family:FontAwesome;font-weight:normal;font-style:normal;display:inline-block;font-size:1.3333333333333333em;}.panel-collapse a{color:#555;} .panel-collapse .drag{position:absolute;top:0;right:0;padding:0 5px;text-align:center;height:25px;width:20px;background-image:url(../images/visualization/draggable_horizontal.png);background-repeat:no-repeat;background-position:50% 50%;cursor:w-resize;} -.panel-collapse:before{content:'\2190';} -.panel-collapse.hidden:before{content:'\2192';} -.panel-collapse.right{left:inherit;right:0;border-right:none;border-left:solid #999999 1px;}.panel-collapse.right.right:before{content:'\2192';} -.panel-collapse.right.right.hidden:before{content:'\2190';} +.panel-collapse:before{content:'\f053';} +.panel-collapse.hidden:before{content:'\f054';} +.panel-collapse.right{left:inherit;right:0;border-right:none;border-left:solid #999999 1px;}.panel-collapse.right.right:before{content:'\f054';} +.panel-collapse.right.right.hidden:before{content:'\f053';} .menu-bg{background:whiteSmoke top repeat-x;} div.unified-panel-body{position:absolute;top:30px;bottom:0;width:100%;margin-top:1px;} #left>div.unified-panel-body,#right>div.unified-panel-body{bottom:25px;} @@ -547,16 +694,6 @@ .quota-meter-bar-warn{background-color:#ffb400;} .quota-meter-bar-error{background-color:#ff4343;} .quota-meter-text{position:absolute;top:50%;left:0;width:100px;height:16px;margin-top:-6px;text-align:center;z-index:9001;color:#000000;} -div.toolForm{border:solid #d8b365 1px;} -div.toolFormTitle{font-weight:bold;padding:5px;padding-left:10px;padding-right:10px;background:#ebd9b2;background-repeat:repeat-x;background-position:top;border-bottom:solid #d8b365 1px;} -div.toolParamHelp{color:#666;} -div.toolParamHelp a{color:#666;} -div.toolFormBody{background:#ffffff;background-image:url(form_body_bg.png);background-repeat:repeat-x;background-position:top;padding:5px 0;} -div.toolFormBody div.toolFormTitle{background:transparent;border:none;font-weight:bold;border-bottom:solid #d8b365 1px;margin-bottom:5px;} -div.toolFormDisabled div.toolFormTitle{background:#eeeeee;border-color:#999999;} -div.toolFormDisabled{border-color:#999999;} -div.toolHelp{margin-top:10px;} -div.toolHelpBody{width:100%;} div.metadataForm{border:solid #aaaaaa 1px;} div.metadataFormTitle{font-weight:bold;padding:5px;padding-left:10px;padding-right:10px;background:#cccccc;background-repeat:repeat-x;background-position:top;border-bottom:solid #aaaaaa 1px;} div.metadataFormBody{background:#FFFFFF;background-image:url(form_body_bg.png);background-repeat:repeat-x;background-position:top;padding:5px 0;} @@ -565,8 +702,13 @@ div.metadataFormDisabled{border-color:#999;} div.metadataHelpBody{width:100%;overflow:auto;} div.titleRow{font-weight:bold;border-bottom:dotted gray 1px;margin-bottom:0.5em;padding-bottom:0.25em;} -div.form{border:solid #d8b365 1px;} -div.form-title{font-weight:bold;padding:5px 10px;background:#ebd9b2;background-image:url(form_title_bg.png);background-repeat:repeat-x;background-position:top;border-bottom:solid #d8b365 1px;} +div.toolFormBody{background:#ffffff;background-image:url(form_body_bg.png);background-repeat:repeat-x;background-position:top;padding:5px 0;} +div.toolFormBody div.toolFormTitle{background:transparent;border:none;font-weight:bold;border-bottom:solid #d8b365 1px;margin-bottom:5px;} +div.toolFormDisabled div.toolFormTitle{background:#eeeeee;border-color:#999999;} +div.toolFormDisabled{border-color:#999999;} +div.toolHelp{margin-top:15px;padding:5px;} +div.toolHelpBody{width:100%;} +div.form-title,div.toolFormTitle{font-size:15px;line-height:24px;padding:5px 10px;background:#ebd9b2;border-bottom:solid #d8b365 1px;} div.form-body{padding:5px 0;} div.form-row{padding:5px 10px;} div.form-title-row{padding:5px 10px;} @@ -577,13 +719,16 @@ div.form-row-input{width:300px;float:left;} div.form-row-input label{font-weight:normal;display:inline;} div.form-row-error-message{width:300px;float:left;color:red;font-weight:bold;padding:3px 0;} -.form-row .help{color:#666;} +.form-row .help,.toolParamHelp{color:#666;}.form-row .help a,.toolParamHelp a{color:#666;} +.form-row.form-actions{background:whiteSmoke;border-top:solid #ddd 1px;padding-top:10px;padding-bottom:10px;margin-top:5px;} +select{padding:4px;font-size:12px;line-height:16px;} select,input,textarea{font:inherit;} select,textarea,input[type="text"],input[type="file"],input[type="password"]{max-width:300px;} -.search-query{display:inline-block;padding:4px;margin-bottom:9px;font-size:12px;line-height:16px;color:#555555;border:1px solid #999999;padding-left:14px;padding-right:14px;margin-bottom:0;-webkit-border-radius:14px;-moz-border-radius:14px;border-radius:14px;max-width:auto;} -.search-query:focus{border-color:rgba(82, 168, 236, 0.8);-webkit-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);-moz-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);outline:0;outline:thin dotted \9;} +textarea,input[type="text"],input[type="password"]{font-size:12px;line-height:16px;border:1px solid #999999;padding:3px;} +.search-query{display:inline-block;padding:4px;font-size:12px;line-height:16px;color:#555555;border:1px solid #999999;padding-left:14px !important;padding-right:14px !important;margin-bottom:0;-webkit-border-radius:14px;-moz-border-radius:14px;border-radius:14px;max-width:auto;} +.search-query:focus{border-color:rgba(24, 132, 218, 0.8);-webkit-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);-moz-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);outline:0;outline:thin dotted \9;} .search-spinner{position:absolute;display:none;right:8px;top:10px;} -.errormessagelarge,.warningmessagelarge,.donemessagelarge,.infomessagelarge{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#ffffcc;border:1px solid #ffdd33;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#666600;min-height:32px;padding-left:52px;background-image:url(error_message_icon.png);background-repeat:no-repeat;background-position:10px 10px;} +.errormessagelarge,.warningmessagelarge,.donemessagelarge,.infomessagelarge{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#ffffcc;border:1px solid #ffdd33;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#666600;min-height:36px;padding-left:52px;background-image:url(error_message_icon.png);background-repeat:no-repeat;background-position:10px 10px;} .errormessagelarge{background-color:#ffcccc;border-color:#ff3355;color:#660000;padding-left:52px;} .warningmessagelarge{background-image:url(warn_message_icon.png);border-color:#aaaa66;background-color:#ffffcc;} .donemessagelarge{background-color:#ccffcc;border-color:#1a9900;color:#006600;padding-left:52px;background-image:url(done_message_icon.png);} @@ -622,6 +767,18 @@ .grid thead th{line-height:16px;background:#ebd9b2;background-repeat:repeat-x;background-position:top;border-top:solid #d8b365 1px;border-bottom:solid #d8b365 1px;padding:5px;text-align:left;white-space:nowrap;} .grid tfoot td{background-color:#F8F8F8;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:5px;} .grid .current{background-color:#EEEEFF;} +.count-box{min-width:1.1em;padding:5px;border-width:1px;border-style:solid;text-align:center;display:inline-block;} +.text-filter-val{border:solid 1px #AAAAAA;padding:1px 2px 1px 3px;margin-right:5px;-moz-border-radius:.5em;-webkit-border-radius:.5em;font-style:italic;} +.page-link a,.inactive-link{padding:0px 7px 0px 7px;color:#555;} +.inactive-link,.current-filter{font-weight:bold;color:#000;} +.submit-image{background:url(../images/fugue/magnifier-left.png) no-repeat center transparent;background-color:#eee;width:24px;height:24px;cursor:pointer;margin:0;padding:0;display:block;border:1px solid #aaa;border-left:none;} +#advanced-search td{padding:3px;} +#advanced-search table{border-collapse:separate;} +.delete-search-icon{background:url(../images/delete_tag_icon_gray.png) center no-repeat;display:inline-block;width:10px;cursor:pointer;height:18px;vertical-align:middle;margin-left:2px;} +.search-box-input{border:0;float:left;outline:medium none;font-style:italic;font-size:inherit;} +.search-box{vertical-align:bottom;display:inline-block;padding:0;} +.gray-background{background-color:#DDDDDD;} +.loading-elt-overlay{background-color:white;opacity:0.5;width:100%;height:100%;z-index:14000;position:fixed;display:none;} div.odd_row{background:#dadfef;} #footer{display:none;} span.toolParameterExpandableCollapsable{font-weight:bold;cursor:pointer;} @@ -644,13 +801,14 @@ .state-fg-ok{color:#66AA66;} .state-fg-error{color:#AA6666;} .state-fg-deleted{color:#3399FF;} -button{display:inline-block;padding:4px 10px 4px;font-size:12px;line-height:16px;color:#333333;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border:1px solid #999999;border-bottom-color:#888888;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);cursor:pointer;*margin-left:.3em;}button:first-child{*margin-left:0;} -.action-button{display:inline-block;padding:4px 10px 4px;font-size:12px;line-height:16px;color:#333333;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border:1px solid #999999;border-bottom-color:#888888;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);cursor:pointer;*margin-left:.3em;}.action-button:first-child{*margin-left:0;} +.action-button{display:inline-block;padding:4px 10px 4px;font-size:12px;line-height:16px;color:#111111;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border:1px solid #999999;border-bottom-color:#888888;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);cursor:pointer;*margin-left:.3em;}.action-button:first-child{*margin-left:0;} +.action-button [class^="ficon"],.action-button [class*=" ficon"]{line-height:.9em;} a.action-button{text-decoration:none;} .action-button>img{vertical-align:middle;} -.action-button:hover{color:#333333;text-decoration:none;background-color:#e6e6e6;background-position:0 -15px;-webkit-transition:background-position 0.1s linear;-moz-transition:background-position 0.1s linear;-ms-transition:background-position 0.1s linear;-o-transition:background-position 0.1s linear;transition:background-position 0.1s linear;} +.action-button:hover{color:#111111;text-decoration:none;background-color:#e6e6e6;background-position:0 -15px;-webkit-transition:background-position 0.1s linear;-moz-transition:background-position 0.1s linear;-ms-transition:background-position 0.1s linear;-o-transition:background-position 0.1s linear;transition:background-position 0.1s linear;} .action-button:active{background-image:none;-webkit-box-shadow:inset 0 2px 4px rgba(0, 0, 0, 0.15),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 2px 4px rgba(0, 0, 0, 0.15),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 2px 4px rgba(0, 0, 0, 0.15),0 1px 2px rgba(0, 0, 0, 0.05);background-color:#e6e6e6;background-color:#d9d9d9 \9;outline:0;} -.menubutton{display:inline-block;padding:4px 10px 4px;font-size:12px;line-height:16px;color:#333333;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border:1px solid #999999;border-bottom-color:#888888;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);cursor:pointer;*margin-left:.3em;display:inline-block;cursor:pointer;position:relative;-webkit-user-select:none;-moz-user-select:none;-o-user-select:none;user-select:none;}.menubutton:first-child{*margin-left:0;} +.menubutton{display:inline-block;padding:4px 10px 4px;font-size:12px;line-height:16px;color:#111111;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border:1px solid #999999;border-bottom-color:#888888;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);cursor:pointer;*margin-left:.3em;display:inline-block;cursor:pointer;position:relative;-webkit-user-select:none;-moz-user-select:none;-o-user-select:none;user-select:none;}.menubutton:first-child{*margin-left:0;} +.menubutton [class^="ficon"],.menubutton [class*=" ficon"]{line-height:.9em;} .menubutton .label{position:relative;border-right:none;text-decoration:none;} .menubutton.popup .label{border-right:solid #999999 1px;padding-right:6px;} .menubutton.popup:after{margin-top:6px;display:inline-block;width:0;height:0;text-indent:-99999px;*text-indent:0;vertical-align:top;border-left:4px solid transparent;border-right:4px solid transparent;border-top:4px solid #000000;opacity:0.3;filter:alpha(opacity=30);content:"\2193";} diff -r 484c3bfb7f3e24213447ea45ed273c328e599eb8 -r 551adce80d002272ce47a850834c26b8b63028a7 static/june_2007_style/bootstrap/buttons.less --- a/static/june_2007_style/bootstrap/buttons.less +++ b/static/june_2007_style/bootstrap/buttons.less @@ -11,7 +11,7 @@ padding: 4px 10px 4px; font-size: @baseFontSize; line-height: @baseLineHeight; - color: @grayDark; + color: @textColor; text-align: center; text-shadow: 0 1px 1px rgba(255,255,255,.75); #gradient > .vertical-three-colors(@white, @white, 25%, darken(@white, 10%)); // Don't use .gradientbar() here since it does a three-color gradient @@ -29,7 +29,7 @@ // Hover state .btn.hover, .btn:hover { - color: @grayDark; + color: @textColor; text-decoration: none; background-color: darken(@white, 10%); background-position: 0 -15px; diff -r 484c3bfb7f3e24213447ea45ed273c328e599eb8 -r 551adce80d002272ce47a850834c26b8b63028a7 static/june_2007_style/fontawesome/font-awesome.less --- /dev/null +++ b/static/june_2007_style/fontawesome/font-awesome.less @@ -0,0 +1,218 @@ +@font-face { + font-family: 'FontAwesome'; + src: url('../images/fonts/fontawesome-webfont.eot'); + src: url('../images/fonts/fontawesome-webfont.eot?#iefix') format('embedded-opentype'), + url('../images/fonts/fontawesome-webfont.woff') format('woff'), + url('../images/fonts/fontawesome-webfont.ttf') format('truetype'), + url('../images/fonts/fontawesome-webfont.svgz#FontAwesomeRegular') format('svg'), + url('../images/fonts/fontawesome-webfont.svg#FontAwesomeRegular') format('svg'); + font-weight: normal; + font-style: normal; +} + +// ICONS +// Glyphs and icons for buttons, nav, and more +// ------------------------------------------- +// Font Awesome courtesy of Dave Gandy at fortaweso.me/font-awesome + +.ficon, +[class^="ficon"]:before, +[class*=" ficon"]:before { + font-family: FontAwesome; + font-weight: normal; + font-style: normal; + display: inline-block; +} + +// makes the font 33% larger relative to the icon container +.ficon.large:before { +// display: inline-block; + font-size: 4/3em; +} + +.btn { + [class^="ficon"], + [class*=" ficon"] { + line-height: .9em; // keeps button heights with and without icons the same + } +} + +li { + [class^="ficon"], + [class*=" ficon"] { + display: inline-block; + width: 1.25em; + text-align: center; + } + .ficon.large[class^="ficon"], + .ficon.large[class*=" ficon"] { + width: 1.5*1.25em; // 1.5 increased font size for icon-large * 1.25 width + } +} + +li[class^="ficon"], +li[class*=" ficon"] { + margin-left: 0; + list-style-type: none; + + &:before { + text-indent: -2em; + text-align: center; + } + &.ficon.large:before { + text-indent: -4/3em; + } +} + +// Uses Unicode Private Use Area (PUA) to ensure screen readers do not read off +// random characters that represent icons +.ficon.glass:before { content: "\f000"; } +.ficon.music:before { content: "\f001"; } +.ficon.search:before { content: "\f002"; } +.ficon.envelope:before { content: "\f003"; } +.ficon.heart:before { content: "\f004"; } +.ficon.star:before { content: "\f005"; } +.ficon.star-empty:before { content: "\f006"; } +.ficon.user:before { content: "\f007"; } +.ficon.film:before { content: "\f008"; } +.ficon.th-large:before { content: "\f009"; } +.ficon.th:before { content: "\f00a"; } +.ficon.th-list:before { content: "\f00b"; } +.ficon.ok:before { content: "\f00c"; } +.ficon.remove:before { content: "\f00d"; } +.ficon.zoom-in:before { content: "\f00e"; } + +.ficon.zoom-out:before { content: "\f010"; } +.ficon.off:before { content: "\f011"; } +.ficon.signal:before { content: "\f012"; } +.ficon.cog:before { content: "\f013"; } +.ficon.trash:before { content: "\f014"; } +.ficon.home:before { content: "\f015"; } +.ficon.file:before { content: "\f016"; } +.ficon.time:before { content: "\f017"; } +.ficon.road:before { content: "\f018"; } +.ficon.download-alt:before { content: "\f019"; } +.ficon.download:before { content: "\f01a"; } +.ficon.upload:before { content: "\f01b"; } +.ficon.inbox:before { content: "\f01c"; } +.ficon.play-circle:before { content: "\f01d"; } +.ficon.repeat:before { content: "\f01e"; } + +// \f020 is not a valid unicode character. all shifted one down +.ficon.refresh:before { content: "\f021"; } +.ficon.list-alt:before { content: "\f022"; } +.ficon.lock:before { content: "\f023"; } +.ficon.flag:before { content: "\f024"; } +.ficon.headphones:before { content: "\f025"; } +.ficon.volume-off:before { content: "\f026"; } +.ficon.volume-down:before { content: "\f027"; } +.ficon.volume-up:before { content: "\f028"; } +.ficon.qrcode:before { content: "\f029"; } +.ficon.barcode:before { content: "\f02a"; } +.ficon.tag:before { content: "\f02b"; } +.ficon.tags:before { content: "\f02c"; } +.ficon.book:before { content: "\f02d"; } +.ficon.bookmark:before { content: "\f02e"; } +.ficon.print:before { content: "\f02f"; } + +.ficon.camera:before { content: "\f030"; } +.ficon.font:before { content: "\f031"; } +.ficon.bold:before { content: "\f032"; } +.ficon.italic:before { content: "\f033"; } +.ficon.text-height:before { content: "\f034"; } +.ficon.text-width:before { content: "\f035"; } +.ficon.align-left:before { content: "\f036"; } +.ficon.align-center:before { content: "\f037"; } +.ficon.align-right:before { content: "\f038"; } +.ficon.align-justify:before { content: "\f039"; } +.ficon.list:before { content: "\f03a"; } +.ficon.indent-left:before { content: "\f03b"; } +.ficon.indent-right:before { content: "\f03c"; } +.ficon.facetime-video:before { content: "\f03d"; } +.ficon.picture:before { content: "\f03e"; } + +.ficon.pencil:before { content: "\f040"; } +.ficon.map-marker:before { content: "\f041"; } +.ficon.adjust:before { content: "\f042"; } +.ficon.tint:before { content: "\f043"; } +.ficon.edit:before { content: "\f044"; } +.ficon.share:before { content: "\f045"; } +.ficon.check:before { content: "\f046"; } +.ficon.move:before { content: "\f047"; } +.ficon.step-backward:before { content: "\f048"; } +.ficon.fast-backward:before { content: "\f049"; } +.ficon.backward:before { content: "\f04a"; } +.ficon.play:before { content: "\f04b"; } +.ficon.pause:before { content: "\f04c"; } +.ficon.stop:before { content: "\f04d"; } +.ficon.forward:before { content: "\f04e"; } + +.ficon.fast-forward:before { content: "\f050"; } +.ficon.step-forward:before { content: "\f051"; } +.ficon.eject:before { content: "\f052"; } +.ficon.chevron-left:before { content: "\f053"; } +.ficon.chevron-right:before { content: "\f054"; } +.ficon.plus-sign:before { content: "\f055"; } +.ficon.minus-sign:before { content: "\f056"; } +.ficon.remove-sign:before { content: "\f057"; } +.ficon.ok-sign:before { content: "\f058"; } +.ficon.question-sign:before { content: "\f059"; } +.ficon.info-sign:before { content: "\f05a"; } +.ficon.screenshot:before { content: "\f05b"; } +.ficon.remove-circle:before { content: "\f05c"; } +.ficon.ok-circle:before { content: "\f05d"; } +.ficon.ban-circle:before { content: "\f05e"; } + +.ficon.arrow-left:before { content: "\f060"; } +.ficon.arrow-right:before { content: "\f061"; } +.ficon.arrow-up:before { content: "\f062"; } +.ficon.arrow-down:before { content: "\f063"; } +.ficon.share-alt:before { content: "\f064"; } +.ficon.resize-full:before { content: "\f065"; } +.ficon.resize-small:before { content: "\f066"; } +.ficon.plus:before { content: "\f067"; } +.ficon.minus:before { content: "\f068"; } +.ficon.asterisk:before { content: "\f069"; } +.ficon.exclamation-sign:before { content: "\f06a"; } +.ficon.gift:before { content: "\f06b"; } +.ficon.leaf:before { content: "\f06c"; } +.ficon.fire:before { content: "\f06d"; } +.ficon.eye-open:before { content: "\f06e"; } + +.ficon.eye-close:before { content: "\f070"; } +.ficon.warning-sign:before { content: "\f071"; } +.ficon.plane:before { content: "\f072"; } +.ficon.calendar:before { content: "\f073"; } +.ficon.random:before { content: "\f074"; } +.ficon.comment:before { content: "\f075"; } +.ficon.magnet:before { content: "\f076"; } +.ficon.chevron-up:before { content: "\f077"; } +.ficon.chevron-down:before { content: "\f078"; } +.ficon.retweet:before { content: "\f079"; } +.ficon.shopping-cart:before { content: "\f07a"; } +.ficon.folder-close:before { content: "\f07b"; } +.ficon.folder-open:before { content: "\f07c"; } +.ficon.resize-vertical:before { content: "\f07d"; } +.ficon.resize-horizontal:before { content: "\f07e"; } + +.ficon.bar-chart:before { content: "\f080"; } +.ficon.twitter-sign:before { content: "\f081"; } +.ficon.facebook-sign:before { content: "\f082"; } +.ficon.camera-retro:before { content: "\f083"; } +.ficon.key:before { content: "\f084"; } +.ficon.cogs:before { content: "\f085"; } +.ficon.comments:before { content: "\f086"; } +.ficon.thumbs-up:before { content: "\f087"; } +.ficon.thumbs-down:before { content: "\f088"; } +.ficon.star-half:before { content: "\f089"; } +.ficon.heart-empty:before { content: "\f08a"; } +.ficon.signout:before { content: "\f08b"; } +.ficon.linkedin-sign:before { content: "\f08c"; } +.ficon.pushpin:before { content: "\f08d"; } +.ficon.external-link:before { content: "\f08e"; } + +.ficon.signin:before { content: "\f090"; } +.ficon.trophy:before { content: "\f091"; } +.ficon.github-sign:before { content: "\f092"; } +.ficon.upload-alt:before { content: "\f093"; } +.ficon.lemon:before { content: "\f094"; } diff -r 484c3bfb7f3e24213447ea45ed273c328e599eb8 -r 551adce80d002272ce47a850834c26b8b63028a7 static/june_2007_style/galaxy_bootstrap.less --- a/static/june_2007_style/galaxy_bootstrap.less +++ b/static/june_2007_style/galaxy_bootstrap.less @@ -35,10 +35,10 @@ @monospaceFontFamily: Menlo, Monaco, "Courier New", monospace; @baseFontFamily: @sansFontFamily; @baseLineHeight: 16px; -@textColor: @grayDark; +@textColor: #111; // Buttons -@primaryButtonBackground: @linkColor; +@primaryButtonBackground: @blueDark; @buttonBorder: #999; @buttonBorderBottom: #888; diff -r 484c3bfb7f3e24213447ea45ed273c328e599eb8 -r 551adce80d002272ce47a850834c26b8b63028a7 static/june_2007_style/iconic_stroke.less --- a/static/june_2007_style/iconic_stroke.less +++ b/static/june_2007_style/iconic_stroke.less @@ -1,7 +1,7 @@ @font-face { font-family: 'IconicStroke'; - src: url('../images/fonts/iconic_stroke.eot'); - src: url('../images/fonts/iconic_stroke.eot?#iefix') format('embedded-opentype'), url('../images/fonts/iconic_stroke.ttf') format('truetype'), url('../images/fonts/iconic_stroke.svg#iconic') format('svg'); + src: url('/static/images/fonts/iconic_stroke.eot'); + src: url('/static/images/fonts/iconic_stroke.eot?#iefix') format('embedded-opentype'), url('../images/fonts/iconic_stroke.ttf') format('truetype'), url('../images/fonts/iconic_stroke.svg#iconic') format('svg'); font-weight: normal; font-style: normal; } diff -r 484c3bfb7f3e24213447ea45ed273c328e599eb8 -r 551adce80d002272ce47a850834c26b8b63028a7 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -62,15 +62,12 @@ } $.each( options, function( k, v ) { if (v) { - $("<a href='#'>").html(k).click(v).appendTo(menu_element).wrap( "<li />" ); + menu_element.append( $("<li></li>").append( $("<a href='#'></a>").html(k).click(v) ) ); } else { - $("<a href='#'>").html(k).appendTo(menu_element).wrap( "<li class='head'/>" ); + menu_element.append( $("<li></li>").addClass( "head" ).append( $("<a href='#'></a>").html(k) ) ); } }); - var wrapper = $( "<div class='popmenu-wrapper' style='position: absolute;left: 0; top: -1000;'>" ); - wrapper.append( menu_element ) - .append( "<div class='overlay-border'>" ) - .appendTo( "body" ); + var wrapper = $( "<div class='popmenu-wrapper' style='position: absolute;left: 0; top: -1000;'></div>" ).append( menu_element ).appendTo( "body" ); var x = e.pageX - wrapper.width() / 2 ; x = Math.min( x, $(document).scrollLeft() + $(window).width() - $(wrapper).width() - 5 ); diff -r 484c3bfb7f3e24213447ea45ed273c328e599eb8 -r 551adce80d002272ce47a850834c26b8b63028a7 templates/base_panels.mako --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -1,5 +1,4 @@ -## This needs to be on the first line, otherwise IE6 goes into quirks mode -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> +<!DOCTYPE HTML><% self.has_left_panel=True @@ -204,7 +203,10 @@ <head><title>${self.title()}</title><meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + ## For mobile browsers, don't scale up <meta name = "viewport" content = "maximum-scale=1.0"> + ## Force IE to standards mode, and prefer Google Chrome Frame if the user has already installed it + <meta http-equiv="X-UA-Compatible" content="IE=Edge,chrome=1"> ${self.stylesheets()} ${self.javascripts()} </head> diff -r 484c3bfb7f3e24213447ea45ed273c328e599eb8 -r 551adce80d002272ce47a850834c26b8b63028a7 templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -619,85 +619,6 @@ ${parent.stylesheets()} ${h.css( "autocomplete_tagging", "jquery.rating" )} <style> - .count-box { - min-width: 1.1em; - padding: 5px; - border-width: 1px; - border-style: solid; - text-align: center; - display: inline-block; - } - .text-filter-val { - border: solid 1px #AAAAAA; - padding: 1px 2px 1px 3px; - margin-right: 5px; - -moz-border-radius: .5em; - -webkit-border-radius: .5em; - font-style: italic; - } - .page-link a, .inactive-link { - padding: 0px 7px 0px 7px; - color: #555; - } - .inactive-link, .current-filter { - font-weight: bold; - color: #000; - } - .submit-image { - background: url(${h.url_for('/static/images/fugue/magnifier-left.png')}) no-repeat right transparent; - background-color: #eee; - width: 20px; - height: 20px; - cursor: pointer; - border: 0; - border-left: 1px solid #ccc; - margin: 0; - padding: 0; - display: block; - float: right; - } - #advanced-search td { - padding: 3px; - } - #advanced-search table { - border-collapse: separate; - } - .delete-search-icon { - background: url(${h.url_for("/static/images/delete_tag_icon_gray.png")}) center no-repeat; - display: inline-block; - width: 10px; - cursor: pointer; - height: 18px; - vertical-align: middle; - margin-left: 2px; - - } - .search-box-input { - border: 0; - margin: 1px 0 0 2px; - float: left; - outline: medium none; - font-style: italic; - font-size: inherit; - } - .search-box { - vertical-align: bottom; - display: inline-block; - padding: 0; - border: 1px solid #aaa; - } - .gray-background { - background-color: #DDDDDD; - } - .loading-elt-overlay { - background-color : white; - opacity : 0.5; - width : 100%; - height : 100%; - z-index : 14000; - position : fixed; - display: none; - } ## If page is displayed in panels, pad from edges for readability. %if context.get('use_panels'): div#center { diff -r 484c3bfb7f3e24213447ea45ed273c328e599eb8 -r 551adce80d002272ce47a850834c26b8b63028a7 templates/root/index.mako --- a/templates/root/index.mako +++ b/templates/root/index.mako @@ -201,7 +201,7 @@ <div class="unified-panel-header" unselectable="on"><div class='unified-panel-header-inner'><div style="float: right"> - <a class='panel-header-button' id="tools-options-button" href="#"><span class="iconic cog"></span></a> + <a class='panel-header-button' id="tools-options-button" href="#"><span class="ficon large cog"></span></a></div> ${n_('Tools')} </div> @@ -235,7 +235,7 @@ <div class="unified-panel-header" unselectable="on"><div class="unified-panel-header-inner"><div style="float: right"> - <a id="history-options-button" class='panel-header-button' href="${h.url_for( controller='root', action='history_options' )}" target="galaxy_main"><span class="iconic cog"></span></a> + <a id="history-options-button" class='panel-header-button' href="${h.url_for( controller='root', action='history_options' )}" target="galaxy_main"><span class="ficon large cog"></span></a></div><div class="panel-header-text">${_('History')}</div></div> diff -r 484c3bfb7f3e24213447ea45ed273c328e599eb8 -r 551adce80d002272ce47a850834c26b8b63028a7 templates/root/tool_menu.mako --- a/templates/root/tool_menu.mako +++ b/templates/root/tool_menu.mako @@ -50,7 +50,7 @@ </div></%def> -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> +<!DOCTYPE HTML><html><head><title>${_('Galaxy Tools')}</title> @@ -59,7 +59,6 @@ <link href="${h.url_for('/static/style/tool_menu.css')}" rel="stylesheet" type="text/css" /><link href="${h.url_for('/static/style/autocomplete_tagging.css')}" rel="stylesheet" type="text/css" /> - ##<script type="text/javascript" src="${h.url_for('/static/scripts/jquery.js')}"></script> ${h.js( "jquery", "galaxy.base", "json2", "autocomplete_tagging" )} <script type="text/javascript"> diff -r 484c3bfb7f3e24213447ea45ed273c328e599eb8 -r 551adce80d002272ce47a850834c26b8b63028a7 templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -139,13 +139,13 @@ %><div class="form-title-row"><strong>${input.title} ${i + 1}</strong></div> ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} - <div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> + <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div></div> %if rep_errors.has_key( '__index__' ): <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${rep_errors['__index__']}</span></div> %endif %endfor - <div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> + <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div></div> %elif input.type == "conditional": <% @@ -290,14 +290,14 @@ <input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}"> %if tool.display_by_page[tool_state.page]: ${trans.fill_template_string( tool.display_by_page[tool_state.page], context=tool.get_param_html_map( trans, tool_state.page, tool_state.inputs ) )} - <input type="submit" class="primary-button" name="runtool_btn" value="Execute"> + <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute"> %else: ${do_inputs( tool.inputs_by_page[ tool_state.page ], tool_state.inputs, errors, "" )} - <div class="form-row"> + <div class="form-row form-actions"> %if tool_state.page == tool.last_page: - <input type="submit" class="primary-button" name="runtool_btn" value="Execute"> + <input type="submit" class="btn btn-primary" name="runtool_btn" value="Execute"> %else: - <input type="submit" class="primary-button" name="runtool_btn" value="Next step"> + <input type="submit" class="btn btn-primary" name="runtool_btn" value="Next step"> %endif </div> %endif diff -r 484c3bfb7f3e24213447ea45ed273c328e599eb8 -r 551adce80d002272ce47a850834c26b8b63028a7 templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -44,31 +44,28 @@ <a class="${a_cls}" data-toggle="dropdown">${display}${extra}</a> %endif %if menu_options: - ## <div class="submenu"><ul class="dropdown-menu"> %for menu_item in menu_options: %if not menu_item: - <li class="divider" /> + <li class="divider"></li> %else: <li> %if len ( menu_item ) == 1: ${menu_item[0]} %elif len ( menu_item ) == 2: <% name, link = menu_item %> - <a href="${link}">${name}</a></li> + <a href="${link}">${name}</a> %else: <% name, link, target = menu_item %> - <a target="${target}" href="${link}">${name}</a></li> + <a target="${target}" href="${link}">${name}</a> %endif </li> %endif %endfor </ul> - ## </div> %endif </li></%def> - ## Analyze data tab. ${tab( "analysis", _("Analyze Data"), h.url_for( controller='/root', action='index' ) )} @@ -151,7 +148,7 @@ email = trans.user.email else: email = "" - menu_options = [ [ '<li><a>Logged in as <span id="user-email">%s</span></a></li>' % email ] ] + menu_options = [ [ '<a>Logged in as <span id="user-email">%s</span></a>' % email ] ] if app.config.use_remote_user: if app.config.remote_user_logout_href: menu_options.append( [ _('Logout'), app.config.remote_user_logout_href, "_top" ] ) @@ -173,7 +170,7 @@ menu_options.append( [ _('API Keys'), h.url_for( controller='/user', action='api_keys', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) if app.config.use_remote_user: menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) - + extra_class = "loggedin-only" visible = ( trans.user != None ) tab( "user", "User", None, visible=visible, menu_options=menu_options ) @@ -187,9 +184,9 @@ </div> ## Logo, layered over tabs to be clickable - <div class="title" style="position: absolute; top: 0; left: 0;"> + <div class="title" style="position: absolute; top: 0; left: 0; white-space: nowrap;"><a href="${app.config.get( 'logo_url', '/' )}"> - <img border="0" src="${h.url_for('/static/images/galaxyIcon_noText.png')}" style="width: 26px; vertical-align: top;"> + <img border="0" src="${h.url_for('/static/images/galaxyIcon_noText.png')}" style="display: inline; width: 26px; vertical-align: top;"> Galaxy %if app.config.brand: <span class='brand'>/ ${app.config.brand}</span> https://bitbucket.org/galaxy/galaxy-central/changeset/9017c8ecb8a6/ changeset: 9017c8ecb8a6 user: james_taylor date: 2012-03-09 19:38:13 summary: Automated merge with https://bitbucket.org/galaxy/galaxy-central affected #: 81 files Diff too large to display. https://bitbucket.org/galaxy/galaxy-central/changeset/e5603d63ea14/ changeset: e5603d63ea14 user: james_taylor date: 2012-03-09 20:41:52 summary: style: smaller button height, fix toolForm styles in workflow editor affected #: 5 files diff -r 9017c8ecb8a641482e75c512b09ef8ce0651ba64 -r e5603d63ea141605327204a889f8fb48173e02f0 static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -573,6 +573,15 @@ width: 100%; } +// In workflow + +.toolForm.toolFormInCanvas { + border: solid @form_border 1px; + .toolFormTitle { + font-size: @baseFontSize; + line-height: @baseLineHeight; + } +} div.form, div.toolForm { @@ -658,7 +667,7 @@ // Selects select { //border: 1px solid @formElementBorder; - padding: 4px; + padding: 2px; font-size: @baseFontSize; line-height: @baseLineHeight; } diff -r 9017c8ecb8a641482e75c512b09ef8ce0651ba64 -r e5603d63ea141605327204a889f8fb48173e02f0 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -95,7 +95,7 @@ .fade{-webkit-transition:opacity 0.15s linear;-moz-transition:opacity 0.15s linear;-ms-transition:opacity 0.15s linear;-o-transition:opacity 0.15s linear;transition:opacity 0.15s linear;opacity:0;}.fade.in{opacity:1;} .collapse{-webkit-transition:height 0.35s ease;-moz-transition:height 0.35s ease;-ms-transition:height 0.35s ease;-o-transition:height 0.35s ease;transition:height 0.35s ease;position:relative;overflow:hidden;height:0;}.collapse.in{height:auto;} .close{float:right;font-size:20px;font-weight:bold;line-height:16px;color:#000000;text-shadow:0 1px 0 #ffffff;opacity:0.2;filter:alpha(opacity=20);}.close:hover{color:#000000;text-decoration:none;opacity:0.4;filter:alpha(opacity=40);cursor:pointer;} -.btn{display:inline-block;padding:4px 10px 4px;font-size:12px;line-height:16px;color:#111111;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border:1px solid #999999;border-bottom-color:#888888;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);cursor:pointer;*margin-left:.3em;}.btn:first-child{*margin-left:0;} +.btn{display:inline-block;padding:2px 10px 2px;font-size:12px;line-height:16px;color:#111111;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border:1px solid #999999;border-bottom-color:#888888;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);cursor:pointer;*margin-left:.3em;}.btn:first-child{*margin-left:0;} .btn.hover,.btn:hover{color:#111111;text-decoration:none;background-color:#e6e6e6;background-position:0 -15px;-webkit-transition:background-position 0.1s linear;-moz-transition:background-position 0.1s linear;-ms-transition:background-position 0.1s linear;-o-transition:background-position 0.1s linear;transition:background-position 0.1s linear;} .btn:focus{outline:thin dotted;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;} .btn.active,.btn:active{background-image:none;-webkit-box-shadow:inset 0 2px 4px rgba(0, 0, 0, 0.15),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 2px 4px rgba(0, 0, 0, 0.15),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 2px 4px rgba(0, 0, 0, 0.15),0 1px 2px rgba(0, 0, 0, 0.05);background-color:#e6e6e6;background-color:#d9d9d9 \9;outline:0;} @@ -329,157 +329,6 @@ .hide{display:none;} .show{display:block;} .invisible{visibility:hidden;} -@font-face{font-family:'IconicStroke';src:url('/static/images/fonts/iconic_stroke.eot');src:url('/static/images/fonts/iconic_stroke.eot?#iefix') format('embedded-opentype'),url('../images/fonts/iconic_stroke.ttf') format('truetype'),url('../images/fonts/iconic_stroke.svg#iconic') format('svg');font-weight:normal;font-style:normal;}.iconic{display:inline-block;font-family:'IconicStroke';} -.iconic.lightbulb:before{content:'\e063';} -.iconic.equalizer:before{content:'\e052';} -.iconic.map_pin_stroke:before{content:'\e068';} -.iconic.brush_alt:before{content:'\e01c';} -.iconic.move:before{content:'\e03e';} -.iconic.pen_alt_stroke:before{content:'\e005';} -.iconic.move_vertical:before{content:'\e03b';} -.iconic.book_alt2:before{content:'\e06a';} -.iconic.layers:before{content:'\e01f';} -.iconic.pause:before{content:'\e049';} -.iconic.layers_alt:before{content:'\e020';} -.iconic.cloud_upload:before{content:'\e045';} -.iconic.chart_alt:before{content:'\e029';} -.iconic.fullscreen_exit_alt:before{content:'\e051';} -.iconic.cloud_download:before{content:'\e044';} -.iconic.comment_alt2_stroke:before{content:'\e004';} -.iconic.mail:before{content:'\2709';} -.iconic.check_alt:before{content:'\2718';} -.iconic.document_stroke:before{content:'\e066';} -.iconic.battery_charging:before{content:'\e05d';} -.iconic.stop:before{content:'\e04a';} -.iconic.arrow_up:before{content:'\2191';} -.iconic.move_horizontal:before{content:'\e038';} -.iconic.compass:before{content:'\e021';} -.iconic.minus_alt:before{content:'\e009';} -.iconic.battery_empty:before{content:'\e05c';} -.iconic.map_pin_alt:before{content:'\e002';} -.iconic.unlock_stroke:before{content:'\e076';} -.iconic.lock_stroke:before{content:'\e075';} -.iconic.question_mark:before{content:'\003f';} -.iconic.list:before{content:'\e055';} -.iconic.upload:before{content:'\e043';} -.iconic.reload:before{content:'\e030';} -.iconic.loop_alt4:before{content:'\e035';} -.iconic.loop_alt3:before{content:'\e034';} -.iconic.loop_alt2:before{content:'\e033';} -.iconic.loop_alt1:before{content:'\e032';} -.iconic.left_quote:before{content:'\275d';} -.iconic.x:before{content:'\2713';} -.iconic.last:before{content:'\e04d';} -.iconic.document_alt_stroke:before{content:'\e000';} -.iconic.bars:before{content:'\e06f';} -.iconic.arrow_left:before{content:'\2190';} -.iconic.arrow_down:before{content:'\2193';} -.iconic.download:before{content:'\e042';} -.iconic.home:before{content:'\2302';} -.iconic.calendar:before{content:'\e001';} -.iconic.right_quote_alt:before{content:'\e012';} -.iconic.fullscreen:before{content:'\e04e';} -.iconic.dial:before{content:'\e058';} -.iconic.plus_alt:before{content:'\e008';} -.iconic.clock:before{content:'\e079';} -.iconic.movie:before{content:'\e060';} -.iconic.steering_wheel:before{content:'\e024';} -.iconic.pen:before{content:'\270e';} -.iconic.tag_stroke:before{content:'\e02b';} -.iconic.pin:before{content:'\e067';} -.iconic.denied:before{content:'\26d4';} -.iconic.left_quote_alt:before{content:'\e011';} -.iconic.volume_mute:before{content:'\e071';} -.iconic.arrow_up_alt2:before{content:'\e018';} -.iconic.list_nested:before{content:'\e056';} -.iconic.arrow_up_alt1:before{content:'\e014';} -.iconic.comment_stroke:before{content:'\e06d';} -.iconic.undo:before{content:'\e02f';} -.iconic.umbrella:before{content:'\2602';} -.iconic.bolt:before{content:'\26a1';} -.iconic.article:before{content:'\e053';} -.iconic.read_more:before{content:'\e054';} -.iconic.beaker:before{content:'\e023';} -.iconic.beaker_alt:before{content:'\e010';} -.iconic.battery_full:before{content:'\e073';} -.iconic.arrow_right:before{content:'\2192';} -.iconic.new_window:before{content:'\e059';} -.iconic.plus:before{content:'\2795';} -.iconic.cog:before{content:'\2699';} -.iconic.key_stroke:before{content:'\26bf';} -.iconic.first:before{content:'\e04c';} -.iconic.comment_alt1_stroke:before{content:'\e003';} -.iconic.trash_stroke:before{content:'\e05a';} -.iconic.image:before{content:'\e027';} -.iconic.chat_alt_stroke:before{content:'\e007';} -.iconic.cd:before{content:'\e064';} -.iconic.right_quote:before{content:'\275e';} -.iconic.brush:before{content:'\e01b';} -.iconic.cloud:before{content:'\2601';} -.iconic.eye:before{content:'\e025';} -.iconic.play_alt:before{content:'\e048';} -.iconic.transfer:before{content:'\e041';} -.iconic.pen_alt2:before{content:'\e006';} -.iconic.camera:before{content:'\e070';} -.iconic.move_horizontal_alt2:before{content:'\e03a';} -.iconic.curved_arrow:before{content:'\2935';} -.iconic.move_horizontal_alt1:before{content:'\e039';} -.iconic.aperture:before{content:'\e026';} -.iconic.reload_alt:before{content:'\e031';} -.iconic.magnifying_glass:before{content:'\e074';} -.iconic.iphone:before{content:'\e06e';} -.iconic.fork:before{content:'\e046';} -.iconic.box:before{content:'\e06b';} -.iconic.bars_alt:before{content:'\e00a';} -.iconic.heart_stroke:before{content:'\2764';} -.iconic.volume:before{content:'\e072';} -.iconic.x_alt:before{content:'\2714';} -.iconic.link:before{content:'\e077';} -.iconic.moon_stroke:before{content:'\263e';} -.iconic.eyedropper:before{content:'\e01e';} -.iconic.spin:before{content:'\e036';} -.iconic.rss:before{content:'\e02c';} -.iconic.info:before{content:'\2139';} -.iconic.target:before{content:'\e02a';} -.iconic.cursor:before{content:'\e057';} -.iconic.minus:before{content:'\2796';} -.iconic.book_alt:before{content:'\e00b';} -.iconic.headphones:before{content:'\e061';} -.iconic.hash:before{content:'\0023';} -.iconic.arrow_left_alt1:before{content:'\e013';} -.iconic.arrow_left_alt2:before{content:'\e017';} -.iconic.fullscreen_exit:before{content:'\e050';} -.iconic.share:before{content:'\e02e';} -.iconic.fullscreen_alt:before{content:'\e04f';} -.iconic.at:before{content:'\0040';} -.iconic.chat:before{content:'\e05e';} -.iconic.move_vertical_alt2:before{content:'\e03d';} -.iconic.move_vertical_alt1:before{content:'\e03c';} -.iconic.check:before{content:'\2717';} -.iconic.mic:before{content:'\e05f';} -.iconic.calendar_alt_stroke:before{content:'\e06c';} -.iconic.book:before{content:'\e069';} -.iconic.move_alt1:before{content:'\e03f';} -.iconic.move_alt2:before{content:'\e040';} -.iconic.award_stroke:before{content:'\e022';} -.iconic.wrench:before{content:'\e078';} -.iconic.play:before{content:'\e047';} -.iconic.star:before{content:'\2605';} -.iconic.chart:before{content:'\e028';} -.iconic.rain:before{content:'\26c6';} -.iconic.folder_stroke:before{content:'\e065';} -.iconic.sun_stroke:before{content:'\2600';} -.iconic.user:before{content:'\e062';} -.iconic.battery_half:before{content:'\e05b';} -.iconic.aperture_alt:before{content:'\e00c';} -.iconic.eject:before{content:'\e04b';} -.iconic.arrow_down_alt1:before{content:'\e016';} -.iconic.pilcrow:before{content:'\00b6';} -.iconic.arrow_down_alt2:before{content:'\e01a';} -.iconic.arrow_right_alt1:before{content:'\e015';} -.iconic.arrow_right_alt2:before{content:'\e019';} -.iconic.rss_alt:before{content:'\e02d';} -.iconic.spin_alt:before{content:'\e037';} @font-face{font-family:'FontAwesome';src:url('../images/fonts/fontawesome-webfont.eot');src:url('../images/fonts/fontawesome-webfont.eot?#iefix') format('embedded-opentype'),url('../images/fonts/fontawesome-webfont.woff') format('woff'),url('../images/fonts/fontawesome-webfont.ttf') format('truetype'),url('../images/fonts/fontawesome-webfont.svgz#FontAwesomeRegular') format('svg'),url('../images/fonts/fontawesome-webfont.svg#FontAwesomeRegular') format('svg');font-weight:normal;font-style:normal;}.ficon,[class^="ficon"]:before,[class*=" ficon"]:before{font-family:FontAwesome;font-weight:normal;font-style:normal;display:inline-block;} .ficon.large:before{font-size:1.3333333333333333em;} .btn [class^="ficon"],.btn [class*=" ficon"]{line-height:.9em;} @@ -708,6 +557,7 @@ div.toolFormDisabled{border-color:#999999;} div.toolHelp{margin-top:15px;padding:5px;} div.toolHelpBody{width:100%;} +.toolForm.toolFormInCanvas{border:solid #d8b365 1px;}.toolForm.toolFormInCanvas .toolFormTitle{font-size:12px;line-height:16px;} div.form-title,div.toolFormTitle{font-size:15px;line-height:24px;padding:5px 10px;background:#ebd9b2;border-bottom:solid #d8b365 1px;} div.form-body{padding:5px 0;} div.form-row{padding:5px 10px;} @@ -721,7 +571,7 @@ div.form-row-error-message{width:300px;float:left;color:red;font-weight:bold;padding:3px 0;} .form-row .help,.toolParamHelp{color:#666;}.form-row .help a,.toolParamHelp a{color:#666;} .form-row.form-actions{background:whiteSmoke;border-top:solid #ddd 1px;padding-top:10px;padding-bottom:10px;margin-top:5px;} -select{padding:4px;font-size:12px;line-height:16px;} +select{padding:2px;font-size:12px;line-height:16px;} select,input,textarea{font:inherit;} select,textarea,input[type="text"],input[type="file"],input[type="password"]{max-width:300px;} textarea,input[type="text"],input[type="password"]{font-size:12px;line-height:16px;border:1px solid #999999;padding:3px;} @@ -801,13 +651,13 @@ .state-fg-ok{color:#66AA66;} .state-fg-error{color:#AA6666;} .state-fg-deleted{color:#3399FF;} -.action-button{display:inline-block;padding:4px 10px 4px;font-size:12px;line-height:16px;color:#111111;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border:1px solid #999999;border-bottom-color:#888888;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);cursor:pointer;*margin-left:.3em;}.action-button:first-child{*margin-left:0;} +.action-button{display:inline-block;padding:2px 10px 2px;font-size:12px;line-height:16px;color:#111111;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border:1px solid #999999;border-bottom-color:#888888;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);cursor:pointer;*margin-left:.3em;}.action-button:first-child{*margin-left:0;} .action-button [class^="ficon"],.action-button [class*=" ficon"]{line-height:.9em;} a.action-button{text-decoration:none;} .action-button>img{vertical-align:middle;} .action-button:hover{color:#111111;text-decoration:none;background-color:#e6e6e6;background-position:0 -15px;-webkit-transition:background-position 0.1s linear;-moz-transition:background-position 0.1s linear;-ms-transition:background-position 0.1s linear;-o-transition:background-position 0.1s linear;transition:background-position 0.1s linear;} .action-button:active{background-image:none;-webkit-box-shadow:inset 0 2px 4px rgba(0, 0, 0, 0.15),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 2px 4px rgba(0, 0, 0, 0.15),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 2px 4px rgba(0, 0, 0, 0.15),0 1px 2px rgba(0, 0, 0, 0.05);background-color:#e6e6e6;background-color:#d9d9d9 \9;outline:0;} -.menubutton{display:inline-block;padding:4px 10px 4px;font-size:12px;line-height:16px;color:#111111;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border:1px solid #999999;border-bottom-color:#888888;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);cursor:pointer;*margin-left:.3em;display:inline-block;cursor:pointer;position:relative;-webkit-user-select:none;-moz-user-select:none;-o-user-select:none;user-select:none;}.menubutton:first-child{*margin-left:0;} +.menubutton{display:inline-block;padding:2px 10px 2px;font-size:12px;line-height:16px;color:#111111;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border:1px solid #999999;border-bottom-color:#888888;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:inset 0 1px 0 rgba(255, 255, 255, 0.2),0 1px 2px rgba(0, 0, 0, 0.05);cursor:pointer;*margin-left:.3em;display:inline-block;cursor:pointer;position:relative;-webkit-user-select:none;-moz-user-select:none;-o-user-select:none;user-select:none;}.menubutton:first-child{*margin-left:0;} .menubutton [class^="ficon"],.menubutton [class*=" ficon"]{line-height:.9em;} .menubutton .label{position:relative;border-right:none;text-decoration:none;} .menubutton.popup .label{border-right:solid #999999 1px;padding-right:6px;} diff -r 9017c8ecb8a641482e75c512b09ef8ce0651ba64 -r e5603d63ea141605327204a889f8fb48173e02f0 static/june_2007_style/bootstrap/buttons.less --- a/static/june_2007_style/bootstrap/buttons.less +++ b/static/june_2007_style/bootstrap/buttons.less @@ -8,7 +8,7 @@ // Core .btn { display: inline-block; - padding: 4px 10px 4px; + padding: 2px 10px 2px; font-size: @baseFontSize; line-height: @baseLineHeight; color: @textColor; diff -r 9017c8ecb8a641482e75c512b09ef8ce0651ba64 -r e5603d63ea141605327204a889f8fb48173e02f0 static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js +++ b/static/scripts/galaxy.panels.js @@ -144,14 +144,14 @@ var $buttons = this.$footer.find( ".buttons" ).html( "" ); if ( options.buttons ) { $.each( options.buttons, function( name, value ) { - $buttons.append( $( '<button>' ).text( name ).click( value ) ); + $buttons.append( $( '<button></button> ' ).text( name ).click( value ) ).append( " " ); }); this.$footer.show(); } var $extraButtons = this.$footer.find( ".extra_buttons" ).html( "" ); if ( options.extra_buttons ) { $.each( options.extra_buttons, function( name, value ) { - $extraButtons.append( $( '<button>' ).text( name ).click( value ) ); + $extraButtons.append( $( '<button></button>' ).text( name ).click( value ) ).append( " " ); }); this.$footer.show(); } diff -r 9017c8ecb8a641482e75c512b09ef8ce0651ba64 -r e5603d63ea141605327204a889f8fb48173e02f0 templates/workflow/editor.mako --- a/templates/workflow/editor.mako +++ b/templates/workflow/editor.mako @@ -955,8 +955,8 @@ display = "none" %><div id="tool-search" style="padding-bottom: 5px; position: relative; display: ${display}; width: 100%"> - <input type="text" name="query" value="search tools" id="tool-search-query" style="width: 100%; font-style:italic; font-size: inherit" autocomplete="off"/> - <img src="${h.url_for('/static/images/loading_small_white_bg.gif')}" id="search-spinner" style="display: none; position: absolute; right: 0; top: 5px;"/> + <input type="text" name="query" value="search tools" id="tool-search-query" class="search-query parent-width" /> + <img src="${h.url_for('/static/images/loading_small_white_bg.gif')}" id="search-spinner" class="search-spinner" /></div><div class="toolSectionList"> %for key, val in app.toolbox.tool_panel.items(): https://bitbucket.org/galaxy/galaxy-central/changeset/9e73daf2a338/ changeset: 9e73daf2a338 user: james_taylor date: 2012-03-12 18:09:19 summary: style: force monospace font and smaller size for pre.peek affected #: 2 files diff -r e5603d63ea141605327204a889f8fb48173e02f0 -r 9e73daf2a33878b35d2adc6d5b2eed5978bac7dc static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -1591,11 +1591,16 @@ background: white; color: black; width: 100%; + font-size: 10px; overflow: auto; th { color: white; background: @peek_table_header; } + table, th, tr, td { + font-family: @monospaceFontFamily; + font-size: 10px; + } } // ==== Tool menu styles diff -r e5603d63ea141605327204a889f8fb48173e02f0 -r 9e73daf2a33878b35d2adc6d5b2eed5978bac7dc static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -730,7 +730,8 @@ div.historyItemTitleBar.spinner .state-icon{background:url(data_running.gif) 0 1px no-repeat !important;} div.historyItemButtons{float:right;} div.historyItemBody div{padding-top:2px;} -pre.peek{background:white;color:black;width:100%;overflow:auto;}pre.peek th{color:white;background:#023858;} +pre.peek{background:white;color:black;width:100%;font-size:10px;overflow:auto;}pre.peek th{color:white;background:#023858;} +pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Menlo,Monaco,"Courier New",monospace;font-size:10px;} body.toolMenuPage{background:white;color:#303030;background:#dfe5f9;margin:5px;margin-right:10px;margin-left:10px;} hr{border:none;height:0px;margin-top:0px;} div.toolSectionPad{margin:0;padding:0;height:5px;font-size:0px;} https://bitbucket.org/galaxy/galaxy-central/changeset/fe149b078c86/ changeset: fe149b078c86 user: james_taylor date: 2012-03-12 18:09:38 summary: Automated merge with https://bitbucket.org/galaxy/galaxy-central affected #: 81 files Diff too large to display. https://bitbucket.org/galaxy/galaxy-central/changeset/35024e38e729/ changeset: 35024e38e729 user: james_taylor date: 2012-03-12 19:49:05 summary: style: use images with transparency for message boxes affected #: 17 files diff -r fe149b078c865e6d2b3f969f76195b3f53d9cb48 -r 35024e38e7292bb26474f10723754dbf96dea316 static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -728,7 +728,7 @@ .alert(); min-height: 36px; padding-left: 52px; - background-image: url(error_message_icon.png); + background-image: url(error_large.png); background-repeat: no-repeat; background-position: 10px 10px; } @@ -739,7 +739,7 @@ } .warningmessagelarge { - background-image: url(warn_message_icon.png); + background-image: url(warn_large.png); border-color: @warn_message_border; background-color: @warn_message_bg; } @@ -747,14 +747,14 @@ .donemessagelarge { .alert-success(); padding-left: 52px; - background-image: url(done_message_icon.png); + background-image: url(done_large.png); //border-color: @done_message_border; //background-color: @done_message_bg; } .infomessagelarge { .alert-info(); - background-image: url(info_message_icon.png); + background-image: url(info_large.png); border-color: @info_message_border; background-color: @info_message_bg; } diff -r fe149b078c865e6d2b3f969f76195b3f53d9cb48 -r 35024e38e7292bb26474f10723754dbf96dea316 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -578,11 +578,11 @@ .search-query{display:inline-block;padding:4px;font-size:12px;line-height:16px;color:#555555;border:1px solid #999999;padding-left:14px !important;padding-right:14px !important;margin-bottom:0;-webkit-border-radius:14px;-moz-border-radius:14px;border-radius:14px;max-width:auto;} .search-query:focus{border-color:rgba(24, 132, 218, 0.8);-webkit-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);-moz-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);outline:0;outline:thin dotted \9;} .search-spinner{position:absolute;display:none;right:8px;top:10px;} -.errormessagelarge,.warningmessagelarge,.donemessagelarge,.infomessagelarge{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#ffffcc;border:1px solid #ffdd33;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#666600;min-height:36px;padding-left:52px;background-image:url(error_message_icon.png);background-repeat:no-repeat;background-position:10px 10px;} +.errormessagelarge,.warningmessagelarge,.donemessagelarge,.infomessagelarge{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#ffffcc;border:1px solid #ffdd33;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#666600;min-height:36px;padding-left:52px;background-image:url(error_large.png);background-repeat:no-repeat;background-position:10px 10px;} .errormessagelarge{background-color:#ffcccc;border-color:#ff3355;color:#660000;padding-left:52px;} -.warningmessagelarge{background-image:url(warn_message_icon.png);border-color:#aaaa66;background-color:#ffffcc;} -.donemessagelarge{background-color:#ccffcc;border-color:#1a9900;color:#006600;padding-left:52px;background-image:url(done_message_icon.png);} -.infomessagelarge{background-color:#d9edf7;border-color:#1b7183;color:#134158;background-image:url(info_message_icon.png);border-color:#6666aa;background-color:#d9edf7;} +.warningmessagelarge{background-image:url(warn_large.png);border-color:#aaaa66;background-color:#ffffcc;} +.donemessagelarge{background-color:#ccffcc;border-color:#1a9900;color:#006600;padding-left:52px;background-image:url(done_large.png);} +.infomessagelarge{background-color:#d9edf7;border-color:#1b7183;color:#134158;background-image:url(info_large.png);border-color:#6666aa;background-color:#d9edf7;} .screencastBox{padding-left:10px;border-color:#AAAA66;background-color:#FFFFCC;background-image:none;} .errormessage,.warningmessage,.donemessage,.infomessage,.errormessagesmall,.warningmessagesmall,.donemessagesmall,.infomessagesmall{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#ffffcc;border:1px solid #ffdd33;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#666600;padding:5px;padding-left:25px;min-height:15px;background-image:url(error_small.png);background-repeat:no-repeat;background-position:5px 5px;} .errormessage{background-color:#ffcccc;border-color:#ff3355;color:#660000;} diff -r fe149b078c865e6d2b3f969f76195b3f53d9cb48 -r 35024e38e7292bb26474f10723754dbf96dea316 static/june_2007_style/blue/data_empty.png Binary file static/june_2007_style/blue/data_empty.png has changed diff -r fe149b078c865e6d2b3f969f76195b3f53d9cb48 -r 35024e38e7292bb26474f10723754dbf96dea316 static/june_2007_style/blue/data_error.png Binary file static/june_2007_style/blue/data_error.png has changed diff -r fe149b078c865e6d2b3f969f76195b3f53d9cb48 -r 35024e38e7292bb26474f10723754dbf96dea316 static/june_2007_style/blue/data_ok.png Binary file static/june_2007_style/blue/data_ok.png has changed diff -r fe149b078c865e6d2b3f969f76195b3f53d9cb48 -r 35024e38e7292bb26474f10723754dbf96dea316 static/june_2007_style/blue/data_queued.png Binary file static/june_2007_style/blue/data_queued.png has changed diff -r fe149b078c865e6d2b3f969f76195b3f53d9cb48 -r 35024e38e7292bb26474f10723754dbf96dea316 static/june_2007_style/blue/error_large.png Binary file static/june_2007_style/blue/error_large.png has changed diff -r fe149b078c865e6d2b3f969f76195b3f53d9cb48 -r 35024e38e7292bb26474f10723754dbf96dea316 static/june_2007_style/blue/error_small.png Binary file static/june_2007_style/blue/error_small.png has changed diff -r fe149b078c865e6d2b3f969f76195b3f53d9cb48 -r 35024e38e7292bb26474f10723754dbf96dea316 static/june_2007_style/blue/info_large.png Binary file static/june_2007_style/blue/info_large.png has changed diff -r fe149b078c865e6d2b3f969f76195b3f53d9cb48 -r 35024e38e7292bb26474f10723754dbf96dea316 static/june_2007_style/blue/info_small.png Binary file static/june_2007_style/blue/info_small.png has changed diff -r fe149b078c865e6d2b3f969f76195b3f53d9cb48 -r 35024e38e7292bb26474f10723754dbf96dea316 static/june_2007_style/blue/ok_large.png Binary file static/june_2007_style/blue/ok_large.png has changed diff -r fe149b078c865e6d2b3f969f76195b3f53d9cb48 -r 35024e38e7292bb26474f10723754dbf96dea316 static/june_2007_style/blue/ok_small.png Binary file static/june_2007_style/blue/ok_small.png has changed diff -r fe149b078c865e6d2b3f969f76195b3f53d9cb48 -r 35024e38e7292bb26474f10723754dbf96dea316 static/june_2007_style/blue/trackster.css --- a/static/june_2007_style/blue/trackster.css +++ b/static/june_2007_style/blue/trackster.css @@ -31,11 +31,11 @@ .overlay{position:absolute;left:0;top:0;} .track-name{float:left;margin-top:2px;height:16px;} .label-track .track-content{background:white;} -.track-content{position:relative;} .track-tile{background:white;} .track-tile canvas{position:relative;z-index:100;} .tile-message{border-bottom:solid 1px red;text-align:center;color:red;background-color:white;} .track.error .track-content{background-color:#ECB4AF;background-image:none;} +.track-content{position:relative;} .track.nodata .track-content{background-color:#eee;background-image:none;} .track.pending .track-content{background-color:white;background-image:none;} .loading{min-height:100px;} diff -r fe149b078c865e6d2b3f969f76195b3f53d9cb48 -r 35024e38e7292bb26474f10723754dbf96dea316 static/june_2007_style/blue/wait_large.png Binary file static/june_2007_style/blue/wait_large.png has changed diff -r fe149b078c865e6d2b3f969f76195b3f53d9cb48 -r 35024e38e7292bb26474f10723754dbf96dea316 static/june_2007_style/blue/wait_small.png Binary file static/june_2007_style/blue/wait_small.png has changed diff -r fe149b078c865e6d2b3f969f76195b3f53d9cb48 -r 35024e38e7292bb26474f10723754dbf96dea316 static/june_2007_style/blue/warn_large.png Binary file static/june_2007_style/blue/warn_large.png has changed diff -r fe149b078c865e6d2b3f969f76195b3f53d9cb48 -r 35024e38e7292bb26474f10723754dbf96dea316 static/june_2007_style/blue/warn_small.png Binary file static/june_2007_style/blue/warn_small.png has changed https://bitbucket.org/galaxy/galaxy-central/changeset/fe460cfa0f00/ changeset: fe460cfa0f00 user: james_taylor date: 2012-03-12 20:02:02 summary: style: fix for ok/done icon affected #: 2 files diff -r 35024e38e7292bb26474f10723754dbf96dea316 -r fe460cfa0f00e0a23ec161b1c780f654dbdcb2af static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -358,7 +358,7 @@ .panel-done-message { - background-image: url(done_small.png); + background-image: url(ok_small.png); background-color: @done_message_bg; } @@ -480,6 +480,7 @@ text-align: center; z-index: 9001; color: @quota_meter_text; + white-space: nowrap; } @@ -747,7 +748,7 @@ .donemessagelarge { .alert-success(); padding-left: 52px; - background-image: url(done_large.png); + background-image: url(ok_large.png); //border-color: @done_message_border; //background-color: @done_message_bg; } diff -r 35024e38e7292bb26474f10723754dbf96dea316 -r fe460cfa0f00e0a23ec161b1c780f654dbdcb2af static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -525,7 +525,7 @@ .dialog-box .buttons{padding:5px;} .panel-error-message,.panel-warning-message,.panel-done-message,.panel-info-message{height:24px;line-height:24px;color:#303030;padding:0px;padding-left:26px;background-color:#ffcccc;background-image:url(error_small.png);background-repeat:no-repeat;background-position:6px 50%;} .panel-warning-message{background-image:url(warn_small.png);background-color:#ffffcc;} -.panel-done-message{background-image:url(done_small.png);background-color:#ccffcc;} +.panel-done-message{background-image:url(ok_small.png);background-color:#ccffcc;} .panel-info-message{background-image:url(info_small.png);background-color:#d9edf7;} #masthead{-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;overflow:visible;margin-bottom:16px;position:absolute;top:0;left:0;width:100%;min-width:900px;height:32px;border-bottom:solid #444444 1px;z-index:15000;padding:0;}#masthead .brand:hover{text-decoration:none;} #masthead .brand{float:left;display:block;padding:8px 20px 12px;margin-left:-20px;font-size:20px;font-weight:200;line-height:1;color:#ffffff;} @@ -542,7 +542,7 @@ .quota-meter-bar{position:absolute;top:0;left:0;height:16px;background-color:#969db3;} .quota-meter-bar-warn{background-color:#ffb400;} .quota-meter-bar-error{background-color:#ff4343;} -.quota-meter-text{position:absolute;top:50%;left:0;width:100px;height:16px;margin-top:-6px;text-align:center;z-index:9001;color:#000000;} +.quota-meter-text{position:absolute;top:50%;left:0;width:100px;height:16px;margin-top:-6px;text-align:center;z-index:9001;color:#000000;white-space:nowrap;} div.metadataForm{border:solid #aaaaaa 1px;} div.metadataFormTitle{font-weight:bold;padding:5px;padding-left:10px;padding-right:10px;background:#cccccc;background-repeat:repeat-x;background-position:top;border-bottom:solid #aaaaaa 1px;} div.metadataFormBody{background:#FFFFFF;background-image:url(form_body_bg.png);background-repeat:repeat-x;background-position:top;padding:5px 0;} @@ -581,7 +581,7 @@ .errormessagelarge,.warningmessagelarge,.donemessagelarge,.infomessagelarge{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#ffffcc;border:1px solid #ffdd33;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#666600;min-height:36px;padding-left:52px;background-image:url(error_large.png);background-repeat:no-repeat;background-position:10px 10px;} .errormessagelarge{background-color:#ffcccc;border-color:#ff3355;color:#660000;padding-left:52px;} .warningmessagelarge{background-image:url(warn_large.png);border-color:#aaaa66;background-color:#ffffcc;} -.donemessagelarge{background-color:#ccffcc;border-color:#1a9900;color:#006600;padding-left:52px;background-image:url(done_large.png);} +.donemessagelarge{background-color:#ccffcc;border-color:#1a9900;color:#006600;padding-left:52px;background-image:url(ok_large.png);} .infomessagelarge{background-color:#d9edf7;border-color:#1b7183;color:#134158;background-image:url(info_large.png);border-color:#6666aa;background-color:#d9edf7;} .screencastBox{padding-left:10px;border-color:#AAAA66;background-color:#FFFFCC;background-image:none;} .errormessage,.warningmessage,.donemessage,.infomessage,.errormessagesmall,.warningmessagesmall,.donemessagesmall,.infomessagesmall{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#ffffcc;border:1px solid #ffdd33;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#666600;padding:5px;padding-left:25px;min-height:15px;background-image:url(error_small.png);background-repeat:no-repeat;background-position:5px 5px;} https://bitbucket.org/galaxy/galaxy-central/changeset/243ad28621be/ changeset: 243ad28621be user: james_taylor date: 2012-03-21 17:44:43 summary: Automated merge with https://bitbucket.org/galaxy/galaxy-central affected #: 95 files Diff too large to display. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Branch close for pull request.
by Bitbucket 21 Mar '12

21 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c94957ac5454/ changeset: c94957ac5454 branch: workflow_import_menu_api user: dannon date: 2012-03-21 14:50:44 summary: Branch close for pull request. affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 21 Mar '12

21 Mar '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/44c6cbd425e9/ changeset: 44c6cbd425e9 branch: workflow_import_menu_api user: jmchilton date: 2012-03-19 18:13:59 summary: Augment workflow import api to allow add_to_menu argument which (when true) adds imported workflow to user's workflow menu. Augment api example script to take in an optional fourth parameter --add_to_menu to enable this. affected #: 2 files diff -r f61e924a5463e2f2232635e36d5b2e20745abe24 -r 44c6cbd425e9dc61a5a054d0d417847890e532aa lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -1127,6 +1127,7 @@ # id being imported from a Galaxy tool shed repository. tool_shed_url = kwd.get( 'tool_shed_url', '' ) repository_metadata_id = kwd.get( 'repository_metadata_id', '' ) + add_to_menu = kwd.get( 'add_to_menu', False ) # The workflow_name parameter is in the request only if the import originated # from a Galaxy tool shed, in which case the value was encoded. workflow_name = kwd.get( 'workflow_name', '' ) @@ -1193,7 +1194,7 @@ src = None if cntrller != 'api': src="uploaded file" - workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source=src ) + workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source=src, add_to_menu=add_to_menu ) workflow = workflow.latest_workflow if workflow_name: workflow.name = workflow_name @@ -1824,7 +1825,7 @@ # Add to return value data['steps'][step.order_index] = step_dict return data - def _workflow_from_dict( self, trans, data, source=None ): + def _workflow_from_dict( self, trans, data, source=None, add_to_menu=False ): """ Creates a workflow from a dict. Created workflow is stored in the database and returned. """ @@ -1901,6 +1902,15 @@ # Persist trans.sa_session.add( stored ) trans.sa_session.flush() + + if add_to_menu: + if trans.user.stored_workflow_menu_entries == None: + trans.user.stored_workflow_menu_entries = [] + menuEntry = model.StoredWorkflowMenuEntry() + menuEntry.stored_workflow = stored + trans.user.stored_workflow_menu_entries.append( menuEntry ) + trans.sa_session.flush() + return stored, missing_tool_tups ## ---- Utility methods ------------------------------------------------------- diff -r f61e924a5463e2f2232635e36d5b2e20745abe24 -r 44c6cbd425e9dc61a5a054d0d417847890e532aa scripts/api/workflow_import.py --- a/scripts/api/workflow_import.py +++ b/scripts/api/workflow_import.py @@ -2,7 +2,7 @@ """ Import workflows from the command line. Example calls: -python workflow_import.py <api_key><galaxy_url> '/path/to/workflow/file' +python workflow_import.py <api_key><galaxy_url> '/path/to/workflow/file [--add_to_menu]' """ import os, sys @@ -16,6 +16,8 @@ try: data = {} data['installed_repository_file'] = sys.argv[3] + if len(sys.argv) > 4 and sys.argv[4] == "--add_to_menu": + data['add_to_menu'] = True except IndexError: print 'usage: %s key galaxy_url workflow_file' % os.path.basename(sys.argv[0]) sys.exit(1) https://bitbucket.org/galaxy/galaxy-central/changeset/1a3d01b09f7a/ changeset: 1a3d01b09f7a branch: workflow_import_menu_api user: jmchilton date: 2012-03-19 18:37:37 summary: Improving string vs. bool handling of add_to_menu API option in workflow controller. affected #: 1 file diff -r 44c6cbd425e9dc61a5a054d0d417847890e532aa -r 1a3d01b09f7acf05d465f3eb5906525507a52807 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -16,6 +16,7 @@ from galaxy.util.topsort import topsort, topsort_levels, CycleError from galaxy.workflow.modules import * from galaxy import model +from galaxy import util from galaxy.model.mapping import desc from galaxy.model.orm import * from galaxy.model.item_attrs import * @@ -1127,7 +1128,7 @@ # id being imported from a Galaxy tool shed repository. tool_shed_url = kwd.get( 'tool_shed_url', '' ) repository_metadata_id = kwd.get( 'repository_metadata_id', '' ) - add_to_menu = kwd.get( 'add_to_menu', False ) + add_to_menu = util.string_as_bool( kwd.get( 'add_to_menu', False ) ) # The workflow_name parameter is in the request only if the import originated # from a Galaxy tool shed, in which case the value was encoded. workflow_name = kwd.get( 'workflow_name', '' ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for viewport generation in display_applications/ucsc/interval_as_bed.xml.
by Bitbucket 20 Mar '12

20 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7b85f800362c/ changeset: 7b85f800362c user: dan date: 2012-03-20 18:10:21 summary: Fix for viewport generation in display_applications/ucsc/interval_as_bed.xml. affected #: 1 file diff -r e8e36170786518dc8d31ba3d6758e08d345875b5 -r 7b85f800362c738f7296f5d09f71fbe100a52d58 display_applications/ucsc/interval_as_bed.xml --- a/display_applications/ucsc/interval_as_bed.xml +++ b/display_applications/ucsc/interval_as_bed.xml @@ -14,7 +14,7 @@ <param type="template" name="position" strip="True" > #set chrom, start, end = $bed_file.datatype.get_estimated_display_viewport( $bed_file ) #if $chrom is not None: -${chrom}:${start}-${end + 1} +${chrom}:${start}-${int( end ) + 1} #else: :- #end if Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Fix owner_tag mapping of StoredWorkflow. Previously this mapping incorrectly retrieved *all* workflow tags owned by the user.
by Bitbucket 20 Mar '12

20 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e8e361707865/ changeset: e8e361707865 user: dannon date: 2012-03-20 15:34:01 summary: Fix owner_tag mapping of StoredWorkflow. Previously this mapping incorrectly retrieved *all* workflow tags owned by the user. affected #: 1 file diff -r d388551528e97128401a048c7638d1b4becaca53 -r e8e36170786518dc8d31ba3d6758e08d345875b5 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -1566,7 +1566,7 @@ assign_mapper( context, StoredWorkflow, StoredWorkflow.table, - properties=dict( user=relation( User, + properties=dict( user=relation( User, primaryjoin=( User.table.c.id == StoredWorkflow.table.c.user_id ), backref='stored_workflows' ), workflows=relation( Workflow, backref='stored_workflow', @@ -1575,16 +1575,15 @@ latest_workflow=relation( Workflow, post_update=True, primaryjoin=( StoredWorkflow.table.c.latest_workflow_id == Workflow.table.c.id ), lazy=False ), - tags=relation( StoredWorkflowTagAssociation, order_by=StoredWorkflowTagAssociation.table.c.id, backref="stored_workflows" ), - owner_tags=relation( StoredWorkflowTagAssociation, + tags=relation( StoredWorkflowTagAssociation, order_by=StoredWorkflowTagAssociation.table.c.id, backref="stored_workflows" ), + owner_tags=relation( StoredWorkflowTagAssociation, primaryjoin=and_( StoredWorkflow.table.c.id == StoredWorkflowTagAssociation.table.c.stored_workflow_id, StoredWorkflow.table.c.user_id == StoredWorkflowTagAssociation.table.c.user_id ), - foreign_keys=[StoredWorkflowTagAssociation.table.c.user_id], order_by=StoredWorkflowTagAssociation.table.c.id ), annotations=relation( StoredWorkflowAnnotationAssociation, order_by=StoredWorkflowAnnotationAssociation.table.c.id, backref="stored_workflows" ), ratings=relation( StoredWorkflowRatingAssociation, order_by=StoredWorkflowRatingAssociation.table.c.id, backref="stored_workflows" ) ) ) - + # Set up proxy so that # StoredWorkflow.users_shared_with # returns a list of users that workflow is shared with. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Add fugue hammer icons.
by Bitbucket 18 Mar '12

18 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d388551528e9/ changeset: d388551528e9 user: jgoecks date: 2012-03-18 19:43:32 summary: Add fugue hammer icons. affected #: 2 files diff -r f89751a0110713afb868caf72c80fc75890509bb -r d388551528e97128401a048c7638d1b4becaca53 static/images/fugue/hammer-bw.png Binary file static/images/fugue/hammer-bw.png has changed diff -r f89751a0110713afb868caf72c80fc75890509bb -r d388551528e97128401a048c7638d1b4becaca53 static/images/fugue/hammer.png Binary file static/images/fugue/hammer.png has changed Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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