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[hg] galaxy 3250: c.log
by Greg Von Kuster 22 Jan '10

22 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/82082fd1da62 changeset: 3250:82082fd1da62 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Tue Jan 19 14:22:31 2010 -0500 description: c.log diffstat: lib/galaxy/tools/parameters/validation.py | 8 ++++---- 1 files changed, 4 insertions(+), 4 deletions(-) diffs (26 lines): diff -r 85d032d94db1 -r 82082fd1da62 lib/galaxy/tools/parameters/validation.py --- a/lib/galaxy/tools/parameters/validation.py Tue Jan 19 13:41:53 2010 -0500 +++ b/lib/galaxy/tools/parameters/validation.py Tue Jan 19 14:22:31 2010 -0500 @@ -105,18 +105,18 @@ """ @classmethod def from_element( cls, param, elem ): - return cls( elem.get( 'message', None ), elem.get( 'min' ), elem.get( 'max' ) ) + return cls( elem.get( 'message', None ), elem.get( 'min', '-inf' ), elem.get( 'max', '+inf' ) ) def __init__( self, message, range_min, range_max ): - self.message = message or ( "Value must be between %f and %f" % ( range_min, range_max ) ) self.min = float( range_min ) - self.max = float( range_max ) + self.max = float( range_max ) + self.message = message or ( "Value must be between %f and %f" % ( self.min, self.max ) ) def validate( self, value, history=None ): if not( self.min <= float( value ) <= self.max ): raise ValueError( self.message ) class LengthValidator( Validator ): """ - Validator that ensures a number is in a specific range + Validator that ensures the length of the provided string (value) is in a specific range >>> from galaxy.tools.parameters import ToolParameter >>> p = ToolParameter.build( None, XML( '''

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[hg] galaxy 3249: redo panel template change
by Greg Von Kuster 22 Jan '10

22 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/85d032d94db1 changeset: 3249:85d032d94db1 user: Kanwei Li <kanwei(a)gmail.com> date: Tue Jan 19 13:41:53 2010 -0500 description: redo panel template change diffstat: static/june_2007_style/panel_layout.css.tmpl | 5 +++-- 1 files changed, 3 insertions(+), 2 deletions(-) diffs (27 lines): diff -r 08e1f40f2b93 -r 85d032d94db1 static/june_2007_style/panel_layout.css.tmpl --- a/static/june_2007_style/panel_layout.css.tmpl Fri Jan 15 17:29:19 2010 -0500 +++ b/static/june_2007_style/panel_layout.css.tmpl Tue Jan 19 13:41:53 2010 -0500 @@ -139,12 +139,13 @@ 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; - background: #bbb; } .panel-header-button.popup { @@ -154,7 +155,7 @@ .panel-header-button:hover { color: black; - background-color: #aaaaaa; + background-color: #ccc; } .panel-header-button:active {

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[hg] galaxy 3248: Use Lucida Grande for better unicode support, ...
by Greg Von Kuster 22 Jan '10

22 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/08e1f40f2b93 changeset: 3248:08e1f40f2b93 user: Kanwei Li <kanwei(a)gmail.com> date: Fri Jan 15 17:29:19 2010 -0500 description: Use Lucida Grande for better unicode support, clean up some css diffstat: static/june_2007_style/base.css.tmpl | 4 ++-- static/june_2007_style/blue/base.css | 4 ++-- static/june_2007_style/blue/history.css | 2 +- static/june_2007_style/blue/panel_layout.css | 9 ++------- static/june_2007_style/history.css.tmpl | 1 + static/june_2007_style/panel_layout.css.tmpl | 13 ++++--------- templates/root/history_common.mako | 2 +- 7 files changed, 13 insertions(+), 22 deletions(-) diffs (134 lines): diff -r 4e7c1fe8fab8 -r 08e1f40f2b93 static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl Fri Jan 15 17:12:50 2010 -0500 +++ b/static/june_2007_style/base.css.tmpl Fri Jan 15 17:29:19 2010 -0500 @@ -1,5 +1,5 @@ -## Font settings from YUI + verdana -body{font:13px/1.231 verdana,arial,helvetica,clean,sans-serif;*font-size:small;*font:x-small;}select,input,button,textarea,button{font:99% verdana,arial,helvetica,clean,sans-serif;}table{font-size:inherit;font:100%;}pre,code,kbd,samp,tt{font-family:monospace;*font-size:108%;line-height:100%;} +## 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 diff -r 4e7c1fe8fab8 -r 08e1f40f2b93 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Fri Jan 15 17:12:50 2010 -0500 +++ b/static/june_2007_style/blue/base.css Fri Jan 15 17:29:19 2010 -0500 @@ -1,5 +1,5 @@ -body{font:13px/1.231 verdana,arial,helvetica,clean,sans-serif;*font-size:small;*font:x-small;} -select,input,button,textarea,button{font:99% verdana,arial,helvetica,clean,sans-serif;} +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%;} diff -r 4e7c1fe8fab8 -r 08e1f40f2b93 static/june_2007_style/blue/history.css --- a/static/june_2007_style/blue/history.css Fri Jan 15 17:12:50 2010 -0500 +++ b/static/june_2007_style/blue/history.css Fri Jan 15 17:29:19 2010 -0500 @@ -3,7 +3,7 @@ div.historyLinks{padding:5px;margin:5px 0 5px 0;} div.historyItem{margin:5px -5px 5px 0px;padding:5px 11px 5px 5px;border:solid #888888 1px;border-left:solid #888888 5px;border-right:none;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{line-height:16px;} +div.historyItem .historyItemTitle{font-weight:bold;line-height:16px;} div.historyItem div.historyItem{margin-right:-11px;} div.historyItem-ok{border-color:#66AA66;background:#CCFFCC;} div.historyItem-ok .state-icon{display:none;} diff -r 4e7c1fe8fab8 -r 08e1f40f2b93 static/june_2007_style/blue/panel_layout.css --- a/static/june_2007_style/blue/panel_layout.css Fri Jan 15 17:12:50 2010 -0500 +++ b/static/june_2007_style/blue/panel_layout.css Fri Jan 15 17:29:19 2010 -0500 @@ -1,10 +1,5 @@ -body{font:13px/1.231 verdana,arial,helvetica,clean,sans-serif;*font-size:small;*font:x-small;} -select,input,button,textarea,button{font:99% verdana,arial,helvetica,clean,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%;} body,html{overflow:hidden;margin:0;padding:0;width:100%;height:100%;} -body{font:75% verdana, "Bitstream Vera Sans", geneva, arial, helvetica, helve, sans-serif;background:#eee;} +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%;} @@ -37,7 +32,7 @@ .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{font-family: verdana;arial;sans-serif;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{padding:3px 10px;font-size:175%;font-weight:bold;} #masthead a:hover{text-decoration:underline;} diff -r 4e7c1fe8fab8 -r 08e1f40f2b93 static/june_2007_style/history.css.tmpl --- a/static/june_2007_style/history.css.tmpl Fri Jan 15 17:12:50 2010 -0500 +++ b/static/june_2007_style/history.css.tmpl Fri Jan 15 17:29:19 2010 -0500 @@ -36,6 +36,7 @@ background-repeat: no-repeat; } .historyItemTitle { + font-weight: bold; line-height: 16px; } } diff -r 4e7c1fe8fab8 -r 08e1f40f2b93 static/june_2007_style/panel_layout.css.tmpl --- a/static/june_2007_style/panel_layout.css.tmpl Fri Jan 15 17:12:50 2010 -0500 +++ b/static/june_2007_style/panel_layout.css.tmpl Fri Jan 15 17:29:19 2010 -0500 @@ -1,8 +1,3 @@ -## Font settings from YUI + verdana -body{font:13px/1.231 verdana,arial,helvetica,clean,sans-serif;*font-size:small;*font:x-small;}select,input,button,textarea,button{font:99% verdana,arial,helvetica,clean,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%;} - - body, html { overflow: hidden; margin: 0; @@ -12,7 +7,7 @@ } body { - font: 75% verdana, "Bitstream Vera Sans", geneva, arial, helvetica, helve, sans-serif; + font: 75% "Lucida Grande",verdana,arial,helvetica,sans-serif; background: ${layout_bg}; } @@ -144,13 +139,12 @@ display: inline-block; cursor: pointer; margin: -1px; padding: 1px; - margin-top: -0.2em; - border: solid #999 1px; padding-right: 0.5em; padding-left: 0.5em; -moz-border-radius: 0.5em; -webkit-border-radius: 0.5em; border-radius: 0.5em; + background: #bbb; } .panel-header-button.popup { @@ -160,7 +154,7 @@ .panel-header-button:hover { color: black; - background-color: #ccc; + background-color: #aaaaaa; } .panel-header-button:active { @@ -235,6 +229,7 @@ ## Masthead #masthead { + font-family: verdana;arial;sans-serif; position:absolute; top:0; left:0; diff -r 4e7c1fe8fab8 -r 08e1f40f2b93 templates/root/history_common.mako --- a/templates/root/history_common.mako Fri Jan 15 17:12:50 2010 -0500 +++ b/templates/root/history_common.mako Fri Jan 15 17:29:19 2010 -0500 @@ -43,7 +43,7 @@ %endif </div> <span class="state-icon"></span> - <span class="historyItemTitle"><b>${hid}: ${data.display_name()}</b></span> + <span class="historyItemTitle">${hid}: ${data.display_name()}</span> </div> ## Body for history items, extra info and actions, data "peek"

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[hg] galaxy 3247: Updated csFasta sniff method to handle sequenc...
by Greg Von Kuster 22 Jan '10

22 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/4e7c1fe8fab8 changeset: 3247:4e7c1fe8fab8 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Fri Jan 15 17:12:50 2010 -0500 description: Updated csFasta sniff method to handle sequences with dots in them (T123..32.020......23) instead of being just numbers with a leading capital letter diffstat: lib/galaxy/datatypes/sequence.py | 4 ++-- 1 files changed, 2 insertions(+), 2 deletions(-) diffs (21 lines): diff -r 9cc57a489be0 -r 4e7c1fe8fab8 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py Fri Jan 15 12:51:45 2010 -0500 +++ b/lib/galaxy/datatypes/sequence.py Fri Jan 15 17:12:50 2010 -0500 @@ -66,7 +66,7 @@ A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than (">") symbol in the first column. - All lines should be shorter than 80 charcters + All lines should be shorter than 80 characters For complete details see http://www.ncbi.nlm.nih.gov/blast/fasta.shtml @@ -139,7 +139,7 @@ break elif line[0] not in string.ascii_uppercase: return False - elif len( line ) > 1 and not re.search( '^\d+$', line[1:] ): + elif len( line ) > 1 and not re.search( '^[\d.]+$', line[1:] ): return False return True else:

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[hg] galaxy 3246: Corrected counting of sequences in fastq set_meta
by Greg Von Kuster 22 Jan '10

22 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/9cc57a489be0 changeset: 3246:9cc57a489be0 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Fri Jan 15 12:51:45 2010 -0500 description: Corrected counting of sequences in fastq set_meta diffstat: lib/galaxy/datatypes/sequence.py | 18 +++++++++++++++--- 1 files changed, 15 insertions(+), 3 deletions(-) diffs (35 lines): diff -r fa318a093bf2 -r 9cc57a489be0 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py Thu Jan 14 17:49:20 2010 -0500 +++ b/lib/galaxy/datatypes/sequence.py Fri Jan 15 12:51:45 2010 -0500 @@ -160,16 +160,28 @@ """ data_lines = 0 sequences = 0 + seq_counter = 0 # blocks should be 4 lines long for line in file( dataset.file_name ): line = line.strip() if line and line.startswith( '#' ): # We don't count comment lines for sequence data types continue - if line and line.startswith( '@' ): - sequences += 1 - data_lines +=1 + if line and line.startswith( '@' ): + if seq_counter >= 4: + # count previous block + # blocks should be 4 lines long + sequences += 1 + seq_counter = 1 + else: + # in case quality line starts with @ + seq_counter += 1 + data_lines += 1 else: data_lines += 1 + seq_counter += 1 + if seq_counter >= 4: + # count final block + sequences += 1 dataset.metadata.data_lines = data_lines dataset.metadata.sequences = sequences def sniff ( self, filename ):

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[hg] galaxy 3245: trackster: fix thick region display bug, stack...
by Greg Von Kuster 22 Jan '10

22 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/fa318a093bf2 changeset: 3245:fa318a093bf2 user: Kanwei Li <kanwei(a)gmail.com> date: Thu Jan 14 17:49:20 2010 -0500 description: trackster: fix thick region display bug, stacking bugs, enable right-panel diffstat: lib/galaxy/web/controllers/tracks.py | 1 - lib/galaxy/web/controllers/visualization.py | 15 +-- static/scripts/packed/galaxy.panels.js | 2 +- static/scripts/packed/trackster.js | 2 +- static/scripts/trackster.js | 110 ++++++++++++++++----------- static/trackster.css | 6 +- templates/base_panels.mako | 2 +- templates/panels.mako | 2 +- templates/tracks/browser.mako | 35 ++++++-- 9 files changed, 105 insertions(+), 70 deletions(-) diffs (447 lines): diff -r 44526498cd00 -r fa318a093bf2 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Thu Jan 14 15:22:10 2010 -0500 +++ b/lib/galaxy/web/controllers/tracks.py Thu Jan 14 17:49:20 2010 -0500 @@ -221,7 +221,6 @@ converted dataset (possibly new) is returned, if it cannot be converted, None is returned. """ - log.debug("Inside dataset as type") # Already of correct type if dataset.extension == type: return dataset diff -r 44526498cd00 -r fa318a093bf2 lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py Thu Jan 14 15:22:10 2010 -0500 +++ b/lib/galaxy/web/controllers/visualization.py Thu Jan 14 17:49:20 2010 -0500 @@ -25,17 +25,16 @@ return query.filter_by( user=trans.user ) class VisualizationController( BaseController ): - + list_grid = VisualizationListGrid() @web.expose @web.require_login() - def index( self, trans ): - return trans.fill_template( "panels.mako", active_view='visualization', main_url=url_for( action='list' ) ) + def index( self, trans, *args, **kwargs ): + return trans.fill_template( "panels.mako", grid=self.list_grid( trans, *args, **kwargs ), active_view='visualization', main_url=url_for( action='list' ) ) - list_grid = VisualizationListGrid() - @web.expose - @web.require_login() - def list( self, trans, *args, **kwargs ): - return self.list_grid( trans, *args, **kwargs ) + # @web.expose + # @web.require_login() + # def list( self, trans, *args, **kwargs ): + # return self.list_grid( trans, *args, **kwargs ) #(a)web.expose #(a)web.require_admin diff -r 44526498cd00 -r fa318a093bf2 static/scripts/packed/galaxy.panels.js --- a/static/scripts/packed/galaxy.panels.js Thu Jan 14 15:22:10 2010 -0500 +++ b/static/scripts/packed/galaxy.panels.js Thu Jan 14 17:49:20 2010 -0500 @@ -1,1 +1,1 @@ -function ensure_dd_helper(){if($("#DD-helper").length==0){$("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_left_panel(h,c,e){var g=false;var f=null;var d=function(i){var j=i;if(i<0){i=0}$(h).css("width",i);$(e).css("left",j);$(c).css("left",i+7);if(document.recalc){document.recalc()}};var 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crolling='"+a+"' frameborder='0'></iframe></div>"));$("#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 diff -r 44526498cd00 -r fa318a093bf2 static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js Thu Jan 14 15:22:10 2010 -0500 +++ b/static/scripts/packed/trackster.js Thu Jan 14 17:49:20 2010 -0500 @@ -1,1 +1,1 @@ -var DEBUG=false;var DENSITY=1000,FEATURE_LEVELS=100,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_ img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c}});var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=3;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=thi s.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/DENSITY)/Math.LN10));this.zoom_res=Math.max(1,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS)));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;thi s.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var l=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(l);var m=this.content_div.width()/f;var i=20;var h;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b=(g-j)*m;if(this.left_off set){b-=this.left_offset}c.css({left:b});l.append(c);i=Math.max(i,c.height())}else{h=this.draw_tile(d,a,l,m);if(h){this.tile_cache.set(k,h);i=Math.max(i,h.height())}}this.content_div.css("height",i);a+=1}}});var LabelTrack=function(a){Track.call(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,d,a){this.tile_cache=new Cache(CACHED_TILES_LINE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=(a?a:100);this.container_div.addClass("line -track");this.dataset_id=b;this.data_queue={};this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,indexer:a.indexer,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){if(!c||c=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(c=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(c=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.min_value=c.min;a.max_value=c.max;a.vertical_range=a.max_value-a.min_value;var d=$("<div class='yaxislabel'>"+a.min_value+"</div>");var b=$("<div class='yaxislabel'>"+a.max_value+"</div>");b.css({position:"relative",top:"35px"});b.prependTo(a.container_div);d.css({position:"relative",top:a.height_ px+32+"px"});d.prependTo(a.container_div);a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.getJSON(data_url,{indexer:this.indexer,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},function(g){c.cache.set(e,g);delete c.data_queue[e];c.draw()})}},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache.get(l)){this.get_data(d,a);return}var g=this.cache.get(l);c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n.stroke();m.append(c);retu rn c}});var FeatureTrack=function(c,b,d,a){this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10;this.base_color="#2C3143";this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.data_cache=new Cache(20)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{indexer:a.indexer,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.addCla ss("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{indexer:b.indexer,chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,include_blocks:true},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},calc_slots:function(){var c=[],b=this.content_div.width()/(this.view.high-this.view.low),a=this.view.max_high,e=this.view.max_low;for(var f=0,g=this.values.length;f<g;f++){var h,k,l=this.values[f];h=Math.floor((l.start-e)*b);k=Math.ceil((l.end-e)*b);var d=0;while(true){if(c[d]===undefined||c[d]<h){c[d]=k;this.zo_slots[l.uid]=d;break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},incremental_slots:function(a,b){if(!this.inc_slots[a]){this.inc _slots[a]={};this.inc_slots[a].w_scale=DENSITY/Math.pow(FEATURE_LEVELS,a+1)}var k=this.inc_slots[a];var d=[],l=[],c=0,m=$("<canvas></canvas>").get(0).getContext("2d"),f=this.view.max_low;for(var g=0,h=b.length;g<h;g++){var n=b[g];if(k[n.uid]){c=Math.max(c,k[n.uid]);d[k[n.uid]]=Math.ceil((n.end-f)*k.w_scale)}else{l.push(n)}}for(var g=0,h=l.length;g<h;g++){var n=l[g];f_start=Math.floor((n.start-f)*k.w_scale);f_start-=m.measureText(n.name).width;f_end=Math.ceil((n.end-f)*k.w_scale);var e=0;while(true){if(d[e]===undefined||d[e]<f_start){d[e]=f_end;k[n.uid]=e;c=Math.max(c,e);break}e++}}return c},draw_tile:function(A,F,n,r){if(!this.values){return}var G=F*DENSITY*A,c=(F+1)*DENSITY*A,v=DENSITY*A;var K,u,h;if(r>this.show_labels_scale){if(!this.showing_labels){this.showing_labels=true}for(var B in this.data_cache.obj_cache){var p=B.split("_"),e=p[0],d=p[1];if(e<=G&&d>=c){K=this.data_cache.get(B);break}}if(!K){this.data_queue[[G,c]]=true;this.get_data(G,c);return}h=this.incremental_sl ots(this.view.zoom_res,K)*this.vertical_gap+15;u=this.inc_slots[this.view.zoom_res]}else{if(this.showing_labels){this.showing_labels=false}h=this.height_px;u=this.zo_slots;K=this.values}var y=Math.ceil(v*r),x=$("<canvas class='tile'></canvas>");x.css({position:"absolute",top:0,left:(G-this.view.low)*r-this.left_offset});x.get(0).width=y+this.left_offset;x.get(0).height=h;var z=x.get(0).getContext("2d");z.fillStyle=this.base_color;z.font=this.default_font;z.textAlign="right";var C=0;for(var D=0,E=K.length;D<E;D++){var m=K[D];if(m.start<=c&&m.end>=G){var g=Math.floor(Math.max(0,(m.start-G)*r)),l=Math.ceil(Math.min(y,(m.end-G)*r)),f=u[m.uid]*this.vertical_gap;var a,L,b=null,s=null;if(m.thick_start&&m.thick_end){b=Math.floor(Math.max(0,(m.thick_start-G)*r));s=Math.ceil(Math.min(y,(m.thick_end-G)*r))}if(!this.showing_labels){z.fillRect(g+this.left_offset,f+5,l-g,1)}else{if(z.fillText&&m.start>G){z.fillText(m.name,g-1+this.left_offset,f+8)}var I=m.blocks;if(I){if(m.strand){if(m.st rand=="+"){z.fillStyle=RIGHT_STRAND}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}for(var B=0,J=I.length;B<J;B++){var q=I[B],o=Math.floor(Math.max(0,(q[0]-G)*r)),H=Math.ceil(Math.min(y,(q[1]-G)*r));if(o>H){continue}a=5;L=3;z.fillRect(o+this.left_offset,f+L,H-o,a);if(b&&(o<s||H>b)){a=9;L=1;var w=Math.max(o,b),t=Math.min(H,s);z.fillRect(w+this.left_offset,f+L,t-w,a)}}}else{a=9;L=1;z.fillRect(g+this.left_offset,f+L,l-g,a);if(m.strand){if(m.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}}}C++}}n.append(x);return x}});var ReadTrack=function(c,b,d,a){this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);FeatureTrack.call(this,c,b,d,a);this.default_font="9px Monaco, Lucida Console, monospace"};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureT rack.prototype,{draw_tile:function(w,A,n,o){if(!this.values){return}var B=A*DENSITY*w,f=(A+1)*DENSITY*w,r=DENSITY*w;var E,q,k;k=this.height_px;q=this.zo_slots;E=this.values;var u=Math.ceil(r*o),s=$("<canvas class='tile'></canvas>");var b=$("<canvas></canvas>").get(0).getContext("2d");s.css({position:"absolute",top:0,left:(B-this.view.low)*o-this.left_offset});s.get(0).width=u+this.left_offset;s.get(0).height=k;var v=s.get(0).getContext("2d");v.fillStyle=this.base_color;v.font=this.default_font;v.textAlign="right";var t=v.measureText("A").width;var x=0;for(var y=0,z=E.length;y<z;y++){var m=E[y];if(m.start<=f&&m.end>=B){var h=Math.floor(Math.max(0,(m.start-B)*o)),l=Math.ceil(Math.min(u,(m.end-B)*o)),g=q[m.uid]*this.vertical_gap;var a,F,e=null,p=null;if(o>t){for(var C=0,d=m.name.length;C<d;C++){var D=Math.floor(Math.max(0,(m.start+C-B)*o));v.fillText(m.name[C],D+this.left_offset,g+8)}}else{v.fillRect(h+this.left_offset,g+4,l-h,3)}}}n.append(s);return s}}); \ No newline at end of file +var DEBUG=false;var DENSITY=1000,FEATURE_LEVELS=100,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_ img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c}});var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=3;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=thi s.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/DENSITY)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;retu rn}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var l=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(l);var m=this.content_div.width()/f;var i=20;var h;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b =(g-j)*m;if(this.left_offset){b-=this.left_offset}c.css({left:b});l.append(c);i=Math.max(i,c.height())}else{h=this.draw_tile(d,a,l,m);if(h){this.tile_cache.set(k,h);i=Math.max(i,h.height())}}this.content_div.css("height",i);a+=1}}});var LabelTrack=function(a){Track.call(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,d,a){this.tile_cache=new Cache(CACHED_TILES_LINE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=(a?a:100);this.con tainer_div.addClass("line-track");this.dataset_id=b;this.data_queue={};this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,indexer:a.indexer,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){if(!c||c=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(c=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(c=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.min_value=c.min;a.max_value=c.max;a.vertical_range=a.max_value-a.min_value;var d=$("<div class='yaxislabel'>"+a.min_value+"</div>");var b=$("<div class='yaxislabel'>"+a.max_value+"</div>");b.css({position:"relative",top:"25px"});b.prependTo(a.container_div);d.css({position :"relative",top:a.height_px+55+"px"});d.prependTo(a.container_div);a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.getJSON(data_url,{indexer:this.indexer,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},function(g){c.cache.set(e,g);delete c.data_queue[e];c.draw()})}},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache.get(l)){this.get_data(d,a);return}var g=this.cache.get(l);c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n. stroke();m.append(c);return c}});var FeatureTrack=function(c,b,d,a){this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.base_color="#2C3143";this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.data_cache=new Cache(20)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{indexer:a.indexer,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nod ata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{indexer:b.indexer,chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,include_blocks:true},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},calc_slots:function(){var b=[],a=this.content_div.width()/(this.view.high-this.view.low),d=this.view.max_low;for(var e=0,f=this.values.length;e<f;e++){var g,h,k=this.values[e];g=Math.floor((k.start-d)*a);h=Math.ceil((k.end-d)*a);var c=0;while(true){if(b[c]===undefined||b[c]<g){b[c]=h;this.zo_slots[k.uid]=c;break}c++}}this.height_px=b.length*this.vertical_nodetail_px+15;this.content_div.css("height",this.height_px+"px ")},incremental_slots:function(a,f){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var h=this.inc_slots[a].w_scale,s=[],g=0,b=$("<canvas></canvas>").get(0).getContext("2d"),l=this.view.max_low;var c,e,u=[];for(var p=0,q=f.length;p<q;p++){var d=f[p];if(this.inc_slots[a][d.uid]!==undefined){g=Math.max(g,this.inc_slots[a][d.uid]);u.push(this.inc_slots[a][d.uid])}else{s.push(p)}}for(var p=0,q=s.length;p<q;p++){var d=f[s[p]];c=Math.floor((d.start-l)*h);c-=b.measureText(d.name).width;e=Math.ceil((d.end-l)*h);var o=0;while(true){var m=true;if(this.s_e_by_tile[a][o]!==undefined){for(var n=0,t=this.s_e_by_tile[a][o].length;n<t;n++){var r=this.s_e_by_tile[a][o][n];if(e>r[0]&&c<r[1]){m=false;break}}}if(m){if(this.s_e_by_tile[a][o]===undefined){this.s_e_by_tile[a][o]=[]}this.s_e_by_tile[a][o].push([c,e]);this.inc_slots[a][d.uid]=o;g=Math.max(g,o);break}o++}}return g},draw_tile:function(A,F,n,r){if(!this.values){return}var G=F*DENSITY*A,c =(F+1)*DENSITY*A,v=DENSITY*A;var K,u,h;if(r>this.show_labels_scale){if(!this.showing_details){this.showing_details=true}for(var B in this.data_cache.obj_cache){var p=B.split("_"),e=p[0],d=p[1];if(e<=G&&d>=c){K=this.data_cache.get(B);break}}if(!K){this.data_queue[[G,c]]=true;this.get_data(G,c);return}h=this.incremental_slots(this.view.zoom_res,K)*this.vertical_detail_px+15;u=this.inc_slots[this.view.zoom_res]}else{if(this.showing_details){this.showing_details=false}h=this.height_px;u=this.zo_slots;K=this.values}var y=Math.ceil(v*r),x=$("<canvas class='tile'></canvas>");x.css({position:"absolute",top:0,left:(G-this.view.low)*r-this.left_offset});x.get(0).width=y+this.left_offset;x.get(0).height=h;var z=x.get(0).getContext("2d");z.fillStyle=this.base_color;z.font=this.default_font;z.textAlign="right";var C=0;for(var D=0,E=K.length;D<E;D++){var m=K[D];if(m.start<=c&&m.end>=G){var g=Math.floor(Math.max(0,(m.start-G)*r)),l=Math.ceil(Math.min(y,(m.end-G)*r)),f=u[m.uid]*(this.showin g_details?this.vertical_detail_px:this.vertical_nodetail_px);var a,L,b=null,s=null;if(m.thick_start&&m.thick_end){b=Math.floor(Math.max(0,(m.thick_start-G)*r));s=Math.ceil(Math.min(y,(m.thick_end-G)*r))}if(!this.showing_details){z.fillRect(g+this.left_offset,f+5,l-g,1)}else{if(z.fillText&&m.start>G){z.fillText(m.name,g-1+this.left_offset,f+8)}var I=m.blocks;if(I){if(m.strand){if(m.strand=="+"){z.fillStyle=RIGHT_STRAND}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}for(var B=0,J=I.length;B<J;B++){var q=I[B],o=Math.floor(Math.max(0,(q[0]-G)*r)),H=Math.ceil(Math.min(y,(q[1]-G)*r));if(o>H){continue}a=5;L=3;z.fillRect(o+this.left_offset,f+L,H-o,a);if(b!==undefined&&(o<=s||H>=b)){a=9;L=1;var w=Math.max(o,b),t=Math.min(H,s);z.fillRect(w+this.left_offset,f+L,t-w,a)}}}else{a=9;L=1;z.fillRect(g+this.left_offset,f+L,l-g,a);if(m.strand){if(m.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(m.strand=="-"){z.fillStyle=L EFT_STRAND_INV}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}}}C++}}n.append(x);return x}});var ReadTrack=function(c,b,d,a){this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);FeatureTrack.call(this,c,b,d,a);this.default_font="9px Monaco, Lucida Console, monospace"};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_tile:function(v,z,m,n){if(!this.values){return}var A=z*DENSITY*v,e=(z+1)*DENSITY*v,q=DENSITY*v;var D,p,h;h=this.height_px;p=this.zo_slots;D=this.values;var t=Math.ceil(q*n),r=$("<canvas class='tile'></canvas>");r.css({position:"absolute",top:0,left:(A-this.view.low)*n-this.left_offset});r.get(0).width=t+this.left_offset;r.get(0).height=h;var u=r.get(0).getContext("2d");u.fillStyle=this.base_color;u.font=this.default_font;u.textAlign="right";var s=u.measureText("A").width;var w=0;for(var x=0,y=D.length;x<y;x++){var l=D[x];if(l.start<=e&&l.end>=A){var g=Math.floor (Math.max(0,(l.start-A)*n)),k=Math.ceil(Math.min(t,(l.end-A)*n)),f=p[l.uid]*this.vertical_detail_px;var a,E,d=null,o=null;if(n>s){for(var B=0,b=l.name.length;B<b;B++){var C=Math.floor(Math.max(0,(l.start+B-A)*n));u.fillText(l.name[B],C+this.left_offset,f+8)}}else{u.fillRect(g+this.left_offset,f+4,k-g,3)}}}m.append(r);return r}}); \ No newline at end of file diff -r 44526498cd00 -r fa318a093bf2 static/scripts/trackster.js --- a/static/scripts/trackster.js Thu Jan 14 15:22:10 2010 -0500 +++ b/static/scripts/trackster.js Thu Jan 14 17:49:20 2010 -0500 @@ -1,5 +1,5 @@ /* Trackster - 2009, James Taylor, Kanwei Li + 2010, James Taylor, Kanwei Li */ var DEBUG = false; @@ -19,22 +19,22 @@ right_img.src = "../images/visualization/strand_right.png"; right_img.onload = function() { RIGHT_STRAND = CONTEXT.createPattern(right_img, "repeat"); -} +}; var left_img = new Image(); left_img.src = "../images/visualization/strand_left.png"; left_img.onload = function() { LEFT_STRAND = CONTEXT.createPattern(left_img, "repeat"); -} +}; var right_img_inv = new Image(); right_img_inv.src = "../images/visualization/strand_right_inv.png"; right_img_inv.onload = function() { RIGHT_STRAND_INV = CONTEXT.createPattern(right_img_inv, "repeat"); -} +}; var left_img_inv = new Image(); left_img_inv.src = "../images/visualization/strand_left_inv.png"; left_img_inv.onload = function() { LEFT_STRAND_INV = CONTEXT.createPattern(left_img_inv, "repeat"); -} +}; function commatize( number ) { number += ''; // Convert to string @@ -49,7 +49,7 @@ this.num_elements = num_elements; this.obj_cache = {}; this.key_ary = []; -} +}; $.extend( Cache.prototype, { get: function( key ) { var index = this.key_ary.indexOf(key); @@ -109,7 +109,7 @@ // 10^log10(range / DENSITY) Close approximation for browser window, assuming DENSITY = window width this.resolution = Math.pow( 10, Math.ceil( Math.log( (this.high - this.low) / DENSITY ) / Math.LN10 ) ); - this.zoom_res = Math.max(1,Math.ceil( Math.log( this.resolution, FEATURE_LEVELS ) / Math.log(FEATURE_LEVELS) )); + this.zoom_res = Math.pow( FEATURE_LEVELS, Math.max(0,Math.ceil( Math.log( this.resolution, FEATURE_LEVELS ) / Math.log(FEATURE_LEVELS) ))); // Overview $("#overview-box").css( { @@ -282,10 +282,10 @@ var min_label = $("<div class='yaxislabel'>" + track.min_value + "</div>"); var max_label = $("<div class='yaxislabel'>" + track.max_value + "</div>"); - max_label.css({ position: "relative", top: "35px" }); - max_label.prependTo(track.container_div) + max_label.css({ position: "relative", top: "25px" }); + max_label.prependTo(track.container_div); - min_label.css({ position: "relative", top: track.height_px + 32 + "px" }); + min_label.css({ position: "relative", top: track.height_px + 55 + "px" }); min_label.prependTo(track.container_div); track.draw(); @@ -371,13 +371,15 @@ this.dataset_id = dataset_id; this.zo_slots = {}; this.show_labels_scale = 0.001; - this.showing_labels = false; - this.vertical_gap = 10; + this.showing_details = false; + this.vertical_detail_px = 10; + this.vertical_nodetail_px = 3; this.base_color = "#2C3143"; this.default_font = "9px Monaco, Lucida Console, monospace"; this.left_offset = 200; this.inc_slots = {}; this.data_queue = {}; + this.s_e_by_tile = {}; this.data_cache = new Cache(20); }; $.extend( FeatureTrack.prototype, TiledTrack.prototype, { @@ -425,10 +427,8 @@ } }, calc_slots: function() { - // console.log("num vals: " + this.values.length); var end_ary = [], scale = this.content_div.width() / (this.view.high - this.view.low), - max_high = this.view.max_high, max_low = this.view.max_low; // console.log(scale, this.view.high, this.view.low); for (var i = 0, len = this.values.length; i < len; i++) { @@ -447,43 +447,62 @@ j++; } } - this.height_px = end_ary.length * this.vertical_gap + 15; + this.height_px = end_ary.length * this.vertical_nodetail_px + 15; this.content_div.css( "height", this.height_px + "px" ); }, incremental_slots: function( level, features ) { if (!this.inc_slots[level]) { this.inc_slots[level] = {}; - this.inc_slots[level].w_scale = DENSITY / Math.pow(FEATURE_LEVELS, level+1); + this.inc_slots[level].w_scale = 1 / level; + this.s_e_by_tile[level] = {}; } - var slots = this.inc_slots[level]; - // console.log(level, slots.w_scale, slots); - var end_ary = [], + // TODO: Should calculate zoom tile index, which will improve performance + // by only having to look at a smaller subset + // if (this.s_e_by_tile[0] === undefined) { this.s_e_by_tile[0] = []; } + var w_scale = this.inc_slots[level].w_scale, undone = [], highest_slot = 0, // To measure how big to draw canvas dummy_canvas = $("<canvas></canvas>").get(0).getContext("2d"), max_low = this.view.max_low; + var f_start, f_end, slotted = []; + + // If feature already exists in slots (from previously seen tiles), use the same slot, + // otherwise if not seen, add to "undone" list for slot calculation for (var i = 0, len = features.length; i < len; i++) { var feature = features[i]; - // console.log(feature.name, feature.uid, slots[feature.uid]); - if (slots[feature.uid]) { - highest_slot = Math.max(highest_slot, slots[feature.uid]); - end_ary[ slots[feature.uid] ] = Math.ceil( (feature.end - max_low) * slots.w_scale ); + if (this.inc_slots[level][feature.uid] !== undefined) { + highest_slot = Math.max(highest_slot, this.inc_slots[level][feature.uid]); + slotted.push(this.inc_slots[level][feature.uid]); } else { - undone.push(feature); - } + undone.push(i); + } } + + // console.log("Slotted: ", features.length - undone.length, "/", features.length, slotted); for (var i = 0, len = undone.length; i < len; i++) { - var feature = undone[i]; - f_start = Math.floor( (feature.start - max_low) * slots.w_scale ); + var feature = features[undone[i]]; + f_start = Math.floor( (feature.start - max_low) * w_scale ); f_start -= dummy_canvas.measureText(feature.name).width; - f_end = Math.ceil( (feature.end - max_low) * slots.w_scale ); - // console.log(f_start, f_end, feature.name); + f_end = Math.ceil( (feature.end - max_low) * w_scale ); + var j = 0; + // Try to fit the feature to the first slot that doesn't overlap any other features in that slot while (true) { - if (end_ary[j] === undefined || end_ary[j] < f_start) { - end_ary[j] = f_end; - slots[feature.uid] = j; + var found = true; + if (this.s_e_by_tile[level][j] !== undefined) { + for (var k = 0, k_len = this.s_e_by_tile[level][j].length; k < k_len; k++) { + var s_e = this.s_e_by_tile[level][j][k]; + if (f_end > s_e[0] && f_start < s_e[1]) { + found = false; + break; + } + } + } + if (found) { + if (this.s_e_by_tile[level][j] === undefined) { this.s_e_by_tile[level][j] = []; } + this.s_e_by_tile[level][j].push([f_start, f_end]); + this.inc_slots[level][feature.uid] = j; highest_slot = Math.max(highest_slot, j); break; } @@ -504,8 +523,8 @@ // Once we zoom in enough, show name labels var data, slots, required_height; if (w_scale > this.show_labels_scale) { - if (!this.showing_labels) { - this.showing_labels = true; + if (!this.showing_details) { + this.showing_details = true; } for (var k in this.data_cache.obj_cache) { var k_split = k.split("_"), k_low = k_split[0], k_high = k_split[1]; @@ -519,12 +538,13 @@ this.get_data(tile_low, tile_high); return; } - required_height = this.incremental_slots( this.view.zoom_res, data ) * this.vertical_gap + 15; + // Calculate new slots incrementally for this new chunk of data and update height if necessary + required_height = this.incremental_slots( this.view.zoom_res, data ) * this.vertical_detail_px + 15; // console.log(required_height); slots = this.inc_slots[this.view.zoom_res]; } else { - if (this.showing_labels) { - this.showing_labels = false; + if (this.showing_details) { + this.showing_details = false; } required_height = this.height_px; slots = this.zo_slots; @@ -554,14 +574,14 @@ if (feature.start <= tile_high && feature.end >= tile_low) { var f_start = Math.floor( Math.max(0, (feature.start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, (feature.end - tile_low) * w_scale) ), - y_center = slots[feature.uid] * this.vertical_gap; + y_center = slots[feature.uid] * (this.showing_details ? this.vertical_detail_px : this.vertical_nodetail_px); var thickness, y_start, thick_start = null, thick_end = null; if (feature.thick_start && feature.thick_end) { thick_start = Math.floor( Math.max(0, (feature.thick_start - tile_low) * w_scale) ); thick_end = Math.ceil( Math.min(width, (feature.thick_end - tile_low) * w_scale) ); } - if (!this.showing_labels) { + if (!this.showing_details) { // Non-detail levels ctx.fillRect(f_start + this.left_offset, y_center + 5, f_end - f_start, 1); } else { @@ -569,6 +589,7 @@ if (ctx.fillText && feature.start > tile_low) { ctx.fillText(feature.name, f_start - 1 + this.left_offset, y_center + 8); // ctx.fillText(commatize(feature.start), f_start - 1 + this.left_offset, y_center + 8); + // ctx.fillText(slots[feature.uid], f_start - 1 + this.left_offset, y_center + 8); } var blocks = feature.blocks; if (blocks) { @@ -592,13 +613,12 @@ thickness = 5; y_start = 3; ctx.fillRect(block_start + this.left_offset, y_center + y_start, block_end - block_start, thickness); - - if (thick_start && (block_start < thick_end || block_end > thick_start) ) { + + if (thick_start !== undefined && (block_start <= thick_end || block_end >= thick_start) ) { thickness = 9; y_start = 1; var block_thick_start = Math.max(block_start, thick_start), block_thick_end = Math.min(block_end, thick_end); - ctx.fillRect(block_thick_start + this.left_offset, y_center + y_start, block_thick_end - block_thick_start, thickness); } @@ -654,9 +674,7 @@ // console.log(tile_low, tile_high, tile_length, w_scale); var width = Math.ceil( tile_span * w_scale ), new_canvas = $("<canvas class='tile'></canvas>"); - - var dummy_canvas = $("<canvas></canvas>").get(0).getContext("2d"); - + new_canvas.css({ position: "absolute", top: 0, @@ -677,7 +695,7 @@ if (feature.start <= tile_high && feature.end >= tile_low) { var f_start = Math.floor( Math.max(0, (feature.start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, (feature.end - tile_low) * w_scale) ), - y_center = slots[feature.uid] * this.vertical_gap; + y_center = slots[feature.uid] * this.vertical_detail_px; var thickness, y_start, thick_start = null, thick_end = null; if (w_scale > px_per_char) { diff -r 44526498cd00 -r fa318a093bf2 static/trackster.css --- a/static/trackster.css Thu Jan 14 15:22:10 2010 -0500 +++ b/static/trackster.css Thu Jan 14 17:49:20 2010 -0500 @@ -22,7 +22,6 @@ #nav-container { position: fixed; bottom: 0; - width: 100%; } input { @@ -60,7 +59,8 @@ width: 100%; margin: 0px; color: white; - margin-top: 10px; + margin-top: -6px; + margin-bottom: -3px; } #overview-viewport { @@ -82,7 +82,7 @@ } #viewport { - overflow-x: hidden; +/* overflow-x: hidden;*/ background-color: #fff; /* overflow: scroll;*/ /* border-bottom: 2px solid black;*/ diff -r 44526498cd00 -r fa318a093bf2 templates/base_panels.mako --- a/templates/base_panels.mako Thu Jan 14 15:22:10 2010 -0500 +++ b/templates/base_panels.mako Thu Jan 14 17:49:20 2010 -0500 @@ -318,8 +318,8 @@ <head> <title>${self.title()}</title> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + ${self.stylesheets()} ${self.javascripts()} - ${self.stylesheets()} </head> <body scroll="no" class="${self.body_class}"> diff -r 44526498cd00 -r fa318a093bf2 templates/panels.mako --- a/templates/panels.mako Thu Jan 14 15:22:10 2010 -0500 +++ b/templates/panels.mako Thu Jan 14 17:49:20 2010 -0500 @@ -11,6 +11,6 @@ <%def name="center_panel()"> - <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${main_url}"> </iframe> + ${grid} </%def> diff -r 44526498cd00 -r fa318a093bf2 templates/tracks/browser.mako --- a/templates/tracks/browser.mako Thu Jan 14 15:22:10 2010 -0500 +++ b/templates/tracks/browser.mako Thu Jan 14 17:49:20 2010 -0500 @@ -1,4 +1,13 @@ -<%inherit file="/base.mako"/> +<%inherit file="/base_panels.mako"/> + +<%def name="init()"> +<% + self.has_left_panel=False + self.has_right_panel=True + self.active_view="visualization" + self.message_box_visible=False +%> +</%def> <%def name="stylesheets()"> ${parent.stylesheets()} @@ -53,13 +62,16 @@ }); // To adjust the size of the viewport to fit the fixed-height footer - $(window).resize( function( e ) { - $("#content").height( $(window).height() - $("#nav-container").height() ); + var refresh = function( e ) { + $("#content").height( $(window).height() - $("#nav-container").height() - $("#masthead").height()); $("#viewport-container").height( $("#content").height() - $("#top-labeltrack").height() - $("#nav-labeltrack").height() ); + $("#nav-container").width( $("#center").width() ); view.redraw(); - }); - - $(window).resize(); + }; + $(window).bind( "resize", function(e) { refresh(e); } ); + $("#right-border").bind( "click", function(e) { refresh(e); } ); + $("#right-border").bind( "dragend", function(e) { refresh(e); } ); + $(window).trigger( "resize" ); $("#viewport").bind( "dragstart", function( e ) { this.original_low = view.low; @@ -103,15 +115,16 @@ </script> </%def> +<%def name="center_panel()"> <div id="content"> <div id="top-labeltrack"></div> <div id="viewport-container" style="overflow-x: hidden; overflow-y: auto;"> <div id="viewport"></div> </div> - <div id="nav-labeltrack"></div> + </div> <div id="nav-container"> - ## <div style="height: 5px; border-top: solid #ccc 1px"></div> + <div id="nav-labeltrack"></div> <div id="nav"> <div id="overview"> <div id="overview-viewport"> @@ -133,3 +146,9 @@ </div> </div> </div> +</%def> + +<%def name="right_panel()"> + <div>Configs</div> + +</%def> \ No newline at end of file

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[hg] galaxy 3244: Fix typo in last commit.
by Greg Von Kuster 22 Jan '10

22 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/44526498cd00 changeset: 3244:44526498cd00 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Jan 14 15:22:10 2010 -0500 description: Fix typo in last commit. diffstat: templates/tool_form.mako | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r 54a31dda709b -r 44526498cd00 templates/tool_form.mako --- a/templates/tool_form.mako Thu Jan 14 15:13:01 2010 -0500 +++ b/templates/tool_form.mako Thu Jan 14 15:22:10 2010 -0500 @@ -166,7 +166,7 @@ # Field may contain characters submitted by user and these characters may be unicode; handle non-ascii characters gracefully. field_html = field.get_html( prefix ) - if field_html is not unicode: + if type( field_html ) is not unicode: field_html = unicode( field_html, 'utf-8' ) %> <div class="form-row-input">${field_html}</div>

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[hg] galaxy 3243: Fix unicode bug when displaying dataset names ...
by Greg Von Kuster 22 Jan '10

22 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/54a31dda709b changeset: 3243:54a31dda709b user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Jan 14 15:13:01 2010 -0500 description: Fix unicode bug when displaying dataset names in HTML select boxes in tool forms. diffstat: templates/tool_form.mako | 11 ++++++++--- 1 files changed, 8 insertions(+), 3 deletions(-) diffs (22 lines): diff -r 5d5e5da2fcda -r 54a31dda709b templates/tool_form.mako --- a/templates/tool_form.mako Thu Jan 14 14:20:01 2010 -0500 +++ b/templates/tool_form.mako Thu Jan 14 15:13:01 2010 -0500 @@ -161,10 +161,15 @@ </label> %endif <% - field = param.get_html_field( trans, parent_state[ param.name ], other_values ) - field.refresh_on_change = param.refresh_on_change + field = param.get_html_field( trans, parent_state[ param.name ], other_values ) + field.refresh_on_change = param.refresh_on_change + + # Field may contain characters submitted by user and these characters may be unicode; handle non-ascii characters gracefully. + field_html = field.get_html( prefix ) + if field_html is not unicode: + field_html = unicode( field_html, 'utf-8' ) %> - <div class="form-row-input">${field.get_html( prefix )}</div> + <div class="form-row-input">${field_html}</div> %if parent_errors.has_key( param.name ): <div class="form-row-error-message"> <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${parent_errors[param.name]}</span></div>

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[hg] galaxy 3242: Small edit for the help section
by Greg Von Kuster 22 Jan '10

22 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/5d5e5da2fcda changeset: 3242:5d5e5da2fcda user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Thu Jan 14 14:20:01 2010 -0500 description: Small edit for the help section diffstat: tools/samtools/pileup_parser.xml | 6 +++--- 1 files changed, 3 insertions(+), 3 deletions(-) diffs (16 lines): diff -r ec77ae7f9b4f -r 5d5e5da2fcda tools/samtools/pileup_parser.xml --- a/tools/samtools/pileup_parser.xml Thu Jan 14 14:13:42 2010 -0500 +++ b/tools/samtools/pileup_parser.xml Thu Jan 14 14:20:01 2010 -0500 @@ -272,9 +272,9 @@ will report everything from the original file:: - chrM 412 A 2 ., II 0 0 0 0 2 - chrM 413 G 4 ..t, III2 0 0 0 1 3 - chrM 414 C 4 ...a III2 0 0 0 0 3 + chrM 412 A 2 ., II 2 0 0 0 2 + chrM 413 G 4 ..t, III2 0 0 2 1 3 + chrM 414 C 4 ...a III2 3 0 0 0 3 chrM 415 C 4 TTTt III7 0 0 0 4 4 Here, you can see that although the total coverage at position 414 is 4 (column 4), the quality adjusted coverage is 3 (last column). This is because only three out of four reads have bases with quality above the set threshold of 20 (the actual qualities are III2 or, after conversion, 40, 40, 40, 17).

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[hg] galaxy 3241: restoring welcome.html
by Greg Von Kuster 22 Jan '10

22 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/ec77ae7f9b4f changeset: 3241:ec77ae7f9b4f user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Thu Jan 14 14:13:42 2010 -0500 description: restoring welcome.html diffstat: static/welcome.html | 158 ++++----------------------------------------------- 1 files changed, 13 insertions(+), 145 deletions(-) diffs (169 lines): diff -r be8f54671d56 -r ec77ae7f9b4f static/welcome.html --- a/static/welcome.html Thu Jan 14 14:07:05 2010 -0500 +++ b/static/welcome.html Thu Jan 14 14:13:42 2010 -0500 @@ -2,152 +2,20 @@ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> -<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -<meta name="generator" content="Docutils 0.3.9: http://docutils.sourceforge.net/" /> -<link rel="stylesheet" href="style/base.css" type="text/css" /> -<style type="text/css"> - - .quickie { - text-align: center; - background: black; - margin: 10px; - } - - .current-quickie { - width: 300px; - background: white; - margin: auto; - } - - .current-quickie img { - padding: 15px; - border: 1px solid #ccc; - margin: auto; - background-color: white; - -moz-border-radius:4px; - -webkit-border-radius:4px; - - } - - .previous { - width: 100%; - overflow: auto; - border: solid #ccc 1px; - -moz-border-radius:4px; - -webkit-border-radius:4px; - - } - .previous .quickie { - padding-top: 10px; - min-height: 90px; - min-width: 150px; - } - #screencasts { - max-width: 50em; - margin-left: auto; - margin-right: auto; - } - -</style> -<script type="text/javascript" src="http://galaxy.psu.edu/welcome_img/jquery.min.js"></script> -<script type="text/javascript" src="http://galaxy.psu.edu/welcome_img/jquery.cycle.all.2.72.js"></script> -<script type="text/javascript"> - -$(document).ready(function() { - $('.current-quickie').cycle({ - fx: 'fade', - pause: 1, - speed: 100 - }); -}); -</script> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + <link rel="stylesheet" href="style/base.css" type="text/css" /> </head> <body> -<div class="document"> -<h3 align="center">Galaxy in 2010...</h3> -<div align="center" class="current-quickie"> - <a target="_blank" href="http://galaxy.psu.edu/dev2010/"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.001.png" width="300" height="200"/></a> - <a target="_blank" href="http://www.iscb.org/ismb2010"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.002.png" width="300" height="200" /></a> - <img src="http://galaxy.psu.edu/welcome_img/welcome_images.003.png" width="300" height="200" /> - <img src="http://galaxy.psu.edu/welcome_img/welcome_images.004.png" width="300" height="200" /> - <a target="_blank" href="http://main.g2.bx.psu.edu/u/aun1/p/windshield-splatter"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.005.png" width="300" height="200" /></a> -</div> -<br> -<hr> - -<h3 align="center">Galaxy Quickies</h3> - -<div class="previous" id="previous"> - <table border="0" cellpadding="0" cellspacing="0" width="100%"> - <tr> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie1_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie2_Grouping/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie2_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie3_Intervals/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie3_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie4_whatsNew/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie4_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie5_join/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie5_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie6_share/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie6_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie7_sr_beta/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie7_small.png" border="0"> - </div> - </a> - </td> - </tr> - </table> -</div> - -<script type="text/javascript"> - // Scroll to last quickie in box - document.getElementById("previous").scrollLeft = 100000000; -</script> - -<br/> -<br/> -<br/> -<hr/> - -<p><a target="_blank" class="reference" href="http://g2.trac.bx.psu.edu/wiki/GalaxyTeam">The Galaxy team</a> is a part of <a target="_blank" class="reference" href="http://www.bx.psu.edu">BX</a> at <a target="_blank" class="reference" href="http://www.psu.edu">Penn State</a>.</p> - -This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>. -<p><small>Galaxy build: <b>$Rev 1733:a4214de3752e$</b></small></p> -</div> -</div> + <div class="document"> + <div class="warningmessagelarge"> + <strong>Hello world! It's running...</strong> + <hr> + To customize this page edit <code>static/welcome.html</code> + </div> + <br/> + <img src="images/noodles.png" alt="WWFSMD?" style="display: block; margin-left: auto; margin-right: auto;" /> + <hr/> + This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>. + </div> </body> </html>

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