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galaxy-dist commit 477eb3cceae7: Updated a caption for consistency, removed an old comment
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285944657 -3600 # Node ID 477eb3cceae79d93be845a8540572033f208ae73 # Parent 36086d5bd8fa174ce88443eeeefec52b8fada5bd Updated a caption for consistency, removed an old comment --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -33,7 +33,7 @@ </when><when value="file"><param name="database" type="hidden" value="" /> - <param name="subject" type="data" format="fasta" label="Protein subject sequence(s)"/> + <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/></when></conditional><param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -59,7 +59,6 @@ </conditional></inputs><outputs> - <data name="output1" format="tabular" label="tblastn on ${db_opts.db_opts_selector}"><change_format><when input="out_format" value="0" format="txt"/>

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galaxy-dist commit aa7f4bdc2eab: Use a select parameter for picking just column 1 or 2. Less flexible but works better for BLAST output I think
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285929247 -3600 # Node ID aa7f4bdc2eab6be57fc1311137ce423eb39750cd # Parent 55f909b601c49dc0bb53f4fee538605df04d19f4 Use a select parameter for picking just column 1 or 2. Less flexible but works better for BLAST output I think --- a/tools/ncbi_blast_plus/blast_filter_fasta.xml +++ b/tools/ncbi_blast_plus/blast_filter_fasta.xml @@ -1,12 +1,15 @@ -<tool id="blast_filter_fasta" name="BLAST filter FASTA file" version="0.0.1"> +<tool id="blast_filter_fasta" name="Filter FASTA using BLAST output" version="0.0.1"><description>Divide a FASTA file based on BLAST hits</description><command interpreter="python"> blast_filter_fasta.py $blast_file $blast_col $in_file $out_positive_file $out_negative_file </command><inputs> + <param name="in_file" type="data" format="fasta" label="FASTA file to filter"/><param name="blast_file" type="data" format="tabular" label="Tabular BLAST output"/> - <param name="blast_col" type="data_column" data_ref="blast_file" numerical="true" value="1" label="Column containing FASTA identifiers" /> - <param name="in_file" type="data" format="fasta" label="BLAST query FASTA file"/> + <param name="blast_col" type="select" label="Column containing FASTA identifiers"> + <option value="1">Column 1 - BLAST query ID</option> + <option value="2">Column 2 - BLAST match ID</option> + </param></inputs><outputs><data name="out_positive_file" format="fasta" label="Sequences with BLAST hits" /> @@ -21,11 +24,14 @@ **What it does** Typical use would be to take a multi-sequence FASTA and the tabular output of -running BLAST on it, and divides the FASTA file in two: those sequence with a +running BLAST on it, and divide the FASTA file in two: those sequence with a BLAST hit, and those without. In the default NCBI BLAST+ tabular output, the query sequence ID is in column one, and the ID of the match from the database is in column two. +This allows you to filter the FASTA file for the subjects in the BLAST search, +rather than filtering the FASTA file for the queries in the BLAST search. + </help></tool>

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galaxy-dist commit 36086d5bd8fa: Support -db (database) or -subject (FASTA file)
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285940235 -3600 # Node ID 36086d5bd8fa174ce88443eeeefec52b8fada5bd # Parent 5176fa11ef2f45df4a7bb0b82f2ca0871aaf2465 Support -db (database) or -subject (FASTA file) --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -3,7 +3,11 @@ <command> blastn -query "$query" - -db "$database" +#if $db_opts.db_opts_selector == "db": + -db "$db_opts.database" +#else: + -subject "$db_opts.subject" +#end if -task $blast_type -evalue $evalue_cutoff $adv_opts.filter_query @@ -14,12 +18,25 @@ </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> - <param name="database" type="select" display="radio" label="Nucleotide BLAST database"> - <options from_file="blastdb.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> - </options> - </param> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="True">BLAST Database</option> + <option value="file">FASTA file</option> + </param> + <when value="db"> + <param name="database" type="select" display="radio" label="Nucleotide BLAST database"> + <options from_file="blastdb.loc"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + <param name="subject" type="hidden" value="" /> + </when> + <when value="file"> + <param name="database" type="hidden" value="" /> + <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> + </when> + </conditional><param name="blast_type" type="select" display="radio" label="Type of BLAST"><option value="megablast">megablast</option><option value="blastn">blastn</option> @@ -57,8 +74,7 @@ </conditional></inputs><outputs> -  - <data name="output1" format="tabular" label="${blast_type.value_label} on ${database.value_label}"> + <data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}"><change_format><when input="out_format" value="0" format="txt"/></change_format> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -3,7 +3,11 @@ <command> blastp -query "$query" - -db "$database" +#if $db_opts.db_opts_selector == "db": + -db "$db_opts.database" +#else: + -subject "$db_opts.subject" +#end if -task $blast_type -evalue $evalue_cutoff $adv_opts.filter_query @@ -13,12 +17,25 @@ </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> - <param name="database" type="select" display="radio" label="Protein BLAST database"> - <options from_file="blastdb_p.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> - </options> - </param> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="True">BLAST Database</option> + <option value="file">FASTA file</option> + </param> + <when value="db"> + <param name="database" type="select" display="radio" label="Protein BLAST database"> + <options from_file="blastdb_p.loc"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + <param name="subject" type="hidden" value="" /> + </when> + <when value="file"> + <param name="database" type="hidden" value="" /> + <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> + </when> + </conditional><param name="blast_type" type="select" display="radio" label="Type of BLAST"><option value="blastp">blastp</option><option value="blastp-short">blastp-short</option> @@ -47,8 +64,7 @@ </conditional></inputs><outputs> -  - <data name="output1" format="tabular" label="${blast_type.value_label} on ${database.value_label}"> + <data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}"><change_format><when input="out_format" value="0" format="txt"/></change_format> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -3,7 +3,11 @@ <command> tblastx -query "$query" - -db "$database" +#if $db_opts.db_opts_selector == "db": + -db "$db_opts.database" +#else: + -subject "$db_opts.subject" +#end if -evalue $evalue_cutoff $adv_opts.filter_query $adv_opts.strand @@ -13,12 +17,25 @@ </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> - <param name="database" type="select" display="radio" label="Nucelotide BLAST database"> - <options from_file="blastdb.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> - </options> - </param> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="True">BLAST Database</option> + <option value="file">FASTA file</option> + </param> + <when value="db"> + <param name="database" type="select" display="radio" label="Nucleotide BLAST database"> + <options from_file="blastdb.loc"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + <param name="subject" type="hidden" value="" /> + </when> + <when value="file"> + <param name="database" type="hidden" value="" /> + <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> + </when> + </conditional><param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /><param name="out_format" type="select" label="Output format"><option value="6">Tabular</option> @@ -49,8 +66,7 @@ </conditional></inputs><outputs> -  - <data name="output1" format="tabular" label="tblastx on ${database.value_label}"> + <data name="output1" format="tabular" label="tblastx on ${db_opts.db_opts_selector}"><change_format><when input="out_format" value="0" format="txt"/></change_format> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -3,7 +3,11 @@ <command> blastx -query "$query" - -db "$database" +#if $db_opts.db_opts_selector == "db": + -db "$db_opts.database" +#else: + -subject "$db_opts.subject" +#end if -evalue $evalue_cutoff $adv_opts.filter_query $adv_opts.strand @@ -13,12 +17,25 @@ </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> - <param name="database" type="select" display="radio" label="Protein BLAST database"> - <options from_file="blastdb_p.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> - </options> - </param> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="True">BLAST Database</option> + <option value="file">FASTA file</option> + </param> + <when value="db"> + <param name="database" type="select" display="radio" label="Protein BLAST database"> + <options from_file="blastdb_p.loc"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + <param name="subject" type="hidden" value="" /> + </when> + <when value="file"> + <param name="database" type="hidden" value="" /> + <param name="subject" type="data" format="fasta" label="Protein subject sequence(s)"/> + </when> + </conditional><param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /><param name="out_format" type="select" label="Output format"><option value="6">Tabular</option> @@ -49,8 +66,7 @@ </conditional></inputs><outputs> -  - <data name="output1" format="tabular" label="blastx on ${database.value_label}"> + <data name="output1" format="tabular" label="blastx on ${db_opts.db_opts_selector}"><change_format><when input="out_format" value="0" format="txt"/></change_format> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -3,7 +3,11 @@ <command> tblastn -query "$query" - -db "$database" +#if $db_opts.db_opts_selector == "db": + -db "$db_opts.database" +#else: + -subject "$db_opts.subject" +#end if -evalue $evalue_cutoff $adv_opts.filter_query -out $output1 @@ -12,12 +16,25 @@ </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> - <param name="database" type="select" display="radio" label="Nucelotide BLAST database"> - <options from_file="blastdb.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> - </options> - </param> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="True">BLAST Database</option> + <option value="file">FASTA file</option> + </param> + <when value="db"> + <param name="database" type="select" display="radio" label="Nucleotide BLAST database"> + <options from_file="blastdb.loc"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + <param name="subject" type="hidden" value="" /> + </when> + <when value="file"> + <param name="database" type="hidden" value="" /> + <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> + </when> + </conditional><param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /><param name="out_format" type="select" label="Output format"><option value="6">Tabular</option> @@ -43,7 +60,7 @@ </inputs><outputs> - <data name="output1" format="tabular" label="tblastn on ${database.value_label}"> + <data name="output1" format="tabular" label="tblastn on ${db_opts.db_opts_selector}"><change_format><when input="out_format" value="0" format="txt"/></change_format>

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galaxy-dist commit 5498ff5b31ac: Allow filter to pick ID column
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285873215 -3600 # Node ID 5498ff5b31ac871c7d22df60146fd96c61b74aab # Parent ad83deba645811d8b9509a6e3c58e986ffa89e3b Allow filter to pick ID column --- a/tools/ncbi_blast_plus/blast_filter_fasta.py +++ b/tools/ncbi_blast_plus/blast_filter_fasta.py @@ -1,22 +1,26 @@ #!/usr/bin/env python -"""Filter a FASTA file using tabular BLAST output. +"""Filter a FASTA file using tabular output, e.g. from BLAST. -Takes four command line options, tabular BLAST filename, input FASTA filename, -and two output FASTA filenames (for records with and without any BLAST hits). +Takes five command line options, tabular BLAST filename, ID column number +(using one based counting), input FASTA filename, and two output FASTA +filenames (for records with and without any BLAST hits). + +In the default NCBI BLAST+ tabular output, the query sequence ID is in column +one, and the ID of the match from the database is in column two. """ -#TODO - Option to define which column to use for ID? - import sys from galaxy_utils.sequence.fasta import fastaReader, fastaWriter #Parse Command Line -blast_file, in_file, out_positive_file, out_negative_file = sys.argv[1:] +blast_file, blast_col, in_file, out_positive_file, out_negative_file = sys.argv[1:] +blast_col = int(blast_col)-1 +assert blast_col >= 0 #Read tabular BLAST file and record all queries with hit(s) ids = set() blast_handle = open(blast_file, "rU") for line in blast_handle: - ids.add(line.split("\t")[0]) + ids.add(line.split("\t")[blast_col]) blast_handle.close() #Write filtered FASTA file based on IDs from BLAST file --- a/tools/ncbi_blast_plus/blast_filter_fasta.xml +++ b/tools/ncbi_blast_plus/blast_filter_fasta.xml @@ -1,10 +1,13 @@ <tool id="blast_filter_fasta" name="BLAST filter FASTA file" version="0.0.1"><description>Divide a FASTA file based on BLAST hits</description><command interpreter="python"> - blast_filter_fasta.py $blast_file $in_file $out_positive_file $out_negative_file + blast_filter_fasta.py $blast_file $blast_col $in_file $out_positive_file $out_negative_file </command><inputs><param name="blast_file" type="data" format="tabular" label="Tabular BLAST output"/> + <param name="blast_col" type="integer" value="1" label="Column containing FASTA identifiers"> + <validator type="in_range" min="1" /> + </param><param name="in_file" type="data" format="fasta" label="BLAST query FASTA file"/></inputs><outputs> @@ -19,8 +22,12 @@ **What it does** -Takes a multi-sequence FASTA and the tabular output of running BLAST on it, and -divides the FASTA file in two: those sequence with a BLAST hit, and those without. +Typical use would be to take a multi-sequence FASTA and the tabular output of +running BLAST on it, and divides the FASTA file in two: those sequence with a +BLAST hit, and those without. + +In the default NCBI BLAST+ tabular output, the query sequence ID is in column +one, and the ID of the match from the database is in column two. </help></tool>

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galaxy-dist commit 5176fa11ef2f: Add -strand as adv opt to blastn, blastx and tblastx wrappers
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285931141 -3600 # Node ID 5176fa11ef2f45df4a7bb0b82f2ca0871aaf2465 # Parent 6c1d520f25d44f80de926285cbd927bc35f69a6a Add -strand as adv opt to blastn, blastx and tblastx wrappers --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -7,6 +7,7 @@ -task $blast_type -evalue $evalue_cutoff $adv_opts.filter_query + $adv_opts.strand -out $output1 -outfmt $out_format -num_threads 8 @@ -42,10 +43,16 @@ </param><when value="basic"><param name="filter_query" type="hidden" value="" /> + <param name="strand" type="hidden" value="" /></when><when value="advanced"><param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" /> + <param name="strand" type="select" label="Query strand(s) to search against database/subject"> + <option value="-strand both">Both</option> + <option value="-strand plus">Plus (forward)</option> + <option value="-strand minus">Minus (reverse complement)</option> + </param></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -6,6 +6,7 @@ -db "$database" -evalue $evalue_cutoff $adv_opts.filter_query + $adv_opts.strand -out $output1 -outfmt $out_format -num_threads 8 @@ -34,10 +35,16 @@ </param><when value="basic"><param name="filter_query" type="hidden" value="" /> + <param name="strand" type="hidden" value="" /></when><when value="advanced"><param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> + <param name="strand" type="select" label="Query strand(s) to search against database/subject"> + <option value="-strand both">Both</option> + <option value="-strand plus">Plus (forward)</option> + <option value="-strand minus">Minus (reverse complement)</option> + </param></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -6,6 +6,7 @@ -db "$database" -evalue $evalue_cutoff $adv_opts.filter_query + $adv_opts.strand -out $output1 -outfmt $out_format -num_threads 8 @@ -34,10 +35,16 @@ </param><when value="basic"><param name="filter_query" type="hidden" value="" /> + <param name="strand" type="hidden" value="" /></when><when value="advanced"><param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> + <param name="strand" type="select" label="Query strand(s) to search against database/subject"> + <option value="-strand both">Both</option> + <option value="-strand plus">Plus (forward)</option> + <option value="-strand minus">Minus (reverse complement)</option> + </param></when></conditional></inputs>

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galaxy-dist commit 5244ad54beba: Make descriptions more concise (don't need to repeat infor from name)
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285670784 -3600 # Node ID 5244ad54bebadf57e8bede36643afa49c58ac579 # Parent 6dd6224f571deb34c01c7fd0c3c4daccf948eda1 Make descriptions more concise (don't need to repeat infor from name) --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -1,5 +1,5 @@ <tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.1"> - <description>Use NCBI BLAST+ tool to search a nucleotide database with nucleotide query sequence(s)</description> + <description>Search nucleotide database with nucleotide query sequence(s)</description><command> blastn -query "$query" --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -1,5 +1,5 @@ <tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.1"> - <description>Use NCBI BLAST+ tool to search a protein database with protein query sequence(s)</description> + <description>Search protein database with protein query sequence(s)</description><command> blastp -query "$query"

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galaxy-dist commit 92bb0d0d7e90: Adding basic tblastn wrapper
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285685499 -3600 # Node ID 92bb0d0d7e9058bc4b6b43eaa015349241bc13e0 # Parent 34794995b12f700d50c12bb013431c882dca9c10 Adding basic tblastn wrapper --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -264,6 +264,7 @@ --><section name="NCBI BLAST+" id="ncbi_blast_plus_tools"><tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" /> + <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" /><tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" /><tool file="ncbi_blast_plus/blast_filter_fasta.xml" /></section> --- /dev/null +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -0,0 +1,97 @@ +<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.1"> + <description>Search translated nucleotide database with protein query sequence(s)</description> + <command> + tblastn + -query "$query" + -db "$database" + -evalue $evalue_cutoff + -seg $adv_opts.filter_query + -out $output1 + -outfmt $out_format + -num_threads 8 + </command> + <inputs> + <param name="query" type="data" format="fasta" label="Query sequence(s)"/> + <param name="database" type="select" display="radio" label="Nucelotide BLAST database"> + <options from_file="blastdb.loc"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> + <param name="out_format" type="select" label="Output format"> + <option value="6">Tabular</option> + <option value="5">BLAST XML</option> + <option value="0">Pairwise text</option> +  + </param> + <conditional name="adv_opts"> + <param name="adv_opts_selector" type="select" label="Advanced Options"> + <option value="basic" selected="True">Hide Advanced Options</option> + <option value="advanced">Show Advanced Options</option> + </param> + <when value="basic"> + <param name="filter_query" type="hidden" value="yes" /> + </when> + <when value="advanced"> + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="yes" falsevalue="no" checked="true" /> + </when> + </conditional> + </inputs> + <outputs> +  + <data name="output1" format="tabular" label="tblastn on ${database.value_label}"> + <change_format> + <when input="out_format" value="0" format="txt"/> + </change_format> + <change_format> + <when input="out_format" value="5" format="blastxml"/> + </change_format> + </data> + </outputs> + <requirements> + <requirement type="binary">blastn</requirement> + </requirements> + <tests> + </tests> + <help> + +.. class:: warningmark + +**Note**. Database searches may take substantial amount of time. For large input datasets it is advisable to allow overnight processing. + +----- + +**What it does** + +This tool runs NCBI BLAST+ tblastn tool. + +----- + +**Output format** + +The default Output of this tool is tabular, containing 12 columns: + +1. Id of your sequence +2. GI of the database hit +3. % identity +4. Alignment length +5. # mismatches +6. # gaps +7. Start position in your sequence +8. End position in your sequence +9. Start position in database hit +10. End position in database hit +11. E-value +12. Bit score + +------- + +**References** + +Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. + + </help> +</tool>

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galaxy-dist commit 55f909b601c4: Use the data_column type (great except on empty tabular files)
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285874190 -3600 # Node ID 55f909b601c49dc0bb53f4fee538605df04d19f4 # Parent 5498ff5b31ac871c7d22df60146fd96c61b74aab Use the data_column type (great except on empty tabular files) --- a/tools/ncbi_blast_plus/blast_filter_fasta.xml +++ b/tools/ncbi_blast_plus/blast_filter_fasta.xml @@ -5,9 +5,7 @@ </command><inputs><param name="blast_file" type="data" format="tabular" label="Tabular BLAST output"/> - <param name="blast_col" type="integer" value="1" label="Column containing FASTA identifiers"> - <validator type="in_range" min="1" /> - </param> + <param name="blast_col" type="data_column" data_ref="blast_file" numerical="true" value="1" label="Column containing FASTA identifiers" /><param name="in_file" type="data" format="fasta" label="BLAST query FASTA file"/></inputs><outputs>

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galaxy-dist commit 6c1d520f25d4: Don't default to setting seg/dust explicitly (allow BLAST+ to use its own defaults)
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285930037 -3600 # Node ID 6c1d520f25d44f80de926285cbd927bc35f69a6a # Parent aa7f4bdc2eab6be57fc1311137ce423eb39750cd Don't default to setting seg/dust explicitly (allow BLAST+ to use its own defaults) --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -6,7 +6,7 @@ -db "$database" -task $blast_type -evalue $evalue_cutoff - -dust $adv_opts.filter_query + $adv_opts.filter_query -out $output1 -outfmt $out_format -num_threads 8 @@ -41,10 +41,11 @@ <option value="advanced">Show Advanced Options</option></param><when value="basic"> - <param name="filter_query" type="hidden" value="yes" /> + <param name="filter_query" type="hidden" value="" /></when><when value="advanced"> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="yes" falsevalue="no" checked="true" /> +  + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" /></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -6,7 +6,7 @@ -db "$database" -task $blast_type -evalue $evalue_cutoff - -seg $adv_opts.filter_query + $adv_opts.filter_query -out $output1 -outfmt $out_format -num_threads 8 @@ -38,10 +38,11 @@ <option value="advanced">Show Advanced Options</option></param><when value="basic"> - <param name="filter_query" type="hidden" value="yes" /> + <param name="filter_query" type="hidden" value="" /></when><when value="advanced"> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="yes" falsevalue="no" checked="true" /> +  + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -5,7 +5,7 @@ -query "$query" -db "$database" -evalue $evalue_cutoff - -seg $adv_opts.filter_query + $adv_opts.filter_query -out $output1 -outfmt $out_format -num_threads 8 @@ -33,10 +33,11 @@ <option value="advanced">Show Advanced Options</option></param><when value="basic"> - <param name="filter_query" type="hidden" value="yes" /> + <param name="filter_query" type="hidden" value="" /></when><when value="advanced"> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="yes" falsevalue="no" checked="true" /> +  + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -5,7 +5,7 @@ -query "$query" -db "$database" -evalue $evalue_cutoff - -seg $adv_opts.filter_query + $adv_opts.filter_query -out $output1 -outfmt $out_format -num_threads 8 @@ -33,10 +33,11 @@ <option value="advanced">Show Advanced Options</option></param><when value="basic"> - <param name="filter_query" type="hidden" value="yes" /> + <param name="filter_query" type="hidden" value="" /></when><when value="advanced"> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="yes" falsevalue="no" checked="true" /> +  + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -5,7 +5,7 @@ -query "$query" -db "$database" -evalue $evalue_cutoff - -seg $adv_opts.filter_query + $adv_opts.filter_query -out $output1 -outfmt $out_format -num_threads 8 @@ -33,10 +33,11 @@ <option value="advanced">Show Advanced Options</option></param><when value="basic"> - <param name="filter_query" type="hidden" value="yes" /> + <param name="filter_query" type="hidden" value="" /></when><when value="advanced"> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="yes" falsevalue="no" checked="true" /> +  + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /></when></conditional></inputs>

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galaxy-dist commit 34794995b12f: Adding simple python script to split a FASTA file into those sequence with/without BLAST hits using tabular output
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285681430 -3600 # Node ID 34794995b12f700d50c12bb013431c882dca9c10 # Parent 5244ad54bebadf57e8bede36643afa49c58ac579 Adding simple python script to split a FASTA file into those sequence with/without BLAST hits using tabular output --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -265,6 +265,7 @@ <section name="NCBI BLAST+" id="ncbi_blast_plus_tools"><tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" /><tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" /> + <tool file="ncbi_blast_plus/blast_filter_fasta.xml" /></section><section name="NGS: Mapping" id="solexa_tools"><tool file="sr_mapping/lastz_wrapper.xml" /> --- /dev/null +++ b/tools/ncbi_blast_plus/blast_filter_fasta.py @@ -0,0 +1,34 @@ +#!/usr/bin/env python +"""Filter a FASTA file using tabular BLAST output. + +Takes four command line options, tabular BLAST filename, input FASTA filename, +and two output FASTA filenames (for records with and without any BLAST hits). +""" +#TODO - Option to define which column to use for ID? + +import sys +from galaxy_utils.sequence.fasta import fastaReader, fastaWriter + +#Parse Command Line +blast_file, in_file, out_positive_file, out_negative_file = sys.argv[1:] + +#Read tabular BLAST file and record all queries with hit(s) +ids = set() +blast_handle = open(blast_file, "rU") +for line in blast_handle: + ids.add(line.split("\t")[0]) +blast_handle.close() + +#Write filtered FASTA file based on IDs from BLAST file +reader = fastaReader(open(in_file, "rU")) +positive_writer = fastaWriter(open(out_positive_file, "w")) +negative_writer = fastaWriter(open(out_negative_file, "w")) +for record in reader: + #The [1:] is because the fastaReader leaves the > on the identifer. + if record.identifier and record.identifier.split()[0][1:] in ids: + positive_writer.write(record) + else: + negative_writer.write(record) +positive_writer.close() +negative_writer.close() +reader.close() --- /dev/null +++ b/tools/ncbi_blast_plus/blast_filter_fasta.xml @@ -0,0 +1,26 @@ +<tool id="blast_filter_fasta" name="BLAST filter FASTA file" version="0.0.1"> + <description>Divide a FASTA file based on BLAST hits</description> + <command interpreter="python"> + blast_filter_fasta.py $blast_file $in_file $out_positive_file $out_negative_file + </command> + <inputs> + <param name="blast_file" type="data" format="tabular" label="Tabular BLAST output"/> + <param name="in_file" type="data" format="fasta" label="BLAST query FASTA file"/> + </inputs> + <outputs> + <data name="out_positive_file" format="fasta" label="Sequences with BLAST hits" /> + <data name="out_negative_file" format="fasta" label="Sequences without BLAST hits" /> + </outputs> + <requirements> + </requirements> + <tests> + </tests> + <help> + +**What it does** + +Takes a multi-sequence FASTA and the tabular output of running BLAST on it, and +divides the FASTA file in two: those sequence with a BLAST hit, and those without. + + </help> +</tool>

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galaxy-dist commit ad83deba6458: Adding blastx and tblastx wrappers, tidying
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285688573 -3600 # Node ID ad83deba645811d8b9509a6e3c58e986ffa89e3b # Parent 92bb0d0d7e9058bc4b6b43eaa015349241bc13e0 Adding blastx and tblastx wrappers, tidying --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -12,8 +12,8 @@ -num_threads 8 </command><inputs> - <param name="query" type="data" format="fasta" label="Query sequence(s)"/> - <param name="database" type="select" display="radio" label="Nucelotide BLAST database"> + <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> + <param name="database" type="select" display="radio" label="Nucleotide BLAST database"><options from_file="blastdb.loc"><column name="name" index="0"/><column name="value" index="1"/> @@ -26,13 +26,6 @@ <option value="dc-megablast">dc-megablast</option><option value="vecscreen">vecscreen</option></param> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /><param name="out_format" type="select" label="Output format"><option value="6">Tabular</option> @@ -89,19 +82,22 @@ .. class:: warningmark -**Note**. Database searches may take substantial amount of time. For large input datasets it is advisable to allow overnight processing. +**Note**. Database searches may take substantial amount of time. +For large input datasets it is advisable to allow overnight processing. ----- **What it does** -This tool runs NCBI BLAST+ blastn tool (which include *megablast*). +Search a *nucleotide database* using a *nucleotide query*, +using the NCBI BLAST+ blastn command line tool. +Algorithms include blastn, megablast, and discontiguous megablast. ----- **Output format** -The default Output of this tool is tabular, containing 12 columns: +The default output of this tool is tabular, containing 12 columns: 1. Id of your sequence 2. GI of the database hit --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -11,7 +11,7 @@ -num_threads 8 </command><inputs> - <param name="query" type="data" format="fasta" label="Query sequence(s)"/> + <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/><param name="database" type="select" display="radio" label="Nucelotide BLAST database"><options from_file="blastdb.loc"><column name="name" index="0"/> @@ -60,19 +60,21 @@ .. class:: warningmark -**Note**. Database searches may take substantial amount of time. For large input datasets it is advisable to allow overnight processing. +**Note**. Database searches may take substantial amount of time. +For large input datasets it is advisable to allow overnight processing. ----- **What it does** -This tool runs NCBI BLAST+ tblastn tool. +Search a *translated nucleotide database* using a *protein query*, +using the NCBI BLAST+ tblastn command line tool. ----- **Output format** -The default Output of this tool is tabular, containing 12 columns: +The default output of this tool is tabular, containing 12 columns: 1. Id of your sequence 2. GI of the database hit --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -264,8 +264,10 @@ --><section name="NCBI BLAST+" id="ncbi_blast_plus_tools"><tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" /> + <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" /> + <tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" /><tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" /> - <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" /> + <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" /><tool file="ncbi_blast_plus/blast_filter_fasta.xml" /></section><section name="NGS: Mapping" id="solexa_tools"> --- /dev/null +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -0,0 +1,112 @@ +<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.1"> + <description>Search translated nucleotide database with translated nucleotide query sequence(s)</description> + <command> + tblastx + -query "$query" + -db "$database" + -evalue $evalue_cutoff + -seg $adv_opts.filter_query + -out $output1 + -outfmt $out_format + -num_threads 8 + </command> + <inputs> + <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> + <param name="database" type="select" display="radio" label="Nucelotide BLAST database"> + <options from_file="blastdb.loc"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> + <param name="out_format" type="select" label="Output format"> + <option value="6">Tabular</option> + <option value="5">BLAST XML</option> + <option value="0">Pairwise text</option> +  + </param> + <conditional name="adv_opts"> + <param name="adv_opts_selector" type="select" label="Advanced Options"> + <option value="basic" selected="True">Hide Advanced Options</option> + <option value="advanced">Show Advanced Options</option> + </param> + <when value="basic"> + <param name="filter_query" type="hidden" value="yes" /> + </when> + <when value="advanced"> + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="yes" falsevalue="no" checked="true" /> + </when> + </conditional> + </inputs> + <outputs> +  + <data name="output1" format="tabular" label="tblastx on ${database.value_label}"> + <change_format> + <when input="out_format" value="0" format="txt"/> + </change_format> + <change_format> + <when input="out_format" value="5" format="blastxml"/> + </change_format> + </data> + </outputs> + <requirements> + <requirement type="binary">blastn</requirement> + </requirements> + <tests> + <test> + <param name="input_query" value="megablast_wrapper_test1.fa" ftype="fasta"/> +  + <param name="database" value="phiX" /> + <param name="blast_type" value="megablast" /> +  + <param name="evalue_cutoff" value="10.0" /> + <param name="filter_query" value="yes" /> + <param name="out_format" value="6" /> + <output name="output1" file="megablast_wrapper_test1.out"/> + </test> + </tests> + <help> + +.. class:: warningmark + +**Note**. Database searches may take substantial amount of time. For large input datasets it is advisable to allow overnight processing. + +----- + +**What it does** + +Search a *translated nucleotide database* using a *protein query*, +using the NCBI BLAST+ tblastx command line tool. + +----- + +**Output format** + +The default output of this tool is tabular, containing 12 columns: + +1. Id of your sequence +2. GI of the database hit +3. % identity +4. Alignment length +5. # mismatches +6. # gaps +7. Start position in your sequence +8. End position in your sequence +9. Start position in database hit +10. End position in database hit +11. E-value +12. Bit score + +------- + +**References** + +Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. + + </help> +</tool> --- /dev/null +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -0,0 +1,99 @@ +<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.1"> + <description>Search protein database with translated nucleotide query sequence(s)</description> + <command> + blastx + -query "$query" + -db "$database" + -evalue $evalue_cutoff + -seg $adv_opts.filter_query + -out $output1 + -outfmt $out_format + -num_threads 8 + </command> + <inputs> + <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> + <param name="database" type="select" display="radio" label="Protein BLAST database"> + <options from_file="blastdb_p.loc"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> + <param name="out_format" type="select" label="Output format"> + <option value="6">Tabular</option> + <option value="5">BLAST XML</option> + <option value="0">Pairwise text</option> +  + </param> + <conditional name="adv_opts"> + <param name="adv_opts_selector" type="select" label="Advanced Options"> + <option value="basic" selected="True">Hide Advanced Options</option> + <option value="advanced">Show Advanced Options</option> + </param> + <when value="basic"> + <param name="filter_query" type="hidden" value="yes" /> + </when> + <when value="advanced"> + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="yes" falsevalue="no" checked="true" /> + </when> + </conditional> + </inputs> + <outputs> +  + <data name="output1" format="tabular" label="blastx on ${database.value_label}"> + <change_format> + <when input="out_format" value="0" format="txt"/> + </change_format> + <change_format> + <when input="out_format" value="5" format="blastxml"/> + </change_format> + </data> + </outputs> + <requirements> + <requirement type="binary">blastn</requirement> + </requirements> + <tests> + </tests> + <help> + +.. class:: warningmark + +**Note**. Database searches may take substantial amount of time. +For large input datasets it is advisable to allow overnight processing. + +----- + +**What it does** + +Search a *protein database* using a *translated nucleotide query*, +using the NCBI BLAST+ blastx command line tool. + +----- + +**Output format** + +The default output of this tool is tabular, containing 12 columns: + +1. Id of your sequence +2. GI of the database hit +3. % identity +4. Alignment length +5. # mismatches +6. # gaps +7. Start position in your sequence +8. End position in your sequence +9. Start position in database hit +10. End position in database hit +11. E-value +12. Bit score + +------- + +**References** + +Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. + + </help> +</tool> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -12,7 +12,7 @@ -num_threads 8 </command><inputs> - <param name="query" type="data" format="fasta" label="Query sequence(s)"/> + <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/><param name="database" type="select" display="radio" label="Protein BLAST database"><options from_file="blastdb_p.loc"><column name="name" index="0"/> @@ -23,13 +23,6 @@ <option value="blastp">blastp</option><option value="blastp-short">blastp-short</option></param> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /><param name="out_format" type="select" label="Output format"><option value="6">Tabular</option> @@ -72,19 +65,21 @@ .. class:: warningmark -**Note**. Database searches may take substantial amount of time. For large input datasets it is advisable to allow overnight processing. +**Note**. Database searches may take substantial amount of time. +For large input datasets it is advisable to allow overnight processing. ----- **What it does** -This runs the command line NCBI BLAST+ blastp tool. +Search a *protein database* using a *protein query*, +using the NCBI BLAST+ blastp command line tool. ----- **Output format** -The default Output of this tool is tabular, containing 12 columns: +The default output of this tool is tabular, containing 12 columns: 1. Id of your sequence 2. GI of the database hit

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galaxy-dist commit dc68de280ac7: Adding basic NCBI BLAST+ blastn wrapper with multiple output format support
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285090213 -3600 # Node ID dc68de280ac7f2ff2ff97068694a7ecded62ee0c # Parent e902e11cd57c7b5e4b0b43bdf0bde459535e8a0c Adding basic NCBI BLAST+ blastn wrapper with multiple output format support --- /dev/null +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -0,0 +1,117 @@ +<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.1"> + <description>Use NCBI BLAST+ tool to search a nucleotide database with nucleotide query sequence(s)</description> + <command> + blastn + -query "$query" + -db "$database" + -task $blast_type + -evalue $evalue_cutoff + -dust $filter_query + -out $output1 + -outfmt $out_format + </command> + <inputs> + <param name="query" type="data" format="fasta" label="Query sequence(s)"/> + <param name="database" type="select" display="radio" label="Nucelotide BLAST database"> + <options from_file="blastdb.loc"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + <param name="blast_type" type="select" display="radio" label="Type of BLAST"> + <option value="megablast">megablast</option> + <option value="blastn">blastn</option> + <option value="blastn-short">blastn-short</option> + <option value="dc-megablast">dc-megablast</option> + <option value="vecscreen">vecscreen</option> + </param> +  + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> + <param name="filter_query" type="select" label="Filter out low complexity regions (with DUST)?"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="out_format" type="select" label="Output format"> + <option value="6">Tabular</option> + <option value="5">BLAST XML</option> + <option value="0">Pairwise text</option> +  + </param> + </inputs> + <outputs> +  + <data name="output1" format="tabular" label="${blast_type.value_label} on ${database.value_label}"> + <change_format> + <when input="out_format" value="0" format="txt"/> + </change_format> + <change_format> + <when input="out_format" value="5" format="blastxml"/> + </change_format> + </data> + </outputs> + <requirements> + <requirement type="binary">blastn</requirement> + </requirements> + <tests> + <test> + <param name="input_query" value="megablast_wrapper_test1.fa" ftype="fasta"/> +  + <param name="database" value="phiX" /> + <param name="blast_type" value="megablast" /> +  + <param name="evalue_cutoff" value="10.0" /> + <param name="filter_query" value="yes" /> + <param name="out_format" value="6" /> + <output name="output1" file="megablast_wrapper_test1.out"/> + </test> + </tests> + <help> + +.. class:: warningmark + +**Note**. Database searches may take substantial amount of time. For large input datasets it is advisable to allow overnight processing. + +----- + +**What it does** + +This tool runs NCBI BLAST+ blastn tool (which include *megablast*). + +----- + +**Output format** + +The default Output of this tool is tabular, containing 12 columns: + +1. Id of your sequence +2. GI of the database hit +3. % identity +4. Alignment length +5. # mismatches +6. # gaps +7. Start position in your sequence +8. End position in your sequence +9. Start position in database hit +10. End position in database hit +11. E-value +12. Bit score + +------- + +**References** + +Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214. + + </help> +</tool> --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -262,6 +262,9 @@ <tool file="sr_assembly/velveth.xml" /></section> --> + <section name="NCBI BLAST+" id="ncbi_blast_plus_tools"> + <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" /> + </section><section name="NGS: Mapping" id="solexa_tools"><tool file="sr_mapping/lastz_wrapper.xml" /><tool file="sr_mapping/lastz_paired_reads_wrapper.xml" />

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galaxy-dist commit 59995b9b461b: Make the dust option a boolean (checkbox)
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285335392 -3600 # Node ID 59995b9b461bfe40b48807a9ea1e81af3292d96e # Parent dc68de280ac7f2ff2ff97068694a7ecded62ee0c Make the dust option a boolean (checkbox) --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -33,10 +33,7 @@ <param name="iden_cutoff" type="float" size="15" value="90.0" label="report hits above this identity" help="no cutoff if 0" /> --><param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> - <param name="filter_query" type="select" label="Filter out low complexity regions (with DUST)?"> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="yes" falsevalue="no" checked="true" /><param name="out_format" type="select" label="Output format"><option value="6">Tabular</option><option value="5">BLAST XML</option>

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galaxy-dist commit 6dd6224f571d: Add basic blastp wrapper
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285670500 -3600 # Node ID 6dd6224f571deb34c01c7fd0c3c4daccf948eda1 # Parent fbc4d5d45649043ac57270cac5741ec153f6de66 Add basic blastp wrapper --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -264,6 +264,7 @@ --><section name="NCBI BLAST+" id="ncbi_blast_plus_tools"><tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" /> + <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" /></section><section name="NGS: Mapping" id="solexa_tools"><tool file="sr_mapping/lastz_wrapper.xml" /> --- /dev/null +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -0,0 +1,111 @@ +<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.1"> + <description>Use NCBI BLAST+ tool to search a protein database with protein query sequence(s)</description> + <command> + blastp + -query "$query" + -db "$database" + -task $blast_type + -evalue $evalue_cutoff + -seg $adv_opts.filter_query + -out $output1 + -outfmt $out_format + -num_threads 8 + </command> + <inputs> + <param name="query" type="data" format="fasta" label="Query sequence(s)"/> + <param name="database" type="select" display="radio" label="Protein BLAST database"> + <options from_file="blastdb_p.loc"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + <param name="blast_type" type="select" display="radio" label="Type of BLAST"> + <option value="blastp">blastp</option> + <option value="blastp-short">blastp-short</option> + </param> +  + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> + <param name="out_format" type="select" label="Output format"> + <option value="6">Tabular</option> + <option value="5">BLAST XML</option> + <option value="0">Pairwise text</option> +  + </param> + <conditional name="adv_opts"> + <param name="adv_opts_selector" type="select" label="Advanced Options"> + <option value="basic" selected="True">Hide Advanced Options</option> + <option value="advanced">Show Advanced Options</option> + </param> + <when value="basic"> + <param name="filter_query" type="hidden" value="yes" /> + </when> + <when value="advanced"> + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="yes" falsevalue="no" checked="true" /> + </when> + </conditional> + </inputs> + <outputs> +  + <data name="output1" format="tabular" label="${blast_type.value_label} on ${database.value_label}"> + <change_format> + <when input="out_format" value="0" format="txt"/> + </change_format> + <change_format> + <when input="out_format" value="5" format="blastxml"/> + </change_format> + </data> + </outputs> + <requirements> + <requirement type="binary">blastn</requirement> + </requirements> + <tests> + </tests> + <help> + +.. class:: warningmark + +**Note**. Database searches may take substantial amount of time. For large input datasets it is advisable to allow overnight processing. + +----- + +**What it does** + +This runs the command line NCBI BLAST+ blastp tool. + +----- + +**Output format** + +The default Output of this tool is tabular, containing 12 columns: + +1. Id of your sequence +2. GI of the database hit +3. % identity +4. Alignment length +5. # mismatches +6. # gaps +7. Start position in your sequence +8. End position in your sequence +9. Start position in database hit +10. End position in database hit +11. E-value +12. Bit score + +------- + +**References** + +Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. + +Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005. + + </help> +</tool>

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galaxy-dist commit 87a75fed920e: Create basic/advanced options split using <conditional> construct
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285336016 -3600 # Node ID 87a75fed920e0509dc5270000edf3758d97bd2f1 # Parent 59995b9b461bfe40b48807a9ea1e81af3292d96e Create basic/advanced options split using <conditional> construct --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -6,7 +6,7 @@ -db "$database" -task $blast_type -evalue $evalue_cutoff - -dust $filter_query + -dust $adv_opts.filter_query -out $output1 -outfmt $out_format </command> @@ -33,7 +33,6 @@ <param name="iden_cutoff" type="float" size="15" value="90.0" label="report hits above this identity" help="no cutoff if 0" /> --><param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="yes" falsevalue="no" checked="true" /><param name="out_format" type="select" label="Output format"><option value="6">Tabular</option><option value="5">BLAST XML</option> @@ -42,6 +41,18 @@ <option value="11">BLAST archive format (ASN.1)</option> --></param> + <conditional name="adv_opts"> + <param name="adv_opts_selector" type="select" label="Advanced Options"> + <option value="basic" selected="True">Hide Advanced Options</option> + <option value="advanced">Show Advanced Options</option> + </param> + <when value="basic"> + <param name="filter_query" type="hidden" value="yes" /> + </when> + <when value="advanced"> + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="yes" falsevalue="no" checked="true" /> + </when> + </conditional></inputs><outputs>

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galaxy-dist commit e902e11cd57c: Introduce blastdb_p.loc for protein BLAST databases
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285085124 -3600 # Node ID e902e11cd57c7b5e4b0b43bdf0bde459535e8a0c # Parent 63a43c1d230a6b42dda6d4f8d225d2620bdb9a8c Introduce blastdb_p.loc for protein BLAST databases --- a/tool-data/blastdb.loc.sample +++ b/tool-data/blastdb.loc.sample @@ -28,3 +28,5 @@ #wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk #test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test #...etc... +# +#See also blastdb_p.loc which is for any protein BLAST database. --- /dev/null +++ b/tool-data/blastdb_p.loc.sample @@ -0,0 +1,12 @@ +#This is a sample file distributed with Galaxy that is used to define a +#list of protein BLAST databases, using two columns tab separated: +# +#<database caption><path to base name> +# +#For example: +# +#NCBI NR (non redundant) /data/blastdb/nr +# +#where /data/blastdb/nr.* are the files making up the NR database. +# +#See also the blastdb.loc file which is for any nucleotide databases.

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galaxy-dist commit 054e0b2c15d4: Clean up the code in the request_admin controller.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1286912182 14400 # Node ID 054e0b2c15d412c3b1d99cbbd7ccb7a653b2a637 # Parent 45fdae2622ad9f989f6f15e6b081a268430683f3 Clean up the code in the request_admin controller. --- a/test/functional/test_forms_and_requests.py +++ b/test/functional/test_forms_and_requests.py @@ -164,7 +164,7 @@ class TestFormsAndRequests( TwillTestCas str( sample_form.id ), sample_states, strings_displayed=[ 'Create a new sequencer configuration' ], - strings_displayed_after_submit=[ "Sequencer configuration <b>%s</b> has been created" % name ] ) + strings_displayed_after_submit=[ "Sequencer configuration (%s) has been created" % name ] ) global request_type1 request_type1 = get_request_type_by_name( name ) assert request_type1 is not None, 'Problem retrieving sequencer configuration named "%s" from the database' % name --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1433,7 +1433,7 @@ class TwillTestCase( unittest.TestCase ) self.check_page_for_string( check_str ) def request_type_permissions( self, request_type_id, request_type_name, role_ids_str, permissions_in, permissions_out ): # role_ids_str must be a comma-separated string of role ids - url = "requests_admin/manage_request_types?operation=permissions&id=%s&update_roles_button=Save" % ( request_type_id ) + url = "requests_admin/request_type_permissions?id=%s&update_roles_button=Save" % ( request_type_id ) for po in permissions_out: key = '%s_out' % po url ="%s&%s=%s" % ( url, key, role_ids_str ) --- a/templates/admin/requests/get_data.mako +++ b/templates/admin/requests/get_data.mako @@ -2,18 +2,15 @@ <%namespace file="/message.mako" import="render_msg" /><script type="text/javascript"> -$(document).ready(function(){ - //hide the all of the element with class msg_body - $(".msg_body").hide(); - //toggle the component with class msg_body - $(".msg_head").click(function(){ - $(this).next(".msg_body").slideToggle(450); + $(document).ready(function(){ + //hide the all of the element with class msg_body + $(".msg_body").hide(); + //toggle the component with class msg_body + $(".msg_head").click(function(){ + $(this).next(".msg_body").slideToggle(450); + }); }); -}); -</script> - -<script type="text/javascript"> function display_file_details(request_id, folder_path) { var w = document.get_data.files_list.selectedIndex; @@ -37,9 +34,7 @@ cell.html( '' ) } } -</script> -<script type="text/javascript"> function open_folder1( request_id, folder_path ) { var w = document.get_data.files_list.selectedIndex; @@ -80,25 +75,24 @@ } </style> +<br/> +<br/> +<ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='view_request_type', id=trans.security.encode_id( request.type.id ) )}">Sequencer configuration "${request.type.name}"</a> + </li> + <li> + <a class="action-button" href="${h.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a> + </li> +</ul> + %if message: ${render_msg( message, status )} %endif -<br/> -<br/> -<ul class="manage-table-actions"> - <li> - <a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_request_types', operation='view', id=trans.security.encode_id( request.type.id ) )}"> - <span>Sequencer configuration "${request.type.name}"</span></a> - </li> - <li> - <a class="action-button" href="${h.url_for( controller='requests_common', action='manage_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}"> - <span>Browse this request</span></a> - </li> -</ul> -<form name="get_data" id="get_data" action="${h.url_for( controller='requests_admin', cntrller=cntrller, action='get_data', request_id=trans.security.encode_id( request.id ) )}" method="post" > - <div class="toolForm"> - <div class="toolFormTitle">Select files for transfer</div> +<div class="toolForm"> + <div class="toolFormTitle">Select files for transfer</div> + <form name="get_data" id="get_data" action="${h.url_for( controller='requests_admin', action='get_data', cntrller=cntrller, request_id=trans.security.encode_id( request.id )}" method="post" ><div class="form-row"><label>Sample:</label> ${sample_id_select_field.get_html()} @@ -123,5 +117,5 @@ <input type="submit" name="select_show_datasets_button" value="Select & show datasets"/><input type="submit" name="select_more_button" value="Select more"/></div> - </div> -</form> + </form> +</div> --- a/templates/requests/common/manage_request.mako +++ b/templates/requests/common/manage_request.mako @@ -146,6 +146,8 @@ </div><br/><br/> +<font color="red"><b><i>A dataset can be renamed only if its status is "Not Started"</i></b></font> + <ul class="manage-table-actions"><li><a class="action-button" id="seqreq-${request.id}-popup" class="menubutton">Sequencing Request Actions</a></li><div popupmenu="seqreq-${request.id}-popup"> @@ -157,7 +159,7 @@ %if is_admin: %if request.is_submitted: <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a> - <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', show_page=True, request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> %endif %endif </div> --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -106,6 +106,7 @@ class RequestsGrid( grids.Grid ): class RequestsCommon( BaseController, UsesFormDefinitionWidgets ): @web.json def sample_state_updates( self, trans, ids=None, states=None, cntrller=None ): + # TODO fix this mthod - cntrller is required in the signature. # Avoid caching trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' --- a/templates/webapps/galaxy/admin/index.mako +++ b/templates/webapps/galaxy/admin/index.mako @@ -114,7 +114,7 @@ </div><div class="toolSectionBody"><div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='requests_admin', action='manage_request_types' )}" target="galaxy_main">Sequencer configurations</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='requests_admin', action='browse_request_types' )}" target="galaxy_main">Sequencer configurations</a></div><div class="toolTitle"><a href="${h.url_for( controller='requests_admin', action='browse_requests' )}" target="galaxy_main">Sequencing requests</a></div><div class="toolTitle"><a href="${h.url_for( controller='requests_common', action='find_samples', cntrller='requests_admin' )}" target="galaxy_main">Find samples</a></div></div> --- a/templates/admin/requests/rename_datasets.mako +++ b/templates/admin/requests/rename_datasets.mako @@ -1,12 +1,10 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> -%if message: - ${render_msg( message, status )} -%endif -<h3>Rename datasets for Sample "${sample.name}"</h3> -<br/> -${render_msg('A dataset can be renamed only if its status is "Not Started"', 'ok')} +<% from galaxy.web.controllers.requests_admin import build_rename_datasets_for_sample_select_field %> + +<br/><br/> +<font color="red"><b><i>A dataset can be renamed only if its status is "Not Started"</i></b></font><ul class="manage-table-actions"><li> @@ -17,48 +15,44 @@ </li></ul> -<form name="rename_datasets" id="rename_datasets" action="${h.url_for( controller='requests_admin', action='rename_datasets', id_list=id_list, sample_id=trans.security.encode_id( sample.id ) )}" method="post" > - <table class="grid"> - <thead> - <tr> - <th>Prepend directory name</th> - <th>Name</th> - <th>Path on Sequencer</th> - </tr> - <thead> - <tbody> - %for id in id_list: - <% - sample_dataset = trans.sa_session.query( trans.app.model.SampleDataset ).get( trans.security.decode_id(id) ) - import os - id = trans.security.decode_id(id) - %> - %if sample_dataset.status == trans.app.model.Sample.transfer_status.NOT_STARTED: - <tr> - <td> - <select name="prepend_${sample_dataset.id}" last_selected_value="2"> - <option value="None" selected></option> - %for option_index, option in enumerate(sample_dataset.file_path.split(os.sep)[:-1]): - %if option.strip(): - <option value="${option}">${option}</option> - %endif - %endfor - </select> - </td> - <td> - <input type="text" name="name_${sample_dataset.id}" value="${sample_dataset.name}" size="100"/> - </td> - <td> - ${sample_dataset.file_path} - </td> - </tr> - %endif - %endfor - </tbody> - </table> - <br/> - <div class="form-row"> - <input type="submit" name="save_button" value="Save"/> - <input type="submit" name="cancel_button" value="Close"/> +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Rename datasets for Sample "${sample.name}"</div> + <div class="toolFormBody"> + <form name="rename_datasets" id="rename_datasets" action="${h.url_for( controller='requests_admin', action='rename_datasets', id_list=id_list, sample_id=trans.security.encode_id( sample.id ) )}" method="post" > + <table class="grid"> + <thead> + <tr> + <th>Prepend directory name</th> + <th>Name</th> + <th>Path on sequencer</th> + </tr> + <thead> + <tbody> + %for sample_dataset in sample_datasets: + %if sample_dataset.status == trans.app.model.Sample.transfer_status.NOT_STARTED: + <tr> + <td> + <% rename_datasets_for_sample_select_field = build_rename_datasets_for_sample_select_field( trans, sample_dataset ) %> + ${rename_datasets_for_sample_select_field} + </td> + <td> + <input type="text" name="new_name_${trans.security.encode_id( sample_dataset.id} )" value="${sample_dataset.name}" size="100"/> + </td> + <td>${sample_dataset.file_path}</td> + </tr> + %endif + %endfor + </tbody> + </table> + <br/> + <div class="form-row"> + <input type="submit" name="rename_datasets_button" value="Save"/> + <input type="submit" name="cancel_rename_datasets_button" value="Close"/> + </div> + </form></div> -</form> +</div> --- a/templates/admin/requests/create_request_type.mako +++ b/templates/admin/requests/create_request_type.mako @@ -70,7 +70,7 @@ </div><div class="form-row"><label>Add experiment name and the sample name to the dataset name?</label> - ${rename_dataset_selectbox.get_html()} + ${rename_dataset_select_field.get_html()} <div class="toolParamHelp" style="clear: both;"> The datasets are renamed by prepending the experiment name and the sample name to the dataset name. <br/>This makes sure that dataset names remain unique in Galaxy even when they have the --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -67,9 +67,9 @@ class RequestTypeGrid( grids.Grid ): key='desc', filterable="advanced" ), RequestFormColumn( "Request Form", - link=( lambda item: iff( item.deleted, None, dict( operation="view_form", id=item.request_form.id ) ) ) ), + link=( lambda item: iff( item.deleted, None, dict( operation="view_form_definition", id=item.request_form.id ) ) ) ), SampleFormColumn( "Sample Form", - link=( lambda item: iff( item.deleted, None, dict( operation="view_form", id=item.sample_form.id ) ) ) ), + link=( lambda item: iff( item.deleted, None, dict( operation="view_form_definition", id=item.sample_form.id ) ) ) ), grids.DeletedColumn( "Deleted", key="deleted", visible=False, @@ -110,18 +110,15 @@ class DataTransferGrid( grids.Grid ): use_paging = True columns = [ NameColumn( "Name", - #key="name", link=( lambda item: dict( operation="view", id=item.id ) ), attach_popup=True, filterable="advanced" ), SizeColumn( "Size", - #key='size', filterable="advanced" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), StatusColumn( "Status", - #key='status', filterable="advanced" ), ] columns.append( grids.MulticolFilterColumn( "Search", @@ -197,15 +194,6 @@ class RequestsAdmin( BaseController, Use events={ '.ssword:*' : datatx_info[ 'password'] + '\r\n', pexpect.TIMEOUT : print_ticks }, timeout=10 ) return unicode( output.replace( '\n', '<br/>' ) ) - @web.json - def open_folder( self, trans, id, folder_path ): - def print_ticks( d ): - pass - # Avoid caching - trans.response.headers['Pragma'] = 'no-cache' - trans.response.headers['Expires'] = '0' - request = trans.sa_session.query( trans.model.Request ).get( int( id ) ) - return self.__get_files( trans, request.type, folder_path ) @web.expose @web.require_admin def reject( self, trans, **kwd ): @@ -246,29 +234,30 @@ class RequestsAdmin( BaseController, Use @web.expose @web.require_admin def manage_datasets( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) if 'operation' in kwd: operation = kwd[ 'operation' ].lower() - dataset_id = kwd.get( 'id', None ) - if not dataset_id: - return invalid_id_redirect( trans, 'requests_admin', dataset_id ) - id_list = util.listify( dataset_id ) + sample_dataset_id = params.get( 'id', None ) + if not sample_dataset_id: + return invalid_id_redirect( trans, 'requests_admin', sample_dataset_id ) + id_list = util.listify( sample_dataset_id ) if operation == "view": - sample_dataset_id = trans.security.decode_id( kwd['id'] ) - sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( sample_dataset_id ) + sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) return trans.fill_template( '/admin/requests/dataset.mako', sample_dataset=sample_dataset ) elif operation == "delete": not_deleted = [] - for id in id_list: - sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( id ) ) + for sample_dataset_id in id_list: + sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) sample_id = sample_dataset.sample_id if sample_dataset.status == sample_dataset.sample.transfer_status.NOT_STARTED: trans.sa_session.delete( sample_dataset ) trans.sa_session.flush() else: not_deleted.append( sample_dataset.name ) - message = '%i datasets have been successfully deleted. ' % ( len( id_list ) - len( not_deleted ) ) - status = 'done' + message = '%i datasets have been deleted. ' % ( len( id_list ) - len( not_deleted ) ) if not_deleted: status = 'warning' message = message + '%s could not be deleted because their transfer status is not "Not Started". ' % str( not_deleted ) @@ -278,21 +267,21 @@ class RequestsAdmin( BaseController, Use status=status, message=message ) ) elif operation == "rename": - sample_dataset_id = id_list[0] sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) return trans.fill_template( '/admin/requests/rename_datasets.mako', sample=sample_dataset.sample, id_list=id_list ) elif operation == "start transfer": - sample_dataset_id = id_list[0] sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) self.__start_datatx( trans, sample_dataset.sample, id_list ) # Render the grid view - sample_id = kwd.get( 'sample_id', None ) + sample_id = params.get( 'sample_id', None ) try: sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id ( sample_id ) ) except: return invalid_id_redirect( trans, 'requests_admin', sample_id ) + request_id = trans.security.encode_id( sample.request.id ) + library_id = trans.security.encode_id( sample.library.id ) self.datatx_grid.title = 'Datasets of sample "%s"' % sample.name self.datatx_grid.global_actions = [ grids.GridAction( "Refresh", dict( controller='requests_admin', @@ -301,24 +290,25 @@ class RequestsAdmin( BaseController, Use grids.GridAction( "Select datasets", dict( controller='requests_admin', action='get_data', - request_id=trans.security.encode_id( sample.request.id ), + request_id=request_id, folder_path=sample.request.type.datatx_info[ 'data_dir' ], - sample_id=sample_id, - show_page=True ) ), + sample_id=sample_id ) ), grids.GridAction( 'Data library "%s"' % sample.library.name, dict( controller='library_common', action='browse_library', cntrller='library_admin', - id=trans.security.encode_id( sample.library.id ) ) ), + id=library_id ) ), grids.GridAction( "Browse this request", dict( controller='requests_common', action='manage_request', cntrller='requests_admin', - id=trans.security.encode_id( sample.request.id ) ) ) ] + id=request_id ) ) ] return self.datatx_grid( trans, **kwd ) @web.expose @web.require_admin def rename_datasets( self, trans, **kwd ): + # This method is called from the DataTransferGrid when a user is renaming 1 or more + # SampleDatasets. params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -327,64 +317,35 @@ class RequestsAdmin( BaseController, Use sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) except: return invalid_id_redirect( trans, 'requests_admin', sample_id ) - if params.get( 'save_button', False ): - id_list = util.listify( kwd['id_list'] ) - for id in id_list: - sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( id ) ) - prepend = util.restore_text( params.get( 'prepend_%i' % sample_dataset.id, '' ) ) - name = util.restore_text( params.get( 'name_%i' % sample_dataset.id, sample_dataset.name ) ) - if prepend == 'None': - sample_dataset.name = name + # id_list is list of SampleDataset ids, which is a subset of all + # of the SampleDatasets associated with the Sample. The user may + # or may not have selected all of the SampleDatasets for renaming. + id_list = util.listify( kwd.get( 'id_list', [] ) ) + # Get all of the SampleDatasets + sample_datasets = [] + for sample_dataset_id in id_list: + sample_dataset = trans.sa_session.query( trans.app.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) + sample_datasets.append( sample_dataset ) + if params.get( 'rename_datasets_button', False ): + for sample_dataset in sample_datasets: + encoded_id = trans.security.encode_id( sample_dataset.id ) + selected_option = util.restore_text( params.get( 'rename_datasets_for_sample_%s' % encoded_id, '' ) ) + new_name = util.restore_text( params.get( 'new_name_%s' % encoded_id, '' ) ) + if selected_option == 'none': + sample_dataset.name = new_name else: - sample_dataset.name = '%s_%s' % ( prepend, name ) + sample_dataset.name = '%s_%s' % ( selected_option, new_name ) trans.sa_session.add( sample_dataset ) trans.sa_session.flush() + message = 'Changes saved successfully.' return trans.fill_template( '/admin/requests/rename_datasets.mako', sample=sample, - id_list=id_list, - message='Changes saved successfully.', - status='done' ) + sample_datasets=sample_datasets, + message=message, + status=status ) return trans.response.send_redirect( web.url_for( controller='requests_admin', action='manage_datasets', sample_id=sample_id ) ) - def __get_files( self, trans, request_type, folder_path ): - # Retrieves the filenames to be transferred from the remote host. - # FIXME: sample is used in this method, but no sample obj is received... - datatx_info = request_type.datatx_info - if not datatx_info[ 'host' ] or not datatx_info[ 'username' ] or not datatx_info[ 'password' ]: - status = 'error' - message = "Error in sequencer login information." - return trans.response.send_redirect( web.url_for( controller='requests_common', - action='view_dataset_transfer', - cntrller='requests_admin' , - sample_id=trans.security.encode_id( sample.id ), - status=status, - message=message ) ) - def print_ticks( d ): - pass - cmd = 'ssh %s@%s "ls -p \'%s\'"' % ( datatx_info['username'], datatx_info['host'], folder_path ) - output = pexpect.run( cmd, - events={ '.ssword:*' : datatx_info['password'] + '\r\n', pexpect.TIMEOUT : print_ticks }, - timeout=10 ) - if 'No such file or directory' in output: - status = 'error' - message = "No folder named (%s) exists on the sequencer." % folder_path - return trans.response.send_redirect( web.url_for( controller='requests_common', - action='view_dataset_transfer', - cntrller='requests_admin' , - sample_id=trans.security.encode_id( sample.id ), - folder_path=folder_path, - status=status, - message=message ) ) - - return output.splitlines() - def __check_path( self, a_path ): - # Return a valid folder_path - if a_path and not a_path.endswith( os.sep ): - a_path += os.sep - return a_path - def __build_sample_id_select_field( self, trans, request, selected_value ): - return build_select_field( trans, request.samples, 'name', 'sample_id', selected_value=selected_value, refresh_on_change=False ) @web.expose @web.require_admin def get_data( self, trans, **kwd ): @@ -396,132 +357,129 @@ class RequestsAdmin( BaseController, Use request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) except: return invalid_id_redirect( trans, 'requests_admin', request_id ) - files_list = util.listify( params.get( 'files_list', '' ) ) + files_list = util.listify( params.get( 'files_list', [] ) ) folder_path = util.restore_text( params.get( 'folder_path', request.type.datatx_info[ 'data_dir' ] ) ) selected_value = kwd.get( 'sample_id', 'none' ) - sample_id_select_field = self.__build_sample_id_select_field( trans, request, selected_value ) - if not folder_path: - return trans.fill_template( '/admin/requests/get_data.mako', - cntrller='requests_admin', - request=request, - sample_id_select_field=sample_id_select_field, - files=[], - folder_path=folder_path ) - folder_path = self.__check_path( folder_path ) - sample_id = kwd.get( 'sample_id', None ) - if params.get( 'show_page', False ): - if sample_id: + sample_id_select_field = self.__build_sample_id_select_field( request, selected_value ) + # The __get_files() method redirects here with a status of 'error' and a message if there + # was a problem retrieving the files. + if folder_path and status != 'error': + folder_path = self.__check_path( folder_path ) + sample_id = params.get( 'sample_id', None ) + try: sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) - if sample.datasets: - folder_path = os.path.dirname( sample.datasets[-1].file_path ) - return trans.fill_template( '/admin/requests/get_data.mako', - cntrller='requests_admin', - request=request, - sample_id_select_field=sample_id_select_field, - files=[], - folder_path=folder_path, - status=status, - message=message ) - elif params.get( 'browse_button', False ): - # get the filenames from the remote host - files = self.__get_files( trans, request.type, folder_path ) - return trans.fill_template( '/admin/requests/get_data.mako', - cntrller='requests_admin', - request=request, - sample_id_select_field=sample_id_select_field, - files=files, - folder_path=folder_path, - status=status, - message=message ) - elif params.get( 'folder_up', False ): - # get the filenames from the remote host - files = self.__get_files( trans, request.type, folder_path ) - return trans.fill_template( '/admin/requests/get_data.mako', - cntrller='requests_admin', - request=request, - sample_id_select_field=sample_id_select_field, - files=files, - folder_path=folder_path, - status=status, - message=message ) - elif params.get( 'open_folder', False ): - if len( files_list ) == 1: - folder_path = os.path.join( folder_path, files_list[0] ) - folder_path = self.__check_path( folder_path ) - # get the filenames from the remote host - files = self.__get_files( trans, request.type, folder_path ) - return trans.fill_template( '/admin/requests/get_data.mako', - cntrller='requests_admin', - request=request, - sample_id_select_field=sample_id_select_field, - files=files, - folder_path=folder_path, - status=status, - message=message ) - elif params.get( 'select_show_datasets_button', False ): - sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) - retval = self.__save_sample_datasets( trans, sample, files_list, folder_path ) - if retval: - message = 'The datasets %s have been selected for sample <b>%s</b>' % ( str( retval )[1:-1].replace( "'", "" ), sample.name ) - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='manage_datasets', - sample_id=sample_id, - message=message, - status=status ) ) - elif params.get( 'select_more_button', False ): - sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) - retval = self.__save_sample_datasets( trans, sample, files_list, folder_path ) - if retval: - message='The datasets %s have been selected for sample <b>%s</b>' % ( str( retval )[1:-1].replace( "'", "" ), sample.name ) - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='get_data', - request_id=trans.security.encode_id( sample.request.id ), + except: + return invalid_id_redirect( trans, 'requests_admin', sample_id ) + # Get the filenames from the remote host + files = self.__get_files( trans, request, folder_path ) + if params.get( 'open_folder', False ): + if len( files_list ) == 1: + folder_path = os.path.join( folder_path, files_list[0] ) + folder_path = self.__check_path( folder_path ) + elif params.get( 'select_show_datasets_button', False ) or params.get( 'select_more_button', False ): + sample_dataset_file_names = self.__save_sample_datasets( trans, sample, files_list, folder_path ) + if sample_dataset_file_names: + message = 'Datasets (%s) have been selected for sample (%s)' % \ + ( str( sample_dataset_file_names )[1:-1].replace( "'", "" ), sample.name ) + if params.get( 'select_show_datasets_button', False ): + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='manage_datasets', + sample_id=sample_id, + message=message, + status=status ) ) + else: # 'select_more_button' was clicked + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='get_data', + request_id=request_id, + folder_path=folder_path, + sample_id=sample_id, + open_folder=True, + message=message, + status=status ) ) + return trans.fill_template( '/admin/requests/dataset_transfer.mako', + cntrller='requests_admin', + request=request, + sample_id_select_field=sample_id_select_field, + files=files, + folder_path=folder_path, + status=status, + message=message ) + @web.json + def open_folder( self, trans, id, folder_path ): + def print_ticks( d ): + pass + # Avoid caching + trans.response.headers['Pragma'] = 'no-cache' + trans.response.headers['Expires'] = '0' + request = trans.sa_session.query( trans.model.Request ).get( int( id ) ) + return self.__get_files( trans, request, folder_path ) + def __get_files( self, trans, request, folder_path ): + # Retrieves the filenames to be transferred from the remote host. + ok = True + datatx_info = request.type.datatx_info + if not datatx_info[ 'host' ] or not datatx_info[ 'username' ] or not datatx_info[ 'password' ]: + status = 'error' + message = "Error in sequencer login information." + ok = False + def print_ticks( d ): + pass + cmd = 'ssh %s@%s "ls -p \'%s\'"' % ( datatx_info['username'], datatx_info['host'], folder_path ) + output = pexpect.run( cmd, + events={ '.ssword:*' : datatx_info['password'] + '\r\n', pexpect.TIMEOUT : print_ticks }, + timeout=10 ) + if 'No such file or directory' in output: + status = 'error' + message = "No folder named (%s) exists on the sequencer." % folder_path + ok = False + if ok: + return output.splitlines() + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='get_data', + request_id=trans.security.encode_id( request.id ), folder_path=folder_path, - sample_id=sample_id, - open_folder=True, - message=message, - status=status ) ) - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='get_data', - request_id=trans.security.encode_id( sample.request.id ), - folder_path=folder_path, - show_page=True ) ) + status=status, + message=message ) ) + def __check_path( self, a_path ): + # Return a valid folder_path + if a_path and not a_path.endswith( os.sep ): + a_path += os.sep + return a_path def __save_sample_datasets( self, trans, sample, files_list, folder_path ): - files = [] + sample_dataset_file_names = [] if files_list: for f in files_list: filepath = os.path.join( folder_path, f ) if f[-1] == os.sep: - # the selected item is a folder so transfer all the folder contents - # FIXME - #self.__get_files_in_dir(trans, sample, filepath) + # FIXME: The selected item is a folder so transfer all the folder contents + request_id = trans.security.ecnode_id( sample.request.id ) return trans.response.send_redirect( web.url_for( controller='requests_admin', action='get_data', - request=sample.request, + request_id=request_id, folder_path=folder_path, open_folder=True ) ) else: + name = self.__dataset_name( sample, filepath.split( '/' )[-1] ) sample_dataset = trans.model.SampleDataset( sample=sample, file_path=filepath, status=sample.transfer_status.NOT_STARTED, - name=self.__dataset_name( sample, filepath.split( '/' )[-1] ), + name=name, error_msg='', size=sample.dataset_size( filepath ) ) trans.sa_session.add( sample_dataset ) trans.sa_session.flush() - files.append( str( sample_dataset.name ) ) - return files + sample_dataset_file_names.append( str( sample_dataset.name ) ) + return sample_dataset_file_names def __dataset_name( self, sample, filepath ): name = filepath.split( '/' )[-1] options = sample.request.type.rename_dataset_options option = sample.request.type.datatx_info.get( 'rename_dataset', options.NO ) if option == options.NO: return name - elif option == options.SAMPLE_NAME: + if option == options.SAMPLE_NAME: return sample.name + '_' + name - elif option == options.EXPERIMENT_AND_SAMPLE_NAME: + if option == options.EXPERIMENT_AND_SAMPLE_NAME: return sample.request.name + '_' + sample.name + '_' + name - elif opt == options.EXPERIMENT_NAME: + if opt == options.EXPERIMENT_NAME: return sample.request.name + '_' + name def __setup_datatx_user( self, trans, library, folder ): """ @@ -625,7 +583,7 @@ class RequestsAdmin( BaseController, Use status = "error" else: self.__send_message( trans, datatx_info, sample, id_list ) - message = "%i datasets have been queued for transfer from the sequencer. Click on <b>Refresh</b> button above to get the latest transfer status." % len( id_list ) + message = "%i datasets have been queued for transfer from the sequencer. Click the Refresh button above to see the latest transfer status." % len( id_list ) status = "done" return trans.response.send_redirect( web.url_for( controller='requests_admin', action='manage_datasets', @@ -635,91 +593,46 @@ class RequestsAdmin( BaseController, Use # Request Type Stuff @web.expose @web.require_admin - def manage_request_types( self, trans, **kwd ): + def browse_request_types( self, trans, **kwd ): if 'operation' in kwd: operation = kwd['operation'].lower() obj_id = kwd.get( 'id', None ) - if obj_id is None: - return invalid_id_redirect( trans, 'requests_admin', obj_id, action='manage_request_types' ) - if operation == "view": - return self.__view_request_type( trans, **kwd ) - elif operation == "view_form": - return self.__view_form( trans, **kwd ) - elif operation == "delete": - return self.__delete_request_type( trans, **kwd ) - elif operation == "undelete": - return self.__undelete_request_type( trans, **kwd ) - elif operation == "clone": - return self.__clone_request_type( trans, **kwd ) - elif operation == "permissions": - return self.__show_request_type_permissions( trans, **kwd ) + if operation == "view_form_definition": + return self.view_form_definition( trans, **kwd ) # Render the grid view return self.requesttype_grid( trans, **kwd ) - def __view_request_type( self, trans, **kwd ): - request_type_id = kwd.get( 'id', None ) - try: - request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) ) - except: - return invalid_id_redirect( trans, 'requests_admin', request_type_id, action='manage_request_types' ) - forms = self.get_all_forms( trans ) - rename_dataset_selectbox = self.__build_rename_dataset_select_list( trans, request_type ) - return trans.fill_template( '/admin/requests/view_request_type.mako', - request_type=request_type, - forms=forms, - rename_dataset_selectbox=rename_dataset_selectbox ) - def __view_form(self, trans, **kwd): - form_definition_id = kwd.get( 'id', None ) - try: - form_definition = trans.sa_session.query( trans.model.FormDefinition ).get( trans.security.decode_id( form_definition_id ) ) - except: - return invalid_id_redirect( trans, 'requests_admin', form_definition_id, action='manage_request_types' ) - return trans.fill_template( '/admin/forms/show_form_read_only.mako', - form_definition=form_definition ) @web.expose @web.require_admin def create_request_type( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + status = params.get( 'status', 'done' ) + rt_info_widgets, rt_states_widgets = self.__create_request_type_form( trans, **kwd ) + rename_dataset_select_field = self.__build_rename_dataset_select_field( trans ) if params.get( 'add_state_button', False ): - rt_info_widgets, rt_states_widgets = self.__create_request_type_form( trans, **kwd ) + # FIXME: why do we append a tuple of 2 empty strings???? rt_states_widgets.append( ( "", "" ) ) - rename_dataset_selectbox = self.__build_rename_dataset_select_list( trans ) - return trans.fill_template( '/admin/requests/create_request_type.mako', - rt_info_widgets=rt_info_widgets, - rt_states_widgets=rt_states_widgets, - rename_dataset_selectbox=rename_dataset_selectbox, - message=message, - status=status ) elif params.get( 'remove_state_button', False ): - rt_info_widgets, rt_states_widgets = self.__create_request_type_form( trans, **kwd ) index = int( params.get( 'remove_state_button', '' ).split(" ")[2] ) del rt_states_widgets[ index-1 ] - rename_dataset_selectbox = self.__build_rename_dataset_select_list( trans ) - return trans.fill_template( '/admin/requests/create_request_type.mako', - rt_info_widgets=rt_info_widgets, - rt_states_widgets=rt_states_widgets, - rename_dataset_selectbox=rename_dataset_selectbox, - message=message, - status=status ) elif params.get( 'save_request_type', False ): request_type, message = self.__save_request_type( trans, **kwd ) if not request_type: - return trans.fill_template( '/admin/requests/create_request_type.mako', - message=message, - status='error' ) - message = 'Sequencer configuration <b>%s</b> has been created' % request_type.name - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='manage_request_types', - message=message, - status=status ) ) + status='error' + else: + message = 'Sequencer configuration (%s) has been created' % request_type.name + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='browse_request_types', + message=message, + status=status ) ) elif params.get( 'save_changes', False ): - request_type_id = kwd.get( 'rt_id', None ) + request_type_id = params.get( 'rt_id', None ) try: request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) ) except: - return invalid_id_redirect( trans, 'requests_admin', request_type_id, action='manage_request_types' ) - # Data transfer info - make sure password is retrieved from kwd rathe rthan Params since Params may have munged the characters. + return invalid_id_redirect( trans, 'requests_admin', request_type_id, action='browse_request_types' ) + # Data transfer info - make sure password is retrieved from kwd rather + # than Params since Params may have munged the characters. request_type.datatx_info = dict( host=util.restore_text( params.get( 'host', '' ) ), username=util.restore_text( params.get( 'username', '' ) ), password=kwd.get( 'password', '' ), @@ -731,51 +644,48 @@ class RequestsAdmin( BaseController, Use trans.sa_session.flush() message = 'Changes made to sequencer configuration <b>%s</b> has been saved' % request_type.name return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='manage_request_types', - operation='view', + action='view_request_type', id=request_type_id, message=message, status=status ) ) - else: - rt_info_widgets, rt_states_widgets = self.__create_request_type_form( trans, **kwd ) - rename_dataset_selectbox = self.__build_rename_dataset_select_list( trans ) - return trans.fill_template( '/admin/requests/create_request_type.mako', - rt_info_widgets=rt_info_widgets, - rt_states_widgets=rt_states_widgets, - rename_dataset_selectbox=rename_dataset_selectbox, - message=message, - status=status ) + return trans.fill_template( '/admin/requests/create_request_type.mako', + rt_info_widgets=rt_info_widgets, + rt_states_widgets=rt_states_widgets, + rename_dataset_select_field=rename_dataset_select_field, + message=message, + status=status ) def __create_request_type_form( self, trans, **kwd ): - request_forms = self.get_all_forms( trans, - filter=dict( deleted=False ), - form_type=trans.model.FormDefinition.types.REQUEST ) - sample_forms = self.get_all_forms( trans, - filter=dict( deleted=False ), - form_type=trans.model.FormDefinition.types.SAMPLE ) - if not request_forms or not sample_forms: + request_form_definitionss = self.get_all_forms( trans, + filter=dict( deleted=False ), + form_type=trans.model.FormDefinition.types.REQUEST ) + sample_form_definitions = self.get_all_forms( trans, + filter=dict( deleted=False ), + form_type=trans.model.FormDefinition.types.SAMPLE ) + if not request_form_definitionss or not sample_form_definitions: return [],[] params = util.Params( kwd ) - rt_info_widgets = [] - rt_info_widgets.append( dict( label='Name', - widget=TextField( 'name', 40, util.restore_text( params.get( 'name', '' ) ) ) ) ) - rt_info_widgets.append( dict( label='Description', - widget=TextField( 'desc', 40, util.restore_text( params.get( 'desc', '' ) ) ) ) ) - rf_selectbox = SelectField( 'request_form_id' ) - for fd in request_forms: - if str( fd.id ) == params.get( 'request_form_id', '' ): - rf_selectbox.add_option( fd.name, fd.id, selected=True ) - else: - rf_selectbox.add_option( fd.name, fd.id ) - rt_info_widgets.append( dict( label='Request form', - widget=rf_selectbox ) ) - sf_selectbox = SelectField( 'sample_form_id' ) - for fd in sample_forms: - if str( fd.id ) == params.get( 'sample_form_id', '' ): - sf_selectbox.add_option( fd.name, fd.id, selected=True ) - else: - sf_selectbox.add_option( fd.name, fd.id ) - rt_info_widgets.append( dict( label='Sample form', - widget=sf_selectbox ) ) + request_form_id = params.get( 'request_form_id', 'none' ) + sample_form_id = params.get( 'sample_form_id', 'none' ) + request_form_id_select_field = build_select_field( trans, + objs=request_form_definitionss, + label_attr='id', + select_field_name='request_form_id', + selected_value=request_form_id, + refresh_on_change=False ) + sample_form_id_select_field = build_select_field( trans, + objs=sample_form_definitions, + label_attr='id', + select_field_name='sample_form_id', + selected_value=sample_form_id, + refresh_on_change=False ) + rt_info_widgets = [ dict( label='Name', + widget=TextField( 'name', 40, util.restore_text( params.get( 'name', '' ) ) ) ), + dict( label='Description', + widget=TextField( 'desc', 40, util.restore_text( params.get( 'desc', '' ) ) ) ), + dict( label='Request form', + widget=request_form_id_select_field ), + dict( label='Sample form', + widget=sample_form_id_select_field ) ] # Possible sample states rt_states = [] i=0 @@ -787,26 +697,14 @@ class RequestsAdmin( BaseController, Use else: break return rt_info_widgets, rt_states - def __build_rename_dataset_select_list( self, trans, rt=None ): - if rt: - sel_opt = rt.datatx_info.get( 'rename_dataset', trans.model.RequestType.rename_dataset_options.NO ) - else: - sel_opt = trans.model.RequestType.rename_dataset_options.NO - rename_dataset_selectbox = SelectField( 'rename_dataset' ) - for opt, opt_name in trans.model.RequestType.rename_dataset_options.items(): - if sel_opt == opt_name: - rename_dataset_selectbox.add_option( opt_name, opt_name, selected=True ) - else: - rename_dataset_selectbox.add_option( opt_name, opt_name ) - return rename_dataset_selectbox def __save_request_type(self, trans, **kwd): params = util.Params( kwd ) name = util.restore_text( params.get( 'name', '' ) ) desc = util.restore_text( params.get( 'desc', '' ) ) request_form_id = params.get( 'request_form_id', None ) - request_form = trans.sa_session.query( trans.model.FormDefinition ).get( int( request_form_id ) ) + request_form = trans.sa_session.query( trans.model.FormDefinition ).get( trans.security.decode_id( request_form_id ) ) sample_form_id = params.get( 'sample_form_id', None ) - sample_form = trans.sa_session.query( trans.model.FormDefinition ).get( int( sample_form_id ) ) + sample_form = trans.sa_session.query( trans.model.FormDefinition ).get( trans.security.decode_id( sample_form_id ) ) data_dir = util.restore_text( params.get( 'data_dir', '' ) ) data_dir = self.__check_path( data_dir ) # Data transfer info - Make sure password is retrieved from kwd rather than Params @@ -836,43 +734,73 @@ class RequestsAdmin( BaseController, Use i = i + 1 else: break - message = "The new sequencer configuration named '%s' with %s states has been created" % ( request_type.name, i ) + message = "The new sequencer configuration named (%s) with %s states has been created" % ( request_type.name, i ) return request_type, message - def __delete_request_type( self, trans, **kwd ): + @web.expose + @web.require_admin + def view_request_type( self, trans, **kwd ): + request_type_id = kwd.get( 'id', None ) + try: + request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) ) + except: + return invalid_id_redirect( trans, 'requests_admin', request_type_id, action='browse_request_types' ) + forms = self.get_all_forms( trans ) + rename_dataset_select_field = self.__build_rename_dataset_select_field( trans, request_type ) + return trans.fill_template( '/admin/requests/view_request_type.mako', + request_type=request_type, + forms=forms, + rename_dataset_select_field=rename_dataset_select_field ) + @web.expose + @web.require_admin + def view_form_definition( self, trans, **kwd ): + form_definition_id = kwd.get( 'id', None ) + try: + form_definition = trans.sa_session.query( trans.model.FormDefinition ).get( trans.security.decode_id( form_definition_id ) ) + except: + return invalid_id_redirect( trans, 'requests_admin', form_definition_id, action='browse_request_types' ) + return trans.fill_template( '/admin/forms/show_form_read_only.mako', + form_definition=form_definition ) + @web.expose + @web.require_admin + def delete_request_type( self, trans, **kwd ): rt_id = kwd.get( 'id', '' ) rt_id_list = util.listify( rt_id ) for rt_id in rt_id_list: try: request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( rt_id ) ) except: - return invalid_id_redirect( trans, 'requests_admin', rt_id, action='manage_request_types' ) + return invalid_id_redirect( trans, 'requests_admin', rt_id, action='browse_request_types' ) request_type.deleted = True trans.sa_session.add( request_type ) trans.sa_session.flush() status = 'done' message = '%i sequencer configurations has been deleted' % len( rt_id_list ) return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='manage_request_types', + action='browse_request_types', message=message, status='done' ) ) - def __undelete_request_type( self, trans, **kwd ): + @web.expose + @web.require_admin + def undelete_request_type( self, trans, **kwd ): rt_id = kwd.get( 'id', '' ) rt_id_list = util.listify( rt_id ) for rt_id in rt_id_list: try: request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( rt_id ) ) except: - return invalid_id_redirect( trans, 'requests_admin', rt_id, action='manage_request_types' ) + return invalid_id_redirect( trans, 'requests_admin', rt_id, action='browse_request_types' ) request_type.deleted = False trans.sa_session.add( request_type ) trans.sa_session.flush() status = 'done' message = '%i sequencer configurations have been undeleted' % len( rt_id_list ) return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='manage_request_types', + action='browse_request_types', message=message, status=status ) ) - def __show_request_type_permissions( self, trans, **kwd ): + @web.expose + @web.require_admin + def request_type_permissions( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -880,7 +808,7 @@ class RequestsAdmin( BaseController, Use try: request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) ) except: - return invalid_id_redirect( trans, 'requests_admin', request_type_id, action='manage_request_types' ) + return invalid_id_redirect( trans, 'requests_admin', request_type_id, action='browse_request_types' ) roles = trans.sa_session.query( trans.model.Role ) \ .filter( trans.model.Role.table.c.deleted==False ) \ .order_by( trans.model.Role.table.c.name ) @@ -897,3 +825,30 @@ class RequestsAdmin( BaseController, Use roles=roles, status=status, message=message ) + # ===== Methods for building SelectFields used on various admin_requests forms + def __build_sample_id_select_field( self, request, selected_value ): + return build_select_field( trans, request.samples, 'name', 'sample_id', selected_value=selected_value, refresh_on_change=False ) + def __build_rename_dataset_select_field( self, trans, request_type=None ): + if request_type: + selected_value = request_type.datatx_info.get( 'rename_dataset', trans.model.RequestType.rename_dataset_options.NO ) + else: + selected_value = trans.model.RequestType.rename_dataset_options.NO + return build_select_field( trans, + objs=[ v for k, v in trans.model.RequestType.rename_dataset_options.items() ], + label_attr='self', + select_field_name='rename_dataset', + selected_value=selected_value, + refresh_on_change=False ) +# ===== Methods for building SelectFields used on various admin_requests forms - used outside this controller ===== +def build_rename_datasets_for_sample_select_field( trans, sample_dataset, selected_value='none' ): + options = [] + for option_index, option in enumerate( sample_dataset.file_path.split( os.sep )[ :-1 ] ): + option = option.strip() + if option: + options.append( option ) + return build_select_field( trans, + objs=options, + label_attr='self', + select_field_name='rename_datasets_for_sample_%s' % trans.security.encode_id( sample_dataset.id ), + selected_value=selected_value, + refresh_on_change=False ) --- a/templates/admin/requests/view_request_type.mako +++ b/templates/admin/requests/view_request_type.mako @@ -64,7 +64,7 @@ </div><div class="form-row"><label>Add experiment name and the sample name to the dataset name?</label> - ${rename_dataset_selectbox.get_html()} + ${rename_dataset_select_field.get_html()} <div class="toolParamHelp" style="clear: both;"> The datasets are renamed by prepending the experiment name and the sample name to the dataset name. <br/>This makes sure that dataset names remain unique in Galaxy even when they have the --- a/templates/admin/requests/request_type_permissions.mako +++ b/templates/admin/requests/request_type_permissions.mako @@ -32,7 +32,7 @@ <div class="toolForm"><div class="toolFormTitle">Manage permissions on "${request_type.name}"</div><div class="toolFormBody"> - <form name="request_type_permissions" id="request_type_permissions" action="${h.url_for( controller='requests_admin', action='manage_request_types', operation="permissions", id=trans.security.encode_id( request_type.id ) )}" method="post"> + <form name="request_type_permissions" id="request_type_permissions" action="${h.url_for( controller='requests_admin', action='request_type_permissions', id=trans.security.encode_id( request_type.id ) )}" method="post"><div class="form-row"><% obj_name = request_type.name --- a/templates/admin/requests/dataset.mako +++ b/templates/admin/requests/dataset.mako @@ -19,51 +19,51 @@ <div class="toolForm"><div class="toolFormTitle">Dataset Information</div><div class="toolFormBody"> - <div class="form-row"> - <label>Name:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.name} - </div> - <div style="clear: both"></div> + <div class="form-row"> + <label>Name:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + ${sample_dataset.name} </div> - <div class="form-row"> - <label>File on the Sequencer:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.file_path} - </div> - <div style="clear: both"></div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>File on the Sequencer:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + ${sample_dataset.file_path} </div> - <div class="form-row"> - <label>Size:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.size} - </div> - <div style="clear: both"></div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Size:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + ${sample_dataset.size} </div> - <div class="form-row"> - <label>Created on:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.create_time} - </div> - <div style="clear: both"></div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Created on:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + ${sample_dataset.create_time} </div> - <div class="form-row"> - <label>Updated on:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.update_time} - </div> - <div style="clear: both"></div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Updated on:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + ${sample_dataset.update_time} </div> - <div class="form-row"> - <label>Transfer status:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.status} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Transfer status:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + ${sample_dataset.status} + %if sample_dataset.status == sample.transfer_status.ERROR: <br/> - %if sample_dataset.status == sample.transfer_status.ERROR: - ${sample_dataset.error_msg} - %endif - </div> - <div style="clear: both"></div> + ${sample_dataset.error_msg} + %endif </div> + <div style="clear: both"></div> + </div></div></div>

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galaxy-dist commit fbc4d5d45649: Use threads in blastn wrapper
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285670387 -3600 # Node ID fbc4d5d45649043ac57270cac5741ec153f6de66 # Parent 87a75fed920e0509dc5270000edf3758d97bd2f1 Use threads in blastn wrapper --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -9,6 +9,7 @@ -dust $adv_opts.filter_query -out $output1 -outfmt $out_format + -num_threads 8 </command><inputs><param name="query" type="data" format="fasta" label="Query sequence(s)"/> @@ -55,7 +56,7 @@ </conditional></inputs><outputs> -  + <data name="output1" format="tabular" label="${blast_type.value_label} on ${database.value_label}"><change_format><when input="out_format" value="0" format="txt"/>

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galaxy-dist commit 63a43c1d230a: Update comments in blastdb.loc.sample for intended usage
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285084879 -3600 # Node ID 63a43c1d230a6b42dda6d4f8d225d2620bdb9a8c # Parent 054e0b2c15d412c3b1d99cbbd7ccb7a653b2a637 Update comments in blastdb.loc.sample for intended usage --- a/tool-data/blastdb.loc.sample +++ b/tool-data/blastdb.loc.sample @@ -1,12 +1,11 @@ -#This is a sample file distributed with Galaxy that is used by some -#short read tools. The blastdb.loc file has this format: +#This is a sample file distributed with Galaxy that is used to define a +#list of nucelotide BLAST databases, using two columns tab separated: # -#<database><build_date><path to base name> +#<database caption><path to base name> # -#where a single space separates the first two and a tab the last two. +#The captions typically contain spaces and might end with the build date. #It is important that the actual database name does not have a space in it, #and that the first tab that appears in the line is right before the path. -#The <build_date> can look any way you want. # #So, for example, if your database is nt and the path to your base name #is /depot/data2/galaxy/blastdb/nt/nt.chunk, then the blastdb.loc entry

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galaxy-dist commit 45fdae2622ad: trackster: Fix refactor breaking bam tracks. Only show draggable handle in editor mode. Update jQuery UI to 1.8.5 and add slider widget
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1286911481 14400 # Node ID 45fdae2622ad9f989f6f15e6b081a268430683f3 # Parent 772d6986c1afc7e78a9543fb5445e4d327df7df1 trackster: Fix refactor breaking bam tracks. Only show draggable handle in editor mode. 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m=this;this.namespace=l;this.widgetName=k;this.widgetEventPrefix=c[l][k].eventPrefix||k;this.widgetBaseClass=l+"-"+k;this.options=c.extend({},c.widget.defaults,c[l][k].defaults,c.metadata&&c.metadata.get(o)[k],n);this.element=c(o).bin d("setData."+k,function(q,p,r){if(q.target==o){return m._setData(p,r)}}).bind("getData."+k,function(q,p){if(q.target==o){return m._getData(p)}}).bind("remove",function(){return m.destroy()})};c[l][k].prototype=c.extend({},c.widget.prototype,j);c[l][k].getterSetter="option"};c.widget.prototype={_init:function(){},destroy:function(){this.element.removeData(this.widgetName).removeClass(this.widgetBaseClass+"-disabled "+this.namespace+"-state-disabled").removeAttr("aria-disabled")},option:function(l,m){var k=l,j=this;if(typeof l=="string"){if(m===undefined){return this._getData(l)}k={};k[l]=m}c.each(k,function(n,o){j._setData(n,o)})},_getData:function(j){return 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false}});if(c.browser.msie){this._mouseUnselectable=this.element.attr("unselectable");this.element.attr("unselectable","on")}this.started=false},_mouseDestroy:function(){this.element.unbind("."+this.widgetName);(c.browser.msie&&this.element.attr("unselectable",this._mouseUnselectable))},_mouseDown:function(l){l.originalEvent=l.originalEvent||{};if(l.originalE vent.mouseHandled){return}(this._mouseStarted&&this._mouseUp(l));this._mouseDownEvent=l;var k=this,m=(l.which==1),j=(typeof this.options.cancel=="string"?c(l.target).parents().add(l.target).filter(this.options.cancel).length:false);if(!m||j||!this._mouseCapture(l)){return true}this.mouseDelayMet=!this.options.delay;if(!this.mouseDelayMet){this._mouseDelayTimer=setTimeout(function(){k.mouseDelayMet=true},this.options.delay)}if(this._mouseDistanceMet(l)&&this._mouseDelayMet(l)){this._mouseStarted=(this._mouseStart(l)!==false);if(!this._mouseStarted){l.preventDefault();return true}}this._mouseMoveDelegate=function(n){return k._mouseMove(n)};this._mouseUpDelegate=function(n){return k._mouseUp(n)};c(document).bind("mousemove."+this.widgetName,this._mouseMoveDelegate).bind("mouseup."+this.widgetName,this._mouseUpDelegate);(c.browser.safari||l.preventDefault());l.originalEvent.mouseHandled=true;return true},_mouseMove:function(j){if(c.browser.msie&&!j.button){return this._mouseUp(j )}if(this._mouseStarted){this._mouseDrag(j);return j.preventDefault()}if(this._mouseDistanceMet(j)&&this._mouseDelayMet(j)){this._mouseStarted=(this._mouseStart(this._mouseDownEvent,j)!==false);(this._mouseStarted?this._mouseDrag(j):this._mouseUp(j))}return !this._mouseStarted},_mouseUp:function(j){c(document).unbind("mousemove."+this.widgetName,this._mouseMoveDelegate).unbind("mouseup."+this.widgetName,this._mouseUpDelegate);if(this._mouseStarted){this._mouseStarted=false;this._preventClickEvent=(j.target==this._mouseDownEvent.target);this._mouseStop(j)}return false},_mouseDistanceMet:function(j){return(Math.max(Math.abs(this._mouseDownEvent.pageX-j.pageX),Math.abs(this._mouseDownEvent.pageY-j.pageY))>=this.options.distance)},_mouseDelayMet:function(j){return this.mouseDelayMet},_mouseStart:function(j){},_mouseDrag:function(j){},_mouseStop:function(j){},_mouseCapture:function(j){return true}};c.ui.mouse.defaults={cancel:null,distance:1,delay:0}})(jQuery); --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +1,1 @@ -var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",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=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function() {RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.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},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,c,e,d,b){this.container=a;this.vis_id=d;this.dbkey=b;this.title=e;this.chrom=c;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this. min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.prototype,{init:function(){var c=this.container,a=this;this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview -close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){void (0)}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(d){if(d.type==="focusout"||(d.keyCode||d.which)===13||(d.keyCode||d.which)===27){if((d.keyCode||d.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<inp ut/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(d){if(d.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=d.chrom_info ;var f='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var e=a.chrom_data[i]["chrom"];f+='<option value="'+e+'">'+e+"</option>"}a.chrom_select.html(f);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-f)});this.overview_close.bind("click",function(){for(var d in a.tracks){a.tracks[d].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("dragstart",function(d){this.origin al_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX;this.enable_pan=(d.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(g){if(!this.enable_pan||this.in_reordering){return}var d=$(this);var j=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);d.scrollTop(f);this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+30,top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j){var f=Math.min(j.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(j.clientX,this.drag_origin_x)-a.container.offset().left,h=(a.high-a. low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(k){var f=Math.min(k.clientX,this.drag_origin_x),d=Math.max(k.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),j=a.low;a.low=Math.round(f/g*h)+j;a.high=Math.round(d/g*h)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack))},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(d,a,f){var c=this;var e=$.grep(c.chrom_data,function(h,j){return h.chrom===d})[0];if(e===undefined){return}if(d!==c.chrom){c.chrom=d;if(c.chrom===""){c.intro_div.show()}else{c.intro_div.hide()}c.chrom_select.val(c.chrom);c.max_high=e.len;c.reset();c.redraw(true);for(var g i n c.tracks){var b=c.tracks[g];if(b.init){b.init()}}}if(a!==undefined&&f!==undefined){c.low=Math.max(a,0);c.high=Math.min(f,c.max_high)}c.overview_viewport.find("canvas").remove();c.redraw()},go_to:function(f){var k=this,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-"),a=parseInt(g[0].replace(/,/g,"")),d=parseInt(g[1].replace(/,/g,""))}catch(c){return false}}k.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()} );delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=this.low/(this.max_high-this.max_low)*this.overview_viewport.width();var e=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width();var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,widt h:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()}});var Track=function(b,a,c){this.name=b;this.parent_element=c;this.view=a;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.container_div=$("<div />").addClass("track");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this. container_div);this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div);this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name)}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+ "</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="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.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var d=this,c=d.view;if(d.hidden){return}if(d.display_modes!==undefined){if(d.mode_div===undefined){d.mode_div=$("<div class='right-float menubutton popup' />").appendTo(d.header_div);var h=d.display_modes[0];d.mode=h;d.mode_div.text(h);var a=function(j){d.mode_div.text(j);d.mode=j;d.tile_cache.clear();d.draw()};var f={};for(var e in d.display_modes){var g=d.display _modes[e];f[g]=function(j){return function(){a(j)}}(g)}make_popupmenu(d.mode_div,f)}else{d.mode_div.hide()}}var b={};b["Set as overview"]=function(){c.overview_viewport.find("canvas").remove();d.is_overview=true;d.set_overview();for(var j in c.tracks){if(c.tracks[j]!==d){c.tracks[j].is_overview=false}}};b["Edit configuration"]=function(){var k=function(){hide_modal()};var j=function(){d.update_options(d.track_id);hide_modal()};show_modal("Configure Track",d.gen_options(d.track_id),{Cancel:k,OK:j})};b.Remove=function(){c.remove_track(d);if(c.num_tracks===0){$("#no-tracks").show()}};make_popupmenu(d.name_div,b)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;var l=$("<div style='position: relative;'></div>"),m=this.content_div.width()/f,h;this.content_div.children(":first").remove();this.content_div.append(l),this.max_height=0;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.conten t_div.width()+"_"+m+"_"+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);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,k,j,e,a,d,l,m)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){if(!c.initial_canvas){c.initial_canvas=$(tile_element).clone();var l=tile_element.get(0).getContext("2d");var j=c.initial_canvas.get(0).getContext("2d");var k=l.getImageData(0,0,l.canvas.width,l.canvas.height);j.putImageData(k,0,0);c.set_overview()}c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)},set_overview:function(){var a=this.view;a.overview_viewport.height(a.default_overview_height);a.overview_box.height(a.default_overv iew_height);if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);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($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrac k";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.height_px=12;this.container_div.addClass("reference-track");this.dummy_canvas=$("<canvas></canvas>").get(0).getContext("2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),n=e.get(0).getContext("2d"),j=f+"_"+b;if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content _div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o-this.left_offset});for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o);n.fillText(m[h],a+this.left_offset,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Line","Filled","Intensity"];this.mode="Line";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){this.prefs.max_value=c.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({s tats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();a.container_div.css("position","relative");var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"22px",left:"10px"});d.prependTo(a.container_div);e.css({position:"absolute",top:a.height_px+11+"px",left:"10px"});e.prependTo(a.container_div)})},get_dat a: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;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(p,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.mode;o.beginPath();if(data.length>1){var f=Math.ceil((data[1][0]- data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;h=data[q][1];if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(k){var a=$("<div />").addClass("form-row");var e="track_"+k+"_minval",h=$("<label></label>").attr("for",e).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),j=$("<input></input>").attr("id",e).val(b),g="track_"+k+"_maxval",d=$("<label></label>").attr("for",g).text("Max value:"),f=(this.prefs.max_value===undefined?"":this.prefs.max_value),c=$("<inp ut></input>").attr("id",g).val(f);return a.append(h).append(j).append(d).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=20;this.default_font="9px Monaco, Lucida Console, mono space";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"black",label_color:"black",show_counts:true};if(c.block_color!==undefined){this.prefs.block_color=c.block_color}if(c.label_color!==undefined){this.prefs.label_color=c.label_color}if(c.show_counts!==undefined){this.prefs.show_counts=c.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b .data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(true){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y[0]&&e<y[1]){p=false; break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]=[]}this.s_e_by_tile[a][v].push([e,f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(n,o,f,m,b,d,k,e,h){n.textAlign="center";var j=Math.round(o/2);if((this.mode==="Pack"||this.mode==="Auto")&&d!==undefined&&o>PX_PER_CHAR){n.fillStyle=this.prefs.block_color;n.fillRect(k,h+1,e,9);n.fillStyle="#eee";for(var g=0,l=d.length;g<l;g++){if(b+g>=f&&b+g<=m){var a=Math.floor(Math.max(0,(b+g-f)*o));n.fillText(d[g],a+this.left_offset+j,h+9)}}}else{n.fillStyle=this.prefs.block_color;n.fillRect(k,h+4,e,3)}},draw_tile:function(ae,o,r,ar){var L=o*DENSITY*ae,ak=(o+1)*DENSITY*ae,K=ak-L;var al=(!this.initial_canvas?"initial":L+"_"+ak);var G=this.data_cache.get(al);var e;if(G===undefined||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[L,ak]]=true;this.get_data(L,ak);return}var a=Math.ceil(K*ar),S=$("<canvas class='tile'></canvas>"),ag=this.prefs.label_color,h=thi s.prefs.block_color,q=this.mode,v=25,ac=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(G.extra_info==="no_detail")),W=this.left_offset,aq,B,at;if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(q==="Dense"){B=v;at=10}else{at=(ac?this.vertical_nodetail_px:this.vertical_detail_px);var w=(ar<0.0001?1/view.zoom_res:ar);B=this.incremental_slots(w,G.data,ac,q)*at+v;aq=this.inc_slots[w]}}S.css({position:"absolute",top:0,left:(L-this.view.low)*ar-W});S.get(0).width=a+W;S.get(0).height=B;r.parent().css("height",Math.max(this.height_px,B)+"px");var H=S.get(0).getContext("2d");H.fillStyle=h;H.font=this.default_font;H.textAlign="right";if(G.dataset_type=="summary_tree"){var R,O=55,aj=255-O,n=aj*2/3,Y=G.data,J=G.max,p=G.avg,b=Math.ceil(G.delta*ar);for(var an=0,F=Y.length;an<F;an++){var aa=Math.floor((Y[an][0]-L)*ar);var Z=Y[an][1];if(!Z){continue}R=Math.floor(aj-(Z/J)*aj);H.fillStyle="rgb("+R+","+R+","+R+")";H.fillRect(aa+W,0,b,this.summary_draw_height);if (this.prefs.show_counts&&H.measureText(Z).width<b){if(R>n){H.fillStyle="black"}else{H.fillStyle="#ddd"}H.textAlign="center";H.fillText(Z,aa+W+(b/2),12)}}e="Summary";r.append(S);return S}if(G.message){S.css({border:"solid red","border-width":"2px 2px 2px 0px"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+W,at)}var ap=G.data;var am=0;for(var an=0,F=ap.length;an<F;an++){var T=ap[an],Q=T[0],ao=T[1],ab=T[2],M=T[3];if(ao<=ak&&ab>=L){var ad=Math.floor(Math.max(0,(ao-L)*ar)),I=Math.ceil(Math.min(a,Math.max(0,(ab-L)*ar))),X=(q==="Dense"?1:(1+aq[Q]))*at;if(G.dataset_type==="bai"){H.fillStyle=h;if(T[4] instanceof Array){var C=Math.floor(Math.max(0,(T[4][0]-L)*ar)),P=Math.ceil(Math.min(a,Math.max(0,(T[4][1]-L)*ar))),A=Math.floor(Math.max(0,(T[5][0]-L)*ar)),u=Math.ceil(Math.min(a,Math.max(0,(T[5][1]-L)*ar)));if(T[4][1]>=L&&T[4][0]<=ak){this.rect_or_text(H,ar,L,ak,T[4][0],T[4][2],C+W,P-C,X)}if(T[5][1]>=L&&T[5][0]<=ak){this.rect_or_text(H,ar,L,ak,T[5][0],T[5][2],A+W,u-A,X )}if(A>P){H.fillStyle="#999";H.fillRect(P+W,X+5,A-P,1)}}else{H.fillStyle=h;this.rect_or_text(H,ar,L,ak,ao,M,ad+W,I-ad,X)}if(q!=="Dense"&&!ac&&ao>L){H.fillStyle=this.prefs.label_color;if(o===0&&ad-H.measureText(M).width<0){H.textAlign="left";H.fillText(Q,I+2+W,X+8)}else{H.textAlign="right";H.fillText(Q,ad-2+W,X+8)}H.fillStyle=h}}else{if(G.dataset_type==="interval_index"){if(ac){H.fillStyle=h;H.fillRect(ad+W,X+5,I-ad,1)}else{var E=T[4],V=T[5],af=T[6],g=T[7];var D,ah,N=null,au=null;if(V&&af){N=Math.floor(Math.max(0,(V-L)*ar));au=Math.ceil(Math.min(a,Math.max(0,(af-L)*ar)))}if(q!=="Dense"&&M!==undefined&&ao>L){H.fillStyle=ag;if(o===0&&ad-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+W,X+8)}else{H.textAlign="right";H.fillText(M,ad-2+W,X+8)}H.fillStyle=h}if(g){if(E){if(E=="+"){H.fillStyle=RIGHT_STRAND}else{if(E=="-"){H.fillStyle=LEFT_STRAND}}H.fillRect(ad+W,X,I-ad,10);H.fillStyle=h}for(var al=0,f=g.length;al<f;al++){var t=g[al],d=Math.floor(Math.max(0,(t[0]-L)*ar)) ,U=Math.ceil(Math.min(a,Math.max((t[1]-L)*ar)));if(d>U){continue}D=5;ah=3;H.fillRect(d+W,X+ah,U-d,D);if(N!==undefined&&!(d>au||U<N)){D=9;ah=1;var ai=Math.max(d,N),z=Math.min(U,au);H.fillRect(ai+W,X+ah,z-ai,D)}}}else{D=9;ah=1;H.fillRect(ad+W,X+ah,I-ad,D);if(T.strand){if(T.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(T.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}H.fillRect(ad+W,X,I-ad,10);H.fillStyle=h}}}}else{if(G.dataset_type==="vcf"){if(ac){H.fillStyle=h;H.fillRect(ad+W,X+5,I-ad,1)}else{var s=T[4],m=T[5],c=T[6];D=9;ah=1;H.fillRect(ad+W,X,I-ad,D);if(q!=="Dense"&&M!==undefined&&ao>L){H.fillStyle=ag;if(o===0&&ad-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+W,X+8)}else{H.textAlign="right";H.fillText(M,ad-2+W,X+8)}H.fillStyle=h}var l=s+" / "+m;if(ao>L&&H.measureText(l).width<(I-ad)){H.fillStyle="white";H.textAlign="center";H.fillText(l,W+ad+(I-ad)/2,X+8);H.fillStyle=h}}}}}am++}}r.append(S);return S},gen_options:function(j){var a=$("<div />").addClass("form-ro w");var e="track_"+j+"_block_color",l=$("<label />").attr("for",e).text("Block color:"),m=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),k="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(l).append(m).append(g).append(h).append(d)},update_options:function(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_label_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs.show_counts=a;this.t ile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,c){FeatureTrack.call(this,d,b,a,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); +var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",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=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function() {RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.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},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,c,e,d,b){this.container=a;this.vis_id=d;this.dbkey=b;this.title=e;this.chrom=c;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this. min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.prototype,{init:function(){var c=this.container,a=this;this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview -close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){void (0)}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(d){if(d.type==="focusout"||(d.keyCode||d.which)===13||(d.keyCode||d.which)===27){if((d.keyCode||d.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<inp ut/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(d){if(d.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=d.chrom_info ;var f='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var e=a.chrom_data[i]["chrom"];f+='<option value="'+e+'">'+e+"</option>"}a.chrom_select.html(f);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-f)});this.overview_close.bind("click",function(){for(var d in a.tracks){a.tracks[d].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("dragstart",function(d){this.origin al_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX;this.enable_pan=(d.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(g){if(!this.enable_pan||this.in_reordering){return}var d=$(this);var j=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);d.scrollTop(f);this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+30,top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j){var f=Math.min(j.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(j.clientX,this.drag_origin_x)-a.container.offset().left,h=(a.high-a. low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(k){var f=Math.min(k.clientX,this.drag_origin_x),d=Math.max(k.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),j=a.low;a.low=Math.round(f/g*h)+j;a.high=Math.round(d/g*h)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack))},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(d,a,f){var c=this;var e=$.grep(c.chrom_data,function(h,j){return h.chrom===d})[0];if(e===undefined){return}if(d!==c.chrom){c.chrom=d;if(c.chrom===""){c.intro_div.show()}else{c.intro_div.hide()}c.chrom_select.val(c.chrom);c.max_high=e.len;c.reset();c.redraw(true);for(var g i n c.tracks){var b=c.tracks[g];if(b.init){b.init()}}}if(a!==undefined&&f!==undefined){c.low=Math.max(a,0);c.high=Math.min(f,c.max_high)}c.overview_viewport.find("canvas").remove();c.redraw()},go_to:function(f){var k=this,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-"),a=parseInt(g[0].replace(/,/g,"")),d=parseInt(g[1].replace(/,/g,""))}catch(c){return false}}k.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()} );delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=this.low/(this.max_high-this.max_low)*this.overview_viewport.width();var e=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width();var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,widt h:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()}});var Track=function(b,a,c){this.name=b;this.parent_element=c;this.view=a;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.container_div=$("<div />").addClass("track");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this. container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name)}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Erro r","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="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.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var d=this,c=d.view;if(d.hidden){return}if(d.display_modes!==undefined){if(d.mode_div===undefined){d.mode_div=$("<div class='right-float menubutton popup' />").appendTo(d.header_div);var h=d.display_modes[0];d.mode=h;d.mode_div.text(h);var a=function(j){d.mode_div.text(j);d.mode=j;d.tile_cache.clear();d.draw()};var f={};for(var e in d.display_m odes){var g=d.display_modes[e];f[g]=function(j){return function(){a(j)}}(g)}make_popupmenu(d.mode_div,f)}else{d.mode_div.hide()}}var b={};b["Set as overview"]=function(){c.overview_viewport.find("canvas").remove();d.is_overview=true;d.set_overview();for(var j in c.tracks){if(c.tracks[j]!==d){c.tracks[j].is_overview=false}}};b["Edit configuration"]=function(){var k=function(){hide_modal()};var j=function(){d.update_options(d.track_id);hide_modal()};show_modal("Configure Track",d.gen_options(d.track_id),{Cancel:k,OK:j})};b.Remove=function(){c.remove_track(d);if(c.num_tracks===0){$("#no-tracks").show()}};make_popupmenu(d.name_div,b)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;var l=$("<div style='position: relative;'></div>"),m=this.content_div.width()/f,h;this.content_div.children(":first").remove();this.content_div.append(l),this.max_height=0;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d) <e){var k=this.content_div.width()+"_"+m+"_"+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);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,k,j,e,a,d,l,m)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){if(!c.initial_canvas){c.initial_canvas=$(tile_element).clone();var l=tile_element.get(0).getContext("2d");var j=c.initial_canvas.get(0).getContext("2d");var k=l.getImageData(0,0,l.canvas.width,l.canvas.height);j.putImageData(k,0,0);c.set_overview()}c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)},set_overview:function(){var a=this.view;a.overview_viewport.height(a.default_overview_height);a.overview_box.h eight(a.default_overview_height);if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);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($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.trac k_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.height_px=12;this.container_div.addClass("reference-track");this.dummy_canvas=$("<canvas></canvas>").get(0).getContext("2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),n=e.get(0).getContext("2d"),j=f+"_"+b;if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m ===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o-this.left_offset});for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o);n.fillText(m[h],a+this.left_offset,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Line","Filled","Intensity"];this.mode="Line";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){this.prefs.max_value=c.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefi ned;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();a.container_div.css("position","relative");var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"22px",left:"10px"});d.prependTo(a.container_div);e.css({position:"absolute",top:a.height_px+11+"px",left:"10px"});e.prependTo(a.cont ainer_div)})},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;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(p,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.mode;o.beginPath();if(data.length>1){var f=M ath.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;h=data[q][1];if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(k){var a=$("<div />").addClass("form-row");var e="track_"+k+"_minval",h=$("<label></label>").attr("for",e).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),j=$("<input></input>").attr("id",e).val(b),g="track_"+k+"_maxval",d=$("<label></label>").attr("for",g).text("Max value:"),f=(this.prefs.max_value===undefined?"":this.prefs .max_value),c=$("<input></input>").attr("id",g).val(f);return a.append(h).append(j).append(d).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=20;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"black",label_color:"black",show_counts:true};if(c.block_color!==undefined){this.prefs.block_color=c.block_color}if(c.label_color!==undefined){this.prefs.label_color=c.label_color}if(c.show_counts!==undefined){this.prefs.show_counts=c.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_ca che.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(true){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y [0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]=[]}this.s_e_by_tile[a][v].push([e,f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(n,o,f,m,b,d,k,e,h){n.textAlign="center";var j=Math.round(o/2);if((this.mode==="Pack"||this.mode==="Auto")&&d!==undefined&&o>PX_PER_CHAR){n.fillStyle=this.prefs.block_color;n.fillRect(k,h+1,e,9);n.fillStyle="#eee";for(var g=0,l=d.length;g<l;g++){if(b+g>=f&&b+g<=m){var a=Math.floor(Math.max(0,(b+g-f)*o));n.fillText(d[g],a+this.left_offset+j,h+9)}}}else{n.fillStyle=this.prefs.block_color;n.fillRect(k,h+4,e,3)}},draw_tile:function(ae,o,r,ar){var L=o*DENSITY*ae,ak=(o+1)*DENSITY*ae,K=ak-L;var al=(!this.initial_canvas?"initial":L+"_"+ak);var G=this.data_cache.get(al);var e;if(G===undefined||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[L,ak]]=true;this.get_data(L,ak);return}var a=Math.ceil(K*ar),S=$("<canvas class='tile'></canvas>"),ag=this.pr efs.label_color,h=this.prefs.block_color,q=this.mode,v=25,ac=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(G.extra_info==="no_detail")),W=this.left_offset,aq,B,at;if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(q==="Dense"){B=v;at=10}else{at=(ac?this.vertical_nodetail_px:this.vertical_detail_px);var w=(ar<0.0001?1/view.zoom_res:ar);B=this.incremental_slots(w,G.data,ac,q)*at+v;aq=this.inc_slots[w]}}S.css({position:"absolute",top:0,left:(L-this.view.low)*ar-W});S.get(0).width=a+W;S.get(0).height=B;r.parent().css("height",Math.max(this.height_px,B)+"px");var H=S.get(0).getContext("2d");H.fillStyle=h;H.font=this.default_font;H.textAlign="right";if(G.dataset_type=="summary_tree"){var R,O=55,aj=255-O,n=aj*2/3,Y=G.data,J=G.max,p=G.avg,b=Math.ceil(G.delta*ar);for(var an=0,F=Y.length;an<F;an++){var aa=Math.floor((Y[an][0]-L)*ar);var Z=Y[an][1];if(!Z){continue}R=Math.floor(aj-(Z/J)*aj);H.fillStyle="rgb("+R+","+R+","+R+")";H.fillRect(aa+W,0,b,this.su mmary_draw_height);if(this.prefs.show_counts&&H.measureText(Z).width<b){if(R>n){H.fillStyle="black"}else{H.fillStyle="#ddd"}H.textAlign="center";H.fillText(Z,aa+W+(b/2),12)}}e="Summary";r.append(S);return S}if(G.message){S.css({border:"solid red","border-width":"2px 2px 2px 0px"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+W,at)}var ap=G.data;var am=0;for(var an=0,F=ap.length;an<F;an++){var T=ap[an],Q=T[0],ao=T[1],ab=T[2],M=T[3];if(ao<=ak&&ab>=L){var ad=Math.floor(Math.max(0,(ao-L)*ar)),I=Math.ceil(Math.min(a,Math.max(0,(ab-L)*ar))),X=(q==="Dense"?1:(1+aq[Q]))*at;if(G.dataset_type==="bai"){H.fillStyle=h;if(T[4] instanceof Array){var C=Math.floor(Math.max(0,(T[4][0]-L)*ar)),P=Math.ceil(Math.min(a,Math.max(0,(T[4][1]-L)*ar))),A=Math.floor(Math.max(0,(T[5][0]-L)*ar)),u=Math.ceil(Math.min(a,Math.max(0,(T[5][1]-L)*ar)));if(T[4][1]>=L&&T[4][0]<=ak){this.rect_or_text(H,ar,L,ak,T[4][0],T[4][2],C+W,P-C,X)}if(T[5][1]>=L&&T[5][0]<=ak){this.rect_or_text(H,ar,L,ak,T[5] [0],T[5][2],A+W,u-A,X)}if(A>P){H.fillStyle="#999";H.fillRect(P+W,X+5,A-P,1)}}else{H.fillStyle=h;this.rect_or_text(H,ar,L,ak,ao,M,ad+W,I-ad,X)}if(q!=="Dense"&&!ac&&ao>L){H.fillStyle=this.prefs.label_color;if(o===0&&ad-H.measureText(M).width<0){H.textAlign="left";H.fillText(Q,I+2+W,X+8)}else{H.textAlign="right";H.fillText(Q,ad-2+W,X+8)}H.fillStyle=h}}else{if(G.dataset_type==="interval_index"){if(ac){H.fillStyle=h;H.fillRect(ad+W,X+5,I-ad,1)}else{var E=T[4],V=T[5],af=T[6],g=T[7];var D,ah,N=null,au=null;if(V&&af){N=Math.floor(Math.max(0,(V-L)*ar));au=Math.ceil(Math.min(a,Math.max(0,(af-L)*ar)))}if(q!=="Dense"&&M!==undefined&&ao>L){H.fillStyle=ag;if(o===0&&ad-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+W,X+8)}else{H.textAlign="right";H.fillText(M,ad-2+W,X+8)}H.fillStyle=h}if(g){if(E){if(E=="+"){H.fillStyle=RIGHT_STRAND}else{if(E=="-"){H.fillStyle=LEFT_STRAND}}H.fillRect(ad+W,X,I-ad,10);H.fillStyle=h}for(var al=0,f=g.length;al<f;al++){var t=g[al],d=Math.floor(Mat h.max(0,(t[0]-L)*ar)),U=Math.ceil(Math.min(a,Math.max((t[1]-L)*ar)));if(d>U){continue}D=5;ah=3;H.fillRect(d+W,X+ah,U-d,D);if(N!==undefined&&!(d>au||U<N)){D=9;ah=1;var ai=Math.max(d,N),z=Math.min(U,au);H.fillRect(ai+W,X+ah,z-ai,D)}}}else{D=9;ah=1;H.fillRect(ad+W,X+ah,I-ad,D);if(T.strand){if(T.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(T.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}H.fillRect(ad+W,X,I-ad,10);H.fillStyle=h}}}}else{if(G.dataset_type==="vcf"){if(ac){H.fillStyle=h;H.fillRect(ad+W,X+5,I-ad,1)}else{var s=T[4],m=T[5],c=T[6];D=9;ah=1;H.fillRect(ad+W,X,I-ad,D);if(q!=="Dense"&&M!==undefined&&ao>L){H.fillStyle=ag;if(o===0&&ad-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+W,X+8)}else{H.textAlign="right";H.fillText(M,ad-2+W,X+8)}H.fillStyle=h}var l=s+" / "+m;if(ao>L&&H.measureText(l).width<(I-ad)){H.fillStyle="white";H.textAlign="center";H.fillText(l,W+ad+(I-ad)/2,X+8);H.fillStyle=h}}}}}am++}}r.append(S);return S},gen_options:function(j){var a=$("<div / >").addClass("form-row");var e="track_"+j+"_block_color",l=$("<label />").attr("for",e).text("Block color:"),m=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),k="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(l).append(m).append(g).append(h).append(d)},update_options:function(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_label_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs .show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,c){FeatureTrack.call(this,d,b,a,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -452,7 +452,7 @@ var Track = function (name, view, parent this.container_div = $("<div />").addClass('track') if (!this.hidden) { this.header_div = $("<div class='track-header' />").appendTo(this.container_div); - this.drag_div = $("<div class='draghandle' />").appendTo(this.header_div); + if (this.view.editor) { this.drag_div = $("<div class='draghandle' />").appendTo(this.header_div); } this.name_div = $("<div class='menubutton popup' />").appendTo(this.header_div); this.name_div.text(this.name); } --- a/static/scripts/packed/ui.sortable.js +++ /dev/null @@ -1,1 +0,0 @@ -(function(a){a.widget("ui.sortable",a.extend({},a.ui.mouse,{_init:function(){var b=this.options;this.containerCache={};this.element.addClass("ui-sortable");this.refresh();this.floating=this.items.length?(/left|right/).test(this.items[0].item.css("float")):false;this.offset=this.element.offset();this._mouseInit()},destroy:function(){this.element.removeClass("ui-sortable ui-sortable-disabled").removeData("sortable").unbind(".sortable");this._mouseDestroy();for(var b=this.items.length-1;b>=0;b--){this.items[b].item.removeData("sortable-item")}},_mouseCapture:function(e,f){if(this.reverting){return false}if(this.options.disabled||this.options.type=="static"){return false}this._refreshItems(e);var d=null,c=this,b=a(e.target).parents().each(function(){if(a.data(this,"sortable-item")==c){d=a(this);return false}});if(a.data(e.target,"sortable-item")==c){d=a(e.target)}if(!d){return false}if(this.options.handle&&!f){var g=false;a(this.options.handle,d).find("*").andSelf().each(functio n(){if(this==e.target){g=true}});if(!g){return false}}this.currentItem=d;this._removeCurrentsFromItems();return true},_mouseStart:function(e,f,b){var g=this.options,c=this;this.currentContainer=this;this.refreshPositions();this.helper=this._createHelper(e);this._cacheHelperProportions();this._cacheMargins();this.scrollParent=this.helper.scrollParent();this.offset=this.currentItem.offset();this.offset={top:this.offset.top-this.margins.top,left:this.offset.left-this.margins.left};this.helper.css("position","absolute");this.cssPosition=this.helper.css("position");a.extend(this.offset,{click:{left:e.pageX-this.offset.left,top:e.pageY-this.offset.top},parent:this._getParentOffset(),relative:this._getRelativeOffset()});this.originalPosition=this._generatePosition(e);this.originalPageX=e.pageX;this.originalPageY=e.pageY;if(g.cursorAt){this._adjustOffsetFromHelper(g.cursorAt)}this.domPosition={prev:this.currentItem.prev()[0],parent:this.currentItem.parent()[0]};if(this.helper[0]!=th is.currentItem[0]){this.currentItem.hide()}this._createPlaceholder();if(g.containment){this._setContainment()}if(g.cursor){if(a("body").css("cursor")){this._storedCursor=a("body").css("cursor")}a("body").css("cursor",g.cursor)}if(g.opacity){if(this.helper.css("opacity")){this._storedOpacity=this.helper.css("opacity")}this.helper.css("opacity",g.opacity)}if(g.zIndex){if(this.helper.css("zIndex")){this._storedZIndex=this.helper.css("zIndex")}this.helper.css("zIndex",g.zIndex)}if(this.scrollParent[0]!=document&&this.scrollParent[0].tagName!="HTML"){this.overflowOffset=this.scrollParent.offset()}this._trigger("start",e,this._uiHash());if(!this._preserveHelperProportions){this._cacheHelperProportions()}if(!b){for(var d=this.containers.length-1;d>=0;d--){this.containers[d]._trigger("activate",e,c._uiHash(this))}}if(a.ui.ddmanager){a.ui.ddmanager.current=this}if(a.ui.ddmanager&&!g.dropBehaviour){a.ui.ddmanager.prepareOffsets(this,e)}this.dragging=true;this.helper.addClass("ui-sorta ble-helper");this._mouseDrag(e);return true},_mouseDrag:function(f){this.position=this._generatePosition(f);this.positionAbs=this._convertPositionTo("absolute");if(!this.lastPositionAbs){this.lastPositionAbs=this.positionAbs}if(this.options.scroll){var g=this.options,b=false;if(this.scrollParent[0]!=document&&this.scrollParent[0].tagName!="HTML"){if((this.overflowOffset.top+this.scrollParent[0].offsetHeight)-f.pageY<g.scrollSensitivity){this.scrollParent[0].scrollTop=b=this.scrollParent[0].scrollTop+g.scrollSpeed}else{if(f.pageY-this.overflowOffset.top<g.scrollSensitivity){this.scrollParent[0].scrollTop=b=this.scrollParent[0].scrollTop-g.scrollSpeed}}if((this.overflowOffset.left+this.scrollParent[0].offsetWidth)-f.pageX<g.scrollSensitivity){this.scrollParent[0].scrollLeft=b=this.scrollParent[0].scrollLeft+g.scrollSpeed}else{if(f.pageX-this.overflowOffset.left<g.scrollSensitivity){this.scrollParent[0].scrollLeft=b=this.scrollParent[0].scrollLeft-g.scrollSpeed}}}else{if(f.page Y-a(document).scrollTop()<g.scrollSensitivity){b=a(document).scrollTop(a(document).scrollTop()-g.scrollSpeed)}else{if(a(window).height()-(f.pageY-a(document).scrollTop())<g.scrollSensitivity){b=a(document).scrollTop(a(document).scrollTop()+g.scrollSpeed)}}if(f.pageX-a(document).scrollLeft()<g.scrollSensitivity){b=a(document).scrollLeft(a(document).scrollLeft()-g.scrollSpeed)}else{if(a(window).width()-(f.pageX-a(document).scrollLeft())<g.scrollSensitivity){b=a(document).scrollLeft(a(document).scrollLeft()+g.scrollSpeed)}}}if(b!==false&&a.ui.ddmanager&&!g.dropBehaviour){a.ui.ddmanager.prepareOffsets(this,f)}}this.positionAbs=this._convertPositionTo("absolute");if(!this.options.axis||this.options.axis!="y"){this.helper[0].style.left=this.position.left+"px"}if(!this.options.axis||this.options.axis!="x"){this.helper[0].style.top=this.position.top+"px"}for(var d=this.items.length-1;d>=0;d--){var e=this.items[d],c=e.item[0],h=this._intersectsWithPointer(e);if(!h){continue}if(c!=thi s.currentItem[0]&&this.placeholder[h==1?"next":"prev"]()[0]!=c&&!a.ui.contains(this.placeholder[0],c)&&(this.options.type=="semi-dynamic"?!a.ui.contains(this.element[0],c):true)){this.direction=h==1?"down":"up";if(this.options.tolerance=="pointer"||this._intersectsWithSides(e)){this._rearrange(f,e)}else{break}this._trigger("change",f,this._uiHash());break}}this._contactContainers(f);if(a.ui.ddmanager){a.ui.ddmanager.drag(this,f)}this._trigger("sort",f,this._uiHash());this.lastPositionAbs=this.positionAbs;return false},_mouseStop:function(c,d){if(!c){return}if(a.ui.ddmanager&&!this.options.dropBehaviour){a.ui.ddmanager.drop(this,c)}if(this.options.revert){var b=this;var e=b.placeholder.offset();b.reverting=true;a(this.helper).animate({left:e.left-this.offset.parent.left-b.margins.left+(this.offsetParent[0]==document.body?0:this.offsetParent[0].scrollLeft),top:e.top-this.offset.parent.top-b.margins.top+(this.offsetParent[0]==document.body?0:this.offsetParent[0].scrollTop)},par seInt(this.options.revert,10)||500,function(){b._clear(c)})}else{this._clear(c,d)}return false},cancel:function(){var b=this;if(this.dragging){this._mouseUp();if(this.options.helper=="original"){this.currentItem.css(this._storedCSS).removeClass("ui-sortable-helper")}else{this.currentItem.show()}for(var c=this.containers.length-1;c>=0;c--){this.containers[c]._trigger("deactivate",null,b._uiHash(this));if(this.containers[c].containerCache.over){this.containers[c]._trigger("out",null,b._uiHash(this));this.containers[c].containerCache.over=0}}}if(this.placeholder[0].parentNode){this.placeholder[0].parentNode.removeChild(this.placeholder[0])}if(this.options.helper!="original"&&this.helper&&this.helper[0].parentNode){this.helper.remove()}a.extend(this,{helper:null,dragging:false,reverting:false,_noFinalSort:null});if(this.domPosition.prev){a(this.domPosition.prev).after(this.currentItem)}else{a(this.domPosition.parent).prepend(this.currentItem)}return true},serialize:function(d){v ar b=this._getItemsAsjQuery(d&&d.connected);var c=[];d=d||{};a(b).each(function(){var e=(a(d.item||this).attr(d.attribute||"id")||"").match(d.expression||(/(.+)[-=_](.+)/));if(e){c.push((d.key||e[1]+"[]")+"="+(d.key&&d.expression?e[1]:e[2]))}});return c.join("&")},toArray:function(d){var b=this._getItemsAsjQuery(d&&d.connected);var c=[];d=d||{};b.each(function(){c.push(a(d.item||this).attr(d.attribute||"id")||"")});return c},_intersectsWith:function(m){var e=this.positionAbs.left,d=e+this.helperProportions.width,k=this.positionAbs.top,j=k+this.helperProportions.height;var f=m.left,c=f+m.width,n=m.top,i=n+m.height;var o=this.offset.click.top,h=this.offset.click.left;var g=(k+o)>n&&(k+o)<i&&(e+h)>f&&(e+h)<c;if(this.options.tolerance=="pointer"||this.options.forcePointerForContainers||(this.options.tolerance!="pointer"&&this.helperProportions[this.floating?"width":"height"]>m[this.floating?"width":"height"])){return g}else{return(f<e+(this.helperProportions.width/2)&&d-(this.he lperProportions.width/2)<c&&n<k+(this.helperProportions.height/2)&&j-(this.helperProportions.height/2)<i)}},_intersectsWithPointer:function(d){var e=a.ui.isOverAxis(this.positionAbs.top+this.offset.click.top,d.top,d.height),c=a.ui.isOverAxis(this.positionAbs.left+this.offset.click.left,d.left,d.width),g=e&&c,b=this._getDragVerticalDirection(),f=this._getDragHorizontalDirection();if(!g){return false}return this.floating?(((f&&f=="right")||b=="down")?2:1):(b&&(b=="down"?2:1))},_intersectsWithSides:function(e){var c=a.ui.isOverAxis(this.positionAbs.top+this.offset.click.top,e.top+(e.height/2),e.height),d=a.ui.isOverAxis(this.positionAbs.left+this.offset.click.left,e.left+(e.width/2),e.width),b=this._getDragVerticalDirection(),f=this._getDragHorizontalDirection();if(this.floating&&f){return((f=="right"&&d)||(f=="left"&&!d))}else{return b&&((b=="down"&&c)||(b=="up"&&!c))}},_getDragVerticalDirection:function(){var b=this.positionAbs.top-this.lastPositionAbs.top;return b!=0&&(b>0?" down":"up")},_getDragHorizontalDirection:function(){var b=this.positionAbs.left-this.lastPositionAbs.left;return b!=0&&(b>0?"right":"left")},refresh:function(b){this._refreshItems(b);this.refreshPositions()},_connectWith:function(){var b=this.options;return b.connectWith.constructor==String?[b.connectWith]:b.connectWith},_getItemsAsjQuery:function(b){var l=this;var g=[];var e=[];var h=this._connectWith();if(h&&b){for(var d=h.length-1;d>=0;d--){var k=a(h[d]);for(var c=k.length-1;c>=0;c--){var f=a.data(k[c],"sortable");if(f&&f!=this&&!f.options.disabled){e.push([a.isFunction(f.options.items)?f.options.items.call(f.element):a(f.options.items,f.element).not(".ui-sortable-helper"),f])}}}}e.push([a.isFunction(this.options.items)?this.options.items.call(this.element,null,{options:this.options,item:this.currentItem}):a(this.options.items,this.element).not(".ui-sortable-helper"),this]);for(var d=e.length-1;d>=0;d--){e[d][0].each(function(){g.push(this)})}return a(g)},_removeCurrentsF romItems:function(){var d=this.currentItem.find(":data(sortable-item)");for(var c=0;c<this.items.length;c++){for(var b=0;b<d.length;b++){if(d[b]==this.items[c].item[0]){this.items.splice(c,1)}}}},_refreshItems:function(b){this.items=[];this.containers=[this];var h=this.items;var p=this;var f=[[a.isFunction(this.options.items)?this.options.items.call(this.element[0],b,{item:this.currentItem}):a(this.options.items,this.element),this]];var l=this._connectWith();if(l){for(var e=l.length-1;e>=0;e--){var m=a(l[e]);for(var d=m.length-1;d>=0;d--){var g=a.data(m[d],"sortable");if(g&&g!=this&&!g.options.disabled){f.push([a.isFunction(g.options.items)?g.options.items.call(g.element[0],b,{item:this.currentItem}):a(g.options.items,g.element),g]);this.containers.push(g)}}}}for(var e=f.length-1;e>=0;e--){var k=f[e][1];var c=f[e][0];for(var d=0,n=c.length;d<n;d++){var o=a(c[d]);o.data("sortable-item",k);h.push({item:o,instance:k,width:0,height:0,left:0,top:0})}}},refreshPositions:function(b ){if(this.offsetParent&&this.helper){this.offset.parent=this._getParentOffset()}for(var d=this.items.length-1;d>=0;d--){var e=this.items[d];if(e.instance!=this.currentContainer&&this.currentContainer&&e.item[0]!=this.currentItem[0]){continue}var c=this.options.toleranceElement?a(this.options.toleranceElement,e.item):e.item;if(!b){e.width=c.outerWidth();e.height=c.outerHeight()}var f=c.offset();e.left=f.left;e.top=f.top}if(this.options.custom&&this.options.custom.refreshContainers){this.options.custom.refreshContainers.call(this)}else{for(var d=this.containers.length-1;d>=0;d--){var f=this.containers[d].element.offset();this.containers[d].containerCache.left=f.left;this.containers[d].containerCache.top=f.top;this.containers[d].containerCache.width=this.containers[d].element.outerWidth();this.containers[d].containerCache.height=this.containers[d].element.outerHeight()}}},_createPlaceholder:function(d){var b=d||this,e=b.options;if(!e.placeholder||e.placeholder.constructor==Stri ng){var c=e.placeholder;e.placeholder={element:function(){var f=a(document.createElement(b.currentItem[0].nodeName)).addClass(c||b.currentItem[0].className+" ui-sortable-placeholder").removeClass("ui-sortable-helper")[0];if(!c){f.style.visibility="hidden"}return f},update:function(f,g){if(c&&!e.forcePlaceholderSize){return}if(!g.height()){g.height(b.currentItem.innerHeight()-parseInt(b.currentItem.css("paddingTop")||0,10)-parseInt(b.currentItem.css("paddingBottom")||0,10))}if(!g.width()){g.width(b.currentItem.innerWidth()-parseInt(b.currentItem.css("paddingLeft")||0,10)-parseInt(b.currentItem.css("paddingRight")||0,10))}}}}b.placeholder=a(e.placeholder.element.call(b.element,b.currentItem));b.currentItem.after(b.placeholder);e.placeholder.update(b,b.placeholder)},_contactContainers:function(d){for(var c=this.containers.length-1;c>=0;c--){if(this._intersectsWith(this.containers[c].containerCache)){if(!this.containers[c].containerCache.over){if(this.currentContainer!=this.cont ainers[c]){var h=10000;var g=null;var e=this.positionAbs[this.containers[c].floating?"left":"top"];for(var b=this.items.length-1;b>=0;b--){if(!a.ui.contains(this.containers[c].element[0],this.items[b].item[0])){continue}var f=this.items[b][this.containers[c].floating?"left":"top"];if(Math.abs(f-e)<h){h=Math.abs(f-e);g=this.items[b]}}if(!g&&!this.options.dropOnEmpty){continue}this.currentContainer=this.containers[c];g?this._rearrange(d,g,null,true):this._rearrange(d,null,this.containers[c].element,true);this._trigger("change",d,this._uiHash());this.containers[c]._trigger("change",d,this._uiHash(this));this.options.placeholder.update(this.currentContainer,this.placeholder)}this.containers[c]._trigger("over",d,this._uiHash(this));this.containers[c].containerCache.over=1}}else{if(this.containers[c].containerCache.over){this.containers[c]._trigger("out",d,this._uiHash(this));this.containers[c].containerCache.over=0}}}},_createHelper:function(c){var d=this.options;var b=a.isFuncti on(d.helper)?a(d.helper.apply(this.element[0],[c,this.currentItem])):(d.helper=="clone"?this.currentItem.clone():this.currentItem);if(!b.parents("body").length){a(d.appendTo!="parent"?d.appendTo:this.currentItem[0].parentNode)[0].appendChild(b[0])}if(b[0]==this.currentItem[0]){this._storedCSS={width:this.currentItem[0].style.width,height:this.currentItem[0].style.height,position:this.currentItem.css("position"),top:this.currentItem.css("top"),left:this.currentItem.css("left")}}if(b[0].style.width==""||d.forceHelperSize){b.width(this.currentItem.width())}if(b[0].style.height==""||d.forceHelperSize){b.height(this.currentItem.height())}return b},_adjustOffsetFromHelper:function(b){if(b.left!=undefined){this.offset.click.left=b.left+this.margins.left}if(b.right!=undefined){this.offset.click.left=this.helperProportions.width-b.right+this.margins.left}if(b.top!=undefined){this.offset.click.top=b.top+this.margins.top}if(b.bottom!=undefined){this.offset.click.top=this.helperProporti ons.height-b.bottom+this.margins.top}},_getParentOffset:function(){this.offsetParent=this.helper.offsetParent();var b=this.offsetParent.offset();if(this.cssPosition=="absolute"&&this.scrollParent[0]!=document&&a.ui.contains(this.scrollParent[0],this.offsetParent[0])){b.left+=this.scrollParent.scrollLeft();b.top+=this.scrollParent.scrollTop()}if((this.offsetParent[0]==document.body)||(this.offsetParent[0].tagName&&this.offsetParent[0].tagName.toLowerCase()=="html"&&a.browser.msie)){b={top:0,left:0}}return{top:b.top+(parseInt(this.offsetParent.css("borderTopWidth"),10)||0),left:b.left+(parseInt(this.offsetParent.css("borderLeftWidth"),10)||0)}},_getRelativeOffset:function(){if(this.cssPosition=="relative"){var b=this.currentItem.position();return{top:b.top-(parseInt(this.helper.css("top"),10)||0)+this.scrollParent.scrollTop(),left:b.left-(parseInt(this.helper.css("left"),10)||0)+this.scrollParent.scrollLeft()}}else{return{top:0,left:0}}},_cacheMargins:function(){this.margins={ left:(parseInt(this.currentItem.css("marginLeft"),10)||0),top:(parseInt(this.currentItem.css("marginTop"),10)||0)}},_cacheHelperProportions:function(){this.helperProportions={width:this.helper.outerWidth(),height:this.helper.outerHeight()}},_setContainment:function(){var e=this.options;if(e.containment=="parent"){e.containment=this.helper[0].parentNode}if(e.containment=="document"||e.containment=="window"){this.containment=[0-this.offset.relative.left-this.offset.parent.left,0-this.offset.relative.top-this.offset.parent.top,a(e.containment=="document"?document:window).width()-this.helperProportions.width-this.margins.left,(a(e.containment=="document"?document:window).height()||document.body.parentNode.scrollHeight)-this.helperProportions.height-this.margins.top]}if(!(/^(document|window|parent)$/).test(e.containment)){var c=a(e.containment)[0];var d=a(e.containment).offset();var b=(a(c).css("overflow")!="hidden");this.containment=[d.left+(parseInt(a(c).css("borderLeftWidth"), 10)||0)+(parseInt(a(c).css("paddingLeft"),10)||0)-this.margins.left,d.top+(parseInt(a(c).css("borderTopWidth"),10)||0)+(parseInt(a(c).css("paddingTop"),10)||0)-this.margins.top,d.left+(b?Math.max(c.scrollWidth,c.offsetWidth):c.offsetWidth)-(parseInt(a(c).css("borderLeftWidth"),10)||0)-(parseInt(a(c).css("paddingRight"),10)||0)-this.helperProportions.width-this.margins.left,d.top+(b?Math.max(c.scrollHeight,c.offsetHeight):c.offsetHeight)-(parseInt(a(c).css("borderTopWidth"),10)||0)-(parseInt(a(c).css("paddingBottom"),10)||0)-this.helperProportions.height-this.margins.top]}},_convertPositionTo:function(f,h){if(!h){h=this.position}var c=f=="absolute"?1:-1;var e=this.options,b=this.cssPosition=="absolute"&&!(this.scrollParent[0]!=document&&a.ui.contains(this.scrollParent[0],this.offsetParent[0]))?this.offsetParent:this.scrollParent,g=(/(html|body)/i).test(b[0].tagName);return{top:(h.top+this.offset.relative.top*c+this.offset.parent.top*c-(a.browser.safari&&this.cssPosition=="fix ed"?0:(this.cssPosition=="fixed"?-this.scrollParent.scrollTop():(g?0:b.scrollTop()))*c)),left:(h.left+this.offset.relative.left*c+this.offset.parent.left*c-(a.browser.safari&&this.cssPosition=="fixed"?0:(this.cssPosition=="fixed"?-this.scrollParent.scrollLeft():g?0:b.scrollLeft())*c))}},_generatePosition:function(e){var h=this.options,b=this.cssPosition=="absolute"&&!(this.scrollParent[0]!=document&&a.ui.contains(this.scrollParent[0],this.offsetParent[0]))?this.offsetParent:this.scrollParent,i=(/(html|body)/i).test(b[0].tagName);if(this.cssPosition=="relative"&&!(this.scrollParent[0]!=document&&this.scrollParent[0]!=this.offsetParent[0])){this.offset.relative=this._getRelativeOffset()}var d=e.pageX;var c=e.pageY;if(this.originalPosition){if(this.containment){if(e.pageX-this.offset.click.left<this.containment[0]){d=this.containment[0]+this.offset.click.left}if(e.pageY-this.offset.click.top<this.containment[1]){c=this.containment[1]+this.offset.click.top}if(e.pageX-this.offset .click.left>this.containment[2]){d=this.containment[2]+this.offset.click.left}if(e.pageY-this.offset.click.top>this.containment[3]){c=this.containment[3]+this.offset.click.top}}if(h.grid){var g=this.originalPageY+Math.round((c-this.originalPageY)/h.grid[1])*h.grid[1];c=this.containment?(!(g-this.offset.click.top<this.containment[1]||g-this.offset.click.top>this.containment[3])?g:(!(g-this.offset.click.top<this.containment[1])?g-h.grid[1]:g+h.grid[1])):g;var f=this.originalPageX+Math.round((d-this.originalPageX)/h.grid[0])*h.grid[0];d=this.containment?(!(f-this.offset.click.left<this.containment[0]||f-this.offset.click.left>this.containment[2])?f:(!(f-this.offset.click.left<this.containment[0])?f-h.grid[0]:f+h.grid[0])):f}}return{top:(c-this.offset.click.top-this.offset.relative.top-this.offset.parent.top+(a.browser.safari&&this.cssPosition=="fixed"?0:(this.cssPosition=="fixed"?-this.scrollParent.scrollTop():(i?0:b.scrollTop())))),left:(d-this.offset.click.left-this.offset.re lative.left-this.offset.parent.left+(a.browser.safari&&this.cssPosition=="fixed"?0:(this.cssPosition=="fixed"?-this.scrollParent.scrollLeft():i?0:b.scrollLeft())))}},_rearrange:function(g,f,c,e){c?c[0].appendChild(this.placeholder[0]):f.item[0].parentNode.insertBefore(this.placeholder[0],(this.direction=="down"?f.item[0]:f.item[0].nextSibling));this.counter=this.counter?++this.counter:1;var d=this,b=this.counter;window.setTimeout(function(){if(b==d.counter){d.refreshPositions(!e)}},0)},_clear:function(d,e){this.reverting=false;var f=[],b=this;if(!this._noFinalSort&&this.currentItem[0].parentNode){this.placeholder.before(this.currentItem)}this._noFinalSort=null;if(this.helper[0]==this.currentItem[0]){for(var c in this._storedCSS){if(this._storedCSS[c]=="auto"||this._storedCSS[c]=="static"){this._storedCSS[c]=""}}this.currentItem.css(this._storedCSS).removeClass("ui-sortable-helper")}else{this.currentItem.show()}if(this.fromOutside&&!e){f.push(function(g){this._trigger("receiv e",g,this._uiHash(this.fromOutside))})}if((this.fromOutside||this.domPosition.prev!=this.currentItem.prev().not(".ui-sortable-helper")[0]||this.domPosition.parent!=this.currentItem.parent()[0])&&!e){f.push(function(g){this._trigger("update",g,this._uiHash())})}if(!a.ui.contains(this.element[0],this.currentItem[0])){if(!e){f.push(function(g){this._trigger("remove",g,this._uiHash())})}for(var c=this.containers.length-1;c>=0;c--){if(a.ui.contains(this.containers[c].element[0],this.currentItem[0])&&!e){f.push((function(g){return function(h){g._trigger("receive",h,this._uiHash(this))}}).call(this,this.containers[c]));f.push((function(g){return function(h){g._trigger("update",h,this._uiHash(this))}}).call(this,this.containers[c]))}}}for(var c=this.containers.length-1;c>=0;c--){if(!e){f.push((function(g){return function(h){g._trigger("deactivate",h,this._uiHash(this))}}).call(this,this.containers[c]))}if(this.containers[c].containerCache.over){f.push((function(g){return function(h) {g._trigger("out",h,this._uiHash(this))}}).call(this,this.containers[c]));this.containers[c].containerCache.over=0}}if(this._storedCursor){a("body").css("cursor",this._storedCursor)}if(this._storedOpacity){this.helper.css("opacity",this._storedOpacity)}if(this._storedZIndex){this.helper.css("zIndex",this._storedZIndex=="auto"?"":this._storedZIndex)}this.dragging=false;if(this.cancelHelperRemoval){if(!e){this._trigger("beforeStop",d,this._uiHash());for(var c=0;c<f.length;c++){f[c].call(this,d)}this._trigger("stop",d,this._uiHash())}return false}if(!e){this._trigger("beforeStop",d,this._uiHash())}this.placeholder[0].parentNode.removeChild(this.placeholder[0]);if(this.helper[0]!=this.currentItem[0]){this.helper.remove()}this.helper=null;if(!e){for(var c=0;c<f.length;c++){f[c].call(this,d)}this._trigger("stop",d,this._uiHash())}this.fromOutside=false;return true},_trigger:function(){if(a.widget.prototype._trigger.apply(this,arguments)===false){this.cancel()}},_uiHash:function(c) {var b=c||this;return{helper:b.helper,placeholder:b.placeholder||a([]),position:b.position,absolutePosition:b.positionAbs,offset:b.positionAbs,item:b.currentItem,sender:c?c.element:null}}}));a.extend(a.ui.sortable,{getter:"serialize toArray",version:"1.7.2",eventPrefix:"sort",defaults:{appendTo:"parent",axis:false,cancel:":input,option",connectWith:false,containment:false,cursor:"auto",cursorAt:false,delay:0,distance:1,dropOnEmpty:true,forcePlaceholderSize:false,forceHelperSize:false,grid:false,handle:false,helper:"original",items:"> *",opacity:false,placeholder:false,revert:false,scroll:true,scrollSensitivity:20,scrollSpeed:20,scope:"default",tolerance:"intersect",zIndex:1000}})})(jQuery); --- /dev/null +++ b/static/scripts/packed/jquery.ui.sortable.slider.js @@ -0,0 +1,33 @@ +/* + * jQuery UI 1.8.5 + * + * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT or GPL Version 2 licenses. + * http://jquery.org/license + * + * http://docs.jquery.com/UI + */ +(function(a,c){a.ui=a.ui||{};if(a.ui.version){return}a.extend(a.ui,{version:"1.8.5",keyCode:{ALT:18,BACKSPACE:8,CAPS_LOCK:20,COMMA:188,COMMAND:91,COMMAND_LEFT:91,COMMAND_RIGHT:93,CONTROL:17,DELETE:46,DOWN:40,END:35,ENTER:13,ESCAPE:27,HOME:36,INSERT:45,LEFT:37,MENU:93,NUMPAD_ADD:107,NUMPAD_DECIMAL:110,NUMPAD_DIVIDE:111,NUMPAD_ENTER:108,NUMPAD_MULTIPLY:106,NUMPAD_SUBTRACT:109,PAGE_DOWN:34,PAGE_UP:33,PERIOD:190,RIGHT:39,SHIFT:16,SPACE:32,TAB:9,UP:38,WINDOWS:91}});a.fn.extend({_focus:a.fn.focus,focus:function(d,e){return typeof d==="number"?this.each(function(){var f=this;setTimeout(function(){a(f).focus();if(e){e.call(f)}},d)}):this._focus.apply(this,arguments)},scrollParent:function(){var d;if((a.browser.msie&&(/(static|relative)/).test(this.css("position")))||(/absolute/).test(this.css("position"))){d=this.parents().filter(function(){return(/(relative|absolute|fixed)/).test(a.curCSS(this,"position",1))&&(/(auto|scroll)/).test(a.curCSS(this,"overflow",1)+a.curCSS(this,"overflo 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uterHeight};function h(l,k,i,m){a.each(e,function(){k-=parseFloat(a.curCSS(l,"padding"+this,true))||0;if(i){k-=parseFloat(a.curCSS(l,"border"+this+"Width",true))||0}if(m){k-=parseFloat(a.curCSS(l,"margin"+this,true))||0}});return k}a.fn["inner"+d]=function(i){if(i===c){return j["inner"+d].call(this)}return this.each(function(){a.style(this,g,h(this,i)+"px")})};a.fn["outer"+d]=function(i,k){if(typeof i!=="number"){return j["outer"+d].call(this,i)}return this.each(function(){a.style(this,g,h(this,i,true,k)+"px")})}});function b(d){return !a(d).parents().andSelf().filter(function(){return a.curCSS(this,"visibility")==="hidden"||a.expr.filters.hidden(this)}).length}a.extend(a.expr[":"],{data:function(f,e,d){return !!a.data(f,d[3])},focusable:function(f){var i=f.nodeName.toLowerCase(),d=a.attr(f,"tabindex");if("area"===i){var h=f.parentNode,g=h.name,e;if(!f.href||!g||h.nodeName.toLowerCase()!=="map"){return false}e=a("img[usemap=#"+g+"]")[0];return !!e&&b(e)}return(/input|select| textarea|button|object/.test(i)?!f.disabled:"a"==i?f.href||!isNaN(d):!isNaN(d))&&b(f)},tabbable:function(e){var d=a.attr(e,"tabindex");return(isNaN(d)||d>=0)&&a(e).is(":focusable")}});a(function(){var e=document.createElement("div"),d=document.body;a.extend(e.style,{minHeight:"100px",height:"auto",padding:0,borderWidth:0});a.support.minHeight=d.appendChild(e).offsetHeight===100;d.removeChild(e).style.display="none"});a.extend(a.ui,{plugin:{add:function(e,f,h){var g=a.ui[e].prototype;for(var d in h){g.plugins[d]=g.plugins[d]||[];g.plugins[d].push([f,h[d]])}},call:function(d,f,e){var h=d.plugins[f];if(!h||!d.element[0].parentNode){return}for(var g=0;g<h.length;g++){if(d.options[h[g][0]]){h[g][1].apply(d.element,e)}}}},contains:function(e,d){return document.compareDocumentPosition?e.compareDocumentPosition(d)&16:e!==d&&e.contains(d)},hasScroll:function(g,e){if(a(g).css("overflow")==="hidden"){return false}var d=(e&&e==="left")?"scrollLeft":"scrollTop",f=false;if(g[d]>0){return true}g[d]=1;f=(g[d]>0);g[d]=0;return f},isOverAxis:function(e,d,f){return(e>d)&&(e<(d+f))},isOver:function(i,e,h,g,d,f){return a.ui.isOverAxis(i,h,d)&&a.ui.isOverAxis(e,g,f)}})})(jQuery); +/* + * jQuery UI Widget 1.8.5 + * + * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT or GPL Version 2 licenses. + * http://jquery.org/license + * + * http://docs.jquery.com/UI/Widget + */ +(function(b,d){if(b.cleanData){var c=b.cleanData;b.cleanData=function(e){for(var f=0,g;(g=e[f])!=null;f++){b(g).triggerHandler("remove")}c(e)}}else{var a=b.fn.remove;b.fn.remove=function(e,f){return this.each(function(){if(!f){if(!e||b.filter(e,[this]).length){b("*",this).add([this]).each(function(){b(this).triggerHandler("remove")})}}return a.call(b(this),e,f)})}}b.widget=function(f,h,e){var g=f.split(".")[0],j;f=f.split(".")[1];j=g+"-"+f;if(!e){e=h;h=b.Widget}b.expr[":"][j]=function(k){return !!b.data(k,f)};b[g]=b[g]||{};b[g][f]=function(k,l){if(arguments.length){this._createWidget(k,l)}};var i=new h();i.options=b.extend(true,{},i.options);b[g][f].prototype=b.extend(true,i,{namespace:g,widgetName:f,widgetEventPrefix:b[g][f].prototype.widgetEventPrefix||f,widgetBaseClass:j},e);b.widget.bridge(f,b[g][f])};b.widget.bridge=function(f,e){b.fn[f]=function(i){var g=typeof i==="string",h=Array.prototype.slice.call(arguments,1),j=this;i=!g&&h.length?b.extend.apply(null,[true,i].con cat(h)):i;if(g&&i.substring(0,1)==="_"){return j}if(g){this.each(function(){var k=b.data(this,f);if(!k){throw"cannot call methods on "+f+" prior to initialization; attempted to call method '"+i+"'"}if(!b.isFunction(k[i])){throw"no such method '"+i+"' for "+f+" widget instance"}var l=k[i].apply(k,h);if(l!==k&&l!==d){j=l;return false}})}else{this.each(function(){var k=b.data(this,f);if(k){k.option(i||{})._init()}else{b.data(this,f,new e(i,this))}})}return j}};b.Widget=function(e,f){if(arguments.length){this._createWidget(e,f)}};b.Widget.prototype={widgetName:"widget",widgetEventPrefix:"",options:{disabled:false},_createWidget:function(f,g){b.data(g,this.widgetName,this);this.element=b(g);this.options=b.extend(true,{},this.options,b.metadata&&b.metadata.get(g)[this.widgetName],f);var e=this;this.element.bind("remove."+this.widgetName,function(){e.destroy()});this._create();this._init()},_create:function(){},_init:function(){},destroy:function(){this.element.unbind("."+this.widg etName).removeData(this.widgetName);this.widget().unbind("."+this.widgetName).removeAttr("aria-disabled").removeClass(this.widgetBaseClass+"-disabled ui-state-disabled")},widget:function(){return this.element},option:function(g,h){var f=g,e=this;if(arguments.length===0){return b.extend({},e.options)}if(typeof g==="string"){if(h===d){return this.options[g]}f={};f[g]=h}b.each(f,function(i,j){e._setOption(i,j)});return e},_setOption:function(e,f){this.options[e]=f;if(e==="disabled"){this.widget()[f?"addClass":"removeClass"](this.widgetBaseClass+"-disabled ui-state-disabled").attr("aria-disabled",f)}return this},enable:function(){return this._setOption("disabled",false)},disable:function(){return this._setOption("disabled",true)},_trigger:function(f,g,h){var k=this.options[f];g=b.Event(g);g.type=(f===this.widgetEventPrefix?f:this.widgetEventPrefix+f).toLowerCase();h=h||{};if(g.originalEvent){for(var e=b.event.props.length,j;e;){j=b.event.props[--e];g[j]=g.originalEvent[j]}}this. element.trigger(g,h);return !(b.isFunction(k)&&k.call(this.element[0],g,h)===false||g.isDefaultPrevented())}}})(jQuery); +/* + * jQuery UI Mouse 1.8.5 + * + * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT or GPL Version 2 licenses. + * http://jquery.org/license + * + * http://docs.jquery.com/UI/Mouse + * + * Depends: + * jquery.ui.widget.js + */ +(function(a,b){a.widget("ui.mouse",{options:{cancel:":input,option",distance:1,delay:0},_mouseInit:function(){var c=this;this.element.bind("mousedown."+this.widgetName,function(d){return c._mouseDown(d)}).bind("click."+this.widgetName,function(d){if(c._preventClickEvent){c._preventClickEvent=false;d.stopImmediatePropagation();return false}});this.started=false},_mouseDestroy:function(){this.element.unbind("."+this.widgetName)},_mouseDown:function(e){e.originalEvent=e.originalEvent||{};if(e.originalEvent.mouseHandled){return}(this._mouseStarted&&this._mouseUp(e));this._mouseDownEvent=e;var d=this,f=(e.which==1),c=(typeof this.options.cancel=="string"?a(e.target).parents().add(e.target).filter(this.options.cancel).length:false);if(!f||c||!this._mouseCapture(e)){return true}this.mouseDelayMet=!this.options.delay;if(!this.mouseDelayMet){this._mouseDelayTimer=setTimeout(function(){d.mouseDelayMet=true},this.options.delay)}if(this._mouseDistanceMet(e)&&this._mouseDelayMet(e)){this ._mouseStarted=(this._mouseStart(e)!==false);if(!this._mouseStarted){e.preventDefault();return true}}this._mouseMoveDelegate=function(g){return d._mouseMove(g)};this._mouseUpDelegate=function(g){return d._mouseUp(g)};a(document).bind("mousemove."+this.widgetName,this._mouseMoveDelegate).bind("mouseup."+this.widgetName,this._mouseUpDelegate);(a.browser.safari||e.preventDefault());e.originalEvent.mouseHandled=true;return true},_mouseMove:function(c){if(a.browser.msie&&!c.button){return this._mouseUp(c)}if(this._mouseStarted){this._mouseDrag(c);return c.preventDefault()}if(this._mouseDistanceMet(c)&&this._mouseDelayMet(c)){this._mouseStarted=(this._mouseStart(this._mouseDownEvent,c)!==false);(this._mouseStarted?this._mouseDrag(c):this._mouseUp(c))}return !this._mouseStarted},_mouseUp:function(c){a(document).unbind("mousemove."+this.widgetName,this._mouseMoveDelegate).unbind("mouseup."+this.widgetName,this._mouseUpDelegate);if(this._mouseStarted){this._mouseStarted=false;this._p reventClickEvent=(c.target==this._mouseDownEvent.target);this._mouseStop(c)}return false},_mouseDistanceMet:function(c){return(Math.max(Math.abs(this._mouseDownEvent.pageX-c.pageX),Math.abs(this._mouseDownEvent.pageY-c.pageY))>=this.options.distance)},_mouseDelayMet:function(c){return this.mouseDelayMet},_mouseStart:function(c){},_mouseDrag:function(c){},_mouseStop:function(c){},_mouseCapture:function(c){return true}})})(jQuery);(function(a,b){a.widget("ui.sortable",a.ui.mouse,{widgetEventPrefix:"sort",options:{appendTo:"parent",axis:false,connectWith:false,containment:false,cursor:"auto",cursorAt:false,dropOnEmpty:true,forcePlaceholderSize:false,forceHelperSize:false,grid:false,handle:false,helper:"original",items:"> *",opacity:false,placeholder:false,revert:false,scroll:true,scrollSensitivity:20,scrollSpeed:20,scope:"default",tolerance:"intersect",zIndex:1000},_create:function(){var c=this.options;this.containerCache={};this.element.addClass("ui-sortable");this.refresh();t his.floating=this.items.length?(/left|right/).test(this.items[0].item.css("float")):false;this.offset=this.element.offset();this._mouseInit()},destroy:function(){this.element.removeClass("ui-sortable ui-sortable-disabled").removeData("sortable").unbind(".sortable");this._mouseDestroy();for(var c=this.items.length-1;c>=0;c--){this.items[c].item.removeData("sortable-item")}return this},_setOption:function(c,d){if(c==="disabled"){this.options[c]=d;this.widget()[d?"addClass":"removeClass"]("ui-sortable-disabled")}else{a.Widget.prototype._setOption.apply(this,arguments)}},_mouseCapture:function(f,g){if(this.reverting){return false}if(this.options.disabled||this.options.type=="static"){return false}this._refreshItems(f);var e=null,d=this,c=a(f.target).parents().each(function(){if(a.data(this,"sortable-item")==d){e=a(this);return false}});if(a.data(f.target,"sortable-item")==d){e=a(f.target)}if(!e){return false}if(this.options.handle&&!g){var h=false;a(this.options.handle,e).find(" *").andSelf().each(function(){if(this==f.target){h=true}});if(!h){return false}}this.currentItem=e;this._removeCurrentsFromItems();return true},_mouseStart:function(f,g,c){var h=this.options,d=this;this.currentContainer=this;this.refreshPositions();this.helper=this._createHelper(f);this._cacheHelperProportions();this._cacheMargins();this.scrollParent=this.helper.scrollParent();this.offset=this.currentItem.offset();this.offset={top:this.offset.top-this.margins.top,left:this.offset.left-this.margins.left};this.helper.css("position","absolute");this.cssPosition=this.helper.css("position");a.extend(this.offset,{click:{left:f.pageX-this.offset.left,top:f.pageY-this.offset.top},parent:this._getParentOffset(),relative:this._getRelativeOffset()});this.originalPosition=this._generatePosition(f);this.originalPageX=f.pageX;this.originalPageY=f.pageY;(h.cursorAt&&this._adjustOffsetFromHelper(h.cursorAt));this.domPosition={prev:this.currentItem.prev()[0],parent:this.currentItem.parent()[ 0]};if(this.helper[0]!=this.currentItem[0]){this.currentItem.hide()}this._createPlaceholder();if(h.containment){this._setContainment()}if(h.cursor){if(a("body").css("cursor")){this._storedCursor=a("body").css("cursor")}a("body").css("cursor",h.cursor)}if(h.opacity){if(this.helper.css("opacity")){this._storedOpacity=this.helper.css("opacity")}this.helper.css("opacity",h.opacity)}if(h.zIndex){if(this.helper.css("zIndex")){this._storedZIndex=this.helper.css("zIndex")}this.helper.css("zIndex",h.zIndex)}if(this.scrollParent[0]!=document&&this.scrollParent[0].tagName!="HTML"){this.overflowOffset=this.scrollParent.offset()}this._trigger("start",f,this._uiHash());if(!this._preserveHelperProportions){this._cacheHelperProportions()}if(!c){for(var e=this.containers.length-1;e>=0;e--){this.containers[e]._trigger("activate",f,d._uiHash(this))}}if(a.ui.ddmanager){a.ui.ddmanager.current=this}if(a.ui.ddmanager&&!h.dropBehaviour){a.ui.ddmanager.prepareOffsets(this,f)}this.dragging=true;this. helper.addClass("ui-sortable-helper");this._mouseDrag(f);return true},_mouseDrag:function(g){this.position=this._generatePosition(g);this.positionAbs=this._convertPositionTo("absolute");if(!this.lastPositionAbs){this.lastPositionAbs=this.positionAbs}if(this.options.scroll){var h=this.options,c=false;if(this.scrollParent[0]!=document&&this.scrollParent[0].tagName!="HTML"){if((this.overflowOffset.top+this.scrollParent[0].offsetHeight)-g.pageY<h.scrollSensitivity){this.scrollParent[0].scrollTop=c=this.scrollParent[0].scrollTop+h.scrollSpeed}else{if(g.pageY-this.overflowOffset.top<h.scrollSensitivity){this.scrollParent[0].scrollTop=c=this.scrollParent[0].scrollTop-h.scrollSpeed}}if((this.overflowOffset.left+this.scrollParent[0].offsetWidth)-g.pageX<h.scrollSensitivity){this.scrollParent[0].scrollLeft=c=this.scrollParent[0].scrollLeft+h.scrollSpeed}else{if(g.pageX-this.overflowOffset.left<h.scrollSensitivity){this.scrollParent[0].scrollLeft=c=this.scrollParent[0].scrollLeft-h.scr ollSpeed}}}else{if(g.pageY-a(document).scrollTop()<h.scrollSensitivity){c=a(document).scrollTop(a(document).scrollTop()-h.scrollSpeed)}else{if(a(window).height()-(g.pageY-a(document).scrollTop())<h.scrollSensitivity){c=a(document).scrollTop(a(document).scrollTop()+h.scrollSpeed)}}if(g.pageX-a(document).scrollLeft()<h.scrollSensitivity){c=a(document).scrollLeft(a(document).scrollLeft()-h.scrollSpeed)}else{if(a(window).width()-(g.pageX-a(document).scrollLeft())<h.scrollSensitivity){c=a(document).scrollLeft(a(document).scrollLeft()+h.scrollSpeed)}}}if(c!==false&&a.ui.ddmanager&&!h.dropBehaviour){a.ui.ddmanager.prepareOffsets(this,g)}}this.positionAbs=this._convertPositionTo("absolute");if(!this.options.axis||this.options.axis!="y"){this.helper[0].style.left=this.position.left+"px"}if(!this.options.axis||this.options.axis!="x"){this.helper[0].style.top=this.position.top+"px"}for(var e=this.items.length-1;e>=0;e--){var f=this.items[e],d=f.item[0],j=this._intersectsWithPointer(f); if(!j){continue}if(d!=this.currentItem[0]&&this.placeholder[j==1?"next":"prev"]()[0]!=d&&!a.ui.contains(this.placeholder[0],d)&&(this.options.type=="semi-dynamic"?!a.ui.contains(this.element[0],d):true)){this.direction=j==1?"down":"up";if(this.options.tolerance=="pointer"||this._intersectsWithSides(f)){this._rearrange(g,f)}else{break}this._trigger("change",g,this._uiHash());break}}this._contactContainers(g);if(a.ui.ddmanager){a.ui.ddmanager.drag(this,g)}this._trigger("sort",g,this._uiHash());this.lastPositionAbs=this.positionAbs;return false},_mouseStop:function(d,e){if(!d){return}if(a.ui.ddmanager&&!this.options.dropBehaviour){a.ui.ddmanager.drop(this,d)}if(this.options.revert){var c=this;var f=c.placeholder.offset();c.reverting=true;a(this.helper).animate({left:f.left-this.offset.parent.left-c.margins.left+(this.offsetParent[0]==document.body?0:this.offsetParent[0].scrollLeft),top:f.top-this.offset.parent.top-c.margins.top+(this.offsetParent[0]==document.body?0:this.offset Parent[0].scrollTop)},parseInt(this.options.revert,10)||500,function(){c._clear(d)})}else{this._clear(d,e)}return false},cancel:function(){var c=this;if(this.dragging){this._mouseUp();if(this.options.helper=="original"){this.currentItem.css(this._storedCSS).removeClass("ui-sortable-helper")}else{this.currentItem.show()}for(var d=this.containers.length-1;d>=0;d--){this.containers[d]._trigger("deactivate",null,c._uiHash(this));if(this.containers[d].containerCache.over){this.containers[d]._trigger("out",null,c._uiHash(this));this.containers[d].containerCache.over=0}}}if(this.placeholder[0].parentNode){this.placeholder[0].parentNode.removeChild(this.placeholder[0])}if(this.options.helper!="original"&&this.helper&&this.helper[0].parentNode){this.helper.remove()}a.extend(this,{helper:null,dragging:false,reverting:false,_noFinalSort:null});if(this.domPosition.prev){a(this.domPosition.prev).after(this.currentItem)}else{a(this.domPosition.parent).prepend(this.currentItem)}return this },serialize:function(e){var c=this._getItemsAsjQuery(e&&e.connected);var d=[];e=e||{};a(c).each(function(){var f=(a(e.item||this).attr(e.attribute||"id")||"").match(e.expression||(/(.+)[-=_](.+)/));if(f){d.push((e.key||f[1]+"[]")+"="+(e.key&&e.expression?f[1]:f[2]))}});if(!d.length&&e.key){d.push(e.key+"=")}return d.join("&")},toArray:function(e){var c=this._getItemsAsjQuery(e&&e.connected);var d=[];e=e||{};c.each(function(){d.push(a(e.item||this).attr(e.attribute||"id")||"")});return d},_intersectsWith:function(m){var e=this.positionAbs.left,d=e+this.helperProportions.width,k=this.positionAbs.top,j=k+this.helperProportions.height;var f=m.left,c=f+m.width,n=m.top,i=n+m.height;var o=this.offset.click.top,h=this.offset.click.left;var g=(k+o)>n&&(k+o)<i&&(e+h)>f&&(e+h)<c;if(this.options.tolerance=="pointer"||this.options.forcePointerForContainers||(this.options.tolerance!="pointer"&&this.helperProportions[this.floating?"width":"height"]>m[this.floating?"width":"height"])){retur n g}else{return(f<e+(this.helperProportions.width/2)&&d-(this.helperProportions.width/2)<c&&n<k+(this.helperProportions.height/2)&&j-(this.helperProportions.height/2)<i)}},_intersectsWithPointer:function(e){var f=a.ui.isOverAxis(this.positionAbs.top+this.offset.click.top,e.top,e.height),d=a.ui.isOverAxis(this.positionAbs.left+this.offset.click.left,e.left,e.width),h=f&&d,c=this._getDragVerticalDirection(),g=this._getDragHorizontalDirection();if(!h){return false}return this.floating?(((g&&g=="right")||c=="down")?2:1):(c&&(c=="down"?2:1))},_intersectsWithSides:function(f){var d=a.ui.isOverAxis(this.positionAbs.top+this.offset.click.top,f.top+(f.height/2),f.height),e=a.ui.isOverAxis(this.positionAbs.left+this.offset.click.left,f.left+(f.width/2),f.width),c=this._getDragVerticalDirection(),g=this._getDragHorizontalDirection();if(this.floating&&g){return((g=="right"&&e)||(g=="left"&&!e))}else{return c&&((c=="down"&&d)||(c=="up"&&!d))}},_getDragVerticalDirection:function(){var c=t his.positionAbs.top-this.lastPositionAbs.top;return c!=0&&(c>0?"down":"up")},_getDragHorizontalDirection:function(){var c=this.positionAbs.left-this.lastPositionAbs.left;return c!=0&&(c>0?"right":"left")},refresh:function(c){this._refreshItems(c);this.refreshPositions();return this},_connectWith:function(){var c=this.options;return c.connectWith.constructor==String?[c.connectWith]:c.connectWith},_getItemsAsjQuery:function(c){var m=this;var h=[];var f=[];var k=this._connectWith();if(k&&c){for(var e=k.length-1;e>=0;e--){var l=a(k[e]);for(var d=l.length-1;d>=0;d--){var g=a.data(l[d],"sortable");if(g&&g!=this&&!g.options.disabled){f.push([a.isFunction(g.options.items)?g.options.items.call(g.element):a(g.options.items,g.element).not(".ui-sortable-helper").not(".ui-sortable-placeholder"),g])}}}}f.push([a.isFunction(this.options.items)?this.options.items.call(this.element,null,{options:this.options,item:this.currentItem}):a(this.options.items,this.element).not(".ui-sortable-helper" ).not(".ui-sortable-placeholder"),this]);for(var e=f.length-1;e>=0;e--){f[e][0].each(function(){h.push(this)})}return a(h)},_removeCurrentsFromItems:function(){var e=this.currentItem.find(":data(sortable-item)");for(var d=0;d<this.items.length;d++){for(var c=0;c<e.length;c++){if(e[c]==this.items[d].item[0]){this.items.splice(d,1)}}}},_refreshItems:function(c){this.items=[];this.containers=[this];var k=this.items;var q=this;var g=[[a.isFunction(this.options.items)?this.options.items.call(this.element[0],c,{item:this.currentItem}):a(this.options.items,this.element),this]];var m=this._connectWith();if(m){for(var f=m.length-1;f>=0;f--){var n=a(m[f]);for(var e=n.length-1;e>=0;e--){var h=a.data(n[e],"sortable");if(h&&h!=this&&!h.options.disabled){g.push([a.isFunction(h.options.items)?h.options.items.call(h.element[0],c,{item:this.currentItem}):a(h.options.items,h.element),h]);this.containers.push(h)}}}}for(var f=g.length-1;f>=0;f--){var l=g[f][1];var d=g[f][0];for(var e=0,o=d.leng th;e<o;e++){var p=a(d[e]);p.data("sortable-item",l);k.push({item:p,instance:l,width:0,height:0,left:0,top:0})}}},refreshPositions:function(c){if(this.offsetParent&&this.helper){this.offset.parent=this._getParentOffset()}for(var e=this.items.length-1;e>=0;e--){var f=this.items[e];var d=this.options.toleranceElement?a(this.options.toleranceElement,f.item):f.item;if(!c){f.width=d.outerWidth();f.height=d.outerHeight()}var g=d.offset();f.left=g.left;f.top=g.top}if(this.options.custom&&this.options.custom.refreshContainers){this.options.custom.refreshContainers.call(this)}else{for(var e=this.containers.length-1;e>=0;e--){var g=this.containers[e].element.offset();this.containers[e].containerCache.left=g.left;this.containers[e].containerCache.top=g.top;this.containers[e].containerCache.width=this.containers[e].element.outerWidth();this.containers[e].containerCache.height=this.containers[e].element.outerHeight()}}return this},_createPlaceholder:function(e){var c=e||this,f=c.options;i f(!f.placeholder||f.placeholder.constructor==String){var d=f.placeholder;f.placeholder={element:function(){var g=a(document.createElement(c.currentItem[0].nodeName)).addClass(d||c.currentItem[0].className+" ui-sortable-placeholder").removeClass("ui-sortable-helper")[0];if(!d){g.style.visibility="hidden"}return g},update:function(g,h){if(d&&!f.forcePlaceholderSize){return}if(!h.height()){h.height(c.currentItem.innerHeight()-parseInt(c.currentItem.css("paddingTop")||0,10)-parseInt(c.currentItem.css("paddingBottom")||0,10))}if(!h.width()){h.width(c.currentItem.innerWidth()-parseInt(c.currentItem.css("paddingLeft")||0,10)-parseInt(c.currentItem.css("paddingRight")||0,10))}}}}c.placeholder=a(f.placeholder.element.call(c.element,c.currentItem));c.currentItem.after(c.placeholder);f.placeholder.update(c,c.placeholder)},_contactContainers:function(c){var e=null,l=null;for(var g=this.containers.length-1;g>=0;g--){if(a.ui.contains(this.currentItem[0],this.containers[g].element[0])){con tinue}if(this._intersectsWith(this.containers[g].containerCache)){if(e&&a.ui.contains(this.containers[g].element[0],e.element[0])){continue}e=this.containers[g];l=g}else{if(this.containers[g].containerCache.over){this.containers[g]._trigger("out",c,this._uiHash(this));this.containers[g].containerCache.over=0}}}if(!e){return}if(this.containers.length===1){this.containers[l]._trigger("over",c,this._uiHash(this));this.containers[l].containerCache.over=1}else{if(this.currentContainer!=this.containers[l]){var k=10000;var h=null;var d=this.positionAbs[this.containers[l].floating?"left":"top"];for(var f=this.items.length-1;f>=0;f--){if(!a.ui.contains(this.containers[l].element[0],this.items[f].item[0])){continue}var m=this.items[f][this.containers[l].floating?"left":"top"];if(Math.abs(m-d)<k){k=Math.abs(m-d);h=this.items[f]}}if(!h&&!this.options.dropOnEmpty){return}this.currentContainer=this.containers[l];h?this._rearrange(c,h,null,true):this._rearrange(c,null,this.containers[l].el ement,true);this._trigger("change",c,this._uiHash());this.containers[l]._trigger("change",c,this._uiHash(this));this.options.placeholder.update(this.currentContainer,this.placeholder);this.containers[l]._trigger("over",c,this._uiHash(this));this.containers[l].containerCache.over=1}}},_createHelper:function(d){var e=this.options;var c=a.isFunction(e.helper)?a(e.helper.apply(this.element[0],[d,this.currentItem])):(e.helper=="clone"?this.currentItem.clone():this.currentItem);if(!c.parents("body").length){a(e.appendTo!="parent"?e.appendTo:this.currentItem[0].parentNode)[0].appendChild(c[0])}if(c[0]==this.currentItem[0]){this._storedCSS={width:this.currentItem[0].style.width,height:this.currentItem[0].style.height,position:this.currentItem.css("position"),top:this.currentItem.css("top"),left:this.currentItem.css("left")}}if(c[0].style.width==""||e.forceHelperSize){c.width(this.currentItem.width())}if(c[0].style.height==""||e.forceHelperSize){c.height(this.currentItem.height())}re turn c},_adjustOffsetFromHelper:function(c){if(typeof c=="string"){c=c.split(" ")}if(a.isArray(c)){c={left:+c[0],top:+c[1]||0}}if("left" in c){this.offset.click.left=c.left+this.margins.left}if("right" in c){this.offset.click.left=this.helperProportions.width-c.right+this.margins.left}if("top" in c){this.offset.click.top=c.top+this.margins.top}if("bottom" in c){this.offset.click.top=this.helperProportions.height-c.bottom+this.margins.top}},_getParentOffset:function(){this.offsetParent=this.helper.offsetParent();var c=this.offsetParent.offset();if(this.cssPosition=="absolute"&&this.scrollParent[0]!=document&&a.ui.contains(this.scrollParent[0],this.offsetParent[0])){c.left+=this.scrollParent.scrollLeft();c.top+=this.scrollParent.scrollTop()}if((this.offsetParent[0]==document.body)||(this.offsetParent[0].tagName&&this.offsetParent[0].tagName.toLowerCase()=="html"&&a.browser.msie)){c={top:0,left:0}}return{top:c.top+(parseInt(this.offsetParent.css("borderTopWidth"),10)||0),left:c .left+(parseInt(this.offsetParent.css("borderLeftWidth"),10)||0)}},_getRelativeOffset:function(){if(this.cssPosition=="relative"){var c=this.currentItem.position();return{top:c.top-(parseInt(this.helper.css("top"),10)||0)+this.scrollParent.scrollTop(),left:c.left-(parseInt(this.helper.css("left"),10)||0)+this.scrollParent.scrollLeft()}}else{return{top:0,left:0}}},_cacheMargins:function(){this.margins={left:(parseInt(this.currentItem.css("marginLeft"),10)||0),top:(parseInt(this.currentItem.css("marginTop"),10)||0)}},_cacheHelperProportions:function(){this.helperProportions={width:this.helper.outerWidth(),height:this.helper.outerHeight()}},_setContainment:function(){var f=this.options;if(f.containment=="parent"){f.containment=this.helper[0].parentNode}if(f.containment=="document"||f.containment=="window"){this.containment=[0-this.offset.relative.left-this.offset.parent.left,0-this.offset.relative.top-this.offset.parent.top,a(f.containment=="document"?document:window).width()-t his.helperProportions.width-this.margins.left,(a(f.containment=="document"?document:window).height()||document.body.parentNode.scrollHeight)-this.helperProportions.height-this.margins.top]}if(!(/^(document|window|parent)$/).test(f.containment)){var d=a(f.containment)[0];var e=a(f.containment).offset();var c=(a(d).css("overflow")!="hidden");this.containment=[e.left+(parseInt(a(d).css("borderLeftWidth"),10)||0)+(parseInt(a(d).css("paddingLeft"),10)||0)-this.margins.left,e.top+(parseInt(a(d).css("borderTopWidth"),10)||0)+(parseInt(a(d).css("paddingTop"),10)||0)-this.margins.top,e.left+(c?Math.max(d.scrollWidth,d.offsetWidth):d.offsetWidth)-(parseInt(a(d).css("borderLeftWidth"),10)||0)-(parseInt(a(d).css("paddingRight"),10)||0)-this.helperProportions.width-this.margins.left,e.top+(c?Math.max(d.scrollHeight,d.offsetHeight):d.offsetHeight)-(parseInt(a(d).css("borderTopWidth"),10)||0)-(parseInt(a(d).css("paddingBottom"),10)||0)-this.helperProportions.height-this.margins.top]}},_con vertPositionTo:function(g,i){if(!i){i=this.position}var e=g=="absolute"?1:-1;var f=this.options,c=this.cssPosition=="absolute"&&!(this.scrollParent[0]!=document&&a.ui.contains(this.scrollParent[0],this.offsetParent[0]))?this.offsetParent:this.scrollParent,h=(/(html|body)/i).test(c[0].tagName);return{top:(i.top+this.offset.relative.top*e+this.offset.parent.top*e-(a.browser.safari&&this.cssPosition=="fixed"?0:(this.cssPosition=="fixed"?-this.scrollParent.scrollTop():(h?0:c.scrollTop()))*e)),left:(i.left+this.offset.relative.left*e+this.offset.parent.left*e-(a.browser.safari&&this.cssPosition=="fixed"?0:(this.cssPosition=="fixed"?-this.scrollParent.scrollLeft():h?0:c.scrollLeft())*e))}},_generatePosition:function(f){var i=this.options,c=this.cssPosition=="absolute"&&!(this.scrollParent[0]!=document&&a.ui.contains(this.scrollParent[0],this.offsetParent[0]))?this.offsetParent:this.scrollParent,j=(/(html|body)/i).test(c[0].tagName);if(this.cssPosition=="relative"&&!(this.scrollPar ent[0]!=document&&this.scrollParent[0]!=this.offsetParent[0])){this.offset.relative=this._getRelativeOffset()}var e=f.pageX;var d=f.pageY;if(this.originalPosition){if(this.containment){if(f.pageX-this.offset.click.left<this.containment[0]){e=this.containment[0]+this.offset.click.left}if(f.pageY-this.offset.click.top<this.containment[1]){d=this.containment[1]+this.offset.click.top}if(f.pageX-this.offset.click.left>this.containment[2]){e=this.containment[2]+this.offset.click.left}if(f.pageY-this.offset.click.top>this.containment[3]){d=this.containment[3]+this.offset.click.top}}if(i.grid){var h=this.originalPageY+Math.round((d-this.originalPageY)/i.grid[1])*i.grid[1];d=this.containment?(!(h-this.offset.click.top<this.containment[1]||h-this.offset.click.top>this.containment[3])?h:(!(h-this.offset.click.top<this.containment[1])?h-i.grid[1]:h+i.grid[1])):h;var g=this.originalPageX+Math.round((e-this.originalPageX)/i.grid[0])*i.grid[0];e=this.containment?(!(g-this.offset.click.left <this.containment[0]||g-this.offset.click.left>this.containment[2])?g:(!(g-this.offset.click.left<this.containment[0])?g-i.grid[0]:g+i.grid[0])):g}}return{top:(d-this.offset.click.top-this.offset.relative.top-this.offset.parent.top+(a.browser.safari&&this.cssPosition=="fixed"?0:(this.cssPosition=="fixed"?-this.scrollParent.scrollTop():(j?0:c.scrollTop())))),left:(e-this.offset.click.left-this.offset.relative.left-this.offset.parent.left+(a.browser.safari&&this.cssPosition=="fixed"?0:(this.cssPosition=="fixed"?-this.scrollParent.scrollLeft():j?0:c.scrollLeft())))}},_rearrange:function(h,g,d,f){d?d[0].appendChild(this.placeholder[0]):g.item[0].parentNode.insertBefore(this.placeholder[0],(this.direction=="down"?g.item[0]:g.item[0].nextSibling));this.counter=this.counter?++this.counter:1;var e=this,c=this.counter;window.setTimeout(function(){if(c==e.counter){e.refreshPositions(!f)}},0)},_clear:function(e,f){this.reverting=false;var g=[],c=this;if(!this._noFinalSort&&this.current Item[0].parentNode){this.placeholder.before(this.currentItem)}this._noFinalSort=null;if(this.helper[0]==this.currentItem[0]){for(var d in this._storedCSS){if(this._storedCSS[d]=="auto"||this._storedCSS[d]=="static"){this._storedCSS[d]=""}}this.currentItem.css(this._storedCSS).removeClass("ui-sortable-helper")}else{this.currentItem.show()}if(this.fromOutside&&!f){g.push(function(h){this._trigger("receive",h,this._uiHash(this.fromOutside))})}if((this.fromOutside||this.domPosition.prev!=this.currentItem.prev().not(".ui-sortable-helper")[0]||this.domPosition.parent!=this.currentItem.parent()[0])&&!f){g.push(function(h){this._trigger("update",h,this._uiHash())})}if(!a.ui.contains(this.element[0],this.currentItem[0])){if(!f){g.push(function(h){this._trigger("remove",h,this._uiHash())})}for(var d=this.containers.length-1;d>=0;d--){if(a.ui.contains(this.containers[d].element[0],this.currentItem[0])&&!f){g.push((function(h){return function(i){h._trigger("receive",i,this._uiHash(this) )}}).call(this,this.containers[d]));g.push((function(h){return function(i){h._trigger("update",i,this._uiHash(this))}}).call(this,this.containers[d]))}}}for(var d=this.containers.length-1;d>=0;d--){if(!f){g.push((function(h){return function(i){h._trigger("deactivate",i,this._uiHash(this))}}).call(this,this.containers[d]))}if(this.containers[d].containerCache.over){g.push((function(h){return function(i){h._trigger("out",i,this._uiHash(this))}}).call(this,this.containers[d]));this.containers[d].containerCache.over=0}}if(this._storedCursor){a("body").css("cursor",this._storedCursor)}if(this._storedOpacity){this.helper.css("opacity",this._storedOpacity)}if(this._storedZIndex){this.helper.css("zIndex",this._storedZIndex=="auto"?"":this._storedZIndex)}this.dragging=false;if(this.cancelHelperRemoval){if(!f){this._trigger("beforeStop",e,this._uiHash());for(var d=0;d<g.length;d++){g[d].call(this,e)}this._trigger("stop",e,this._uiHash())}return false}if(!f){this._trigger("beforeStop", e,this._uiHash())}this.placeholder[0].parentNode.removeChild(this.placeholder[0]);if(this.helper[0]!=this.currentItem[0]){this.helper.remove()}this.helper=null;if(!f){for(var d=0;d<g.length;d++){g[d].call(this,e)}this._trigger("stop",e,this._uiHash())}this.fromOutside=false;return true},_trigger:function(){if(a.Widget.prototype._trigger.apply(this,arguments)===false){this.cancel()}},_uiHash:function(d){var c=d||this;return{helper:c.helper,placeholder:c.placeholder||a([]),position:c.position,originalPosition:c.originalPosition,offset:c.positionAbs,item:c.currentItem,sender:d?d.element:null}}});a.extend(a.ui.sortable,{version:"1.8.5"})})(jQuery);(function(b,c){var a=5;b.widget("ui.slider",b.ui.mouse,{widgetEventPrefix:"slide",options:{animate:false,distance:0,max:100,min:0,orientation:"horizontal",range:false,step:1,value:0,values:null},_create:function(){var d=this,e=this.options;this._keySliding=false;this._mouseSliding=false;this._animateOff=true;this._handleIndex=null;this ._detectOrientation();this._mouseInit();this.element.addClass("ui-slider ui-slider-"+this.orientation+" ui-widget ui-widget-content ui-corner-all");if(e.disabled){this.element.addClass("ui-slider-disabled ui-disabled")}this.range=b([]);if(e.range){if(e.range===true){this.range=b("<div></div>");if(!e.values){e.values=[this._valueMin(),this._valueMin()]}if(e.values.length&&e.values.length!==2){e.values=[e.values[0],e.values[0]]}}else{this.range=b("<div></div>")}this.range.appendTo(this.element).addClass("ui-slider-range");if(e.range==="min"||e.range==="max"){this.range.addClass("ui-slider-range-"+e.range)}this.range.addClass("ui-widget-header")}if(b(".ui-slider-handle",this.element).length===0){b("<a href='#'></a>").appendTo(this.element).addClass("ui-slider-handle")}if(e.values&&e.values.length){while(b(".ui-slider-handle",this.element).length<e.values.length){b("<a href='#'></a>").appendTo(this.element).addClass("ui-slider-handle")}}this.handles=b(".ui-slider-handle",this.el ement).addClass("ui-state-default ui-corner-all");this.handle=this.handles.eq(0);this.handles.add(this.range).filter("a").click(function(f){f.preventDefault()}).hover(function(){if(!e.disabled){b(this).addClass("ui-state-hover")}},function(){b(this).removeClass("ui-state-hover")}).focus(function(){if(!e.disabled){b(".ui-slider .ui-state-focus").removeClass("ui-state-focus");b(this).addClass("ui-state-focus")}else{b(this).blur()}}).blur(function(){b(this).removeClass("ui-state-focus")});this.handles.each(function(f){b(this).data("index.ui-slider-handle",f)});this.handles.keydown(function(k){var h=true,g=b(this).data("index.ui-slider-handle"),l,i,f,j;if(d.options.disabled){return}switch(k.keyCode){case b.ui.keyCode.HOME:case b.ui.keyCode.END:case b.ui.keyCode.PAGE_UP:case b.ui.keyCode.PAGE_DOWN:case b.ui.keyCode.UP:case b.ui.keyCode.RIGHT:case b.ui.keyCode.DOWN:case b.ui.keyCode.LEFT:h=false;if(!d._keySliding){d._keySliding=true;b(this).addClass("ui-state-active");l=d._start(k ,g);if(l===false){return}}break}j=d.options.step;if(d.options.values&&d.options.values.length){i=f=d.values(g)}else{i=f=d.value()}switch(k.keyCode){case b.ui.keyCode.HOME:f=d._valueMin();break;case b.ui.keyCode.END:f=d._valueMax();break;case b.ui.keyCode.PAGE_UP:f=d._trimAlignValue(i+((d._valueMax()-d._valueMin())/a));break;case b.ui.keyCode.PAGE_DOWN:f=d._trimAlignValue(i-((d._valueMax()-d._valueMin())/a));break;case b.ui.keyCode.UP:case b.ui.keyCode.RIGHT:if(i===d._valueMax()){return}f=d._trimAlignValue(i+j);break;case b.ui.keyCode.DOWN:case b.ui.keyCode.LEFT:if(i===d._valueMin()){return}f=d._trimAlignValue(i-j);break}d._slide(k,g,f);return h}).keyup(function(g){var f=b(this).data("index.ui-slider-handle");if(d._keySliding){d._keySliding=false;d._stop(g,f);d._change(g,f);b(this).removeClass("ui-state-active")}});this._refreshValue();this._animateOff=false},destroy:function(){this.handles.remove();this.range.remove();this.element.removeClass("ui-slider ui-slider-horizontal ui-slider-vertical ui-slider-disabled ui-widget ui-widget-content ui-corner-all").removeData("slider").unbind(".slider");this._mouseDestroy();return this},_mouseCapture:function(f){var g=this.options,j,l,e,h,n,k,m,i,d;if(g.disabled){return false}this.elementSize={width:this.element.outerWidth(),height:this.element.outerHeight()};this.elementOffset=this.element.offset();j={x:f.pageX,y:f.pageY};l=this._normValueFromMouse(j);e=this._valueMax()-this._valueMin()+1;n=this;this.handles.each(function(o){var p=Math.abs(l-n.values(o));if(e>p){e=p;h=b(this);k=o}});if(g.range===true&&this.values(1)===g.min){k+=1;h=b(this.handles[k])}m=this._start(f,k);if(m===false){return false}this._mouseSliding=true;n._handleIndex=k;h.addClass("ui-state-active").focus();i=h.offset();d=!b(f.target).parents().andSelf().is(".ui-slider-handle");this._clickOffset=d?{left:0,top:0}:{left:f.pageX-i.left-(h.width()/2),top:f.pageY-i.top-(h.height()/2)-(parseInt(h.css("borderTopWidth"),10)||0)-(parseInt(h.css("b orderBottomWidth"),10)||0)+(parseInt(h.css("marginTop"),10)||0)};this._slide(f,k,l);this._animateOff=true;return true},_mouseStart:function(d){return true},_mouseDrag:function(f){var d={x:f.pageX,y:f.pageY},e=this._normValueFromMouse(d);this._slide(f,this._handleIndex,e);return false},_mouseStop:function(d){this.handles.removeClass("ui-state-active");this._mouseSliding=false;this._stop(d,this._handleIndex);this._change(d,this._handleIndex);this._handleIndex=null;this._clickOffset=null;this._animateOff=false;return false},_detectOrientation:function(){this.orientation=(this.options.orientation==="vertical")?"vertical":"horizontal"},_normValueFromMouse:function(e){var d,h,g,f,i;if(this.orientation==="horizontal"){d=this.elementSize.width;h=e.x-this.elementOffset.left-(this._clickOffset?this._clickOffset.left:0)}else{d=this.elementSize.height;h=e.y-this.elementOffset.top-(this._clickOffset?this._clickOffset.top:0)}g=(h/d);if(g>1){g=1}if(g<0){g=0}if(this.orientation==="vertical" ){g=1-g}f=this._valueMax()-this._valueMin();i=this._valueMin()+g*f;return this._trimAlignValue(i)},_start:function(f,e){var d={handle:this.handles[e],value:this.value()};if(this.options.values&&this.options.values.length){d.value=this.values(e);d.values=this.values()}return this._trigger("start",f,d)},_slide:function(h,g,f){var d,e,i;if(this.options.values&&this.options.values.length){d=this.values(g?0:1);if((this.options.values.length===2&&this.options.range===true)&&((g===0&&f>d)||(g===1&&f<d))){f=d}if(f!==this.values(g)){e=this.values();e[g]=f;i=this._trigger("slide",h,{handle:this.handles[g],value:f,values:e});d=this.values(g?0:1);if(i!==false){this.values(g,f,true)}}}else{if(f!==this.value()){i=this._trigger("slide",h,{handle:this.handles[g],value:f});if(i!==false){this.value(f)}}}},_stop:function(f,e){var d={handle:this.handles[e],value:this.value()};if(this.options.values&&this.options.values.length){d.value=this.values(e);d.values=this.values()}this._trigger("stop",f ,d)},_change:function(f,e){if(!this._keySliding&&!this._mouseSliding){var d={handle:this.handles[e],value:this.value()};if(this.options.values&&this.options.values.length){d.value=this.values(e);d.values=this.values()}this._trigger("change",f,d)}},value:function(d){if(arguments.length){this.options.value=this._trimAlignValue(d);this._refreshValue();this._change(null,0)}return this._value()},values:function(e,h){var g,d,f;if(arguments.length>1){this.options.values[e]=this._trimAlignValue(h);this._refreshValue();this._change(null,e)}if(arguments.length){if(b.isArray(arguments[0])){g=this.options.values;d=arguments[0];for(f=0;f<g.length;f+=1){g[f]=this._trimAlignValue(d[f]);this._change(null,f)}this._refreshValue()}else{if(this.options.values&&this.options.values.length){return this._values(e)}else{return this.value()}}}else{return this._values()}},_setOption:function(e,f){var d,g=0;if(b.isArray(this.options.values)){g=this.options.values.length}b.Widget.prototype._setOption.ap ply(this,arguments);switch(e){case"disabled":if(f){this.handles.filter(".ui-state-focus").blur();this.handles.removeClass("ui-state-hover");this.handles.attr("disabled","disabled");this.element.addClass("ui-disabled")}else{this.handles.removeAttr("disabled");this.element.removeClass("ui-disabled")}break;case"orientation":this._detectOrientation();this.element.removeClass("ui-slider-horizontal ui-slider-vertical").addClass("ui-slider-"+this.orientation);this._refreshValue();break;case"value":this._animateOff=true;this._refreshValue();this._change(null,0);this._animateOff=false;break;case"values":this._animateOff=true;this._refreshValue();for(d=0;d<g;d+=1){this._change(null,d)}this._animateOff=false;break}},_value:function(){var d=this.options.value;d=this._trimAlignValue(d);return d},_values:function(d){var g,f,e;if(arguments.length){g=this.options.values[d];g=this._trimAlignValue(g);return g}else{f=this.options.values.slice();for(e=0;e<f.length;e+=1){f[e]=this._trimAlignValu e(f[e])}return f}},_trimAlignValue:function(g){if(g<this._valueMin()){return this._valueMin()}if(g>this._valueMax()){return this._valueMax()}var d=(this.options.step>0)?this.options.step:1,f=g%d,e=g-f;if(Math.abs(f)*2>=d){e+=(f>0)?d:(-d)}return parseFloat(e.toFixed(5))},_valueMin:function(){return this.options.min},_valueMax:function(){return this.options.max},_refreshValue:function(){var g=this.options.range,f=this.options,m=this,e=(!this._animateOff)?f.animate:false,h,d={},i,k,j,l;if(this.options.values&&this.options.values.length){this.handles.each(function(o,n){h=(m.values(o)-m._valueMin())/(m._valueMax()-m._valueMin())*100;d[m.orientation==="horizontal"?"left":"bottom"]=h+"%";b(this).stop(1,1)[e?"animate":"css"](d,f.animate);if(m.options.range===true){if(m.orientation==="horizontal"){if(o===0){m.range.stop(1,1)[e?"animate":"css"]({left:h+"%"},f.animate)}if(o===1){m.range[e?"animate":"css"]({width:(h-i)+"%"},{queue:false,duration:f.animate})}}else{if(o===0){m.range.stop( 1,1)[e?"animate":"css"]({bottom:(h)+"%"},f.animate)}if(o===1){m.range[e?"animate":"css"]({height:(h-i)+"%"},{queue:false,duration:f.animate})}}}i=h})}else{k=this.value();j=this._valueMin();l=this._valueMax();h=(l!==j)?(k-j)/(l-j)*100:0;d[m.orientation==="horizontal"?"left":"bottom"]=h+"%";this.handle.stop(1,1)[e?"animate":"css"](d,f.animate);if(g==="min"&&this.orientation==="horizontal"){this.range.stop(1,1)[e?"animate":"css"]({width:h+"%"},f.animate)}if(g==="max"&&this.orientation==="horizontal"){this.range[e?"animate":"css"]({width:(100-h)+"%"},{queue:false,duration:f.animate})}if(g==="min"&&this.orientation==="vertical"){this.range.stop(1,1)[e?"animate":"css"]({height:h+"%"},f.animate)}if(g==="max"&&this.orientation==="vertical"){this.range[e?"animate":"css"]({height:(100-h)+"%"},{queue:false,duration:f.animate})}}}});b.extend(b.ui.slider,{version:"1.8.5"})}(jQuery)); --- a/static/scripts/ui.sortable.js +++ /dev/null @@ -1,1019 +0,0 @@ -/* - * jQuery UI Sortable 1.7.2 - * - * Copyright (c) 2009 AUTHORS.txt (http://jqueryui.com/about) - * Dual licensed under the MIT (MIT-LICENSE.txt) - * and GPL (GPL-LICENSE.txt) licenses. - * - * http://docs.jquery.com/UI/Sortables - * - * Depends: - * ui.core.js - */ -(function($) { - -$.widget("ui.sortable", $.extend({}, $.ui.mouse, { - _init: function() { - - var o = this.options; - this.containerCache = {}; - this.element.addClass("ui-sortable"); - - //Get the items - this.refresh(); - - //Let's determine if the items are floating - this.floating = this.items.length ? (/left|right/).test(this.items[0].item.css('float')) : false; - - //Let's determine the parent's offset - this.offset = this.element.offset(); - - //Initialize mouse events for interaction - this._mouseInit(); - - }, - - destroy: function() { - this.element - .removeClass("ui-sortable ui-sortable-disabled") - .removeData("sortable") - .unbind(".sortable"); - this._mouseDestroy(); - - for ( var i = this.items.length - 1; i >= 0; i-- ) - this.items[i].item.removeData("sortable-item"); - }, - - _mouseCapture: function(event, overrideHandle) { - - if (this.reverting) { - return false; - } - - if(this.options.disabled || this.options.type == 'static') return false; - - //We have to refresh the items data once first - this._refreshItems(event); - - //Find out if the clicked node (or one of its parents) is a actual item in this.items - var currentItem = null, self = this, nodes = $(event.target).parents().each(function() { - if($.data(this, 'sortable-item') == self) { - currentItem = $(this); - return false; - } - }); - if($.data(event.target, 'sortable-item') == self) currentItem = $(event.target); - - if(!currentItem) return false; - if(this.options.handle && !overrideHandle) { - var validHandle = false; - - $(this.options.handle, currentItem).find("*").andSelf().each(function() { if(this == event.target) validHandle = true; }); - if(!validHandle) return false; - } - - this.currentItem = currentItem; - this._removeCurrentsFromItems(); - return true; - - }, - - _mouseStart: function(event, overrideHandle, noActivation) { - - var o = this.options, self = this; - this.currentContainer = this; - - //We only need to call refreshPositions, because the refreshItems call has been moved to mouseCapture - this.refreshPositions(); - - //Create and append the visible helper - this.helper = this._createHelper(event); - - //Cache the helper size - this._cacheHelperProportions(); - - /* - * - Position generation - - * This block generates everything position related - it's the core of draggables. - */ - - //Cache the margins of the original element - this._cacheMargins(); - - //Get the next scrolling parent - this.scrollParent = this.helper.scrollParent(); - - //The element's absolute position on the page minus margins - this.offset = this.currentItem.offset(); - this.offset = { - top: this.offset.top - this.margins.top, - left: this.offset.left - this.margins.left - }; - - // Only after we got the offset, we can change the helper's position to absolute - // TODO: Still need to figure out a way to make relative sorting possible - this.helper.css("position", "absolute"); - this.cssPosition = this.helper.css("position"); - - $.extend(this.offset, { - click: { //Where the click happened, relative to the element - left: event.pageX - this.offset.left, - top: event.pageY - this.offset.top - }, - parent: this._getParentOffset(), - relative: this._getRelativeOffset() //This is a relative to absolute position minus the actual position calculation - only used for relative positioned helper - }); - - //Generate the original position - this.originalPosition = this._generatePosition(event); - this.originalPageX = event.pageX; - this.originalPageY = event.pageY; - - //Adjust the mouse offset relative to the helper if 'cursorAt' is supplied - if(o.cursorAt) - this._adjustOffsetFromHelper(o.cursorAt); - - //Cache the former DOM position - this.domPosition = { prev: this.currentItem.prev()[0], parent: this.currentItem.parent()[0] }; - - //If the helper is not the original, hide the original so it's not playing any role during the drag, won't cause anything bad this way - if(this.helper[0] != this.currentItem[0]) { - this.currentItem.hide(); - } - - //Create the placeholder - this._createPlaceholder(); - - //Set a containment if given in the options - if(o.containment) - this._setContainment(); - - if(o.cursor) { // cursor option - if ($('body').css("cursor")) this._storedCursor = $('body').css("cursor"); - $('body').css("cursor", o.cursor); - } - - if(o.opacity) { // opacity option - if (this.helper.css("opacity")) this._storedOpacity = this.helper.css("opacity"); - this.helper.css("opacity", o.opacity); - } - - if(o.zIndex) { // zIndex option - if (this.helper.css("zIndex")) this._storedZIndex = this.helper.css("zIndex"); - this.helper.css("zIndex", o.zIndex); - } - - //Prepare scrolling - if(this.scrollParent[0] != document && this.scrollParent[0].tagName != 'HTML') - this.overflowOffset = this.scrollParent.offset(); - - //Call callbacks - this._trigger("start", event, this._uiHash()); - - //Recache the helper size - if(!this._preserveHelperProportions) - this._cacheHelperProportions(); - - - //Post 'activate' events to possible containers - if(!noActivation) { - for (var i = this.containers.length - 1; i >= 0; i--) { this.containers[i]._trigger("activate", event, self._uiHash(this)); } - } - - //Prepare possible droppables - if($.ui.ddmanager) - $.ui.ddmanager.current = this; - - if ($.ui.ddmanager && !o.dropBehaviour) - $.ui.ddmanager.prepareOffsets(this, event); - - this.dragging = true; - - this.helper.addClass("ui-sortable-helper"); - this._mouseDrag(event); //Execute the drag once - this causes the helper not to be visible before getting its correct position - return true; - - }, - - _mouseDrag: function(event) { - - //Compute the helpers position - this.position = this._generatePosition(event); - this.positionAbs = this._convertPositionTo("absolute"); - - if (!this.lastPositionAbs) { - this.lastPositionAbs = this.positionAbs; - } - - //Do scrolling - if(this.options.scroll) { - var o = this.options, scrolled = false; - if(this.scrollParent[0] != document && this.scrollParent[0].tagName != 'HTML') { - - if((this.overflowOffset.top + this.scrollParent[0].offsetHeight) - event.pageY < o.scrollSensitivity) - this.scrollParent[0].scrollTop = scrolled = this.scrollParent[0].scrollTop + o.scrollSpeed; - else if(event.pageY - this.overflowOffset.top < o.scrollSensitivity) - this.scrollParent[0].scrollTop = scrolled = this.scrollParent[0].scrollTop - o.scrollSpeed; - - if((this.overflowOffset.left + this.scrollParent[0].offsetWidth) - event.pageX < o.scrollSensitivity) - this.scrollParent[0].scrollLeft = scrolled = this.scrollParent[0].scrollLeft + o.scrollSpeed; - else if(event.pageX - this.overflowOffset.left < o.scrollSensitivity) - this.scrollParent[0].scrollLeft = scrolled = this.scrollParent[0].scrollLeft - o.scrollSpeed; - - } else { - - if(event.pageY - $(document).scrollTop() < o.scrollSensitivity) - scrolled = $(document).scrollTop($(document).scrollTop() - o.scrollSpeed); - else if($(window).height() - (event.pageY - $(document).scrollTop()) < o.scrollSensitivity) - scrolled = $(document).scrollTop($(document).scrollTop() + o.scrollSpeed); - - if(event.pageX - $(document).scrollLeft() < o.scrollSensitivity) - scrolled = $(document).scrollLeft($(document).scrollLeft() - o.scrollSpeed); - else if($(window).width() - (event.pageX - $(document).scrollLeft()) < o.scrollSensitivity) - scrolled = $(document).scrollLeft($(document).scrollLeft() + o.scrollSpeed); - - } - - if(scrolled !== false && $.ui.ddmanager && !o.dropBehaviour) - $.ui.ddmanager.prepareOffsets(this, event); - } - - //Regenerate the absolute position used for position checks - this.positionAbs = this._convertPositionTo("absolute"); - - //Set the helper position - if(!this.options.axis || this.options.axis != "y") this.helper[0].style.left = this.position.left+'px'; - if(!this.options.axis || this.options.axis != "x") this.helper[0].style.top = this.position.top+'px'; - - //Rearrange - for (var i = this.items.length - 1; i >= 0; i--) { - - //Cache variables and intersection, continue if no intersection - var item = this.items[i], itemElement = item.item[0], intersection = this._intersectsWithPointer(item); - if (!intersection) continue; - - if(itemElement != this.currentItem[0] //cannot intersect with itself - && this.placeholder[intersection == 1 ? "next" : "prev"]()[0] != itemElement //no useless actions that have been done before - && !$.ui.contains(this.placeholder[0], itemElement) //no action if the item moved is the parent of the item checked - && (this.options.type == 'semi-dynamic' ? !$.ui.contains(this.element[0], itemElement) : true) - ) { - - this.direction = intersection == 1 ? "down" : "up"; - - if (this.options.tolerance == "pointer" || this._intersectsWithSides(item)) { - this._rearrange(event, item); - } else { - break; - } - - this._trigger("change", event, this._uiHash()); - break; - } - } - - //Post events to containers - this._contactContainers(event); - - //Interconnect with droppables - if($.ui.ddmanager) $.ui.ddmanager.drag(this, event); - - //Call callbacks - this._trigger('sort', event, this._uiHash()); - - this.lastPositionAbs = this.positionAbs; - return false; - - }, - - _mouseStop: function(event, noPropagation) { - - if(!event) return; - - //If we are using droppables, inform the manager about the drop - if ($.ui.ddmanager && !this.options.dropBehaviour) - $.ui.ddmanager.drop(this, event); - - if(this.options.revert) { - var self = this; - var cur = self.placeholder.offset(); - - self.reverting = true; - - $(this.helper).animate({ - left: cur.left - this.offset.parent.left - self.margins.left + (this.offsetParent[0] == document.body ? 0 : this.offsetParent[0].scrollLeft), - top: cur.top - this.offset.parent.top - self.margins.top + (this.offsetParent[0] == document.body ? 0 : this.offsetParent[0].scrollTop) - }, parseInt(this.options.revert, 10) || 500, function() { - self._clear(event); - }); - } else { - this._clear(event, noPropagation); - } - - return false; - - }, - - cancel: function() { - - var self = this; - - if(this.dragging) { - - this._mouseUp(); - - if(this.options.helper == "original") - this.currentItem.css(this._storedCSS).removeClass("ui-sortable-helper"); - else - this.currentItem.show(); - - //Post deactivating events to containers - for (var i = this.containers.length - 1; i >= 0; i--){ - this.containers[i]._trigger("deactivate", null, self._uiHash(this)); - if(this.containers[i].containerCache.over) { - this.containers[i]._trigger("out", null, self._uiHash(this)); - this.containers[i].containerCache.over = 0; - } - } - - } - - //$(this.placeholder[0]).remove(); would have been the jQuery way - unfortunately, it unbinds ALL events from the original node! - if(this.placeholder[0].parentNode) this.placeholder[0].parentNode.removeChild(this.placeholder[0]); - if(this.options.helper != "original" && this.helper && this.helper[0].parentNode) this.helper.remove(); - - $.extend(this, { - helper: null, - dragging: false, - reverting: false, - _noFinalSort: null - }); - - if(this.domPosition.prev) { - $(this.domPosition.prev).after(this.currentItem); - } else { - $(this.domPosition.parent).prepend(this.currentItem); - } - - return true; - - }, - - serialize: function(o) { - - var items = this._getItemsAsjQuery(o && o.connected); - var str = []; o = o || {}; - - $(items).each(function() { - var res = ($(o.item || this).attr(o.attribute || 'id') || '').match(o.expression || (/(.+)[-=_](.+)/)); - if(res) str.push((o.key || res[1]+'[]')+'='+(o.key && o.expression ? res[1] : res[2])); - }); - - return str.join('&'); - - }, - - toArray: function(o) { - - var items = this._getItemsAsjQuery(o && o.connected); - var ret = []; o = o || {}; - - items.each(function() { ret.push($(o.item || this).attr(o.attribute || 'id') || ''); }); - return ret; - - }, - - /* Be careful with the following core functions */ - _intersectsWith: function(item) { - - var x1 = this.positionAbs.left, - x2 = x1 + this.helperProportions.width, - y1 = this.positionAbs.top, - y2 = y1 + this.helperProportions.height; - - var l = item.left, - r = l + item.width, - t = item.top, - b = t + item.height; - - var dyClick = this.offset.click.top, - dxClick = this.offset.click.left; - - var isOverElement = (y1 + dyClick) > t && (y1 + dyClick) < b && (x1 + dxClick) > l && (x1 + dxClick) < r; - - if( this.options.tolerance == "pointer" - || this.options.forcePointerForContainers - || (this.options.tolerance != "pointer" && this.helperProportions[this.floating ? 'width' : 'height'] > item[this.floating ? 'width' : 'height']) - ) { - return isOverElement; - } else { - - return (l < x1 + (this.helperProportions.width / 2) // Right Half - && x2 - (this.helperProportions.width / 2) < r // Left Half - && t < y1 + (this.helperProportions.height / 2) // Bottom Half - && y2 - (this.helperProportions.height / 2) < b ); // Top Half - - } - }, - - _intersectsWithPointer: function(item) { - - var isOverElementHeight = $.ui.isOverAxis(this.positionAbs.top + this.offset.click.top, item.top, item.height), - isOverElementWidth = $.ui.isOverAxis(this.positionAbs.left + this.offset.click.left, item.left, item.width), - isOverElement = isOverElementHeight && isOverElementWidth, - verticalDirection = this._getDragVerticalDirection(), - horizontalDirection = this._getDragHorizontalDirection(); - - if (!isOverElement) - return false; - - return this.floating ? - ( ((horizontalDirection && horizontalDirection == "right") || verticalDirection == "down") ? 2 : 1 ) - : ( verticalDirection && (verticalDirection == "down" ? 2 : 1) ); - - }, - - _intersectsWithSides: function(item) { - - var isOverBottomHalf = $.ui.isOverAxis(this.positionAbs.top + this.offset.click.top, item.top + (item.height/2), item.height), - isOverRightHalf = $.ui.isOverAxis(this.positionAbs.left + this.offset.click.left, item.left + (item.width/2), item.width), - verticalDirection = this._getDragVerticalDirection(), - horizontalDirection = this._getDragHorizontalDirection(); - - if (this.floating && horizontalDirection) { - return ((horizontalDirection == "right" && isOverRightHalf) || (horizontalDirection == "left" && !isOverRightHalf)); - } else { - return verticalDirection && ((verticalDirection == "down" && isOverBottomHalf) || (verticalDirection == "up" && !isOverBottomHalf)); - } - - }, - - _getDragVerticalDirection: function() { - var delta = this.positionAbs.top - this.lastPositionAbs.top; - return delta != 0 && (delta > 0 ? "down" : "up"); - }, - - _getDragHorizontalDirection: function() { - var delta = this.positionAbs.left - this.lastPositionAbs.left; - return delta != 0 && (delta > 0 ? "right" : "left"); - }, - - refresh: function(event) { - this._refreshItems(event); - this.refreshPositions(); - }, - - _connectWith: function() { - var options = this.options; - return options.connectWith.constructor == String - ? [options.connectWith] - : options.connectWith; - }, - - _getItemsAsjQuery: function(connected) { - - var self = this; - var items = []; - var queries = []; - var connectWith = this._connectWith(); - - if(connectWith && connected) { - for (var i = connectWith.length - 1; i >= 0; i--){ - var cur = $(connectWith[i]); - for (var j = cur.length - 1; j >= 0; j--){ - var inst = $.data(cur[j], 'sortable'); - if(inst && inst != this && !inst.options.disabled) { - queries.push([$.isFunction(inst.options.items) ? inst.options.items.call(inst.element) : $(inst.options.items, inst.element).not(".ui-sortable-helper"), inst]); - } - }; - }; - } - - queries.push([$.isFunction(this.options.items) ? this.options.items.call(this.element, null, { options: this.options, item: this.currentItem }) : $(this.options.items, this.element).not(".ui-sortable-helper"), this]); - - for (var i = queries.length - 1; i >= 0; i--){ - queries[i][0].each(function() { - items.push(this); - }); - }; - - return $(items); - - }, - - _removeCurrentsFromItems: function() { - - var list = this.currentItem.find(":data(sortable-item)"); - - for (var i=0; i < this.items.length; i++) { - - for (var j=0; j < list.length; j++) { - if(list[j] == this.items[i].item[0]) - this.items.splice(i,1); - }; - - }; - - }, - - _refreshItems: function(event) { - - this.items = []; - this.containers = [this]; - var items = this.items; - var self = this; - var queries = [[$.isFunction(this.options.items) ? this.options.items.call(this.element[0], event, { item: this.currentItem }) : $(this.options.items, this.element), this]]; - var connectWith = this._connectWith(); - - if(connectWith) { - for (var i = connectWith.length - 1; i >= 0; i--){ - var cur = $(connectWith[i]); - for (var j = cur.length - 1; j >= 0; j--){ - var inst = $.data(cur[j], 'sortable'); - if(inst && inst != this && !inst.options.disabled) { - queries.push([$.isFunction(inst.options.items) ? inst.options.items.call(inst.element[0], event, { item: this.currentItem }) : $(inst.options.items, inst.element), inst]); - this.containers.push(inst); - } - }; - }; - } - - for (var i = queries.length - 1; i >= 0; i--) { - var targetData = queries[i][1]; - var _queries = queries[i][0]; - - for (var j=0, queriesLength = _queries.length; j < queriesLength; j++) { - var item = $(_queries[j]); - - item.data('sortable-item', targetData); // Data for target checking (mouse manager) - - items.push({ - item: item, - instance: targetData, - width: 0, height: 0, - left: 0, top: 0 - }); - }; - }; - - }, - - refreshPositions: function(fast) { - - //This has to be redone because due to the item being moved out/into the offsetParent, the offsetParent's position will change - if(this.offsetParent && this.helper) { - this.offset.parent = this._getParentOffset(); - } - - for (var i = this.items.length - 1; i >= 0; i--){ - var item = this.items[i]; - - //We ignore calculating positions of all connected containers when we're not over them - if(item.instance != this.currentContainer && this.currentContainer && item.item[0] != this.currentItem[0]) - continue; - - var t = this.options.toleranceElement ? $(this.options.toleranceElement, item.item) : item.item; - - if (!fast) { - item.width = t.outerWidth(); - item.height = t.outerHeight(); - } - - var p = t.offset(); - item.left = p.left; - item.top = p.top; - }; - - if(this.options.custom && this.options.custom.refreshContainers) { - this.options.custom.refreshContainers.call(this); - } else { - for (var i = this.containers.length - 1; i >= 0; i--){ - var p = this.containers[i].element.offset(); - this.containers[i].containerCache.left = p.left; - this.containers[i].containerCache.top = p.top; - this.containers[i].containerCache.width = this.containers[i].element.outerWidth(); - this.containers[i].containerCache.height = this.containers[i].element.outerHeight(); - }; - } - - }, - - _createPlaceholder: function(that) { - - var self = that || this, o = self.options; - - if(!o.placeholder || o.placeholder.constructor == String) { - var className = o.placeholder; - o.placeholder = { - element: function() { - - var el = $(document.createElement(self.currentItem[0].nodeName)) - .addClass(className || self.currentItem[0].className+" ui-sortable-placeholder") - .removeClass("ui-sortable-helper")[0]; - - if(!className) - el.style.visibility = "hidden"; - - return el; - }, - update: function(container, p) { - - // 1. If a className is set as 'placeholder option, we don't force sizes - the class is responsible for that - // 2. The option 'forcePlaceholderSize can be enabled to force it even if a class name is specified - if(className && !o.forcePlaceholderSize) return; - - //If the element doesn't have a actual height by itself (without styles coming from a stylesheet), it receives the inline height from the dragged item - if(!p.height()) { p.height(self.currentItem.innerHeight() - parseInt(self.currentItem.css('paddingTop')||0, 10) - parseInt(self.currentItem.css('paddingBottom')||0, 10)); }; - if(!p.width()) { p.width(self.currentItem.innerWidth() - parseInt(self.currentItem.css('paddingLeft')||0, 10) - parseInt(self.currentItem.css('paddingRight')||0, 10)); }; - } - }; - } - - //Create the placeholder - self.placeholder = $(o.placeholder.element.call(self.element, self.currentItem)); - - //Append it after the actual current item - self.currentItem.after(self.placeholder); - - //Update the size of the placeholder (TODO: Logic to fuzzy, see line 316/317) - o.placeholder.update(self, self.placeholder); - - }, - - _contactContainers: function(event) { - for (var i = this.containers.length - 1; i >= 0; i--){ - - if(this._intersectsWith(this.containers[i].containerCache)) { - if(!this.containers[i].containerCache.over) { - - if(this.currentContainer != this.containers[i]) { - - //When entering a new container, we will find the item with the least distance and append our item near it - var dist = 10000; var itemWithLeastDistance = null; var base = this.positionAbs[this.containers[i].floating ? 'left' : 'top']; - for (var j = this.items.length - 1; j >= 0; j--) { - if(!$.ui.contains(this.containers[i].element[0], this.items[j].item[0])) continue; - var cur = this.items[j][this.containers[i].floating ? 'left' : 'top']; - if(Math.abs(cur - base) < dist) { - dist = Math.abs(cur - base); itemWithLeastDistance = this.items[j]; - } - } - - if(!itemWithLeastDistance && !this.options.dropOnEmpty) //Check if dropOnEmpty is enabled - continue; - - this.currentContainer = this.containers[i]; - itemWithLeastDistance ? this._rearrange(event, itemWithLeastDistance, null, true) : this._rearrange(event, null, this.containers[i].element, true); - this._trigger("change", event, this._uiHash()); - this.containers[i]._trigger("change", event, this._uiHash(this)); - - //Update the placeholder - this.options.placeholder.update(this.currentContainer, this.placeholder); - - } - - this.containers[i]._trigger("over", event, this._uiHash(this)); - this.containers[i].containerCache.over = 1; - } - } else { - if(this.containers[i].containerCache.over) { - this.containers[i]._trigger("out", event, this._uiHash(this)); - this.containers[i].containerCache.over = 0; - } - } - - }; - }, - - _createHelper: function(event) { - - var o = this.options; - var helper = $.isFunction(o.helper) ? $(o.helper.apply(this.element[0], [event, this.currentItem])) : (o.helper == 'clone' ? this.currentItem.clone() : this.currentItem); - - if(!helper.parents('body').length) //Add the helper to the DOM if that didn't happen already - $(o.appendTo != 'parent' ? o.appendTo : this.currentItem[0].parentNode)[0].appendChild(helper[0]); - - if(helper[0] == this.currentItem[0]) - this._storedCSS = { width: this.currentItem[0].style.width, height: this.currentItem[0].style.height, position: this.currentItem.css("position"), top: this.currentItem.css("top"), left: this.currentItem.css("left") }; - - if(helper[0].style.width == '' || o.forceHelperSize) helper.width(this.currentItem.width()); - if(helper[0].style.height == '' || o.forceHelperSize) helper.height(this.currentItem.height()); - - return helper; - - }, - - _adjustOffsetFromHelper: function(obj) { - if(obj.left != undefined) this.offset.click.left = obj.left + this.margins.left; - if(obj.right != undefined) this.offset.click.left = this.helperProportions.width - obj.right + this.margins.left; - if(obj.top != undefined) this.offset.click.top = obj.top + this.margins.top; - if(obj.bottom != undefined) this.offset.click.top = this.helperProportions.height - obj.bottom + this.margins.top; - }, - - _getParentOffset: function() { - - - //Get the offsetParent and cache its position - this.offsetParent = this.helper.offsetParent(); - var po = this.offsetParent.offset(); - - // This is a special case where we need to modify a offset calculated on start, since the following happened: - // 1. The position of the helper is absolute, so it's position is calculated based on the next positioned parent - // 2. The actual offset parent is a child of the scroll parent, and the scroll parent isn't the document, which means that - // the scroll is included in the initial calculation of the offset of the parent, and never recalculated upon drag - if(this.cssPosition == 'absolute' && this.scrollParent[0] != document && $.ui.contains(this.scrollParent[0], this.offsetParent[0])) { - po.left += this.scrollParent.scrollLeft(); - po.top += this.scrollParent.scrollTop(); - } - - if((this.offsetParent[0] == document.body) //This needs to be actually done for all browsers, since pageX/pageY includes this information - || (this.offsetParent[0].tagName && this.offsetParent[0].tagName.toLowerCase() == 'html' && $.browser.msie)) //Ugly IE fix - po = { top: 0, left: 0 }; - - return { - top: po.top + (parseInt(this.offsetParent.css("borderTopWidth"),10) || 0), - left: po.left + (parseInt(this.offsetParent.css("borderLeftWidth"),10) || 0) - }; - - }, - - _getRelativeOffset: function() { - - if(this.cssPosition == "relative") { - var p = this.currentItem.position(); - return { - top: p.top - (parseInt(this.helper.css("top"),10) || 0) + this.scrollParent.scrollTop(), - left: p.left - (parseInt(this.helper.css("left"),10) || 0) + this.scrollParent.scrollLeft() - }; - } else { - return { top: 0, left: 0 }; - } - - }, - - _cacheMargins: function() { - this.margins = { - left: (parseInt(this.currentItem.css("marginLeft"),10) || 0), - top: (parseInt(this.currentItem.css("marginTop"),10) || 0) - }; - }, - - _cacheHelperProportions: function() { - this.helperProportions = { - width: this.helper.outerWidth(), - height: this.helper.outerHeight() - }; - }, - - _setContainment: function() { - - var o = this.options; - if(o.containment == 'parent') o.containment = this.helper[0].parentNode; - if(o.containment == 'document' || o.containment == 'window') this.containment = [ - 0 - this.offset.relative.left - this.offset.parent.left, - 0 - this.offset.relative.top - this.offset.parent.top, - $(o.containment == 'document' ? document : window).width() - this.helperProportions.width - this.margins.left, - ($(o.containment == 'document' ? document : window).height() || document.body.parentNode.scrollHeight) - this.helperProportions.height - this.margins.top - ]; - - if(!(/^(document|window|parent)$/).test(o.containment)) { - var ce = $(o.containment)[0]; - var co = $(o.containment).offset(); - var over = ($(ce).css("overflow") != 'hidden'); - - this.containment = [ - co.left + (parseInt($(ce).css("borderLeftWidth"),10) || 0) + (parseInt($(ce).css("paddingLeft"),10) || 0) - this.margins.left, - co.top + (parseInt($(ce).css("borderTopWidth"),10) || 0) + (parseInt($(ce).css("paddingTop"),10) || 0) - this.margins.top, - co.left+(over ? Math.max(ce.scrollWidth,ce.offsetWidth) : ce.offsetWidth) - (parseInt($(ce).css("borderLeftWidth"),10) || 0) - (parseInt($(ce).css("paddingRight"),10) || 0) - this.helperProportions.width - this.margins.left, - co.top+(over ? Math.max(ce.scrollHeight,ce.offsetHeight) : ce.offsetHeight) - (parseInt($(ce).css("borderTopWidth"),10) || 0) - (parseInt($(ce).css("paddingBottom"),10) || 0) - this.helperProportions.height - this.margins.top - ]; - } - - }, - - _convertPositionTo: function(d, pos) { - - if(!pos) pos = this.position; - var mod = d == "absolute" ? 1 : -1; - var o = this.options, scroll = this.cssPosition == 'absolute' && !(this.scrollParent[0] != document && $.ui.contains(this.scrollParent[0], this.offsetParent[0])) ? this.offsetParent : this.scrollParent, scrollIsRootNode = (/(html|body)/i).test(scroll[0].tagName); - - return { - top: ( - pos.top // The absolute mouse position - + this.offset.relative.top * mod // Only for relative positioned nodes: Relative offset from element to offset parent - + this.offset.parent.top * mod // The offsetParent's offset without borders (offset + border) - - ($.browser.safari && this.cssPosition == 'fixed' ? 0 : ( this.cssPosition == 'fixed' ? -this.scrollParent.scrollTop() : ( scrollIsRootNode ? 0 : scroll.scrollTop() ) ) * mod) - ), - left: ( - pos.left // The absolute mouse position - + this.offset.relative.left * mod // Only for relative positioned nodes: Relative offset from element to offset parent - + this.offset.parent.left * mod // The offsetParent's offset without borders (offset + border) - - ($.browser.safari && this.cssPosition == 'fixed' ? 0 : ( this.cssPosition == 'fixed' ? -this.scrollParent.scrollLeft() : scrollIsRootNode ? 0 : scroll.scrollLeft() ) * mod) - ) - }; - - }, - - _generatePosition: function(event) { - - var o = this.options, scroll = this.cssPosition == 'absolute' && !(this.scrollParent[0] != document && $.ui.contains(this.scrollParent[0], this.offsetParent[0])) ? this.offsetParent : this.scrollParent, scrollIsRootNode = (/(html|body)/i).test(scroll[0].tagName); - - // This is another very weird special case that only happens for relative elements: - // 1. If the css position is relative - // 2. and the scroll parent is the document or similar to the offset parent - // we have to refresh the relative offset during the scroll so there are no jumps - if(this.cssPosition == 'relative' && !(this.scrollParent[0] != document && this.scrollParent[0] != this.offsetParent[0])) { - this.offset.relative = this._getRelativeOffset(); - } - - var pageX = event.pageX; - var pageY = event.pageY; - - /* - * - Position constraining - - * Constrain the position to a mix of grid, containment. - */ - - if(this.originalPosition) { //If we are not dragging yet, we won't check for options - - if(this.containment) { - if(event.pageX - this.offset.click.left < this.containment[0]) pageX = this.containment[0] + this.offset.click.left; - if(event.pageY - this.offset.click.top < this.containment[1]) pageY = this.containment[1] + this.offset.click.top; - if(event.pageX - this.offset.click.left > this.containment[2]) pageX = this.containment[2] + this.offset.click.left; - if(event.pageY - this.offset.click.top > this.containment[3]) pageY = this.containment[3] + this.offset.click.top; - } - - if(o.grid) { - var top = this.originalPageY + Math.round((pageY - this.originalPageY) / o.grid[1]) * o.grid[1]; - pageY = this.containment ? (!(top - this.offset.click.top < this.containment[1] || top - this.offset.click.top > this.containment[3]) ? top : (!(top - this.offset.click.top < this.containment[1]) ? top - o.grid[1] : top + o.grid[1])) : top; - - var left = this.originalPageX + Math.round((pageX - this.originalPageX) / o.grid[0]) * o.grid[0]; - pageX = this.containment ? (!(left - this.offset.click.left < this.containment[0] || left - this.offset.click.left > this.containment[2]) ? left : (!(left - this.offset.click.left < this.containment[0]) ? left - o.grid[0] : left + o.grid[0])) : left; - } - - } - - return { - top: ( - pageY // The absolute mouse position - - this.offset.click.top // Click offset (relative to the element) - - this.offset.relative.top // Only for relative positioned nodes: Relative offset from element to offset parent - - this.offset.parent.top // The offsetParent's offset without borders (offset + border) - + ($.browser.safari && this.cssPosition == 'fixed' ? 0 : ( this.cssPosition == 'fixed' ? -this.scrollParent.scrollTop() : ( scrollIsRootNode ? 0 : scroll.scrollTop() ) )) - ), - left: ( - pageX // The absolute mouse position - - this.offset.click.left // Click offset (relative to the element) - - this.offset.relative.left // Only for relative positioned nodes: Relative offset from element to offset parent - - this.offset.parent.left // The offsetParent's offset without borders (offset + border) - + ($.browser.safari && this.cssPosition == 'fixed' ? 0 : ( this.cssPosition == 'fixed' ? -this.scrollParent.scrollLeft() : scrollIsRootNode ? 0 : scroll.scrollLeft() )) - ) - }; - - }, - - _rearrange: function(event, i, a, hardRefresh) { - - a ? a[0].appendChild(this.placeholder[0]) : i.item[0].parentNode.insertBefore(this.placeholder[0], (this.direction == 'down' ? i.item[0] : i.item[0].nextSibling)); - - //Various things done here to improve the performance: - // 1. we create a setTimeout, that calls refreshPositions - // 2. on the instance, we have a counter variable, that get's higher after every append - // 3. on the local scope, we copy the counter variable, and check in the timeout, if it's still the same - // 4. this lets only the last addition to the timeout stack through - this.counter = this.counter ? ++this.counter : 1; - var self = this, counter = this.counter; - - window.setTimeout(function() { - if(counter == self.counter) self.refreshPositions(!hardRefresh); //Precompute after each DOM insertion, NOT on mousemove - },0); - - }, - - _clear: function(event, noPropagation) { - - this.reverting = false; - // We delay all events that have to be triggered to after the point where the placeholder has been removed and - // everything else normalized again - var delayedTriggers = [], self = this; - - // We first have to update the dom position of the actual currentItem - // Note: don't do it if the current item is already removed (by a user), or it gets reappended (see #4088) - if(!this._noFinalSort && this.currentItem[0].parentNode) this.placeholder.before(this.currentItem); - this._noFinalSort = null; - - if(this.helper[0] == this.currentItem[0]) { - for(var i in this._storedCSS) { - if(this._storedCSS[i] == 'auto' || this._storedCSS[i] == 'static') this._storedCSS[i] = ''; - } - this.currentItem.css(this._storedCSS).removeClass("ui-sortable-helper"); - } else { - this.currentItem.show(); - } - - if(this.fromOutside && !noPropagation) delayedTriggers.push(function(event) { this._trigger("receive", event, this._uiHash(this.fromOutside)); }); - if((this.fromOutside || this.domPosition.prev != this.currentItem.prev().not(".ui-sortable-helper")[0] || this.domPosition.parent != this.currentItem.parent()[0]) && !noPropagation) delayedTriggers.push(function(event) { this._trigger("update", event, this._uiHash()); }); //Trigger update callback if the DOM position has changed - if(!$.ui.contains(this.element[0], this.currentItem[0])) { //Node was moved out of the current element - if(!noPropagation) delayedTriggers.push(function(event) { this._trigger("remove", event, this._uiHash()); }); - for (var i = this.containers.length - 1; i >= 0; i--){ - if($.ui.contains(this.containers[i].element[0], this.currentItem[0]) && !noPropagation) { - delayedTriggers.push((function(c) { return function(event) { c._trigger("receive", event, this._uiHash(this)); }; }).call(this, this.containers[i])); - delayedTriggers.push((function(c) { return function(event) { c._trigger("update", event, this._uiHash(this)); }; }).call(this, this.containers[i])); - } - }; - }; - - //Post events to containers - for (var i = this.containers.length - 1; i >= 0; i--){ - if(!noPropagation) delayedTriggers.push((function(c) { return function(event) { c._trigger("deactivate", event, this._uiHash(this)); }; }).call(this, this.containers[i])); - if(this.containers[i].containerCache.over) { - delayedTriggers.push((function(c) { return function(event) { c._trigger("out", event, this._uiHash(this)); }; }).call(this, this.containers[i])); - this.containers[i].containerCache.over = 0; - } - } - - //Do what was originally in plugins - if(this._storedCursor) $('body').css("cursor", this._storedCursor); //Reset cursor - if(this._storedOpacity) this.helper.css("opacity", this._storedOpacity); //Reset cursor - if(this._storedZIndex) this.helper.css("zIndex", this._storedZIndex == 'auto' ? '' : this._storedZIndex); //Reset z-index - - this.dragging = false; - if(this.cancelHelperRemoval) { - if(!noPropagation) { - this._trigger("beforeStop", event, this._uiHash()); - for (var i=0; i < delayedTriggers.length; i++) { delayedTriggers[i].call(this, event); }; //Trigger all delayed events - this._trigger("stop", event, this._uiHash()); - } - return false; - } - - if(!noPropagation) this._trigger("beforeStop", event, this._uiHash()); - - //$(this.placeholder[0]).remove(); would have been the jQuery way - unfortunately, it unbinds ALL events from the original node! - this.placeholder[0].parentNode.removeChild(this.placeholder[0]); - - if(this.helper[0] != this.currentItem[0]) this.helper.remove(); this.helper = null; - - if(!noPropagation) { - for (var i=0; i < delayedTriggers.length; i++) { delayedTriggers[i].call(this, event); }; //Trigger all delayed events - this._trigger("stop", event, this._uiHash()); - } - - this.fromOutside = false; - return true; - - }, - - _trigger: function() { - if ($.widget.prototype._trigger.apply(this, arguments) === false) { - this.cancel(); - } - }, - - _uiHash: function(inst) { - var self = inst || this; - return { - helper: self.helper, - placeholder: self.placeholder || $([]), - position: self.position, - absolutePosition: self.positionAbs, //deprecated - offset: self.positionAbs, - item: self.currentItem, - sender: inst ? inst.element : null - }; - } - -})); - -$.extend($.ui.sortable, { - getter: "serialize toArray", - version: "1.7.2", - eventPrefix: "sort", - defaults: { - appendTo: "parent", - axis: false, - cancel: ":input,option", - connectWith: false, - containment: false, - cursor: 'auto', - cursorAt: false, - delay: 0, - distance: 1, - dropOnEmpty: true, - forcePlaceholderSize: false, - forceHelperSize: false, - grid: false, - handle: false, - helper: "original", - items: '> *', - opacity: false, - placeholder: false, - revert: false, - scroll: true, - scrollSensitivity: 20, - scrollSpeed: 20, - scope: "default", - tolerance: "intersect", - zIndex: 1000 - } -}); - -})(jQuery); --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -45,7 +45,10 @@ class TracksDataProvider( object ): try: column_names = self.original_dataset.datatype.column_names except AttributeError: - column_names = range( self.original_dataset.metadata.columns ) + try: + column_names = range( self.original_dataset.metadata.columns ) + except: # Give up + return [] # Dataset must have column types; if not, cannot create filters. try: --- a/static/scripts/ui.core.js +++ /dev/null @@ -1,519 +0,0 @@ -/* - * jQuery UI 1.7.2 - * - * Copyright (c) 2009 AUTHORS.txt (http://jqueryui.com/about) - * Dual licensed under the MIT (MIT-LICENSE.txt) - * and GPL (GPL-LICENSE.txt) licenses. - * - * http://docs.jquery.com/UI - */ -;jQuery.ui || (function($) { - -var _remove = $.fn.remove, - isFF2 = $.browser.mozilla && (parseFloat($.browser.version) < 1.9); - -//Helper functions and ui object -$.ui = { - version: "1.7.2", - - // $.ui.plugin is deprecated. Use the proxy pattern instead. - plugin: { - add: function(module, option, set) { - var proto = $.ui[module].prototype; - for(var i in set) { - proto.plugins[i] = proto.plugins[i] || []; - proto.plugins[i].push([option, set[i]]); - } - }, - call: function(instance, name, args) { - var set = instance.plugins[name]; - if(!set || !instance.element[0].parentNode) { return; } - - for (var i = 0; i < set.length; i++) { - if (instance.options[set[i][0]]) { - set[i][1].apply(instance.element, args); - } - } - } - }, - - contains: function(a, b) { - return document.compareDocumentPosition - ? a.compareDocumentPosition(b) & 16 - : a !== b && a.contains(b); - }, - - hasScroll: function(el, a) { - - //If overflow is hidden, the element might have extra content, but the user wants to hide it - if ($(el).css('overflow') == 'hidden') { return false; } - - var scroll = (a && a == 'left') ? 'scrollLeft' : 'scrollTop', - has = false; - - if (el[scroll] > 0) { return true; } - - // TODO: determine which cases actually cause this to happen - // if the element doesn't have the scroll set, see if it's possible to - // set the scroll - el[scroll] = 1; - has = (el[scroll] > 0); - el[scroll] = 0; - return has; - }, - - isOverAxis: function(x, reference, size) { - //Determines when x coordinate is over "b" element axis - return (x > reference) && (x < (reference + size)); - }, - - isOver: function(y, x, top, left, height, width) { - //Determines when x, y coordinates is over "b" element - return $.ui.isOverAxis(y, top, height) && $.ui.isOverAxis(x, left, width); - }, - - keyCode: { - BACKSPACE: 8, - CAPS_LOCK: 20, - COMMA: 188, - CONTROL: 17, - DELETE: 46, - DOWN: 40, - END: 35, - ENTER: 13, - ESCAPE: 27, - HOME: 36, - INSERT: 45, - LEFT: 37, - NUMPAD_ADD: 107, - NUMPAD_DECIMAL: 110, - NUMPAD_DIVIDE: 111, - NUMPAD_ENTER: 108, - NUMPAD_MULTIPLY: 106, - NUMPAD_SUBTRACT: 109, - PAGE_DOWN: 34, - PAGE_UP: 33, - PERIOD: 190, - RIGHT: 39, - SHIFT: 16, - SPACE: 32, - TAB: 9, - UP: 38 - } -}; - -// WAI-ARIA normalization -if (isFF2) { - var attr = $.attr, - removeAttr = $.fn.removeAttr, - ariaNS = "http://www.w3.org/2005/07/aaa", - ariaState = /^aria-/, - ariaRole = /^wairole:/; - - $.attr = function(elem, name, value) { - var set = value !== undefined; - - return (name == 'role' - ? (set - ? attr.call(this, elem, name, "wairole:" + value) - : (attr.apply(this, arguments) || "").replace(ariaRole, "")) - : (ariaState.test(name) - ? (set - ? elem.setAttributeNS(ariaNS, - name.replace(ariaState, "aaa:"), value) - : attr.call(this, elem, name.replace(ariaState, "aaa:"))) - : attr.apply(this, arguments))); - }; - - $.fn.removeAttr = function(name) { - return (ariaState.test(name) - ? this.each(function() { - this.removeAttributeNS(ariaNS, name.replace(ariaState, "")); - }) : removeAttr.call(this, name)); - }; -} - -//jQuery plugins -$.fn.extend({ - remove: function() { - // Safari has a native remove event which actually removes DOM elements, - // so we have to use triggerHandler instead of trigger (#3037). - $("*", this).add(this).each(function() { - $(this).triggerHandler("remove"); - }); - return _remove.apply(this, arguments ); - }, - - enableSelection: function() { - return this - .attr('unselectable', 'off') - .css('MozUserSelect', '') - .unbind('selectstart.ui'); - }, - - disableSelection: function() { - return this - .attr('unselectable', 'on') - .css('MozUserSelect', 'none') - .bind('selectstart.ui', function() { return false; }); - }, - - scrollParent: function() { - var scrollParent; - if(($.browser.msie && (/(static|relative)/).test(this.css('position'))) || (/absolute/).test(this.css('position'))) { - scrollParent = this.parents().filter(function() { - return (/(relative|absolute|fixed)/).test($.curCSS(this,'position',1)) && (/(auto|scroll)/).test($.curCSS(this,'overflow',1)+$.curCSS(this,'overflow-y',1)+$.curCSS(this,'overflow-x',1)); - }).eq(0); - } else { - scrollParent = this.parents().filter(function() { - return (/(auto|scroll)/).test($.curCSS(this,'overflow',1)+$.curCSS(this,'overflow-y',1)+$.curCSS(this,'overflow-x',1)); - }).eq(0); - } - - return (/fixed/).test(this.css('position')) || !scrollParent.length ? $(document) : scrollParent; - } -}); - - -//Additional selectors -$.extend($.expr[':'], { - data: function(elem, i, match) { - return !!$.data(elem, match[3]); - }, - - focusable: function(element) { - var nodeName = element.nodeName.toLowerCase(), - tabIndex = $.attr(element, 'tabindex'); - return (/input|select|textarea|button|object/.test(nodeName) - ? !element.disabled - : 'a' == nodeName || 'area' == nodeName - ? element.href || !isNaN(tabIndex) - : !isNaN(tabIndex)) - // the element and all of its ancestors must be visible - // the browser may report that the area is hidden - && !$(element)['area' == nodeName ? 'parents' : 'closest'](':hidden').length; - }, - - tabbable: function(element) { - var tabIndex = $.attr(element, 'tabindex'); - return (isNaN(tabIndex) || tabIndex >= 0) && $(element).is(':focusable'); - } -}); - - -// $.widget is a factory to create jQuery plugins -// taking some boilerplate code out of the plugin code -function getter(namespace, plugin, method, args) { - function getMethods(type) { - var methods = $[namespace][plugin][type] || []; - return (typeof methods == 'string' ? methods.split(/,?\s+/) : methods); - } - - var methods = getMethods('getter'); - if (args.length == 1 && typeof args[0] == 'string') { - methods = methods.concat(getMethods('getterSetter')); - } - return ($.inArray(method, methods) != -1); -} - -$.widget = function(name, prototype) { - var namespace = name.split(".")[0]; - name = name.split(".")[1]; - - // create plugin method - $.fn[name] = function(options) { - var isMethodCall = (typeof options == 'string'), - args = Array.prototype.slice.call(arguments, 1); - - // prevent calls to internal methods - if (isMethodCall && options.substring(0, 1) == '_') { - return this; - } - - // handle getter methods - if (isMethodCall && getter(namespace, name, options, args)) { - var instance = $.data(this[0], name); - return (instance ? instance[options].apply(instance, args) - : undefined); - } - - // handle initialization and non-getter methods - return this.each(function() { - var instance = $.data(this, name); - - // constructor - (!instance && !isMethodCall && - $.data(this, name, new $[namespace][name](this, options))._init()); - - // method call - (instance && isMethodCall && $.isFunction(instance[options]) && - instance[options].apply(instance, args)); - }); - }; - - // create widget constructor - $[namespace] = $[namespace] || {}; - $[namespace][name] = function(element, options) { - var self = this; - - this.namespace = namespace; - this.widgetName = name; - this.widgetEventPrefix = $[namespace][name].eventPrefix || name; - this.widgetBaseClass = namespace + '-' + name; - - this.options = $.extend({}, - $.widget.defaults, - $[namespace][name].defaults, - $.metadata && $.metadata.get(element)[name], - options); - - this.element = $(element) - .bind('setData.' + name, function(event, key, value) { - if (event.target == element) { - return self._setData(key, value); - } - }) - .bind('getData.' + name, function(event, key) { - if (event.target == element) { - return self._getData(key); - } - }) - .bind('remove', function() { - return self.destroy(); - }); - }; - - // add widget prototype - $[namespace][name].prototype = $.extend({}, $.widget.prototype, prototype); - - // TODO: merge getter and getterSetter properties from widget prototype - // and plugin prototype - $[namespace][name].getterSetter = 'option'; -}; - -$.widget.prototype = { - _init: function() {}, - destroy: function() { - this.element.removeData(this.widgetName) - .removeClass(this.widgetBaseClass + '-disabled' + ' ' + this.namespace + '-state-disabled') - .removeAttr('aria-disabled'); - }, - - option: function(key, value) { - var options = key, - self = this; - - if (typeof key == "string") { - if (value === undefined) { - return this._getData(key); - } - options = {}; - options[key] = value; - } - - $.each(options, function(key, value) { - self._setData(key, value); - }); - }, - _getData: function(key) { - return this.options[key]; - }, - _setData: function(key, value) { - this.options[key] = value; - - if (key == 'disabled') { - this.element - [value ? 'addClass' : 'removeClass']( - this.widgetBaseClass + '-disabled' + ' ' + - this.namespace + '-state-disabled') - .attr("aria-disabled", value); - } - }, - - enable: function() { - this._setData('disabled', false); - }, - disable: function() { - this._setData('disabled', true); - }, - - _trigger: function(type, event, data) { - var callback = this.options[type], - eventName = (type == this.widgetEventPrefix - ? type : this.widgetEventPrefix + type); - - event = $.Event(event); - event.type = eventName; - - // copy original event properties over to the new event - // this would happen if we could call $.event.fix instead of $.Event - // but we don't have a way to force an event to be fixed multiple times - if (event.originalEvent) { - for (var i = $.event.props.length, prop; i;) { - prop = $.event.props[--i]; - event[prop] = event.originalEvent[prop]; - } - } - - this.element.trigger(event, data); - - return !($.isFunction(callback) && callback.call(this.element[0], event, data) === false - || event.isDefaultPrevented()); - } -}; - -$.widget.defaults = { - disabled: false -}; - - -/** Mouse Interaction Plugin **/ - -$.ui.mouse = { - _mouseInit: function() { - var self = this; - - this.element - .bind('mousedown.'+this.widgetName, function(event) { - return self._mouseDown(event); - }) - .bind('click.'+this.widgetName, function(event) { - if(self._preventClickEvent) { - self._preventClickEvent = false; - event.stopImmediatePropagation(); - return false; - } - }); - - // Prevent text selection in IE - if ($.browser.msie) { - this._mouseUnselectable = this.element.attr('unselectable'); - this.element.attr('unselectable', 'on'); - } - - this.started = false; - }, - - // TODO: make sure destroying one instance of mouse doesn't mess with - // other instances of mouse - _mouseDestroy: function() { - this.element.unbind('.'+this.widgetName); - - // Restore text selection in IE - ($.browser.msie - && this.element.attr('unselectable', this._mouseUnselectable)); - }, - - _mouseDown: function(event) { - // don't let more than one widget handle mouseStart - // TODO: figure out why we have to use originalEvent - event.originalEvent = event.originalEvent || {}; - if (event.originalEvent.mouseHandled) { return; } - - // we may have missed mouseup (out of window) - (this._mouseStarted && this._mouseUp(event)); - - this._mouseDownEvent = event; - - var self = this, - btnIsLeft = (event.which == 1), - elIsCancel = (typeof this.options.cancel == "string" ? $(event.target).parents().add(event.target).filter(this.options.cancel).length : false); - if (!btnIsLeft || elIsCancel || !this._mouseCapture(event)) { - return true; - } - - this.mouseDelayMet = !this.options.delay; - if (!this.mouseDelayMet) { - this._mouseDelayTimer = setTimeout(function() { - self.mouseDelayMet = true; - }, this.options.delay); - } - - if (this._mouseDistanceMet(event) && this._mouseDelayMet(event)) { - this._mouseStarted = (this._mouseStart(event) !== false); - if (!this._mouseStarted) { - event.preventDefault(); - return true; - } - } - - // these delegates are required to keep context - this._mouseMoveDelegate = function(event) { - return self._mouseMove(event); - }; - this._mouseUpDelegate = function(event) { - return self._mouseUp(event); - }; - $(document) - .bind('mousemove.'+this.widgetName, this._mouseMoveDelegate) - .bind('mouseup.'+this.widgetName, this._mouseUpDelegate); - - // preventDefault() is used to prevent the selection of text here - - // however, in Safari, this causes select boxes not to be selectable - // anymore, so this fix is needed - ($.browser.safari || event.preventDefault()); - - event.originalEvent.mouseHandled = true; - return true; - }, - - _mouseMove: function(event) { - // IE mouseup check - mouseup happened when mouse was out of window - if ($.browser.msie && !event.button) { - return this._mouseUp(event); - } - - if (this._mouseStarted) { - this._mouseDrag(event); - return event.preventDefault(); - } - - if (this._mouseDistanceMet(event) && this._mouseDelayMet(event)) { - this._mouseStarted = - (this._mouseStart(this._mouseDownEvent, event) !== false); - (this._mouseStarted ? this._mouseDrag(event) : this._mouseUp(event)); - } - - return !this._mouseStarted; - }, - - _mouseUp: function(event) { - $(document) - .unbind('mousemove.'+this.widgetName, this._mouseMoveDelegate) - .unbind('mouseup.'+this.widgetName, this._mouseUpDelegate); - - if (this._mouseStarted) { - this._mouseStarted = false; - this._preventClickEvent = (event.target == this._mouseDownEvent.target); - this._mouseStop(event); - } - - return false; - }, - - _mouseDistanceMet: function(event) { - return (Math.max( - Math.abs(this._mouseDownEvent.pageX - event.pageX), - Math.abs(this._mouseDownEvent.pageY - event.pageY) - ) >= this.options.distance - ); - }, - - _mouseDelayMet: function(event) { - return this.mouseDelayMet; - }, - - // These are placeholder methods, to be overriden by extending plugin - _mouseStart: function(event) {}, - _mouseDrag: function(event) {}, - _mouseStop: function(event) {}, - _mouseCapture: function(event) { return true; } -}; - -$.ui.mouse.defaults = { - cancel: null, - distance: 1, - delay: 0 -}; - -})(jQuery); --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -51,7 +51,7 @@ <%def name="javascripts()"> ${parent.javascripts()} -${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jquery.event.drag", "jquery.autocomplete", "jquery.mousewheel", "trackster", "ui.core", "ui.sortable" )} +${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jquery.event.drag", "jquery.autocomplete", "trackster", "jquery.ui.sortable.slider" )} <script type="text/javascript"> @@ -64,6 +64,7 @@ %if config: view = new View( $("#center"), "${config.get('chrom')}", "${config.get('title') | h}", "${config.get('vis_id')}", "${config.get('dbkey')}" ); + view.editor = true; %for track in config.get('tracks'): view.add_track( new ${track["track_type"]}( "${track['name'] | h}", view, ${track['dataset_id']}, ${track['prefs']} ) @@ -73,6 +74,7 @@ %else: var continue_fn = function() { view = new View( $("#center"), undefined, $("#new-title").val(), undefined, $("#new-dbkey").val() ); + view.editor = true; init(); hide_modal(); }; @@ -109,7 +111,6 @@ // Execute initializer for EDITOR specific javascript function init() { - if (view.num_tracks === 0) { $("#no-tracks").show(); } --- /dev/null +++ b/static/scripts/jquery.ui.sortable.slider.js @@ -0,0 +1,2458 @@ +/*! + * jQuery UI 1.8.5 + * + * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT or GPL Version 2 licenses. + * http://jquery.org/license + * + * http://docs.jquery.com/UI + */ +(function( $, undefined ) { + +// prevent duplicate loading +// this is only a problem because we proxy existing functions +// and we don't want to double proxy them +$.ui = $.ui || {}; +if ( $.ui.version ) { + return; +} + +$.extend( $.ui, { + version: "1.8.5", + + keyCode: { + ALT: 18, + BACKSPACE: 8, + CAPS_LOCK: 20, + COMMA: 188, + COMMAND: 91, + COMMAND_LEFT: 91, // COMMAND + COMMAND_RIGHT: 93, + CONTROL: 17, + DELETE: 46, + DOWN: 40, + END: 35, + ENTER: 13, + ESCAPE: 27, + HOME: 36, + INSERT: 45, + LEFT: 37, + MENU: 93, // COMMAND_RIGHT + NUMPAD_ADD: 107, + NUMPAD_DECIMAL: 110, + NUMPAD_DIVIDE: 111, + NUMPAD_ENTER: 108, + NUMPAD_MULTIPLY: 106, + NUMPAD_SUBTRACT: 109, + PAGE_DOWN: 34, + PAGE_UP: 33, + PERIOD: 190, + RIGHT: 39, + SHIFT: 16, + SPACE: 32, + TAB: 9, + UP: 38, + WINDOWS: 91 // COMMAND + } +}); + +// plugins +$.fn.extend({ + _focus: $.fn.focus, + focus: function( delay, fn ) { + return typeof delay === "number" ? + this.each(function() { + var elem = this; + setTimeout(function() { + $( elem ).focus(); + if ( fn ) { + fn.call( elem ); + } + }, delay ); + }) : + this._focus.apply( this, arguments ); + }, + + scrollParent: function() { + var scrollParent; + if (($.browser.msie && (/(static|relative)/).test(this.css('position'))) || (/absolute/).test(this.css('position'))) { + scrollParent = this.parents().filter(function() { + return (/(relative|absolute|fixed)/).test($.curCSS(this,'position',1)) && (/(auto|scroll)/).test($.curCSS(this,'overflow',1)+$.curCSS(this,'overflow-y',1)+$.curCSS(this,'overflow-x',1)); + }).eq(0); + } else { + scrollParent = this.parents().filter(function() { + return (/(auto|scroll)/).test($.curCSS(this,'overflow',1)+$.curCSS(this,'overflow-y',1)+$.curCSS(this,'overflow-x',1)); + }).eq(0); + } + + return (/fixed/).test(this.css('position')) || !scrollParent.length ? $(document) : scrollParent; + }, + + zIndex: function( zIndex ) { + if ( zIndex !== undefined ) { + return this.css( "zIndex", zIndex ); + } + + if ( this.length ) { + var elem = $( this[ 0 ] ), position, value; + while ( elem.length && elem[ 0 ] !== document ) { + // Ignore z-index if position is set to a value where z-index is ignored by the browser + // This makes behavior of this function consistent across browsers + // WebKit always returns auto if the element is positioned + position = elem.css( "position" ); + if ( position === "absolute" || position === "relative" || position === "fixed" ) { + // IE returns 0 when zIndex is not specified + // other browsers return a string + // we ignore the case of nested elements with an explicit value of 0 + // <div style="z-index: -10;"><div style="z-index: 0;"></div></div> + value = parseInt( elem.css( "zIndex" ) ); + if ( !isNaN( value ) && value != 0 ) { + return value; + } + } + elem = elem.parent(); + } + } + + return 0; + }, + + disableSelection: function() { + return this.bind( + "mousedown.ui-disableSelection selectstart.ui-disableSelection", + function( event ) { + event.preventDefault(); + }); + }, + + enableSelection: function() { + return this.unbind( ".ui-disableSelection" ); + } +}); + +$.each( [ "Width", "Height" ], function( i, name ) { + var side = name === "Width" ? [ "Left", "Right" ] : [ "Top", "Bottom" ], + type = name.toLowerCase(), + orig = { + innerWidth: $.fn.innerWidth, + innerHeight: $.fn.innerHeight, + outerWidth: $.fn.outerWidth, + outerHeight: $.fn.outerHeight + }; + + function reduce( elem, size, border, margin ) { + $.each( side, function() { + size -= parseFloat( $.curCSS( elem, "padding" + this, true) ) || 0; + if ( border ) { + size -= parseFloat( $.curCSS( elem, "border" + this + "Width", true) ) || 0; + } + if ( margin ) { + size -= parseFloat( $.curCSS( elem, "margin" + this, true) ) || 0; + } + }); + return size; + } + + $.fn[ "inner" + name ] = function( size ) { + if ( size === undefined ) { + return orig[ "inner" + name ].call( this ); + } + + return this.each(function() { + $.style( this, type, reduce( this, size ) + "px" ); + }); + }; + + $.fn[ "outer" + name] = function( size, margin ) { + if ( typeof size !== "number" ) { + return orig[ "outer" + name ].call( this, size ); + } + + return this.each(function() { + $.style( this, type, reduce( this, size, true, margin ) + "px" ); + }); + }; +}); + +// selectors +function visible( element ) { + return !$( element ).parents().andSelf().filter(function() { + return $.curCSS( this, "visibility" ) === "hidden" || + $.expr.filters.hidden( this ); + }).length; +} + +$.extend( $.expr[ ":" ], { + data: function( elem, i, match ) { + return !!$.data( elem, match[ 3 ] ); + }, + + focusable: function( element ) { + var nodeName = element.nodeName.toLowerCase(), + tabIndex = $.attr( element, "tabindex" ); + if ( "area" === nodeName ) { + var map = element.parentNode, + mapName = map.name, + img; + if ( !element.href || !mapName || map.nodeName.toLowerCase() !== "map" ) { + return false; + } + img = $( "img[usemap=#" + mapName + "]" )[0]; + return !!img && visible( img ); + } + return ( /input|select|textarea|button|object/.test( nodeName ) + ? !element.disabled + : "a" == nodeName + ? element.href || !isNaN( tabIndex ) + : !isNaN( tabIndex )) + // the element and all of its ancestors must be visible + && visible( element ); + }, + + tabbable: function( element ) { + var tabIndex = $.attr( element, "tabindex" ); + return ( isNaN( tabIndex ) || tabIndex >= 0 ) && $( element ).is( ":focusable" ); + } +}); + +// support +$(function() { + var div = document.createElement( "div" ), + body = document.body; + + $.extend( div.style, { + minHeight: "100px", + height: "auto", + padding: 0, + borderWidth: 0 + }); + + $.support.minHeight = body.appendChild( div ).offsetHeight === 100; + // set display to none to avoid a layout bug in IE + // http://dev.jquery.com/ticket/4014 + body.removeChild( div ).style.display = "none"; +}); + + + + + +// deprecated +$.extend( $.ui, { + // $.ui.plugin is deprecated. Use the proxy pattern instead. + plugin: { + add: function( module, option, set ) { + var proto = $.ui[ module ].prototype; + for ( var i in set ) { + proto.plugins[ i ] = proto.plugins[ i ] || []; + proto.plugins[ i ].push( [ option, set[ i ] ] ); + } + }, + call: function( instance, name, args ) { + var set = instance.plugins[ name ]; + if ( !set || !instance.element[ 0 ].parentNode ) { + return; + } + + for ( var i = 0; i < set.length; i++ ) { + if ( instance.options[ set[ i ][ 0 ] ] ) { + set[ i ][ 1 ].apply( instance.element, args ); + } + } + } + }, + + // will be deprecated when we switch to jQuery 1.4 - use jQuery.contains() + contains: function( a, b ) { + return document.compareDocumentPosition ? + a.compareDocumentPosition( b ) & 16 : + a !== b && a.contains( b ); + }, + + // only used by resizable + hasScroll: function( el, a ) { + + //If overflow is hidden, the element might have extra content, but the user wants to hide it + if ( $( el ).css( "overflow" ) === "hidden") { + return false; + } + + var scroll = ( a && a === "left" ) ? "scrollLeft" : "scrollTop", + has = false; + + if ( el[ scroll ] > 0 ) { + return true; + } + + // TODO: determine which cases actually cause this to happen + // if the element doesn't have the scroll set, see if it's possible to + // set the scroll + el[ scroll ] = 1; + has = ( el[ scroll ] > 0 ); + el[ scroll ] = 0; + return has; + }, + + // these are odd functions, fix the API or move into individual plugins + isOverAxis: function( x, reference, size ) { + //Determines when x coordinate is over "b" element axis + return ( x > reference ) && ( x < ( reference + size ) ); + }, + isOver: function( y, x, top, left, height, width ) { + //Determines when x, y coordinates is over "b" element + return $.ui.isOverAxis( y, top, height ) && $.ui.isOverAxis( x, left, width ); + } +}); + +})( jQuery ); +/*! + * jQuery UI Widget 1.8.5 + * + * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT or GPL Version 2 licenses. + * http://jquery.org/license + * + * http://docs.jquery.com/UI/Widget + */ +(function( $, undefined ) { + +// jQuery 1.4+ +if ( $.cleanData ) { + var _cleanData = $.cleanData; + $.cleanData = function( elems ) { + for ( var i = 0, elem; (elem = elems[i]) != null; i++ ) { + $( elem ).triggerHandler( "remove" ); + } + _cleanData( elems ); + }; +} else { + var _remove = $.fn.remove; + $.fn.remove = function( selector, keepData ) { + return this.each(function() { + if ( !keepData ) { + if ( !selector || $.filter( selector, [ this ] ).length ) { + $( "*", this ).add( [ this ] ).each(function() { + $( this ).triggerHandler( "remove" ); + }); + } + } + return _remove.call( $(this), selector, keepData ); + }); + }; +} + +$.widget = function( name, base, prototype ) { + var namespace = name.split( "." )[ 0 ], + fullName; + name = name.split( "." )[ 1 ]; + fullName = namespace + "-" + name; + + if ( !prototype ) { + prototype = base; + base = $.Widget; + } + + // create selector for plugin + $.expr[ ":" ][ fullName ] = function( elem ) { + return !!$.data( elem, name ); + }; + + $[ namespace ] = $[ namespace ] || {}; + $[ namespace ][ name ] = function( options, element ) { + // allow instantiation without initializing for simple inheritance + if ( arguments.length ) { + this._createWidget( options, element ); + } + }; + + var basePrototype = new base(); + // we need to make the options hash a property directly on the new instance + // otherwise we'll modify the options hash on the prototype that we're + // inheriting from +// $.each( basePrototype, function( key, val ) { +// if ( $.isPlainObject(val) ) { +// basePrototype[ key ] = $.extend( {}, val ); +// } +// }); + basePrototype.options = $.extend( true, {}, basePrototype.options ); + $[ namespace ][ name ].prototype = $.extend( true, basePrototype, { + namespace: namespace, + widgetName: name, + widgetEventPrefix: $[ namespace ][ name ].prototype.widgetEventPrefix || name, + widgetBaseClass: fullName + }, prototype ); + + $.widget.bridge( name, $[ namespace ][ name ] ); +}; + +$.widget.bridge = function( name, object ) { + $.fn[ name ] = function( options ) { + var isMethodCall = typeof options === "string", + args = Array.prototype.slice.call( arguments, 1 ), + returnValue = this; + + // allow multiple hashes to be passed on init + options = !isMethodCall && args.length ? + $.extend.apply( null, [ true, options ].concat(args) ) : + options; + + // prevent calls to internal methods + if ( isMethodCall && options.substring( 0, 1 ) === "_" ) { + return returnValue; + } + + if ( isMethodCall ) { + this.each(function() { + var instance = $.data( this, name ); + if ( !instance ) { + throw "cannot call methods on " + name + " prior to initialization; " + + "attempted to call method '" + options + "'"; + } + if ( !$.isFunction( instance[options] ) ) { + throw "no such method '" + options + "' for " + name + " widget instance"; + } + var methodValue = instance[ options ].apply( instance, args ); + if ( methodValue !== instance && methodValue !== undefined ) { + returnValue = methodValue; + return false; + } + }); + } else { + this.each(function() { + var instance = $.data( this, name ); + if ( instance ) { + instance.option( options || {} )._init(); + } else { + $.data( this, name, new object( options, this ) ); + } + }); + } + + return returnValue; + }; +}; + +$.Widget = function( options, element ) { + // allow instantiation without initializing for simple inheritance + if ( arguments.length ) { + this._createWidget( options, element ); + } +}; + +$.Widget.prototype = { + widgetName: "widget", + widgetEventPrefix: "", + options: { + disabled: false + }, + _createWidget: function( options, element ) { + // $.widget.bridge stores the plugin instance, but we do it anyway + // so that it's stored even before the _create function runs + $.data( element, this.widgetName, this ); + this.element = $( element ); + this.options = $.extend( true, {}, + this.options, + $.metadata && $.metadata.get( element )[ this.widgetName ], + options ); + + var self = this; + this.element.bind( "remove." + this.widgetName, function() { + self.destroy(); + }); + + this._create(); + this._init(); + }, + _create: function() {}, + _init: function() {}, + + destroy: function() { + this.element + .unbind( "." + this.widgetName ) + .removeData( this.widgetName ); + this.widget() + .unbind( "." + this.widgetName ) + .removeAttr( "aria-disabled" ) + .removeClass( + this.widgetBaseClass + "-disabled " + + "ui-state-disabled" ); + }, + + widget: function() { + return this.element; + }, + + option: function( key, value ) { + var options = key, + self = this; + + if ( arguments.length === 0 ) { + // don't return a reference to the internal hash + return $.extend( {}, self.options ); + } + + if (typeof key === "string" ) { + if ( value === undefined ) { + return this.options[ key ]; + } + options = {}; + options[ key ] = value; + } + + $.each( options, function( key, value ) { + self._setOption( key, value ); + }); + + return self; + }, + _setOption: function( key, value ) { + this.options[ key ] = value; + + if ( key === "disabled" ) { + this.widget() + [ value ? "addClass" : "removeClass"]( + this.widgetBaseClass + "-disabled" + " " + + "ui-state-disabled" ) + .attr( "aria-disabled", value ); + } + + return this; + }, + + enable: function() { + return this._setOption( "disabled", false ); + }, + disable: function() { + return this._setOption( "disabled", true ); + }, + + _trigger: function( type, event, data ) { + var callback = this.options[ type ]; + + event = $.Event( event ); + event.type = ( type === this.widgetEventPrefix ? + type : + this.widgetEventPrefix + type ).toLowerCase(); + data = data || {}; + + // copy original event properties over to the new event + // this would happen if we could call $.event.fix instead of $.Event + // but we don't have a way to force an event to be fixed multiple times + if ( event.originalEvent ) { + for ( var i = $.event.props.length, prop; i; ) { + prop = $.event.props[ --i ]; + event[ prop ] = event.originalEvent[ prop ]; + } + } + + this.element.trigger( event, data ); + + return !( $.isFunction(callback) && + callback.call( this.element[0], event, data ) === false || + event.isDefaultPrevented() ); + } +}; + +})( jQuery ); +/*! + * jQuery UI Mouse 1.8.5 + * + * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT or GPL Version 2 licenses. + * http://jquery.org/license + * + * http://docs.jquery.com/UI/Mouse + * + * Depends: + * jquery.ui.widget.js + */ +(function( $, undefined ) { + +$.widget("ui.mouse", { + options: { + cancel: ':input,option', + distance: 1, + delay: 0 + }, + _mouseInit: function() { + var self = this; + + this.element + .bind('mousedown.'+this.widgetName, function(event) { + return self._mouseDown(event); + }) + .bind('click.'+this.widgetName, function(event) { + if(self._preventClickEvent) { + self._preventClickEvent = false; + event.stopImmediatePropagation(); + return false; + } + }); + + this.started = false; + }, + + // TODO: make sure destroying one instance of mouse doesn't mess with + // other instances of mouse + _mouseDestroy: function() { + this.element.unbind('.'+this.widgetName); + }, + + _mouseDown: function(event) { + // don't let more than one widget handle mouseStart + // TODO: figure out why we have to use originalEvent + event.originalEvent = event.originalEvent || {}; + if (event.originalEvent.mouseHandled) { return; } + + // we may have missed mouseup (out of window) + (this._mouseStarted && this._mouseUp(event)); + + this._mouseDownEvent = event; + + var self = this, + btnIsLeft = (event.which == 1), + elIsCancel = (typeof this.options.cancel == "string" ? $(event.target).parents().add(event.target).filter(this.options.cancel).length : false); + if (!btnIsLeft || elIsCancel || !this._mouseCapture(event)) { + return true; + } + + this.mouseDelayMet = !this.options.delay; + if (!this.mouseDelayMet) { + this._mouseDelayTimer = setTimeout(function() { + self.mouseDelayMet = true; + }, this.options.delay); + } + + if (this._mouseDistanceMet(event) && this._mouseDelayMet(event)) { + this._mouseStarted = (this._mouseStart(event) !== false); + if (!this._mouseStarted) { + event.preventDefault(); + return true; + } + } + + // these delegates are required to keep context + this._mouseMoveDelegate = function(event) { + return self._mouseMove(event); + }; + this._mouseUpDelegate = function(event) { + return self._mouseUp(event); + }; + $(document) + .bind('mousemove.'+this.widgetName, this._mouseMoveDelegate) + .bind('mouseup.'+this.widgetName, this._mouseUpDelegate); + + // preventDefault() is used to prevent the selection of text here - + // however, in Safari, this causes select boxes not to be selectable + // anymore, so this fix is needed + ($.browser.safari || event.preventDefault()); + + event.originalEvent.mouseHandled = true; + return true; + }, + + _mouseMove: function(event) { + // IE mouseup check - mouseup happened when mouse was out of window + if ($.browser.msie && !event.button) { + return this._mouseUp(event); + } + + if (this._mouseStarted) { + this._mouseDrag(event); + return event.preventDefault(); + } + + if (this._mouseDistanceMet(event) && this._mouseDelayMet(event)) { + this._mouseStarted = + (this._mouseStart(this._mouseDownEvent, event) !== false); + (this._mouseStarted ? this._mouseDrag(event) : this._mouseUp(event)); + } + + return !this._mouseStarted; + }, + + _mouseUp: function(event) { + $(document) + .unbind('mousemove.'+this.widgetName, this._mouseMoveDelegate) + .unbind('mouseup.'+this.widgetName, this._mouseUpDelegate); + + if (this._mouseStarted) { + this._mouseStarted = false; + this._preventClickEvent = (event.target == this._mouseDownEvent.target); + this._mouseStop(event); + } + + return false; + }, + + _mouseDistanceMet: function(event) { + return (Math.max( + Math.abs(this._mouseDownEvent.pageX - event.pageX), + Math.abs(this._mouseDownEvent.pageY - event.pageY) + ) >= this.options.distance + ); + }, + + _mouseDelayMet: function(event) { + return this.mouseDelayMet; + }, + + // These are placeholder methods, to be overriden by extending plugin + _mouseStart: function(event) {}, + _mouseDrag: function(event) {}, + _mouseStop: function(event) {}, + _mouseCapture: function(event) { return true; } +}); + +})(jQuery); +/* + * jQuery UI Sortable 1.8.5 + * + * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT or GPL Version 2 licenses. + * http://jquery.org/license + * + * http://docs.jquery.com/UI/Sortables + * + * Depends: + * jquery.ui.core.js + * jquery.ui.mouse.js + * jquery.ui.widget.js + */ +(function( $, undefined ) { + +$.widget("ui.sortable", $.ui.mouse, { + widgetEventPrefix: "sort", + options: { + appendTo: "parent", + axis: false, + connectWith: false, + containment: false, + cursor: 'auto', + cursorAt: false, + dropOnEmpty: true, + forcePlaceholderSize: false, + forceHelperSize: false, + grid: false, + handle: false, + helper: "original", + items: '> *', + opacity: false, + placeholder: false, + revert: false, + scroll: true, + scrollSensitivity: 20, + scrollSpeed: 20, + scope: "default", + tolerance: "intersect", + zIndex: 1000 + }, + _create: function() { + + var o = this.options; + this.containerCache = {}; + this.element.addClass("ui-sortable"); + + //Get the items + this.refresh(); + + //Let's determine if the items are floating + this.floating = this.items.length ? (/left|right/).test(this.items[0].item.css('float')) : false; + + //Let's determine the parent's offset + this.offset = this.element.offset(); + + //Initialize mouse events for interaction + this._mouseInit(); + + }, + + destroy: function() { + this.element + .removeClass("ui-sortable ui-sortable-disabled") + .removeData("sortable") + .unbind(".sortable"); + this._mouseDestroy(); + + for ( var i = this.items.length - 1; i >= 0; i-- ) + this.items[i].item.removeData("sortable-item"); + + return this; + }, + + _setOption: function(key, value){ + if ( key === "disabled" ) { + this.options[ key ] = value; + + this.widget() + [ value ? "addClass" : "removeClass"]( "ui-sortable-disabled" ); + } else { + // Don't call widget base _setOption for disable as it adds ui-state-disabled class + $.Widget.prototype._setOption.apply(this, arguments); + } + }, + + _mouseCapture: function(event, overrideHandle) { + + if (this.reverting) { + return false; + } + + if(this.options.disabled || this.options.type == 'static') return false; + + //We have to refresh the items data once first + this._refreshItems(event); + + //Find out if the clicked node (or one of its parents) is a actual item in this.items + var currentItem = null, self = this, nodes = $(event.target).parents().each(function() { + if($.data(this, 'sortable-item') == self) { + currentItem = $(this); + return false; + } + }); + if($.data(event.target, 'sortable-item') == self) currentItem = $(event.target); + + if(!currentItem) return false; + if(this.options.handle && !overrideHandle) { + var validHandle = false; + + $(this.options.handle, currentItem).find("*").andSelf().each(function() { if(this == event.target) validHandle = true; }); + if(!validHandle) return false; + } + + this.currentItem = currentItem; + this._removeCurrentsFromItems(); + return true; + + }, + + _mouseStart: function(event, overrideHandle, noActivation) { + + var o = this.options, self = this; + this.currentContainer = this; + + //We only need to call refreshPositions, because the refreshItems call has been moved to mouseCapture + this.refreshPositions(); + + //Create and append the visible helper + this.helper = this._createHelper(event); + + //Cache the helper size + this._cacheHelperProportions(); + + /* + * - Position generation - + * This block generates everything position related - it's the core of draggables. + */ + + //Cache the margins of the original element + this._cacheMargins(); + + //Get the next scrolling parent + this.scrollParent = this.helper.scrollParent(); + + //The element's absolute position on the page minus margins + this.offset = this.currentItem.offset(); + this.offset = { + top: this.offset.top - this.margins.top, + left: this.offset.left - this.margins.left + }; + + // Only after we got the offset, we can change the helper's position to absolute + // TODO: Still need to figure out a way to make relative sorting possible + this.helper.css("position", "absolute"); + this.cssPosition = this.helper.css("position"); + + $.extend(this.offset, { + click: { //Where the click happened, relative to the element + left: event.pageX - this.offset.left, + top: event.pageY - this.offset.top + }, + parent: this._getParentOffset(), + relative: this._getRelativeOffset() //This is a relative to absolute position minus the actual position calculation - only used for relative positioned helper + }); + + //Generate the original position + this.originalPosition = this._generatePosition(event); + this.originalPageX = event.pageX; + this.originalPageY = event.pageY; + + //Adjust the mouse offset relative to the helper if 'cursorAt' is supplied + (o.cursorAt && this._adjustOffsetFromHelper(o.cursorAt)); + + //Cache the former DOM position + this.domPosition = { prev: this.currentItem.prev()[0], parent: this.currentItem.parent()[0] }; + + //If the helper is not the original, hide the original so it's not playing any role during the drag, won't cause anything bad this way + if(this.helper[0] != this.currentItem[0]) { + this.currentItem.hide(); + } + + //Create the placeholder + this._createPlaceholder(); + + //Set a containment if given in the options + if(o.containment) + this._setContainment(); + + if(o.cursor) { // cursor option + if ($('body').css("cursor")) this._storedCursor = $('body').css("cursor"); + $('body').css("cursor", o.cursor); + } + + if(o.opacity) { // opacity option + if (this.helper.css("opacity")) this._storedOpacity = this.helper.css("opacity"); + this.helper.css("opacity", o.opacity); + } + + if(o.zIndex) { // zIndex option + if (this.helper.css("zIndex")) this._storedZIndex = this.helper.css("zIndex"); + this.helper.css("zIndex", o.zIndex); + } + + //Prepare scrolling + if(this.scrollParent[0] != document && this.scrollParent[0].tagName != 'HTML') + this.overflowOffset = this.scrollParent.offset(); + + //Call callbacks + this._trigger("start", event, this._uiHash()); + + //Recache the helper size + if(!this._preserveHelperProportions) + this._cacheHelperProportions(); + + + //Post 'activate' events to possible containers + if(!noActivation) { + for (var i = this.containers.length - 1; i >= 0; i--) { this.containers[i]._trigger("activate", event, self._uiHash(this)); } + } + + //Prepare possible droppables + if($.ui.ddmanager) + $.ui.ddmanager.current = this; + + if ($.ui.ddmanager && !o.dropBehaviour) + $.ui.ddmanager.prepareOffsets(this, event); + + this.dragging = true; + + this.helper.addClass("ui-sortable-helper"); + this._mouseDrag(event); //Execute the drag once - this causes the helper not to be visible before getting its correct position + return true; + + }, + + _mouseDrag: function(event) { + + //Compute the helpers position + this.position = this._generatePosition(event); + this.positionAbs = this._convertPositionTo("absolute"); + + if (!this.lastPositionAbs) { + this.lastPositionAbs = this.positionAbs; + } + + //Do scrolling + if(this.options.scroll) { + var o = this.options, scrolled = false; + if(this.scrollParent[0] != document && this.scrollParent[0].tagName != 'HTML') { + + if((this.overflowOffset.top + this.scrollParent[0].offsetHeight) - event.pageY < o.scrollSensitivity) + this.scrollParent[0].scrollTop = scrolled = this.scrollParent[0].scrollTop + o.scrollSpeed; + else if(event.pageY - this.overflowOffset.top < o.scrollSensitivity) + this.scrollParent[0].scrollTop = scrolled = this.scrollParent[0].scrollTop - o.scrollSpeed; + + if((this.overflowOffset.left + this.scrollParent[0].offsetWidth) - event.pageX < o.scrollSensitivity) + this.scrollParent[0].scrollLeft = scrolled = this.scrollParent[0].scrollLeft + o.scrollSpeed; + else if(event.pageX - this.overflowOffset.left < o.scrollSensitivity) + this.scrollParent[0].scrollLeft = scrolled = this.scrollParent[0].scrollLeft - o.scrollSpeed; + + } else { + + if(event.pageY - $(document).scrollTop() < o.scrollSensitivity) + scrolled = $(document).scrollTop($(document).scrollTop() - o.scrollSpeed); + else if($(window).height() - (event.pageY - $(document).scrollTop()) < o.scrollSensitivity) + scrolled = $(document).scrollTop($(document).scrollTop() + o.scrollSpeed); + + if(event.pageX - $(document).scrollLeft() < o.scrollSensitivity) + scrolled = $(document).scrollLeft($(document).scrollLeft() - o.scrollSpeed); + else if($(window).width() - (event.pageX - $(document).scrollLeft()) < o.scrollSensitivity) + scrolled = $(document).scrollLeft($(document).scrollLeft() + o.scrollSpeed); + + } + + if(scrolled !== false && $.ui.ddmanager && !o.dropBehaviour) + $.ui.ddmanager.prepareOffsets(this, event); + } + + //Regenerate the absolute position used for position checks + this.positionAbs = this._convertPositionTo("absolute"); + + //Set the helper position + if(!this.options.axis || this.options.axis != "y") this.helper[0].style.left = this.position.left+'px'; + if(!this.options.axis || this.options.axis != "x") this.helper[0].style.top = this.position.top+'px'; + + //Rearrange + for (var i = this.items.length - 1; i >= 0; i--) { + + //Cache variables and intersection, continue if no intersection + var item = this.items[i], itemElement = item.item[0], intersection = this._intersectsWithPointer(item); + if (!intersection) continue; + + if(itemElement != this.currentItem[0] //cannot intersect with itself + && this.placeholder[intersection == 1 ? "next" : "prev"]()[0] != itemElement //no useless actions that have been done before + && !$.ui.contains(this.placeholder[0], itemElement) //no action if the item moved is the parent of the item checked + && (this.options.type == 'semi-dynamic' ? !$.ui.contains(this.element[0], itemElement) : true) + //&& itemElement.parentNode == this.placeholder[0].parentNode // only rearrange items within the same container + ) { + + this.direction = intersection == 1 ? "down" : "up"; + + if (this.options.tolerance == "pointer" || this._intersectsWithSides(item)) { + this._rearrange(event, item); + } else { + break; + } + + this._trigger("change", event, this._uiHash()); + break; + } + } + + //Post events to containers + this._contactContainers(event); + + //Interconnect with droppables + if($.ui.ddmanager) $.ui.ddmanager.drag(this, event); + + //Call callbacks + this._trigger('sort', event, this._uiHash()); + + this.lastPositionAbs = this.positionAbs; + return false; + + }, + + _mouseStop: function(event, noPropagation) { + + if(!event) return; + + //If we are using droppables, inform the manager about the drop + if ($.ui.ddmanager && !this.options.dropBehaviour) + $.ui.ddmanager.drop(this, event); + + if(this.options.revert) { + var self = this; + var cur = self.placeholder.offset(); + + self.reverting = true; + + $(this.helper).animate({ + left: cur.left - this.offset.parent.left - self.margins.left + (this.offsetParent[0] == document.body ? 0 : this.offsetParent[0].scrollLeft), + top: cur.top - this.offset.parent.top - self.margins.top + (this.offsetParent[0] == document.body ? 0 : this.offsetParent[0].scrollTop) + }, parseInt(this.options.revert, 10) || 500, function() { + self._clear(event); + }); + } else { + this._clear(event, noPropagation); + } + + return false; + + }, + + cancel: function() { + + var self = this; + + if(this.dragging) { + + this._mouseUp(); + + if(this.options.helper == "original") + this.currentItem.css(this._storedCSS).removeClass("ui-sortable-helper"); + else + this.currentItem.show(); + + //Post deactivating events to containers + for (var i = this.containers.length - 1; i >= 0; i--){ + this.containers[i]._trigger("deactivate", null, self._uiHash(this)); + if(this.containers[i].containerCache.over) { + this.containers[i]._trigger("out", null, self._uiHash(this)); + this.containers[i].containerCache.over = 0; + } + } + + } + + //$(this.placeholder[0]).remove(); would have been the jQuery way - unfortunately, it unbinds ALL events from the original node! + if(this.placeholder[0].parentNode) this.placeholder[0].parentNode.removeChild(this.placeholder[0]); + if(this.options.helper != "original" && this.helper && this.helper[0].parentNode) this.helper.remove(); + + $.extend(this, { + helper: null, + dragging: false, + reverting: false, + _noFinalSort: null + }); + + if(this.domPosition.prev) { + $(this.domPosition.prev).after(this.currentItem); + } else { + $(this.domPosition.parent).prepend(this.currentItem); + } + + return this; + + }, + + serialize: function(o) { + + var items = this._getItemsAsjQuery(o && o.connected); + var str = []; o = o || {}; + + $(items).each(function() { + var res = ($(o.item || this).attr(o.attribute || 'id') || '').match(o.expression || (/(.+)[-=_](.+)/)); + if(res) str.push((o.key || res[1]+'[]')+'='+(o.key && o.expression ? res[1] : res[2])); + }); + + if(!str.length && o.key) { + str.push(o.key + '='); + } + + return str.join('&'); + + }, + + toArray: function(o) { + + var items = this._getItemsAsjQuery(o && o.connected); + var ret = []; o = o || {}; + + items.each(function() { ret.push($(o.item || this).attr(o.attribute || 'id') || ''); }); + return ret; + + }, + + /* Be careful with the following core functions */ + _intersectsWith: function(item) { + + var x1 = this.positionAbs.left, + x2 = x1 + this.helperProportions.width, + y1 = this.positionAbs.top, + y2 = y1 + this.helperProportions.height; + + var l = item.left, + r = l + item.width, + t = item.top, + b = t + item.height; + + var dyClick = this.offset.click.top, + dxClick = this.offset.click.left; + + var isOverElement = (y1 + dyClick) > t && (y1 + dyClick) < b && (x1 + dxClick) > l && (x1 + dxClick) < r; + + if( this.options.tolerance == "pointer" + || this.options.forcePointerForContainers + || (this.options.tolerance != "pointer" && this.helperProportions[this.floating ? 'width' : 'height'] > item[this.floating ? 'width' : 'height']) + ) { + return isOverElement; + } else { + + return (l < x1 + (this.helperProportions.width / 2) // Right Half + && x2 - (this.helperProportions.width / 2) < r // Left Half + && t < y1 + (this.helperProportions.height / 2) // Bottom Half + && y2 - (this.helperProportions.height / 2) < b ); // Top Half + + } + }, + + _intersectsWithPointer: function(item) { + + var isOverElementHeight = $.ui.isOverAxis(this.positionAbs.top + this.offset.click.top, item.top, item.height), + isOverElementWidth = $.ui.isOverAxis(this.positionAbs.left + this.offset.click.left, item.left, item.width), + isOverElement = isOverElementHeight && isOverElementWidth, + verticalDirection = this._getDragVerticalDirection(), + horizontalDirection = this._getDragHorizontalDirection(); + + if (!isOverElement) + return false; + + return this.floating ? + ( ((horizontalDirection && horizontalDirection == "right") || verticalDirection == "down") ? 2 : 1 ) + : ( verticalDirection && (verticalDirection == "down" ? 2 : 1) ); + + }, + + _intersectsWithSides: function(item) { + + var isOverBottomHalf = $.ui.isOverAxis(this.positionAbs.top + this.offset.click.top, item.top + (item.height/2), item.height), + isOverRightHalf = $.ui.isOverAxis(this.positionAbs.left + this.offset.click.left, item.left + (item.width/2), item.width), + verticalDirection = this._getDragVerticalDirection(), + horizontalDirection = this._getDragHorizontalDirection(); + + if (this.floating && horizontalDirection) { + return ((horizontalDirection == "right" && isOverRightHalf) || (horizontalDirection == "left" && !isOverRightHalf)); + } else { + return verticalDirection && ((verticalDirection == "down" && isOverBottomHalf) || (verticalDirection == "up" && !isOverBottomHalf)); + } + + }, + + _getDragVerticalDirection: function() { + var delta = this.positionAbs.top - this.lastPositionAbs.top; + return delta != 0 && (delta > 0 ? "down" : "up"); + }, + + _getDragHorizontalDirection: function() { + var delta = this.positionAbs.left - this.lastPositionAbs.left; + return delta != 0 && (delta > 0 ? "right" : "left"); + }, + + refresh: function(event) { + this._refreshItems(event); + this.refreshPositions(); + return this; + }, + + _connectWith: function() { + var options = this.options; + return options.connectWith.constructor == String + ? [options.connectWith] + : options.connectWith; + }, + + _getItemsAsjQuery: function(connected) { + + var self = this; + var items = []; + var queries = []; + var connectWith = this._connectWith(); + + if(connectWith && connected) { + for (var i = connectWith.length - 1; i >= 0; i--){ + var cur = $(connectWith[i]); + for (var j = cur.length - 1; j >= 0; j--){ + var inst = $.data(cur[j], 'sortable'); + if(inst && inst != this && !inst.options.disabled) { + queries.push([$.isFunction(inst.options.items) ? inst.options.items.call(inst.element) : $(inst.options.items, inst.element).not(".ui-sortable-helper").not('.ui-sortable-placeholder'), inst]); + } + }; + }; + } + + queries.push([$.isFunction(this.options.items) ? this.options.items.call(this.element, null, { options: this.options, item: this.currentItem }) : $(this.options.items, this.element).not(".ui-sortable-helper").not('.ui-sortable-placeholder'), this]); + + for (var i = queries.length - 1; i >= 0; i--){ + queries[i][0].each(function() { + items.push(this); + }); + }; + + return $(items); + + }, + + _removeCurrentsFromItems: function() { + + var list = this.currentItem.find(":data(sortable-item)"); + + for (var i=0; i < this.items.length; i++) { + + for (var j=0; j < list.length; j++) { + if(list[j] == this.items[i].item[0]) + this.items.splice(i,1); + }; + + }; + + }, + + _refreshItems: function(event) { + + this.items = []; + this.containers = [this]; + var items = this.items; + var self = this; + var queries = [[$.isFunction(this.options.items) ? this.options.items.call(this.element[0], event, { item: this.currentItem }) : $(this.options.items, this.element), this]]; + var connectWith = this._connectWith(); + + if(connectWith) { + for (var i = connectWith.length - 1; i >= 0; i--){ + var cur = $(connectWith[i]); + for (var j = cur.length - 1; j >= 0; j--){ + var inst = $.data(cur[j], 'sortable'); + if(inst && inst != this && !inst.options.disabled) { + queries.push([$.isFunction(inst.options.items) ? inst.options.items.call(inst.element[0], event, { item: this.currentItem }) : $(inst.options.items, inst.element), inst]); + this.containers.push(inst); + } + }; + }; + } + + for (var i = queries.length - 1; i >= 0; i--) { + var targetData = queries[i][1]; + var _queries = queries[i][0]; + + for (var j=0, queriesLength = _queries.length; j < queriesLength; j++) { + var item = $(_queries[j]); + + item.data('sortable-item', targetData); // Data for target checking (mouse manager) + + items.push({ + item: item, + instance: targetData, + width: 0, height: 0, + left: 0, top: 0 + }); + }; + }; + + }, + + refreshPositions: function(fast) { + + //This has to be redone because due to the item being moved out/into the offsetParent, the offsetParent's position will change + if(this.offsetParent && this.helper) { + this.offset.parent = this._getParentOffset(); + } + + for (var i = this.items.length - 1; i >= 0; i--){ + var item = this.items[i]; + + var t = this.options.toleranceElement ? $(this.options.toleranceElement, item.item) : item.item; + + if (!fast) { + item.width = t.outerWidth(); + item.height = t.outerHeight(); + } + + var p = t.offset(); + item.left = p.left; + item.top = p.top; + }; + + if(this.options.custom && this.options.custom.refreshContainers) { + this.options.custom.refreshContainers.call(this); + } else { + for (var i = this.containers.length - 1; i >= 0; i--){ + var p = this.containers[i].element.offset(); + this.containers[i].containerCache.left = p.left; + this.containers[i].containerCache.top = p.top; + this.containers[i].containerCache.width = this.containers[i].element.outerWidth(); + this.containers[i].containerCache.height = this.containers[i].element.outerHeight(); + }; + } + + return this; + }, + + _createPlaceholder: function(that) { + + var self = that || this, o = self.options; + + if(!o.placeholder || o.placeholder.constructor == String) { + var className = o.placeholder; + o.placeholder = { + element: function() { + + var el = $(document.createElement(self.currentItem[0].nodeName)) + .addClass(className || self.currentItem[0].className+" ui-sortable-placeholder") + .removeClass("ui-sortable-helper")[0]; + + if(!className) + el.style.visibility = "hidden"; + + return el; + }, + update: function(container, p) { + + // 1. If a className is set as 'placeholder option, we don't force sizes - the class is responsible for that + // 2. The option 'forcePlaceholderSize can be enabled to force it even if a class name is specified + if(className && !o.forcePlaceholderSize) return; + + //If the element doesn't have a actual height by itself (without styles coming from a stylesheet), it receives the inline height from the dragged item + if(!p.height()) { p.height(self.currentItem.innerHeight() - parseInt(self.currentItem.css('paddingTop')||0, 10) - parseInt(self.currentItem.css('paddingBottom')||0, 10)); }; + if(!p.width()) { p.width(self.currentItem.innerWidth() - parseInt(self.currentItem.css('paddingLeft')||0, 10) - parseInt(self.currentItem.css('paddingRight')||0, 10)); }; + } + }; + } + + //Create the placeholder + self.placeholder = $(o.placeholder.element.call(self.element, self.currentItem)); + + //Append it after the actual current item + self.currentItem.after(self.placeholder); + + //Update the size of the placeholder (TODO: Logic to fuzzy, see line 316/317) + o.placeholder.update(self, self.placeholder); + + }, + + _contactContainers: function(event) { + + // get innermost container that intersects with item + var innermostContainer = null, innermostIndex = null; + + + for (var i = this.containers.length - 1; i >= 0; i--){ + + // never consider a container that's located within the item itself + if($.ui.contains(this.currentItem[0], this.containers[i].element[0])) + continue; + + if(this._intersectsWith(this.containers[i].containerCache)) { + + // if we've already found a container and it's more "inner" than this, then continue + if(innermostContainer && $.ui.contains(this.containers[i].element[0], innermostContainer.element[0])) + continue; + + innermostContainer = this.containers[i]; + innermostIndex = i; + + } else { + // container doesn't intersect. trigger "out" event if necessary + if(this.containers[i].containerCache.over) { + this.containers[i]._trigger("out", event, this._uiHash(this)); + this.containers[i].containerCache.over = 0; + } + } + + } + + // if no intersecting containers found, return + if(!innermostContainer) return; + + // move the item into the container if it's not there already + if(this.containers.length === 1) { + this.containers[innermostIndex]._trigger("over", event, this._uiHash(this)); + this.containers[innermostIndex].containerCache.over = 1; + } else if(this.currentContainer != this.containers[innermostIndex]) { + + //When entering a new container, we will find the item with the least distance and append our item near it + var dist = 10000; var itemWithLeastDistance = null; var base = this.positionAbs[this.containers[innermostIndex].floating ? 'left' : 'top']; + for (var j = this.items.length - 1; j >= 0; j--) { + if(!$.ui.contains(this.containers[innermostIndex].element[0], this.items[j].item[0])) continue; + var cur = this.items[j][this.containers[innermostIndex].floating ? 'left' : 'top']; + if(Math.abs(cur - base) < dist) { + dist = Math.abs(cur - base); itemWithLeastDistance = this.items[j]; + } + } + + if(!itemWithLeastDistance && !this.options.dropOnEmpty) //Check if dropOnEmpty is enabled + return; + + this.currentContainer = this.containers[innermostIndex]; + itemWithLeastDistance ? this._rearrange(event, itemWithLeastDistance, null, true) : this._rearrange(event, null, this.containers[innermostIndex].element, true); + this._trigger("change", event, this._uiHash()); + this.containers[innermostIndex]._trigger("change", event, this._uiHash(this)); + + //Update the placeholder + this.options.placeholder.update(this.currentContainer, this.placeholder); + + this.containers[innermostIndex]._trigger("over", event, this._uiHash(this)); + this.containers[innermostIndex].containerCache.over = 1; + } + + + }, + + _createHelper: function(event) { + + var o = this.options; + var helper = $.isFunction(o.helper) ? $(o.helper.apply(this.element[0], [event, this.currentItem])) : (o.helper == 'clone' ? this.currentItem.clone() : this.currentItem); + + if(!helper.parents('body').length) //Add the helper to the DOM if that didn't happen already + $(o.appendTo != 'parent' ? o.appendTo : this.currentItem[0].parentNode)[0].appendChild(helper[0]); + + if(helper[0] == this.currentItem[0]) + this._storedCSS = { width: this.currentItem[0].style.width, height: this.currentItem[0].style.height, position: this.currentItem.css("position"), top: this.currentItem.css("top"), left: this.currentItem.css("left") }; + + if(helper[0].style.width == '' || o.forceHelperSize) helper.width(this.currentItem.width()); + if(helper[0].style.height == '' || o.forceHelperSize) helper.height(this.currentItem.height()); + + return helper; + + }, + + _adjustOffsetFromHelper: function(obj) { + if (typeof obj == 'string') { + obj = obj.split(' '); + } + if ($.isArray(obj)) { + obj = {left: +obj[0], top: +obj[1] || 0}; + } + if ('left' in obj) { + this.offset.click.left = obj.left + this.margins.left; + } + if ('right' in obj) { + this.offset.click.left = this.helperProportions.width - obj.right + this.margins.left; + } + if ('top' in obj) { + this.offset.click.top = obj.top + this.margins.top; + } + if ('bottom' in obj) { + this.offset.click.top = this.helperProportions.height - obj.bottom + this.margins.top; + } + }, + + _getParentOffset: function() { + + + //Get the offsetParent and cache its position + this.offsetParent = this.helper.offsetParent(); + var po = this.offsetParent.offset(); + + // This is a special case where we need to modify a offset calculated on start, since the following happened: + // 1. The position of the helper is absolute, so it's position is calculated based on the next positioned parent + // 2. The actual offset parent is a child of the scroll parent, and the scroll parent isn't the document, which means that + // the scroll is included in the initial calculation of the offset of the parent, and never recalculated upon drag + if(this.cssPosition == 'absolute' && this.scrollParent[0] != document && $.ui.contains(this.scrollParent[0], this.offsetParent[0])) { + po.left += this.scrollParent.scrollLeft(); + po.top += this.scrollParent.scrollTop(); + } + + if((this.offsetParent[0] == document.body) //This needs to be actually done for all browsers, since pageX/pageY includes this information + || (this.offsetParent[0].tagName && this.offsetParent[0].tagName.toLowerCase() == 'html' && $.browser.msie)) //Ugly IE fix + po = { top: 0, left: 0 }; + + return { + top: po.top + (parseInt(this.offsetParent.css("borderTopWidth"),10) || 0), + left: po.left + (parseInt(this.offsetParent.css("borderLeftWidth"),10) || 0) + }; + + }, + + _getRelativeOffset: function() { + + if(this.cssPosition == "relative") { + var p = this.currentItem.position(); + return { + top: p.top - (parseInt(this.helper.css("top"),10) || 0) + this.scrollParent.scrollTop(), + left: p.left - (parseInt(this.helper.css("left"),10) || 0) + this.scrollParent.scrollLeft() + }; + } else { + return { top: 0, left: 0 }; + } + + }, + + _cacheMargins: function() { + this.margins = { + left: (parseInt(this.currentItem.css("marginLeft"),10) || 0), + top: (parseInt(this.currentItem.css("marginTop"),10) || 0) + }; + }, + + _cacheHelperProportions: function() { + this.helperProportions = { + width: this.helper.outerWidth(), + height: this.helper.outerHeight() + }; + }, + + _setContainment: function() { + + var o = this.options; + if(o.containment == 'parent') o.containment = this.helper[0].parentNode; + if(o.containment == 'document' || o.containment == 'window') this.containment = [ + 0 - this.offset.relative.left - this.offset.parent.left, + 0 - this.offset.relative.top - this.offset.parent.top, + $(o.containment == 'document' ? document : window).width() - this.helperProportions.width - this.margins.left, + ($(o.containment == 'document' ? document : window).height() || document.body.parentNode.scrollHeight) - this.helperProportions.height - this.margins.top + ]; + + if(!(/^(document|window|parent)$/).test(o.containment)) { + var ce = $(o.containment)[0]; + var co = $(o.containment).offset(); + var over = ($(ce).css("overflow") != 'hidden'); + + this.containment = [ + co.left + (parseInt($(ce).css("borderLeftWidth"),10) || 0) + (parseInt($(ce).css("paddingLeft"),10) || 0) - this.margins.left, + co.top + (parseInt($(ce).css("borderTopWidth"),10) || 0) + (parseInt($(ce).css("paddingTop"),10) || 0) - this.margins.top, + co.left+(over ? Math.max(ce.scrollWidth,ce.offsetWidth) : ce.offsetWidth) - (parseInt($(ce).css("borderLeftWidth"),10) || 0) - (parseInt($(ce).css("paddingRight"),10) || 0) - this.helperProportions.width - this.margins.left, + co.top+(over ? Math.max(ce.scrollHeight,ce.offsetHeight) : ce.offsetHeight) - (parseInt($(ce).css("borderTopWidth"),10) || 0) - (parseInt($(ce).css("paddingBottom"),10) || 0) - this.helperProportions.height - this.margins.top + ]; + } + + }, + + _convertPositionTo: function(d, pos) { + + if(!pos) pos = this.position; + var mod = d == "absolute" ? 1 : -1; + var o = this.options, scroll = this.cssPosition == 'absolute' && !(this.scrollParent[0] != document && $.ui.contains(this.scrollParent[0], this.offsetParent[0])) ? this.offsetParent : this.scrollParent, scrollIsRootNode = (/(html|body)/i).test(scroll[0].tagName); + + return { + top: ( + pos.top // The absolute mouse position + + this.offset.relative.top * mod // Only for relative positioned nodes: Relative offset from element to offset parent + + this.offset.parent.top * mod // The offsetParent's offset without borders (offset + border) + - ($.browser.safari && this.cssPosition == 'fixed' ? 0 : ( this.cssPosition == 'fixed' ? -this.scrollParent.scrollTop() : ( scrollIsRootNode ? 0 : scroll.scrollTop() ) ) * mod) + ), + left: ( + pos.left // The absolute mouse position + + this.offset.relative.left * mod // Only for relative positioned nodes: Relative offset from element to offset parent + + this.offset.parent.left * mod // The offsetParent's offset without borders (offset + border) + - ($.browser.safari && this.cssPosition == 'fixed' ? 0 : ( this.cssPosition == 'fixed' ? -this.scrollParent.scrollLeft() : scrollIsRootNode ? 0 : scroll.scrollLeft() ) * mod) + ) + }; + + }, + + _generatePosition: function(event) { + + var o = this.options, scroll = this.cssPosition == 'absolute' && !(this.scrollParent[0] != document && $.ui.contains(this.scrollParent[0], this.offsetParent[0])) ? this.offsetParent : this.scrollParent, scrollIsRootNode = (/(html|body)/i).test(scroll[0].tagName); + + // This is another very weird special case that only happens for relative elements: + // 1. If the css position is relative + // 2. and the scroll parent is the document or similar to the offset parent + // we have to refresh the relative offset during the scroll so there are no jumps + if(this.cssPosition == 'relative' && !(this.scrollParent[0] != document && this.scrollParent[0] != this.offsetParent[0])) { + this.offset.relative = this._getRelativeOffset(); + } + + var pageX = event.pageX; + var pageY = event.pageY; + + /* + * - Position constraining - + * Constrain the position to a mix of grid, containment. + */ + + if(this.originalPosition) { //If we are not dragging yet, we won't check for options + + if(this.containment) { + if(event.pageX - this.offset.click.left < this.containment[0]) pageX = this.containment[0] + this.offset.click.left; + if(event.pageY - this.offset.click.top < this.containment[1]) pageY = this.containment[1] + this.offset.click.top; + if(event.pageX - this.offset.click.left > this.containment[2]) pageX = this.containment[2] + this.offset.click.left; + if(event.pageY - this.offset.click.top > this.containment[3]) pageY = this.containment[3] + this.offset.click.top; + } + + if(o.grid) { + var top = this.originalPageY + Math.round((pageY - this.originalPageY) / o.grid[1]) * o.grid[1]; + pageY = this.containment ? (!(top - this.offset.click.top < this.containment[1] || top - this.offset.click.top > this.containment[3]) ? top : (!(top - this.offset.click.top < this.containment[1]) ? top - o.grid[1] : top + o.grid[1])) : top; + + var left = this.originalPageX + Math.round((pageX - this.originalPageX) / o.grid[0]) * o.grid[0]; + pageX = this.containment ? (!(left - this.offset.click.left < this.containment[0] || left - this.offset.click.left > this.containment[2]) ? left : (!(left - this.offset.click.left < this.containment[0]) ? left - o.grid[0] : left + o.grid[0])) : left; + } + + } + + return { + top: ( + pageY // The absolute mouse position + - this.offset.click.top // Click offset (relative to the element) + - this.offset.relative.top // Only for relative positioned nodes: Relative offset from element to offset parent + - this.offset.parent.top // The offsetParent's offset without borders (offset + border) + + ($.browser.safari && this.cssPosition == 'fixed' ? 0 : ( this.cssPosition == 'fixed' ? -this.scrollParent.scrollTop() : ( scrollIsRootNode ? 0 : scroll.scrollTop() ) )) + ), + left: ( + pageX // The absolute mouse position + - this.offset.click.left // Click offset (relative to the element) + - this.offset.relative.left // Only for relative positioned nodes: Relative offset from element to offset parent + - this.offset.parent.left // The offsetParent's offset without borders (offset + border) + + ($.browser.safari && this.cssPosition == 'fixed' ? 0 : ( this.cssPosition == 'fixed' ? -this.scrollParent.scrollLeft() : scrollIsRootNode ? 0 : scroll.scrollLeft() )) + ) + }; + + }, + + _rearrange: function(event, i, a, hardRefresh) { + + a ? a[0].appendChild(this.placeholder[0]) : i.item[0].parentNode.insertBefore(this.placeholder[0], (this.direction == 'down' ? i.item[0] : i.item[0].nextSibling)); + + //Various things done here to improve the performance: + // 1. we create a setTimeout, that calls refreshPositions + // 2. on the instance, we have a counter variable, that get's higher after every append + // 3. on the local scope, we copy the counter variable, and check in the timeout, if it's still the same + // 4. this lets only the last addition to the timeout stack through + this.counter = this.counter ? ++this.counter : 1; + var self = this, counter = this.counter; + + window.setTimeout(function() { + if(counter == self.counter) self.refreshPositions(!hardRefresh); //Precompute after each DOM insertion, NOT on mousemove + },0); + + }, + + _clear: function(event, noPropagation) { + + this.reverting = false; + // We delay all events that have to be triggered to after the point where the placeholder has been removed and + // everything else normalized again + var delayedTriggers = [], self = this; + + // We first have to update the dom position of the actual currentItem + // Note: don't do it if the current item is already removed (by a user), or it gets reappended (see #4088) + if(!this._noFinalSort && this.currentItem[0].parentNode) this.placeholder.before(this.currentItem); + this._noFinalSort = null; + + if(this.helper[0] == this.currentItem[0]) { + for(var i in this._storedCSS) { + if(this._storedCSS[i] == 'auto' || this._storedCSS[i] == 'static') this._storedCSS[i] = ''; + } + this.currentItem.css(this._storedCSS).removeClass("ui-sortable-helper"); + } else { + this.currentItem.show(); + } + + if(this.fromOutside && !noPropagation) delayedTriggers.push(function(event) { this._trigger("receive", event, this._uiHash(this.fromOutside)); }); + if((this.fromOutside || this.domPosition.prev != this.currentItem.prev().not(".ui-sortable-helper")[0] || this.domPosition.parent != this.currentItem.parent()[0]) && !noPropagation) delayedTriggers.push(function(event) { this._trigger("update", event, this._uiHash()); }); //Trigger update callback if the DOM position has changed + if(!$.ui.contains(this.element[0], this.currentItem[0])) { //Node was moved out of the current element + if(!noPropagation) delayedTriggers.push(function(event) { this._trigger("remove", event, this._uiHash()); }); + for (var i = this.containers.length - 1; i >= 0; i--){ + if($.ui.contains(this.containers[i].element[0], this.currentItem[0]) && !noPropagation) { + delayedTriggers.push((function(c) { return function(event) { c._trigger("receive", event, this._uiHash(this)); }; }).call(this, this.containers[i])); + delayedTriggers.push((function(c) { return function(event) { c._trigger("update", event, this._uiHash(this)); }; }).call(this, this.containers[i])); + } + }; + }; + + //Post events to containers + for (var i = this.containers.length - 1; i >= 0; i--){ + if(!noPropagation) delayedTriggers.push((function(c) { return function(event) { c._trigger("deactivate", event, this._uiHash(this)); }; }).call(this, this.containers[i])); + if(this.containers[i].containerCache.over) { + delayedTriggers.push((function(c) { return function(event) { c._trigger("out", event, this._uiHash(this)); }; }).call(this, this.containers[i])); + this.containers[i].containerCache.over = 0; + } + } + + //Do what was originally in plugins + if(this._storedCursor) $('body').css("cursor", this._storedCursor); //Reset cursor + if(this._storedOpacity) this.helper.css("opacity", this._storedOpacity); //Reset opacity + if(this._storedZIndex) this.helper.css("zIndex", this._storedZIndex == 'auto' ? '' : this._storedZIndex); //Reset z-index + + this.dragging = false; + if(this.cancelHelperRemoval) { + if(!noPropagation) { + this._trigger("beforeStop", event, this._uiHash()); + for (var i=0; i < delayedTriggers.length; i++) { delayedTriggers[i].call(this, event); }; //Trigger all delayed events + this._trigger("stop", event, this._uiHash()); + } + return false; + } + + if(!noPropagation) this._trigger("beforeStop", event, this._uiHash()); + + //$(this.placeholder[0]).remove(); would have been the jQuery way - unfortunately, it unbinds ALL events from the original node! + this.placeholder[0].parentNode.removeChild(this.placeholder[0]); + + if(this.helper[0] != this.currentItem[0]) this.helper.remove(); this.helper = null; + + if(!noPropagation) { + for (var i=0; i < delayedTriggers.length; i++) { delayedTriggers[i].call(this, event); }; //Trigger all delayed events + this._trigger("stop", event, this._uiHash()); + } + + this.fromOutside = false; + return true; + + }, + + _trigger: function() { + if ($.Widget.prototype._trigger.apply(this, arguments) === false) { + this.cancel(); + } + }, + + _uiHash: function(inst) { + var self = inst || this; + return { + helper: self.helper, + placeholder: self.placeholder || $([]), + position: self.position, + originalPosition: self.originalPosition, + offset: self.positionAbs, + item: self.currentItem, + sender: inst ? inst.element : null + }; + } + +}); + +$.extend($.ui.sortable, { + version: "1.8.5" +}); + +})(jQuery); +/* + * jQuery UI Slider 1.8.5 + * + * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT or GPL Version 2 licenses. + * http://jquery.org/license + * + * http://docs.jquery.com/UI/Slider + * + * Depends: + * jquery.ui.core.js + * jquery.ui.mouse.js + * jquery.ui.widget.js + */ +(function( $, undefined ) { + +// number of pages in a slider +// (how many times can you page up/down to go through the whole range) +var numPages = 5; + +$.widget( "ui.slider", $.ui.mouse, { + + widgetEventPrefix: "slide", + + options: { + animate: false, + distance: 0, + max: 100, + min: 0, + orientation: "horizontal", + range: false, + step: 1, + value: 0, + values: null + }, + + _create: function() { + var self = this, + o = this.options; + + this._keySliding = false; + this._mouseSliding = false; + this._animateOff = true; + this._handleIndex = null; + this._detectOrientation(); + this._mouseInit(); + + this.element + .addClass( "ui-slider" + + " ui-slider-" + this.orientation + + " ui-widget" + + " ui-widget-content" + + " ui-corner-all" ); + + if ( o.disabled ) { + this.element.addClass( "ui-slider-disabled ui-disabled" ); + } + + this.range = $([]); + + if ( o.range ) { + if ( o.range === true ) { + this.range = $( "<div></div>" ); + if ( !o.values ) { + o.values = [ this._valueMin(), this._valueMin() ]; + } + if ( o.values.length && o.values.length !== 2 ) { + o.values = [ o.values[0], o.values[0] ]; + } + } else { + this.range = $( "<div></div>" ); + } + + this.range + .appendTo( this.element ) + .addClass( "ui-slider-range" ); + + if ( o.range === "min" || o.range === "max" ) { + this.range.addClass( "ui-slider-range-" + o.range ); + } + + // note: this isn't the most fittingly semantic framework class for this element, + // but worked best visually with a variety of themes + this.range.addClass( "ui-widget-header" ); + } + + if ( $( ".ui-slider-handle", this.element ).length === 0 ) { + $( "<a href='#'></a>" ) + .appendTo( this.element ) + .addClass( "ui-slider-handle" ); + } + + if ( o.values && o.values.length ) { + while ( $(".ui-slider-handle", this.element).length < o.values.length ) { + $( "<a href='#'></a>" ) + .appendTo( this.element ) + .addClass( "ui-slider-handle" ); + } + } + + this.handles = $( ".ui-slider-handle", this.element ) + .addClass( "ui-state-default" + + " ui-corner-all" ); + + this.handle = this.handles.eq( 0 ); + + this.handles.add( this.range ).filter( "a" ) + .click(function( event ) { + event.preventDefault(); + }) + .hover(function() { + if ( !o.disabled ) { + $( this ).addClass( "ui-state-hover" ); + } + }, function() { + $( this ).removeClass( "ui-state-hover" ); + }) + .focus(function() { + if ( !o.disabled ) { + $( ".ui-slider .ui-state-focus" ).removeClass( "ui-state-focus" ); + $( this ).addClass( "ui-state-focus" ); + } else { + $( this ).blur(); + } + }) + .blur(function() { + $( this ).removeClass( "ui-state-focus" ); + }); + + this.handles.each(function( i ) { + $( this ).data( "index.ui-slider-handle", i ); + }); + + this.handles + .keydown(function( event ) { + var ret = true, + index = $( this ).data( "index.ui-slider-handle" ), + allowed, + curVal, + newVal, + step; + + if ( self.options.disabled ) { + return; + } + + switch ( event.keyCode ) { + case $.ui.keyCode.HOME: + case $.ui.keyCode.END: + case $.ui.keyCode.PAGE_UP: + case $.ui.keyCode.PAGE_DOWN: + case $.ui.keyCode.UP: + case $.ui.keyCode.RIGHT: + case $.ui.keyCode.DOWN: + case $.ui.keyCode.LEFT: + ret = false; + if ( !self._keySliding ) { + self._keySliding = true; + $( this ).addClass( "ui-state-active" ); + allowed = self._start( event, index ); + if ( allowed === false ) { + return; + } + } + break; + } + + step = self.options.step; + if ( self.options.values && self.options.values.length ) { + curVal = newVal = self.values( index ); + } else { + curVal = newVal = self.value(); + } + + switch ( event.keyCode ) { + case $.ui.keyCode.HOME: + newVal = self._valueMin(); + break; + case $.ui.keyCode.END: + newVal = self._valueMax(); + break; + case $.ui.keyCode.PAGE_UP: + newVal = self._trimAlignValue( curVal + ( (self._valueMax() - self._valueMin()) / numPages ) ); + break; + case $.ui.keyCode.PAGE_DOWN: + newVal = self._trimAlignValue( curVal - ( (self._valueMax() - self._valueMin()) / numPages ) ); + break; + case $.ui.keyCode.UP: + case $.ui.keyCode.RIGHT: + if ( curVal === self._valueMax() ) { + return; + } + newVal = self._trimAlignValue( curVal + step ); + break; + case $.ui.keyCode.DOWN: + case $.ui.keyCode.LEFT: + if ( curVal === self._valueMin() ) { + return; + } + newVal = self._trimAlignValue( curVal - step ); + break; + } + + self._slide( event, index, newVal ); + + return ret; + + }) + .keyup(function( event ) { + var index = $( this ).data( "index.ui-slider-handle" ); + + if ( self._keySliding ) { + self._keySliding = false; + self._stop( event, index ); + self._change( event, index ); + $( this ).removeClass( "ui-state-active" ); + } + + }); + + this._refreshValue(); + + this._animateOff = false; + }, + + destroy: function() { + this.handles.remove(); + this.range.remove(); + + this.element + .removeClass( "ui-slider" + + " ui-slider-horizontal" + + " ui-slider-vertical" + + " ui-slider-disabled" + + " ui-widget" + + " ui-widget-content" + + " ui-corner-all" ) + .removeData( "slider" ) + .unbind( ".slider" ); + + this._mouseDestroy(); + + return this; + }, + + _mouseCapture: function( event ) { + var o = this.options, + position, + normValue, + distance, + closestHandle, + self, + index, + allowed, + offset, + mouseOverHandle; + + if ( o.disabled ) { + return false; + } + + this.elementSize = { + width: this.element.outerWidth(), + height: this.element.outerHeight() + }; + this.elementOffset = this.element.offset(); + + position = { x: event.pageX, y: event.pageY }; + normValue = this._normValueFromMouse( position ); + distance = this._valueMax() - this._valueMin() + 1; + self = this; + this.handles.each(function( i ) { + var thisDistance = Math.abs( normValue - self.values(i) ); + if ( distance > thisDistance ) { + distance = thisDistance; + closestHandle = $( this ); + index = i; + } + }); + + // workaround for bug #3736 (if both handles of a range are at 0, + // the first is always used as the one with least distance, + // and moving it is obviously prevented by preventing negative ranges) + if( o.range === true && this.values(1) === o.min ) { + index += 1; + closestHandle = $( this.handles[index] ); + } + + allowed = this._start( event, index ); + if ( allowed === false ) { + return false; + } + this._mouseSliding = true; + + self._handleIndex = index; + + closestHandle + .addClass( "ui-state-active" ) + .focus(); + + offset = closestHandle.offset(); + mouseOverHandle = !$( event.target ).parents().andSelf().is( ".ui-slider-handle" ); + this._clickOffset = mouseOverHandle ? { left: 0, top: 0 } : { + left: event.pageX - offset.left - ( closestHandle.width() / 2 ), + top: event.pageY - offset.top - + ( closestHandle.height() / 2 ) - + ( parseInt( closestHandle.css("borderTopWidth"), 10 ) || 0 ) - + ( parseInt( closestHandle.css("borderBottomWidth"), 10 ) || 0) + + ( parseInt( closestHandle.css("marginTop"), 10 ) || 0) + }; + + this._slide( event, index, normValue ); + this._animateOff = true; + return true; + }, + + _mouseStart: function( event ) { + return true; + }, + + _mouseDrag: function( event ) { + var position = { x: event.pageX, y: event.pageY }, + normValue = this._normValueFromMouse( position ); + + this._slide( event, this._handleIndex, normValue ); + + return false; + }, + + _mouseStop: function( event ) { + this.handles.removeClass( "ui-state-active" ); + this._mouseSliding = false; + + this._stop( event, this._handleIndex ); + this._change( event, this._handleIndex ); + + this._handleIndex = null; + this._clickOffset = null; + this._animateOff = false; + + return false; + }, + + _detectOrientation: function() { + this.orientation = ( this.options.orientation === "vertical" ) ? "vertical" : "horizontal"; + }, + + _normValueFromMouse: function( position ) { + var pixelTotal, + pixelMouse, + percentMouse, + valueTotal, + valueMouse; + + if ( this.orientation === "horizontal" ) { + pixelTotal = this.elementSize.width; + pixelMouse = position.x - this.elementOffset.left - ( this._clickOffset ? this._clickOffset.left : 0 ); + } else { + pixelTotal = this.elementSize.height; + pixelMouse = position.y - this.elementOffset.top - ( this._clickOffset ? this._clickOffset.top : 0 ); + } + + percentMouse = ( pixelMouse / pixelTotal ); + if ( percentMouse > 1 ) { + percentMouse = 1; + } + if ( percentMouse < 0 ) { + percentMouse = 0; + } + if ( this.orientation === "vertical" ) { + percentMouse = 1 - percentMouse; + } + + valueTotal = this._valueMax() - this._valueMin(); + valueMouse = this._valueMin() + percentMouse * valueTotal; + + return this._trimAlignValue( valueMouse ); + }, + + _start: function( event, index ) { + var uiHash = { + handle: this.handles[ index ], + value: this.value() + }; + if ( this.options.values && this.options.values.length ) { + uiHash.value = this.values( index ); + uiHash.values = this.values(); + } + return this._trigger( "start", event, uiHash ); + }, + + _slide: function( event, index, newVal ) { + var otherVal, + newValues, + allowed; + + if ( this.options.values && this.options.values.length ) { + otherVal = this.values( index ? 0 : 1 ); + + if ( ( this.options.values.length === 2 && this.options.range === true ) && + ( ( index === 0 && newVal > otherVal) || ( index === 1 && newVal < otherVal ) ) + ) { + newVal = otherVal; + } + + if ( newVal !== this.values( index ) ) { + newValues = this.values(); + newValues[ index ] = newVal; + // A slide can be canceled by returning false from the slide callback + allowed = this._trigger( "slide", event, { + handle: this.handles[ index ], + value: newVal, + values: newValues + } ); + otherVal = this.values( index ? 0 : 1 ); + if ( allowed !== false ) { + this.values( index, newVal, true ); + } + } + } else { + if ( newVal !== this.value() ) { + // A slide can be canceled by returning false from the slide callback + allowed = this._trigger( "slide", event, { + handle: this.handles[ index ], + value: newVal + } ); + if ( allowed !== false ) { + this.value( newVal ); + } + } + } + }, + + _stop: function( event, index ) { + var uiHash = { + handle: this.handles[ index ], + value: this.value() + }; + if ( this.options.values && this.options.values.length ) { + uiHash.value = this.values( index ); + uiHash.values = this.values(); + } + + this._trigger( "stop", event, uiHash ); + }, + + _change: function( event, index ) { + if ( !this._keySliding && !this._mouseSliding ) { + var uiHash = { + handle: this.handles[ index ], + value: this.value() + }; + if ( this.options.values && this.options.values.length ) { + uiHash.value = this.values( index ); + uiHash.values = this.values(); + } + + this._trigger( "change", event, uiHash ); + } + }, + + value: function( newValue ) { + if ( arguments.length ) { + this.options.value = this._trimAlignValue( newValue ); + this._refreshValue(); + this._change( null, 0 ); + } + + return this._value(); + }, + + values: function( index, newValue ) { + var vals, + newValues, + i; + + if ( arguments.length > 1 ) { + this.options.values[ index ] = this._trimAlignValue( newValue ); + this._refreshValue(); + this._change( null, index ); + } + + if ( arguments.length ) { + if ( $.isArray( arguments[ 0 ] ) ) { + vals = this.options.values; + newValues = arguments[ 0 ]; + for ( i = 0; i < vals.length; i += 1 ) { + vals[ i ] = this._trimAlignValue( newValues[ i ] ); + this._change( null, i ); + } + this._refreshValue(); + } else { + if ( this.options.values && this.options.values.length ) { + return this._values( index ); + } else { + return this.value(); + } + } + } else { + return this._values(); + } + }, + + _setOption: function( key, value ) { + var i, + valsLength = 0; + + if ( $.isArray( this.options.values ) ) { + valsLength = this.options.values.length; + } + + $.Widget.prototype._setOption.apply( this, arguments ); + + switch ( key ) { + case "disabled": + if ( value ) { + this.handles.filter( ".ui-state-focus" ).blur(); + this.handles.removeClass( "ui-state-hover" ); + this.handles.attr( "disabled", "disabled" ); + this.element.addClass( "ui-disabled" ); + } else { + this.handles.removeAttr( "disabled" ); + this.element.removeClass( "ui-disabled" ); + } + break; + case "orientation": + this._detectOrientation(); + this.element + .removeClass( "ui-slider-horizontal ui-slider-vertical" ) + .addClass( "ui-slider-" + this.orientation ); + this._refreshValue(); + break; + case "value": + this._animateOff = true; + this._refreshValue(); + this._change( null, 0 ); + this._animateOff = false; + break; + case "values": + this._animateOff = true; + this._refreshValue(); + for ( i = 0; i < valsLength; i += 1 ) { + this._change( null, i ); + } + this._animateOff = false; + break; + } + }, + + //internal value getter + // _value() returns value trimmed by min and max, aligned by step + _value: function() { + var val = this.options.value; + val = this._trimAlignValue( val ); + + return val; + }, + + //internal values getter + // _values() returns array of values trimmed by min and max, aligned by step + // _values( index ) returns single value trimmed by min and max, aligned by step + _values: function( index ) { + var val, + vals, + i; + + if ( arguments.length ) { + val = this.options.values[ index ]; + val = this._trimAlignValue( val ); + + return val; + } else { + // .slice() creates a copy of the array + // this copy gets trimmed by min and max and then returned + vals = this.options.values.slice(); + for ( i = 0; i < vals.length; i+= 1) { + vals[ i ] = this._trimAlignValue( vals[ i ] ); + } + + return vals; + } + }, + + // returns the step-aligned value that val is closest to, between (inclusive) min and max + _trimAlignValue: function( val ) { + if ( val < this._valueMin() ) { + return this._valueMin(); + } + if ( val > this._valueMax() ) { + return this._valueMax(); + } + var step = ( this.options.step > 0 ) ? this.options.step : 1, + valModStep = val % step, + alignValue = val - valModStep; + + if ( Math.abs(valModStep) * 2 >= step ) { + alignValue += ( valModStep > 0 ) ? step : ( -step ); + } + + // Since JavaScript has problems with large floats, round + // the final value to 5 digits after the decimal point (see #4124) + return parseFloat( alignValue.toFixed(5) ); + }, + + _valueMin: function() { + return this.options.min; + }, + + _valueMax: function() { + return this.options.max; + }, + + _refreshValue: function() { + var oRange = this.options.range, + o = this.options, + self = this, + animate = ( !this._animateOff ) ? o.animate : false, + valPercent, + _set = {}, + lastValPercent, + value, + valueMin, + valueMax; + + if ( this.options.values && this.options.values.length ) { + this.handles.each(function( i, j ) { + valPercent = ( self.values(i) - self._valueMin() ) / ( self._valueMax() - self._valueMin() ) * 100; + _set[ self.orientation === "horizontal" ? "left" : "bottom" ] = valPercent + "%"; + $( this ).stop( 1, 1 )[ animate ? "animate" : "css" ]( _set, o.animate ); + if ( self.options.range === true ) { + if ( self.orientation === "horizontal" ) { + if ( i === 0 ) { + self.range.stop( 1, 1 )[ animate ? "animate" : "css" ]( { left: valPercent + "%" }, o.animate ); + } + if ( i === 1 ) { + self.range[ animate ? "animate" : "css" ]( { width: ( valPercent - lastValPercent ) + "%" }, { queue: false, duration: o.animate } ); + } + } else { + if ( i === 0 ) { + self.range.stop( 1, 1 )[ animate ? "animate" : "css" ]( { bottom: ( valPercent ) + "%" }, o.animate ); + } + if ( i === 1 ) { + self.range[ animate ? "animate" : "css" ]( { height: ( valPercent - lastValPercent ) + "%" }, { queue: false, duration: o.animate } ); + } + } + } + lastValPercent = valPercent; + }); + } else { + value = this.value(); + valueMin = this._valueMin(); + valueMax = this._valueMax(); + valPercent = ( valueMax !== valueMin ) ? + ( value - valueMin ) / ( valueMax - valueMin ) * 100 : + 0; + _set[ self.orientation === "horizontal" ? "left" : "bottom" ] = valPercent + "%"; + this.handle.stop( 1, 1 )[ animate ? "animate" : "css" ]( _set, o.animate ); + + if ( oRange === "min" && this.orientation === "horizontal" ) { + this.range.stop( 1, 1 )[ animate ? "animate" : "css" ]( { width: valPercent + "%" }, o.animate ); + } + if ( oRange === "max" && this.orientation === "horizontal" ) { + this.range[ animate ? "animate" : "css" ]( { width: ( 100 - valPercent ) + "%" }, { queue: false, duration: o.animate } ); + } + if ( oRange === "min" && this.orientation === "vertical" ) { + this.range.stop( 1, 1 )[ animate ? "animate" : "css" ]( { height: valPercent + "%" }, o.animate ); + } + if ( oRange === "max" && this.orientation === "vertical" ) { + this.range[ animate ? "animate" : "css" ]( { height: ( 100 - valPercent ) + "%" }, { queue: false, duration: o.animate } ); + } + } + } + +}); + +$.extend( $.ui.slider, { + version: "1.8.5" +}); + +}(jQuery));

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galaxy-dist commit f91906133f45: Fix bug in 9ddd7c1d4dd5 that prevented data provider from being set correctly.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1286830980 14400 # Node ID f91906133f451758b4be3c711bf1ce85c6d9650b # Parent 9ddd7c1d4dd5075a0878026e59cf04f3d9d768d6 Fix bug in 9ddd7c1d4dd5 that prevented data provider from being set correctly. --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -385,15 +385,14 @@ def get_data_provider( name=None, origin data_provider = value elif original_dataset: # Look for data provider in mapping. - data_provider = \ - dataset_type_to_data_provider.get( original_dataset.datatype.__class__, None ) - - # If get_track_type is available, then dataset can be added to trackster - # and hence has at least a generic data provider. - try: - original_dataset.datatype.get_track_type() - data_provider = TracksDataProvider - except: - pass + data_provider = dataset_type_to_data_provider.get( original_dataset.datatype.__class__, None ) + if not data_provider: + # If get_track_type is available, then dataset can be added to trackster + # and hence has at least a generic data provider. + try: + original_dataset.datatype.get_track_type() + data_provider = TracksDataProvider + except: + pass return data_provider

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galaxy-dist commit d80539104bc3: Re-fix issue from 384c809db93e: show items in user menu when user is remote. Contributed by JJ and Ry4an Brase.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1286831279 14400 # Node ID d80539104bc3f4c20e555864346839be9299c70e # Parent f91906133f451758b4be3c711bf1ce85c6d9650b Re-fix issue from 384c809db93e: show items in user menu when user is remote. Contributed by JJ and Ry4an Brase. --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -141,12 +141,12 @@ logout_url = h.url_for( controller='/user', action='logout' ) menu_options.append( [ 'Logout', logout_url, "_top" ] ) menu_options.append( None ) - menu_options.append( [ 'Saved Histories', h.url_for( controller='/history', action='list' ), "galaxy_main" ] ) - menu_options.append( [ 'Saved Datasets', h.url_for( controller='/dataset', action='list' ), "galaxy_main" ] ) - if app.config.get_bool( 'enable_pages', False ): - menu_options.append( [ 'Saved Pages', h.url_for( controller='/page', action='list' ), "_top" ] ) - if app.config.enable_api: - menu_options.append( [ 'API Keys', h.url_for( controller='/user', action='api_keys' ), "galaxy_main" ] ) + menu_options.append( [ 'Saved Histories', h.url_for( controller='/history', action='list' ), "galaxy_main" ] ) + menu_options.append( [ 'Saved Datasets', h.url_for( controller='/dataset', action='list' ), "galaxy_main" ] ) + if app.config.get_bool( 'enable_pages', False ): + menu_options.append( [ 'Saved Pages', h.url_for( controller='/page', action='list' ), "_top" ] ) + if app.config.enable_api: + menu_options.append( [ 'API Keys', h.url_for( controller='/user', action='api_keys' ), "galaxy_main" ] ) extra_class = "loggedin-only" visible = ( trans.user != None )

1 0

galaxy-dist commit 3c74359b7bb7: sample_tracking bug fixes:
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1286887059 14400 # Node ID 3c74359b7bb72c0d9cfc53e3f0b7a9e3ea426b87 # Parent d80539104bc3f4c20e555864346839be9299c70e sample_tracking bug fixes: - when adding new sample, sample index now starts from 1 instead of 0 - removed searching on user email on the request grid - replaced username with user email in request info page --- a/templates/requests/common/manage_request.mako +++ b/templates/requests/common/manage_request.mako @@ -135,7 +135,7 @@ <div class="toolParamHelp" style="clear: both;"><b>Sequencer</b>: ${request.type.name} %if is_admin: - | <b>User</b>: ${request.user.username} + | <b>User</b>: ${request.user.email} %endif %if request.is_submitted: | <b>State</b>: <i>${request.state}</i> --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -92,7 +92,7 @@ class RequestsGrid( grids.Grid ): ) ] columns.append( grids.MulticolFilterColumn( "Search", - cols_to_filter=[ columns[0], columns[1], columns[6] ], + cols_to_filter=[ columns[0], columns[1] ], key="free-text-search", visible=False, filterable="standard" ) ) @@ -859,7 +859,7 @@ class RequestsCommon( BaseController, Us # The user has selected a sample to copy. library_id = current_samples[ copy_sample_index][ 'library_select_field' ].get_selected( return_value=True ) folder_id = current_samples[ copy_sample_index ][ 'folder_select_field' ].get_selected( return_value=True ) - name = current_samples[ copy_sample_index ][ 'name' ] + '_%i' % ( index ) + name = current_samples[ copy_sample_index ][ 'name' ] + '_%i' % ( index+1 ) library_id = 'none' folder_id = 'none' field_values = [ val for val in current_samples[ copy_sample_index ][ 'field_values' ] ] @@ -867,7 +867,7 @@ class RequestsCommon( BaseController, Us # The user has not selected a sample to copy (may just be adding a sample). library_id = None folder_id = None - name = 'Sample_%i' % sample_index + name = 'Sample_%i' % ( sample_index+1 ) field_values = [ '' for field in request.type.sample_form.fields ] # Build the library_select_field and folder_select_field for the new sample being added. library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans,

1 0

galaxy-dist commit 0e7dbb91575d: sample_tracking bug fixes:
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1286891943 14400 # Node ID 0e7dbb91575d9c8abf39f759cd7bdf54efadcd80 # Parent 1b397ec7f199b8a0581e52af694a12985deb0a64 sample_tracking bug fixes: - undelete request now working - email notification settings for a request can now be changed. --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -516,7 +516,7 @@ class RequestsCommon( BaseController, Us trans.sa_session.add( s ) trans.sa_session.flush() num_undeleted += 1 - message += '%i requests have been undeleted.' % num_deleted + message += '%i requests have been undeleted.' % num_undeleted return trans.response.send_redirect( web.url_for( controller=cntrller, action='browse_requests', status=status, @@ -570,7 +570,7 @@ class RequestsCommon( BaseController, Us email_addresses.append( util.restore_text( email_address ) ) # Make sure email addresses are valid err_msg = '' - for email_address in additional_email_addresses: + for email_address in email_addresses: err_msg += self.__validate_email( email_address ) if err_msg: status = 'error'

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galaxy-dist commit 772d6986c1af: sample_tracking:
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1286910360 14400 # Node ID 772d6986c1afc7e78a9543fb5445e4d327df7df1 # Parent 71dd9ee7b9b945b28359f3e422095d7623841bce sample_tracking: - bug fix in method to set library permissions for the data transfer user - code cleanup --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -102,8 +102,7 @@ class DataTransferGrid( grids.Grid ): return sample_dataset.status # Grid definition title = "Sample Datasets" - # TODO: can this be grid.mako??? - template = "admin/requests/datasets_grid.mako" + template = "admin/requests/grid.mako" model_class = model.SampleDataset default_sort_key = "-create_time" num_rows_per_page = 50 @@ -118,7 +117,9 @@ class DataTransferGrid( grids.Grid ): SizeColumn( "Size", #key='size', filterable="advanced" ), - grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), + grids.GridColumn( "Last Updated", + key="update_time", + format=time_ago ), StatusColumn( "Status", #key='status', filterable="advanced" ), @@ -560,7 +561,7 @@ class RequestsAdmin( BaseController, Use lfp = trans.model.LibraryFolderPermissions( trans.app.security_agent.permitted_actions.LIBRARY_ADD.action, folder, datatx_user_private_role ) - trans.sa_session.add( dp ) + trans.sa_session.add( lfp ) trans.sa_session.flush() return datatx_user def __send_message( self, trans, datatx_info, sample, id_list ): --- a/templates/admin/requests/datasets_grid.mako +++ /dev/null @@ -1,27 +0,0 @@ -<%def name="custom_javascripts()"> - <script type="text/javascript"> - $("#select-dataset-action-button").bind( "click", function(e) { - $.ajax({ - url: "${h.url_for( controller='requests_admin', action='remote_file_browser' )}", - data: {id: 6}, - error: function() { alert( "Couldn't create new browser" ) }, - success: function(form_html) { - show_modal("Select file", form_html, { - "Cancel": function() { window.location = "${h.url_for( controller='requests_admin', action='browse_requests' )}"; }, - "Continue": function() { $(document).trigger("convert_dbkeys"); continue_fn(); } - }); - $("#new-title").focus(); - replace_big_select_inputs(); - } - }); - } - </script> -</%def> - -<%def name="javascripts()"> - ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jquery.event.drag", "jquery.autocomplete", "jquery.mousewheel", "trackster", "ui.core", "ui.sortable" )} - ${self.custom_javascripts()} - ${parent.javascripts()} -</%def> - -<%inherit file="/grid_base.mako"/>

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