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commit/galaxy-central: jgoecks: Add cuffmerge tool wrapper and functional test.
by Bitbucket 01 Feb '12

01 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/724bbcc69c92/ changeset: 724bbcc69c92 user: jgoecks date: 2012-02-02 04:36:17 summary: Add cuffmerge tool wrapper and functional test. affected #: 5 files diff -r 0f7670a67901587a939a93047b6b58bdb93f3516 -r 724bbcc69c921ebe53b780d04f2699178201941e test-data/cuffmerge_out1.gtf --- /dev/null +++ b/test-data/cuffmerge_out1.gtf @@ -0,0 +1,74 @@ +chr1 Cufflinks exon 4797974 4798063 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1"; +chr1 Cufflinks exon 4798536 4798567 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "2"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1"; +chr1 Cufflinks exon 4818665 4818730 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "3"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1"; +chr1 Cufflinks exon 4820349 4820396 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "4"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1"; +chr1 Cufflinks exon 4822392 4822462 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "5"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1"; +chr1 Cufflinks exon 4827082 4827155 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "6"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1"; +chr1 Cufflinks exon 4829468 4829569 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "7"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1"; +chr1 Cufflinks exon 4831037 4831213 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "8"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1"; +chr1 Cufflinks exon 4835044 4836816 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "9"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1"; +chr1 Cufflinks exon 4847775 4848057 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; gene_name "Tcea1"; oId "Tcea1_dup1"; contained_in "TCONS_00000003"; nearest_ref "Tcea1_dup1"; class_code "="; tss_id "TSS2"; +chr1 Cufflinks exon 4857551 4857613 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "2"; gene_name "Tcea1"; oId "Tcea1_dup1"; contained_in "TCONS_00000003"; nearest_ref "Tcea1_dup1"; class_code "="; tss_id "TSS2"; +chr1 Cufflinks exon 4847775 4848057 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "1"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2"; +chr1 Cufflinks exon 4857551 4857613 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "2"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2"; +chr1 Cufflinks exon 4868108 4868213 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "3"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2"; +chr1 Cufflinks exon 4876825 4876912 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "4"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2"; +chr1 Cufflinks exon 4879538 4879683 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "5"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2"; +chr1 Cufflinks exon 4880821 4880877 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "6"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2"; +chr1 Cufflinks exon 4881996 4882150 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "7"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2"; +chr1 Cufflinks exon 4883498 4883644 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "8"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2"; +chr1 Cufflinks exon 4885015 4885086 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "9"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2"; +chr1 Cufflinks exon 4886437 4887987 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "10"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2"; +chr1 Cufflinks exon 3204563 3207049 . - . gene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "1"; gene_name "Xkr4"; oId "Xkr4"; nearest_ref "Xkr4"; class_code "="; tss_id "TSS3"; +chr1 Cufflinks exon 3411783 3411982 . - . gene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "2"; gene_name "Xkr4"; oId "Xkr4"; nearest_ref "Xkr4"; class_code "="; tss_id "TSS3"; +chr1 Cufflinks exon 3660633 3661579 . - . gene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "3"; gene_name "Xkr4"; oId "Xkr4"; nearest_ref "Xkr4"; class_code "="; tss_id "TSS3"; +chr1 Cufflinks exon 4334224 4340172 . - . gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "1"; gene_name "Rp1"; oId "Rp1"; nearest_ref "Rp1"; class_code "="; tss_id "TSS4"; +chr1 Cufflinks exon 4341991 4342162 . - . gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "2"; gene_name "Rp1"; oId "Rp1"; nearest_ref "Rp1"; class_code "="; tss_id "TSS4"; +chr1 Cufflinks exon 4342283 4342918 . - . gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "3"; gene_name "Rp1"; oId "Rp1"; nearest_ref "Rp1"; class_code "="; tss_id "TSS4"; +chr1 Cufflinks exon 4350281 4350473 . - . gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "4"; gene_name "Rp1"; oId "Rp1"; nearest_ref "Rp1"; class_code "="; tss_id "TSS4"; +chr1 Cufflinks exon 4481009 4482749 . - . gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "1"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5"; +chr1 Cufflinks exon 4483181 4483547 . - . gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "2"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5"; +chr1 Cufflinks exon 4483853 4483944 . - . gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "3"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5"; +chr1 Cufflinks exon 4485217 4486023 . - . gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "4"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5"; +chr1 Cufflinks exon 4486372 4486494 . - . gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "5"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5"; +chr1 Cufflinks exon 4763279 4764597 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "1"; gene_name "Mrpl15"; oId "Mrpl15_dup2"; nearest_ref "Mrpl15_dup2"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4767606 4767729 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "2"; gene_name "Mrpl15"; oId "Mrpl15_dup2"; nearest_ref "Mrpl15_dup2"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4772649 4772814 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "3"; gene_name "Mrpl15"; oId "Mrpl15_dup2"; nearest_ref "Mrpl15_dup2"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4775654 4775807 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "4"; gene_name "Mrpl15"; oId "Mrpl15_dup2"; nearest_ref "Mrpl15_dup2"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4763279 4764597 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "1"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4767606 4767729 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "2"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4772649 4772814 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "3"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4774032 4774186 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "4"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4775654 4775807 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "5"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4763279 4766882 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "1"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4767606 4767729 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "2"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4772649 4772814 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "3"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4774032 4774186 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "4"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4775654 4775807 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "5"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 3111450 3111490 . . . gene_id "XLOC_000007"; transcript_id "TCONS_00000010"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS7"; +chr1 Cufflinks exon 3111546 3111576 . . . gene_id "XLOC_000008"; transcript_id "TCONS_00000011"; exon_number "1"; oId "CUFF.2.1"; class_code "u"; tss_id "TSS8"; +chr1 Cufflinks exon 3174766 3174792 . . . gene_id "XLOC_000009"; transcript_id "TCONS_00000012"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS9"; +chr1 Cufflinks exon 3187402 3187428 . . . gene_id "XLOC_000010"; transcript_id "TCONS_00000013"; exon_number "1"; oId "CUFF.4.1"; class_code "u"; tss_id "TSS10"; +chr1 Cufflinks exon 3188522 3188548 . . . gene_id "XLOC_000011"; transcript_id "TCONS_00000014"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS11"; +chr1 Cufflinks exon 3189811 3190789 . . . gene_id "XLOC_000012"; transcript_id "TCONS_00000015"; exon_number "1"; oId "CUFF.6.1"; class_code "u"; tss_id "TSS12"; +chr1 Cufflinks exon 3190859 3191434 . . . gene_id "XLOC_000013"; transcript_id "TCONS_00000016"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS13"; +chr1 Cufflinks exon 3191513 3192077 . . . gene_id "XLOC_000014"; transcript_id "TCONS_00000017"; exon_number "1"; oId "CUFF.8.1"; class_code "u"; tss_id "TSS14"; +chr1 Cufflinks exon 3192251 3192336 . . . gene_id "XLOC_000015"; transcript_id "TCONS_00000018"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS15"; +chr1 Cufflinks exon 3192442 3192494 . . . gene_id "XLOC_000016"; transcript_id "TCONS_00000019"; exon_number "1"; oId "CUFF.10.1"; class_code "u"; tss_id "TSS16"; +chr1 Cufflinks exon 3192551 3192676 . . . gene_id "XLOC_000017"; transcript_id "TCONS_00000020"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS17"; +chr1 Cufflinks exon 3192732 3192811 . . . gene_id "XLOC_000018"; transcript_id "TCONS_00000021"; exon_number "1"; oId "CUFF.12.1"; class_code "u"; tss_id "TSS18"; +chr1 Cufflinks exon 3192941 3193042 . . . gene_id "XLOC_000019"; transcript_id "TCONS_00000022"; exon_number "1"; oId "CUFF.13.1"; class_code "u"; tss_id "TSS19"; +chr1 Cufflinks exon 3194186 3194226 . . . gene_id "XLOC_000020"; transcript_id "TCONS_00000023"; exon_number "1"; oId "CUFF.14.1"; class_code "u"; tss_id "TSS20"; +chr1 Cufflinks exon 3194303 3194329 . . . gene_id "XLOC_000021"; transcript_id "TCONS_00000024"; exon_number "1"; oId "CUFF.15.1"; class_code "u"; tss_id "TSS21"; +chr1 Cufflinks exon 3194707 3194733 . . . gene_id "XLOC_000022"; transcript_id "TCONS_00000025"; exon_number "1"; oId "CUFF.16.1"; class_code "u"; tss_id "TSS22"; +chr1 Cufflinks exon 3195084 3195110 . . . gene_id "XLOC_000023"; transcript_id "TCONS_00000026"; exon_number "1"; oId "CUFF.17.1"; class_code "u"; tss_id "TSS23"; +chr1 Cufflinks exon 3195451 3195477 . . . gene_id "XLOC_000024"; transcript_id "TCONS_00000027"; exon_number "1"; oId "CUFF.18.1"; class_code "u"; tss_id "TSS24"; +chr1 Cufflinks exon 3197090 3197116 . . . gene_id "XLOC_000025"; transcript_id "TCONS_00000028"; exon_number "1"; oId "CUFF.19.1"; class_code "u"; tss_id "TSS25"; +chr1 Cufflinks exon 3197247 3197273 . . . gene_id "XLOC_000026"; transcript_id "TCONS_00000029"; exon_number "1"; oId "CUFF.20.1"; class_code "u"; tss_id "TSS26"; +chr1 Cufflinks exon 3197347 3197373 . . . gene_id "XLOC_000027"; transcript_id "TCONS_00000030"; exon_number "1"; oId "CUFF.21.1"; class_code "u"; tss_id "TSS27"; +chr1 Cufflinks exon 3197426 3197452 . . . gene_id "XLOC_000028"; transcript_id "TCONS_00000031"; exon_number "1"; oId "CUFF.22.1"; class_code "u"; tss_id "TSS28"; +chr1 Cufflinks exon 3200023 3200191 . . . gene_id "XLOC_000029"; transcript_id "TCONS_00000032"; exon_number "1"; oId "CUFF.23.1"; class_code "u"; tss_id "TSS29"; +chr1 Cufflinks exon 3200326 3200352 . . . gene_id "XLOC_000030"; transcript_id "TCONS_00000033"; exon_number "1"; oId "CUFF.24.1"; class_code "u"; tss_id "TSS30"; +chr1 Cufflinks exon 3200431 3200457 . . . gene_id "XLOC_000031"; transcript_id "TCONS_00000034"; exon_number "1"; oId "CUFF.25.1"; class_code "u"; tss_id "TSS31"; +chr1 Cufflinks exon 3201008 3201481 . . . gene_id "XLOC_000032"; transcript_id "TCONS_00000035"; exon_number "1"; oId "CUFF.26.1"; class_code "u"; tss_id "TSS32"; +chr1 Cufflinks exon 3201597 3201809 . . . gene_id "XLOC_000033"; transcript_id "TCONS_00000036"; exon_number "1"; oId "CUFF.27.1"; class_code "u"; tss_id "TSS33"; diff -r 0f7670a67901587a939a93047b6b58bdb93f3516 -r 724bbcc69c921ebe53b780d04f2699178201941e tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -406,6 +406,7 @@ <tool file="ngs_rna/tophat_wrapper.xml" /><tool file="ngs_rna/cufflinks_wrapper.xml" /><tool file="ngs_rna/cuffcompare_wrapper.xml" /> + <tool file="ngs_rna/cuffmerge_wrapper.xml" /><tool file="ngs_rna/cuffdiff_wrapper.xml" /><label text="Filtering" id="filtering" /><tool file="ngs_rna/filter_transcripts_via_tracking.xml" /> diff -r 0f7670a67901587a939a93047b6b58bdb93f3516 -r 724bbcc69c921ebe53b780d04f2699178201941e tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -359,6 +359,7 @@ <tool file="ngs_rna/tophat_color_wrapper.xml" /><tool file="ngs_rna/cufflinks_wrapper.xml" /><tool file="ngs_rna/cuffcompare_wrapper.xml" /> + <tool file="ngs_rna/cuffmerge_wrapper.xml" /><tool file="ngs_rna/cuffdiff_wrapper.xml" /> + <description>merge together several Cufflinks assemblies</description> + <requirements> + <requirement type="package">cufflinks</requirement> + </requirements> + <command interpreter="python"> + cuffmerge_wrapper.py + + ## Use annotation reference? + #if $annotation.use_ref_annotation == "Yes": + -g $annotation.reference_annotation + #end if + + ## Use sequence data? + #if $seq_data.use_seq_data == "Yes": + -s + #if $seq_data.seq_source.index_source == "history": + --ref_file=$seq_data.seq_source.ref_file + #else: + --ref_file="None" + #end if + --dbkey=${first_input.metadata.dbkey} + --index_dir=${GALAXY_DATA_INDEX_DIR} + #end if + + ## Outputs. + --merged-transcripts=${merged_transcripts} + + ## Inputs. + ${first_input} + #for $input_file in $input_files: + ${input_file.additional_input} + #end for + + </command> + <inputs> + <param format="gtf" name="first_input" type="data" label="GTF file produced by Cufflinks" help=""/> + <repeat name="input_files" title="Additional GTF Input Files"> + <param format="gtf" name="additional_input" type="data" label="GTF file produced by Cufflinks" help=""/> + </repeat> + <conditional name="annotation"> + <param name="use_ref_annotation" type="select" label="Use Reference Annotation"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="Yes"> + <param format="gtf" name="reference_annotation" type="data" label="Reference Annotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/> + </when> + <when value="No"> + </when> + </conditional> + <conditional name="seq_data"> + <param name="use_seq_data" type="select" label="Use Sequence Data" help="Use sequence data for some optional classification functions, including the addition of the p_id attribute required by Cuffdiff."> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No"></when> + <when value="Yes"> + <conditional name="seq_source"> + <param name="index_source" type="select" label="Choose the source for the reference list"> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </param> + <when value="cached"></when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + </when> + </conditional> + </when> + </conditional> + </inputs> + + <outputs> + <data format="gtf" name="merged_transcripts" label="${tool.name} on ${on_string}: merged transcripts"/> + </outputs> + + <tests> +  + <test> + <param name="first_input" value="cuffcompare_in1.gtf" ftype="gtf"/> + <param name="additional_input" value="cuffcompare_in2.gtf" ftype="gtf"/> + <param name="use_ref_annotation" value="Yes"/> + <param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/> + <param name="use_seq_data" value="No"/> + <output name="merged_transcripts" file="cuffmerge_out1.gtf"/> + </test> + </tests> + + <help> +**Cuffmerge Overview** + +Cuffmerge is part of Cufflinks_. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621 + +.. _Cufflinks: http://cufflinks.cbcb.umd.edu/ + +------ + +**Know what you are doing** + +.. class:: warningmark + +There is no such thing (yet) as an automated gearshift in expression analysis. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy. + +.. __: http://cufflinks.cbcb.umd.edu/manual.html#cuffmerge + +------ + +**Input format** + +Cuffmerge takes Cufflinks' GTF output as input, and optionally can take a "reference" annotation (such as from Ensembl_) + +.. _Ensembl: http://www.ensembl.org + +------ + +**Outputs** + +Cuffmerge produces the following output files: + +Merged transcripts file: + +Cuffmerge produces a GTF file that contains an assembly that merges together the input assemblies. </help> +</tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 01 Feb '12

01 Feb '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e5f7236a7e3a/ changeset: e5f7236a7e3a user: jgoecks date: 2012-02-01 22:47:32 summary: Change default sort for Pages list to update time. affected #: 1 file diff -r 315515ad52b04d15fe33476b7a33c1079712728c -r e5f7236a7e3ad4e6b6414beb875fc89206deebe7 lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py +++ b/lib/galaxy/web/controllers/page.py @@ -23,7 +23,7 @@ title = "Pages" model_class = model.Page default_filter = { "published" : "All", "tags" : "All", "title" : "All", "sharing" : "All" } - default_sort_key = "-create_time" + default_sort_key = "-update_time" columns = [ grids.TextColumn( "Title", key="title", attach_popup=True, filterable="advanced" ), URLColumn( "Public URL" ), https://bitbucket.org/galaxy/galaxy-central/changeset/0f7670a67901/ changeset: 0f7670a67901 user: jgoecks date: 2012-02-01 23:34:50 summary: To be compatible with distributed object store, use create() when adding data subsets for Trackster. affected #: 1 file diff -r e5f7236a7e3ad4e6b6414beb875fc89206deebe7 -r 0f7670a67901587a939a93047b6b58bdb93f3516 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -961,6 +961,7 @@ data_provider = data_provider_class( original_dataset=input_dataset, converted_dataset=converted_dataset, dependencies=deps ) + trans.app.object_store.create( new_dataset.dataset ) data_provider.write_data_to_file( chrom, low, high, new_dataset.file_name ) # TODO: (a) size not working; (b) need to set peek. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Add overwrite param when setting metadata in Trackster data subsets.
by Bitbucket 01 Feb '12

01 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/315515ad52b0/ changeset: 315515ad52b0 user: jgoecks date: 2012-02-01 21:27:53 summary: Add overwrite param when setting metadata in Trackster data subsets. affected #: 1 file diff -r a8eca62cd5304509a67e598d54d5203411aeb3df -r 315515ad52b04d15fe33476b7a33c1079712728c lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -970,7 +970,7 @@ # Set metadata. if trans.app.config.set_metadata_externally: - trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming = { 'input1':new_dataset } ) + trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming = { 'input1':new_dataset }, overwrite=False ) else: message = 'Attributes updated' new_dataset.set_meta() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Fix bug: when setting chromInfo, do not assume a fasta file exists.
by Bitbucket 01 Feb '12

01 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a8eca62cd530/ changeset: a8eca62cd530 user: jgoecks date: 2012-02-01 20:00:21 summary: Fix bug: when setting chromInfo, do not assume a fasta file exists. affected #: 1 file diff -r 7d97c594b1639bc16aba60ae8a0bf9a2798dbde8 -r a8eca62cd5304509a67e598d54d5203411aeb3df lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -193,12 +193,15 @@ incoming[ "chromInfo" ] = db_dataset.file_name else: # For custom builds, chrom info resides in converted dataset; for built-in builds, chrom info resides in tool-data/shared. + chrom_info = None if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in trans.user.preferences[ 'dbkeys' ] ): # Custom build. custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ input_dbkey ] - build_fasta_dataset = trans.app.model.HistoryDatasetAssociation.get( custom_build_dict[ 'fasta' ] ) - chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name - else: + if 'fasta' in custom_build_dict: + build_fasta_dataset = trans.app.model.HistoryDatasetAssociation.get( custom_build_dict[ 'fasta' ] ) + chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name + + if not chrom_info: # Default to built-in build. chrom_info = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % input_dbkey ) incoming[ "chromInfo" ] = chrom_info Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Workflows:
by Bitbucket 01 Feb '12

01 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d7846ad65544/ changeset: d7846ad65544 user: dannon date: 2012-02-01 17:45:53 summary: Workflows: Add the ability to view your own workflows in plain display mode as if you had shared it. affected #: 3 files diff -r 3097eedaf60b515fceae5d26639f8f4621099040 -r d7846ad655441f7739a903dac4906c3a6c262354 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -222,6 +222,35 @@ user_item_rating = user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings ) @web.expose + def display_by_id( self, trans, id ): + """ Display workflow based on a username and slug. """ + # Get workflow. + stored_workflow = self.get_stored_workflow( trans, id ) + if stored_workflow is None: + raise web.httpexceptions.HTTPNotFound() + # Security check raises error if user cannot access workflow. + self.security_check( trans, stored_workflow, False, True) + + # Get data for workflow's steps. + self.get_stored_workflow_steps( trans, stored_workflow ) + # Get annotations. + stored_workflow.annotation = self.get_item_annotation_str( trans.sa_session, stored_workflow.user, stored_workflow ) + for step in stored_workflow.latest_workflow.steps: + step.annotation = self.get_item_annotation_str( trans.sa_session, stored_workflow.user, step ) + + # Get rating data. + user_item_rating = 0 + if trans.get_user(): + user_item_rating = self.get_user_item_rating( trans.sa_session, trans.get_user(), stored_workflow ) + if user_item_rating: + user_item_rating = user_item_rating.rating + else: + user_item_rating = 0 + ave_item_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, stored_workflow ) + return trans.fill_template_mako( "workflow/display.mako", item=stored_workflow, item_data=stored_workflow.latest_workflow.steps, + user_item_rating = user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings ) + + @web.expose def get_item_content_async( self, trans, id ): """ Returns item content in HTML format. """ diff -r 3097eedaf60b515fceae5d26639f8f4621099040 -r d7846ad655441f7739a903dac4906c3a6c262354 templates/workflow/display.mako --- a/templates/workflow/display.mako +++ b/templates/workflow/display.mako @@ -63,12 +63,14 @@ <%def name="render_item_links( workflow )"> + %if workflow.importable: <a href="${h.url_for( controller='/workflow', action='imp', id=trans.security.encode_id(workflow.id) )}" class="icon-button import" ## Needed to overwide initial width so that link is floated left appropriately. style="width: 100%" title="Import workflow">Import workflow</a> + %endif </%def><%def name="render_item( workflow, steps )"> diff -r 3097eedaf60b515fceae5d26639f8f4621099040 -r d7846ad655441f7739a903dac4906c3a6c262354 templates/workflow/list.mako --- a/templates/workflow/list.mako +++ b/templates/workflow/list.mako @@ -69,6 +69,7 @@ <a class="action-button" href="${h.url_for( controller='workflow', action='export', id=trans.security.encode_id( workflow.id ) )}">Download or Export</a><a class="action-button" href="${h.url_for( controller='workflow', action='clone', id=trans.security.encode_id( workflow.id ) )}">Clone</a><a class="action-button" href="${h.url_for( controller='workflow', action='rename', id=trans.security.encode_id( workflow.id ) )}">Rename</a> + <a class="action-button" href="${h.url_for( controller='workflow', action='display_by_id', id=trans.security.encode_id( workflow.id ) )}" target="_top">View</a><a class="action-button" confirm="Are you sure you want to delete workflow '${h.to_unicode( workflow.name ) | h}'?" href="${h.url_for( controller='workflow', action='delete', id=trans.security.encode_id( workflow.id ) )}">Delete</a></div></td> @@ -118,4 +119,4 @@ </a></div></div> -</%def> \ No newline at end of file +</%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Add a new complete FreeBayes tool configuration.
by Bitbucket 01 Feb '12

01 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3097eedaf60b/ changeset: 3097eedaf60b user: dan date: 2012-02-01 17:25:18 summary: Add a new complete FreeBayes tool configuration. affected #: 4 files diff -r a372c3970447dd0caf123db7c3047d372bfb8092 -r 3097eedaf60b515fceae5d26639f8f4621099040 test-data/variant_detection/freebayes/freebayes_out_1.output_trace --- /dev/null +++ b/test-data/variant_detection/freebayes/freebayes_out_1.output_trace @@ -0,0 +1,8 @@ +phiX174,1411,allele,phiX174,phiX174,A,60,100 +phiX174,1412,allele,phiX174,phiX174,G,60,100 +phiX174,1413,allele,phiX174,phiX174,C,60,100 +phiX174,1414,allele,phiX174,phiX174,G,60,100 +phiX174,1415,allele,phiX174,phiX174,C,60,100 +phiX174,1416,allele,phiX174,phiX174,C,60,100 +phiX174,1417,allele,phiX174,phiX174,G,60,100 +phiX174,1418,allele,phiX174,phiX174,T,60,100 diff -r a372c3970447dd0caf123db7c3047d372bfb8092 -r 3097eedaf60b515fceae5d26639f8f4621099040 test-data/variant_detection/freebayes/freebayes_out_1.vcf.contains --- /dev/null +++ b/test-data/variant_detection/freebayes/freebayes_out_1.vcf.contains @@ -0,0 +1,2 @@ +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A + diff -r a372c3970447dd0caf123db7c3047d372bfb8092 -r 3097eedaf60b515fceae5d26639f8f4621099040 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -415,6 +415,9 @@ <tool file="gatk/variant_eval.xml" /><tool file="gatk/variant_combine.xml" /></section> + <section name="NGS: Variant Detection" id="variant_detection"> + <tool file="variant_detection/freebayes.xml" /> + </section><section name="NGS: Peak Calling" id="peak_calling"><tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /> diff -r a372c3970447dd0caf123db7c3047d372bfb8092 -r 3097eedaf60b515fceae5d26639f8f4621099040 tools/variant_detection/freebayes.xml --- /dev/null +++ b/tools/variant_detection/freebayes.xml @@ -0,0 +1,655 @@ +<?xml version="1.0"?> +<tool id="freebayes" name="FreeBayes" version="0.0.1"> + <requirements> + <requirement type="package" version="0.9.4">freebayes</requirement> + <requirement type="package">samtools</requirement> + </requirements> + <description> - Bayesian genetic variant detector</description> + <command> + ##set up input files + #set $reference_fasta_filename = "localref.fa" + #if str( $reference_source.reference_source_selector ) == "history": + ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && + samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 && + #else: + #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) + #end if + #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ): + ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" && + ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" && + #end for + ##finished setting up inputs + + ##start FreeBayes commandline + freebayes + #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ): + --bam "localbam_${bam_count}.bam" + #end for + --fasta-reference "${reference_fasta_filename}" + + ##outputs + --vcf "${output_vcf}" + --trace "${output_trace}" + --failed-alleles "${output_failed_alleles_bed}" + + ##advanced options + #if str( $options_type.options_type_selector ) == "advanced": + ##additional inputs + #if str( $options_type.target_limit_type.target_limit_type_selector ) == "limit_by_target_file": + --targets "${options_type.target_limit_type.input_target_bed}" + #elif str( $options_type.target_limit_type.target_limit_type_selector ) == "limit_by_region": + --region "${options_type.target_limit_type.region_chromosome}:${options_type.target_limit_type.region_start}..${options_type.target_limit_type.region_end}" + #end if + #if $options_type.input_sample_file: + --samples "${options_type.input_sample_file}" + #end if + #if $options_type.input_populations_file: + --populations "${options_type.input_populations_file}" + #end if + #if $options_type.input_cnv_map_bed: + --cnv-map "${options_type.input_cnv_map_bed}" + #end if + #if str( $options_type.input_variant_type.input_variant_type_selector ) == "provide_vcf": + --variant-input "${options_type.input_variant_type.input_variant_vcf}" + ${options_type.input_variant_type.only_use_input_alleles} + #end if + + ##reporting + #if str( $options_type.section_reporting_type.section_reporting_type_selector ) == "set": + --pvar "${options_type.section_reporting_type.pvar}" + ${options_type.section_reporting_type.show_reference_repeats} + #end if + + ##population model + #if str( $options_type.section_population_model_type.section_population_model_type_selector ) == "set": + --theta "${options_type.section_population_model_type.theta}" + --ploidy "${options_type.section_population_model_type.ploidy}" + ${options_type.section_population_model_type.pooled} + #end if + + ##reference allele + #if str( $options_type.use_reference_allele_type.use_reference_allele_type_selector ) == "include_reference_allele": + --use-reference-allele + ${options_type.use_reference_allele_type.diploid_reference} + --reference-quality "${options_type.use_reference_allele_type.reference_quality_mq},${options_type.use_reference_allele_type.reference_quality_bq}" + #end if + + ##allele scope + #if str( $options_type.section_allele_scope_type.section_allele_scope_type_selector ) == "set": + ${options_type.section_allele_scope_type.no_snps} + ${options_type.section_allele_scope_type.no_indels} + ${options_type.section_allele_scope_type.no_mnps} + ${options_type.section_allele_scope_type.no_complex} + --use-best-n-alleles "${options_type.section_allele_scope_type.use_best_n_alleles}" + #if $options_type.section_allele_scope_type.max_complex_gap: + --max-complex-gap "${options_type.section_allele_scope_type.max_complex_gap}" + #end if + #end if + + ##indel realignment + ${options_type.left_align_indels} + + ##input filters + #if str( $options_type.section_input_filters_type.section_input_filters_type_selector ) == "set": + ${options_type.section_input_filters_type.use_duplicate_reads} + #if str( $options_type.section_input_filters_type.no_filter_type.no_filter_type_selector ) == "apply_filters": + --min-mapping-quality "${options_type.section_input_filters_type.no_filter_type.min_mapping_quality}" + --min-base-quality "${options_type.section_input_filters_type.no_filter_type.min_base_quality}" + --min-supporting-quality "${options_type.section_input_filters_type.no_filter_type.min_supporting_quality_mq},${options_type.section_input_filters_type.no_filter_type.min_supporting_quality_bq}" + #else: + --no-filters + #end if + --mismatch-base-quality-threshold "${options_type.section_input_filters_type.mismatch_base_quality_threshold}" + #if $options_type.section_input_filters_type.read_mismatch_limit: + --read-mismatch-limit "${options_type.section_input_filters_type.read_mismatch_limit}" + #end if + --read-max-mismatch-fraction "${options_type.section_input_filters_type.read_max_mismatch_fraction}" + #if $options_type.section_input_filters_type.read_snp_limit: + --read-snp-limit "${options_type.section_input_filters_type.read_snp_limit}" + #end if + #if $options_type.section_input_filters_type.read_indel_limit: + --read-indel-limit "${options_type.section_input_filters_type.read_indel_limit}" + #end if + --indel-exclusion-window "${options_type.section_input_filters_type.indel_exclusion_window}" + --min-alternate-fraction "${options_type.section_input_filters_type.min_alternate_fraction}" + --min-alternate-count "${options_type.section_input_filters_type.min_alternate_count}" + --min-alternate-qsum "${options_type.section_input_filters_type.min_alternate_qsum}" + --min-alternate-total "${options_type.section_input_filters_type.min_alternate_total}" + --min-coverage "${options_type.section_input_filters_type.min_coverage}" + #end if + + ##bayesian priors + #if str( $options_type.section_bayesian_priors_type.section_bayesian_priors_type_selector ) == "set": + ${options_type.section_bayesian_priors_type.no_ewens_priors} + ${options_type.section_bayesian_priors_type.no_population_priors} + ${options_type.section_bayesian_priors_type.hwe_priors} + #end if + + ##observation prior expectations + #if str( $options_type.section_observation_prior_expectations_type.section_observation_prior_expectations_type_selector ) == "set": + ${options_type.section_observation_prior_expectations_type.binomial_obs_priors} + ${options_type.section_observation_prior_expectations_type.allele_balance_priors} + #end if + + ##algorithmic features + #if str( $options_type.section_algorithmic_features_type.section_algorithmic_features_type_selector ) == "set": + --site-selection-max-iterations "${options_type.section_algorithmic_features_type.site_selection_max_iterations}" + --genotyping-max-iterations "${options_type.section_algorithmic_features_type.genotyping_max_iterations}" + --genotyping-max-banddepth "${options_type.section_algorithmic_features_type.genotyping_max_banddepth}" + --posterior-integration-limits "${options_type.section_algorithmic_features_type.posterior_integration_limits_n},${options_type.section_algorithmic_features_type.posterior_integration_limits_m}" + ${options_type.section_algorithmic_features_type.no_permute} + ${options_type.section_algorithmic_features_type.exclude_unobserved_genotypes} + #if $options_type.section_algorithmic_features_type.genotype_variant_threshold: + --genotype-variant-threshold "${options_type.section_algorithmic_features_type.genotype_variant_threshold}" + #end if + ${options_type.section_algorithmic_features_type.use_mapping_quality} + --read-dependence-factor "${options_type.section_algorithmic_features_type.read_dependence_factor}" + ${options_type.section_algorithmic_features_type.no_marginals} + #end if + + #end if + </command> + <inputs> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </param> + <when value="cached"> + <repeat name="input_bams" title="Sample BAM file" min="1"> + <param name="input_bam" type="data" format="bam" label="BAM file"> + <validator type="unspecified_build" /> + <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="value" message="Sequences are not currently available for the specified build." /> + </param> + </repeat> + <param name="ref_file" type="select" label="Using reference genome"> + <options from_data_table="sam_fa_indexes"> +  + </options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <repeat name="input_bams" title="Sample BAM file" min="1"> + <param name="input_bam" type="data" format="bam" label="BAM file" /> + </repeat> + <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + </when> + </conditional> + + <conditional name="options_type"> + <param name="options_type_selector" type="select" label="Basic or Advanced options"> + <option value="basic" selected="True">Basic</option> + <option value="advanced">Advanced</option> + </param> + <when value="basic"> +  + </when> + <when value="advanced"> + +  + <conditional name="target_limit_type"> + <param name="target_limit_type_selector" type="select" label="Limit analysis to listed targets"> + <option value="do_not_limit" selected="True">Do not limit</option> + <option value="limit_by_target_file">Limit by target file</option> + <option value="limit_by_region">Limit to region</option> + </param> + <when value="do_not_limit"> +  + </when> + <when value="limit_by_target_file"> + <param name="input_target_bed" type="data" format="bed" label="Limit analysis to targets listed in the BED-format FILE." /> + </when> + <when value="limit_by_region"> + <param name="region_chromosome" type="text" label="Region Chromosome" value="" /> + <param name="region_start" type="integer" label="Region Start" value="" /> + <param name="region_end" type="integer" label="Region End" value="" /> + </when> + </conditional> + <param name="input_sample_file" type="data" format="txt" label="Limit analysis to samples listed (one per line) in the FILE" optional="True" /> + <param name="input_populations_file" type="data" format="txt" label="Populations File" optional="True" /> + <param name="input_cnv_map_bed" type="data" format="bed" label="Read a copy number map from the BED file FILE" optional="True" /> + <conditional name="input_variant_type"> + <param name="input_variant_type_selector" type="select" label="Provide variants file"> + <option value="do_not_provide" selected="True">Do not provide</option> + <option value="provide_vcf">Provide VCF file</option> + </param> + <when value="do_not_provide"> +  + </when> + <when value="provide_vcf"> + <param name="input_variant_vcf" type="data" format="vcf" label="Use variants reported in VCF file as input to the algorithm" /> + <param name="only_use_input_alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="False" label="Only provide variant calls and genotype likelihoods for sites in VCF" /> + </when> + </conditional> + + +  + <conditional name="section_reporting_type"> + <param name="section_reporting_type_selector" type="select" label="Set Reporting options"> + <option value="do_not_set" selected="True">Do not set</option> + <option value="set">Set</option> + </param> + <when value="do_no_set"> +  + </when> + <when value="set"> + <param name="pvar" type="float" label="Report sites if the probability that there is a polymorphism at the site is greater" value="0.0001" /> + <param name="show_reference_repeats" type="boolean" truevalue="--show-reference-repeats" falsevalue="" checked="False" label="Calculate and show information about reference repeats" /> + </when> + </conditional> + + +  + <conditional name="section_population_model_type"> + <param name="section_population_model_type_selector" type="select" label="Set population model options"> + <option value="do_not_set" selected="True">Do not set</option> + <option value="set">Set</option> + </param> + <when value="do_no_set"> +  + </when> + <when value="set"> + <param name="theta" type="float" label="expected mutation rate or pairwise nucleotide diversity among the population" value="0.001" help="This serves as the single parameter to the Ewens Sampling Formula prior model"/> + <param name="ploidy" type="integer" label="default ploidy for the analysis" value="2" /> + <param name="pooled" type="boolean" truevalue="--pooled" falsevalue="" checked="False" label="Assume that samples result from pooled sequencing" help="When using this flag, set --ploidy to the number of alleles in each sample." /> + </when> + </conditional> + +  + <conditional name="use_reference_allele_type"> + <param name="use_reference_allele_type_selector" type="select" label="Include the reference allele in the analysis"> + <option value="do_not_include_reference_allele" selected="True">Do not include</option> + <option value="include_reference_allele">Include</option> + </param> + <when value="do_not_include_reference_allele"> +  + </when> + <when value="include_reference_allele"> + <param name="diploid_reference" type="boolean" truevalue="--diploid-reference" falsevalue="" checked="False" label="Treat reference as diploid" /> + <param name="reference_quality_mq" type="integer" label="Assign mapping quality" value="100" /> + <param name="reference_quality_bq" type="integer" label="Assign base quality" value="60" /> + </when> + </conditional> + +  + <conditional name="section_allele_scope_type"> + <param name="section_allele_scope_type_selector" type="select" label="Set allele scope options"> + <option value="do_not_set" selected="True">Do not set</option> + <option value="set">Set</option> + </param> + <when value="do_no_set"> +  + </when> + <when value="set"> + <param name="no_snps" type="boolean" truevalue="--no-snps" falsevalue="" checked="False" label="Ignore SNP alleles" /> + <param name="no_indels" type="boolean" truevalue="--no-indels" falsevalue="" checked="False" label="Ignore insertion and deletion alleles" /> + <param name="no_mnps" type="boolean" truevalue="--no-mnps" falsevalue="" checked="False" label="Ignore multi-nuceotide polymorphisms, MNPs" /> + <param name="no_complex" type="boolean" truevalue="--no-complex" falsevalue="" checked="False" label="Ignore complex events (composites of other classes)" /> + <param name="use_best_n_alleles" type="integer" label="Evaluate only the best N SNP alleles" value="0" min="0" help="Ranked by sum of supporting quality scores; Set to 0 to use all" /> + <param name="max_complex_gap" type="integer" label="Allow complex alleles with contiguous embedded matches of up to this length" value="" optional="True"/> + </when> + </conditional> + +  + <param name="left_align_indels" type="boolean" truevalue="--left-align-indels" falsevalue="" checked="False" label="Left-realign and merge gaps embedded in reads" /> + +  + <conditional name="section_input_filters_type"> + <param name="section_input_filters_type_selector" type="select" label="Set input filters options"> + <option value="do_not_set" selected="True">Do not set</option> + <option value="set">Set</option> + </param> + <when value="do_no_set"> +  + </when> + <when value="set"> + <param name="use_duplicate_reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="False" label="Include duplicate-marked alignments in the analysis" /> + <conditional name="no_filter_type"> + <param name="no_filter_type_selector" type="select" label="Apply filters"> + <option value="apply_filters" selected="True">Apply</option> + <option value="no_filters">Do not apply</option> + </param> + <when value="no_filters"> +  + </when> + <when value="apply_filters"> + <param name="min_mapping_quality" type="integer" label="Exclude alignments from analysis if they have a mapping quality less than" value="30" /> + <param name="min_base_quality" type="integer" label="Exclude alleles from analysis if their supporting base quality less than" value="20" /> + <param name="min_supporting_quality_mq" type="integer" label="In order to consider an alternate allele, at least one supporting alignment must have mapping quality" value="0" /> + <param name="min_supporting_quality_bq" type="integer" label="In order to consider an alternate allele, at least one supporting alignment must have base quality" value="0" /> + </when> + </conditional> + <param name="mismatch_base_quality_threshold" type="integer" label="Count mismatches toward read-mismatch-limit if the base quality of the mismatch is >=" value="10" /> + <param name="read_mismatch_limit" type="integer" label="Exclude reads with more than N mismatches where each mismatch has base quality >= mismatch-base-quality-threshold" value="" optional="True" /> + <param name="read_max_mismatch_fraction" type="float" label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= mismatch-base-quality-threshold" value="1.0" /> + <param name="read_snp_limit" type="integer" label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold" value="" optional="True" /> + <param name="read_indel_limit" type="integer" label="Exclude reads with more than N separate gaps" value="" optional="True" /> + <param name="indel_exclusion_window" type="integer" label="Ignore portions of alignments this many bases from a putative insertion or deletion allele" value="0" /> + <param name="min_alternate_fraction" type="float" label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position" value="0" /> + <param name="min_alternate_count" type="integer" label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position" value="1" /> + <param name="min_alternate_qsum" type="integer" label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" value="0" /> + <param name="min_alternate_total" type="integer" label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis" value="1" /> + <param name="min_coverage" type="integer" label="Require at least this coverage to process a site" value="0" /> + </when> + </conditional> + + +  + <conditional name="section_bayesian_priors_type"> + <param name="section_bayesian_priors_type_selector" type="select" label="Set bayesian priors options"> + <option value="do_not_set" selected="True">Do not set</option> + <option value="set">Set</option> + </param> + <when value="do_no_set"> +  + </when> + <when value="set"> + <param name="no_ewens_priors" type="boolean" truevalue="--no-ewens-priors" falsevalue="" checked="False" label="Turns off the Ewens' Sampling Formula component of the priors" /> + <param name="no_population_priors" type="boolean" truevalue="--no-population-priors" falsevalue="" checked="False" label="No population priors" help="Equivalent to --pooled --no-ewens-priors" /> + <param name="hwe_priors" type="boolean" truevalue="--hwe-priors" falsevalue="" checked="False" label="Use the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency" /> + </when> + </conditional> + +  + <conditional name="section_observation_prior_expectations_type"> + <param name="section_observation_prior_expectations_type_selector" type="select" label="Set observation prior expectations options"> + <option value="do_not_set" selected="True">Do not set</option> + <option value="set">Set</option> + </param> + <when value="do_no_set"> +  + </when> + <when value="set"> + <param name="binomial_obs_priors" type="boolean" truevalue="--binomial-obs-priors" falsevalue="" checked="False" label="Incorporate expectations about osbervations into the priors, Uses read placement probability, strand balance probability, and read position (5'-3') probability" /> + <param name="allele_balance_priors" type="boolean" truevalue="--allele-balance-priors" falsevalue="" checked="False" label="Use aggregate probability of observation balance between alleles as a component of the priors. Best for observations with minimal inherent reference bias" /> + </when> + </conditional> + + +  + <conditional name="section_algorithmic_features_type"> + <param name="section_algorithmic_features_type_selector" type="select" label="Set algorithmic features options"> + <option value="do_not_set" selected="True">Do not set</option> + <option value="set">Set</option> + </param> + <when value="do_no_set"> +  + </when> + <when value="set"> + <param name="site_selection_max_iterations" type="integer" label="Uses hill-climbing algorithm to search posterior space for N iterations to determine if the site should be evaluated." value="5" help="Set to 0 to prevent use of this algorithm for site selection, and to a low integer for improvide site selection at a slight performance penalty" /> + <param name="genotyping_max_iterations" type="integer" label="Iterate no more than N times during genotyping step" value="25" /> + <param name="genotyping_max_banddepth" type="integer" label="Integrate no deeper than the Nth best genotype by likelihood when genotyping" value="6" /> + <param name="posterior_integration_limits_n" type="integer" label="Posteriror integration limit N" help="Integrate all genotype combinations in our posterior space which include no more than N samples with their Mth best data likelihood." value="1" /> + <param name="posterior_integration_limits_m" type="integer" label="Posteriror integration limit M" help="Integrate all genotype combinations in our posterior space which include no more than N samples with their Mth best data likelihood." value="3" /> + <param name="no_permute" type="boolean" truevalue="--no-permute" falsevalue="" checked="False" label="Do not scale prior probability of genotype combination given allele frequency by the number of permutations of included genotypes" /> + <param name="exclude_unobserved_genotypes" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="False" label="Skip sample genotypings for which the sample has no supporting reads" /> + <param name="genotype_variant_threshold" type="integer" label="Limit posterior integration to samples where the second-best genotype likelihood is no more than log(N) from the highest genotype likelihood for the sample" value="" optional="True" /> + <param name="use_mapping_quality" type="boolean" truevalue="--use-mapping-quality" falsevalue="" checked="False" label="Use mapping quality of alleles when calculating data likelihoods" /> + <param name="read_dependence_factor" type="float" label="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations" value="0.9" /> + <param name="no_marginals" type="boolean" truevalue="--no-marginals" falsevalue="" checked="False" label="Do not calculate the marginal probability of genotypes. Saves time and improves scaling performance in large populations" /> + </when> + </conditional> + + + </when> + </conditional> + + </inputs> + <outputs> + <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" /> + <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)" /> + <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)" /> + </outputs> + <tests> + <test> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" ftype="fasta" value="phiX.fasta"/> + <param name="input_bam" ftype="bam" value="gatk/fake_phiX_reads_1.bam"/> + <param name="options_type_selector" value="basic"/> + <output name="output_vcf" file="variant_detection/freebayes/freebayes_out_1.vcf.contains" compare="contains"/> + <output name="output_trace" file="variant_detection/freebayes/freebayes_out_1.output_trace" /> + <output name="output_failed_alleles_bed" file="empty_file.dat" /> + </test> + </tests> + <help> +**What it does** + +This tool uses FreeBayes to call SNPS given a reference sequence and a BAM alignment file. + +FreeBayes is a high-performance, flexible, and open-source Bayesian genetic variant detector. It operates on BAM alignment files, which are produced by most contemporary short-read aligners. + +In addition to substantial performance improvements over its predecessors (PolyBayes, GigaBayes, and BamBayes), it expands the scope of SNP and small-indel variant calling to populations of individuals with heterogeneous copy number. FreeBayes is currently under active development. + +Go `here <http://bioinformatics.bc.edu/marthlab/FreeBayes>`_ for details on FreeBayes. + +------ + +**Inputs** + +FreeBayes accepts an input aligned BAM file. + + +**Outputs** + +The output is in the VCF format. + +------- + +**Settings**:: + + input and output: + + -b --bam FILE Add FILE to the set of BAM files to be analyzed. + -c --stdin Read BAM input on stdin. + -v --vcf FILE Output VCF-format results to FILE. + -f --fasta-reference FILE + Use FILE as the reference sequence for analysis. + An index file (FILE.fai) will be created if none exists. + If neither --targets nor --region are specified, FreeBayes + will analyze every position in this reference. + -t --targets FILE + Limit analysis to targets listed in the BED-format FILE. + -r --region <chrom>:<start_position>..<end_position> + Limit analysis to the specified region, 0-base coordinates, + end_position not included (same as BED format). + -s --samples FILE + Limit analysis to samples listed (one per line) in the FILE. + By default FreeBayes will analyze all samples in its input + BAM files. + --populations FILE + Each line of FILE should list a sample and a population which + it is part of. The population-based bayesian inference model + will then be partitioned on the basis of the populations. + -A --cnv-map FILE + Read a copy number map from the BED file FILE, which has + the format: + reference sequence, start, end, sample name, copy number + ... for each region in each sample which does not have the + default copy number as set by --ploidy. + -L --trace FILE Output an algorithmic trace to FILE. + --failed-alleles FILE + Write a BED file of the analyzed positions which do not + pass --pvar to FILE. + -@ --variant-input VCF + Use variants reported in VCF file as input to the algorithm. + A report will be generated for every record in the VCF file. + -l --only-use-input-alleles + Only provide variant calls and genotype likelihoods for sites + and alleles which are provided in the VCF input, and provide + output in the VCF for all input alleles, not just those which + have support in the data. + + reporting: + + -P --pvar N Report sites if the probability that there is a polymorphism + at the site is greater than N. default: 0.0001 + -_ --show-reference-repeats + Calculate and show information about reference repeats in + the VCF output. + + population model: + + -T --theta N The expected mutation rate or pairwise nucleotide diversity + among the population under analysis. This serves as the + single parameter to the Ewens Sampling Formula prior model + default: 0.001 + -p --ploidy N Sets the default ploidy for the analysis to N. default: 2 + -J --pooled Assume that samples result from pooled sequencing. + When using this flag, set --ploidy to the number of + alleles in each sample. + + reference allele: + + -Z --use-reference-allele + This flag includes the reference allele in the analysis as + if it is another sample from the same population. + -H --diploid-reference + If using the reference sequence as a sample (-Z), + treat it as diploid. default: false (reference is haploid) + --reference-quality MQ,BQ + Assign mapping quality of MQ to the reference allele at each + site and base quality of BQ. default: 100,60 + + allele scope: + + -I --no-snps Ignore SNP alleles. + -i --no-indels Ignore insertion and deletion alleles. + -X --no-mnps Ignore multi-nuceotide polymorphisms, MNPs. + -u --no-complex Ignore complex events (composites of other classes). + -n --use-best-n-alleles N + Evaluate only the best N SNP alleles, ranked by sum of + supporting quality scores. (Set to 0 to use all; default: all) + -E --max-complex-gap N + Allow complex alleles with contiguous embedded matches of up + to this length. + + indel realignment: + + -O --left-align-indels + Left-realign and merge gaps embedded in reads. default: false + + input filters: + + -4 --use-duplicate-reads + Include duplicate-marked alignments in the analysis. + default: exclude duplicates + -m --min-mapping-quality Q + Exclude alignments from analysis if they have a mapping + quality less than Q. default: 30 + -q --min-base-quality Q + Exclude alleles from analysis if their supporting base + quality is less than Q. default: 20 + -R --min-supporting-quality MQ,BQ + In order to consider an alternate allele, at least one supporting + alignment must have mapping quality MQ, and one supporting + allele must have base quality BQ. default: 0,0, unset + -Q --mismatch-base-quality-threshold Q + Count mismatches toward --read-mismatch-limit if the base + quality of the mismatch is >= Q. default: 10 + -U --read-mismatch-limit N + Exclude reads with more than N mismatches where each mismatch + has base quality >= mismatch-base-quality-threshold. + default: ~unbounded + -z --read-max-mismatch-fraction N + Exclude reads with more than N [0,1] fraction of mismatches where + each mismatch has base quality >= mismatch-base-quality-threshold + default: 1.0 + -$ --read-snp-limit N + Exclude reads with more than N base mismatches, ignoring gaps + with quality >= mismatch-base-quality-threshold. + default: ~unbounded + -e --read-indel-limit N + Exclude reads with more than N separate gaps. + default: ~unbounded + -0 --no-filters Do not use any input base and mapping quality filters + Equivalent to -m 0 -q 0 -R 0 -S 0 + -x --indel-exclusion-window + Ignore portions of alignments this many bases from a + putative insertion or deletion allele. default: 0 + -F --min-alternate-fraction N + Require at least this fraction of observations supporting + an alternate allele within a single individual in the + in order to evaluate the position. default: 0.0 + -C --min-alternate-count N + Require at least this count of observations supporting + an alternate allele within a single individual in order + to evaluate the position. default: 1 + -3 --min-alternate-qsum N + Require at least this sum of quality of observations supporting + an alternate allele within a single individual in order + to evaluate the position. default: 0 + -G --min-alternate-total N + Require at least this count of observations supporting + an alternate allele within the total population in order + to use the allele in analysis. default: 1 + -! --min-coverage N + Require at least this coverage to process a site. default: 0 + + bayesian priors: + + -Y --no-ewens-priors + Turns off the Ewens' Sampling Formula component of the priors. + -k --no-population-priors + Equivalent to --pooled --no-ewens-priors + -w --hwe-priors Use the probability of the combination arising under HWE given + the allele frequency as estimated by observation frequency. + + observation prior expectations: + + -V --binomial-obs-priors + Incorporate expectations about osbervations into the priors, + Uses read placement probability, strand balance probability, + and read position (5'-3') probability. + -a --allele-balance-priors + Use aggregate probability of observation balance between alleles + as a component of the priors. Best for observations with minimal + inherent reference bias. + + algorithmic features: + + -M --site-selection-max-iterations N + Uses hill-climbing algorithm to search posterior space for N + iterations to determine if the site should be evaluated. Set to 0 + to prevent use of this algorithm for site selection, and + to a low integer for improvide site selection at a slight + performance penalty. default: 5. + -B --genotyping-max-iterations N + Iterate no more than N times during genotyping step. default: 25. + --genotyping-max-banddepth N + Integrate no deeper than the Nth best genotype by likelihood when + genotyping. default: 6. + -W --posterior-integration-limits N,M + Integrate all genotype combinations in our posterior space + which include no more than N samples with their Mth best + data likelihood. default: 1,3. + -K --no-permute + Do not scale prior probability of genotype combination given allele + frequency by the number of permutations of included genotypes. + -N --exclude-unobserved-genotypes + Skip sample genotypings for which the sample has no supporting reads. + -S --genotype-variant-threshold N + Limit posterior integration to samples where the second-best + genotype likelihood is no more than log(N) from the highest + genotype likelihood for the sample. default: ~unbounded + -j --use-mapping-quality + Use mapping quality of alleles when calculating data likelihoods. + -D --read-dependence-factor N + Incorporate non-independence of reads by scaling successive + observations by this factor during data likelihood + calculations. default: 0.9 + -= --no-marginals + Do not calculate the marginal probability of genotypes. Saves + time and improves scaling performance in large populations. + + +------ + +**Citation** + +For the underlying tool, please cite `FreeBayes <http://bioinformatics.bc.edu/marthlab/FreeBayes>`_. + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + + </help> +</tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Workflow Running: Add a more useful error message when input keys don't map upon executing a workflow instead of tossing to Server Error. This happens in situations where outputs are conditionally filtered (See SICER's significant_islands_summary_output_file) yet still used in the workflows.
by Bitbucket 01 Feb '12

01 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a372c3970447/ changeset: a372c3970447 user: dannon date: 2012-02-01 16:22:51 summary: Workflow Running: Add a more useful error message when input keys don't map upon executing a workflow instead of tossing to Server Error. This happens in situations where outputs are conditionally filtered (See SICER's significant_islands_summary_output_file) yet still used in the workflows. affected #: 1 file diff -r 2edf7a8d376ea6521f7fa20045e57ca58275ce8b -r a372c3970447dd0caf123db7c3047d372bfb8092 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -126,7 +126,7 @@ if operation == "sharing": return self.sharing( trans, id=history_ids ) return self.stored_list_grid( trans, **kwargs ) - + @web.expose @web.require_login( "use Galaxy workflows", use_panels=True ) def list( self, trans ): @@ -1490,7 +1490,10 @@ if prefixed_name in step.input_connections_by_name: conn = step.input_connections_by_name[ prefixed_name ] return outputs[ conn.output_step.id ][ conn.output_name ] - visit_input_values( tool.inputs, step.state.inputs, callback ) + try: + visit_input_values( tool.inputs, step.state.inputs, callback ) + except KeyError, k: + error( "Error due to input mapping of '%s' in '%s'. A common cause of this is conditional outputs that cannot be determined until runtime, please review your workflow." % (tool.name, k.message)) # Execute it job, out_data = tool.execute( trans, step.state.inputs, history=new_history) outputs[ step.id ] = out_data Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Pack scripts.
by Bitbucket 31 Jan '12

31 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2edf7a8d376e/ changeset: 2edf7a8d376e user: jgoecks date: 2012-01-31 21:58:47 summary: Pack scripts. affected #: 1 file diff -r 55a4070a62e73ddd3ff387cb46a27410a2847110 -r 2edf7a8d376ea6521f7fa20045e57ca58275ce8b static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +1,1 @@ -var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(var j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tipsy({gravity:"s"}).click(a)};var trackster_module=function(e,W){var p=e("class").extend,s=e("slotting"),L=e("painters");var ad=function(ae,af){this.document=ae;this.default_font=af!==undefined?af:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ad.prototype,{load_pattern:function(ae,ai){var af=this.patterns,ag=this.dummy_context,ah=new Image();ah.src=image_path+ai;ah.onload=function(){af[ae]=ag.createPattern(ah,"repeat")}},get_pattern:function(ae){return this.patterns[ae]},new_canvas:function(){var ae=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ae)}ae.manager=this;return ae}});var n={};var l=function(ae,af){n[ae.attr("id")]=af};var m=function(ae,ag,ai,ah){ai=".group";var af={};n[ae.attr("id")]=ah;ae.bind("drag",{handle:"."+ag,relative:true},function(aq,ar){var ap=$(this);var av=$(this).parent(),am=av.children(),ao=n[$(this).attr("id")],al,ak,at,aj,an;ak=$(this).parents(ai);if(ak.length!==0){at=ak.position().top;aj=at+ak.outerHeight();if(ar.offsetY<at){$(this).insertBefore(ak);var au=n[ak.attr("id")];au.remove_drawable(ao);au.container.add_drawable_before(ao,au);return}else{if(ar.offsetY>aj){$(this).insertAfter(ak);var au=n[ak.attr("id")];au.remove_drawable(ao);au.container.add_drawable(ao);return}}}ak=null;for(an=0;an<am.length;an++){al=$(am.get(an));at=al.position().top;aj=at+al.outerHeight();if(al.is(ai)&&this!==al.get(0)&&ar.offsetY>=at&&ar.offsetY<=aj){if(ar.offsetY-at<aj-ar.offsetY){al.find(".content-div").prepend(this)}else{al.find(".content-div").append(this)}if(ao.container){ao.container.remove_drawable(ao)}n[al.attr("id")].add_drawable(ao);return}}for(an=0;an<am.length;an++){if(ar.offsetY<$(am.get(an)).position().top){break}}if(an===am.length){if(this!==am.get(an-1)){av.append(this);n[av.attr("id")].move_drawable(ao,an)}}else{if(this!==am.get(an)){$(this).insertBefore(am.get(an));n[av.attr("id")].move_drawable(ao,(ar.deltaY>0?an-1:an))}}}).bind("dragstart",function(){af["border-top"]=ae.css("border-top");af["border-bottom"]=ae.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(af)})};W.moveable=m;var ac=16,F=9,C=20,y=100,I=12000,Q=200,A=5,u=10,K=5000,v=100,o="There was an error in indexing this dataset. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",D="No data for this chrom/contig.",t="Currently indexing... please wait",w="Tool cannot be rerun: ",a="Loading data...",X="Ready for display",R=10,H=20;function Y(af,ae){if(!ae){ae=0}var ag=Math.pow(10,ae);return Math.round(af*ag)/ag}var c=function(ae){this.num_elements=ae;this.clear()};p(c.prototype,{get:function(af){var ae=this.key_ary.indexOf(af);if(ae!==-1){if(this.obj_cache[af].stale){this.key_ary.splice(ae,1);delete this.obj_cache[af]}else{this.move_key_to_end(af,ae)}}return this.obj_cache[af]},set:function(af,ag){if(!this.obj_cache[af]){if(this.key_ary.length>=this.num_elements){var ae=this.key_ary.shift();delete this.obj_cache[ae]}this.key_ary.push(af)}this.obj_cache[af]=ag;return ag},move_key_to_end:function(af,ae){this.key_ary.splice(ae,1);this.key_ary.push(af)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var S=function(af,ae,ag){c.call(this,af);this.track=ae;this.subset=(ag!==undefined?ag:true)};p(S.prototype,c.prototype,{load_data:function(an,ai,al,af,ak){var am=this.track.view.chrom,ah={chrom:am,low:an,high:ai,mode:al,resolution:af,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ah,ak);if(this.track.filters_manager){var ao=[];var ae=this.track.filters_manager.filters;for(var aj=0;aj<ae.length;aj++){ao.push(ae[aj].name)}ah.filter_cols=JSON.stringify(ao)}var ag=this;return $.getJSON(this.track.data_url,ah,function(ap){ag.set_data(an,ai,ap)})},get_data:function(ae,ai,aj,af,ah){var ag=this.get(ae,ai);if(ag&&(is_deferred(ag)||this.track.data_and_mode_compatible(ag,aj))){return ag}ag=this.load_data(ae,ai,aj,af,ah);this.set_data(ae,ai,ag);return ag},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(am,ah,al,ag,ak,ai){var an=this.get(am,ah);if(!(an&&this.track.data_and_mode_compatible(an,al))){console.log("ERROR: no current data for: ",this.track,am,ah,al,ag,ak);return}an.stale=true;var af=am;if(ai===this.DEEP_DATA_REQ){$.extend(ak,{start_val:an.data.length+1})}else{if(ai===this.BROAD_DATA_REQ){af=(an.max_high?an.max_high:an.data[an.data.length-1][2])+1}}var ae=this,aj=this.load_data(af,ah,al,ag,ak);new_data_available=$.Deferred();this.set_data(am,ah,new_data_available);$.when(aj).then(function(ao){if(ao.data){ao.data=an.data.concat(ao.data);if(ao.max_low){ao.max_low=an.max_low}if(ao.message){ao.message=ao.message.replace(/[0-9]+/,ao.data.length)}}ae.set_data(am,ah,ao);new_data_available.resolve(ao)});return new_data_available},get:function(ae,af){return c.prototype.get.call(this,this.gen_key(ae,af))},set_data:function(af,ag,ae){return this.set(this.gen_key(af,ag),ae)},gen_key:function(ae,ag){var af=ae+"_"+ag;return af},split_key:function(ae){return ae.split("_")}});var G=function(af,ae,ag){S.call(this,af,ae,ag)};p(G.prototype,S.prototype,c.prototype,{get:S.prototype.get,load_data:function(ae,ah,ai,af,ag){if(af>1){return{data:null}}return S.prototype.load_data.call(this,ae,ah,ai,af,ag)}});var q=function(ah,af,ae,ag,aj){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=ah;this.view=af;this.container=ae;this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah}],saved_values:ag,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=aj;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ak){ak.stopPropagation()});var ai=this;this.container_div.hover(function(){ai.icons_div.show()},function(){ai.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ae){if(ae.content_visible){ae.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ae.hide_contents();ae.content_visible=false}else{ae.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ae.content_visible=true;ae.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(af){var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){af.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",ag);show_modal("Configure",af.config.build_form(),{Cancel:ah,OK:ae})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ae){$(".tipsy").remove();ae.remove()}}];p(q.prototype,{init:function(){},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},from_dict:function(ae){},update_icons:function(){},set_name:function(ae){this.old_name=this.name;this.name=ae;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.hide(0,function(){$(this).remove();view.update_intro_div();view.has_changes=true})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(af,aj,ai,ah,ae){var ag=this;this.action_icons[af]=$("<a/>").attr("href","javascript:void(0);").attr("title",aj).addClass("icon-button").addClass(ai).tipsy({gravity:"s"}).click(function(){ah(ag)}).appendTo(this.icons_div)},build_action_icons:function(ae){var ag;for(var af=0;af<ae.length;af++){ag=ae[af];this.add_action_icon(ag.name,ag.title,ag.css_class,ag.on_click_fn,ag.prepend)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var x=function(ai,ah,af,ae,ag,aj){q.call(this,ah,af,ae,ag,aj);this.obj_type=ai;this.drawables=[]};p(x.prototype,q.prototype,{init:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].init()}},_draw:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw()}},to_dict:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:af}},from_dict:function(ak,ae){var aj=new this.constructor(ak.name,view,ae,ak.prefs,view.viewport_container,view);var af,ai,ah;for(var ag=0;ag<ak.drawables.length;ag++){af=ak.drawables[ag];ai=af.obj_type;if(!ai){ai=af.track_type}ah=addable_objects[ai].prototype.from_dict(af,aj);aj.add_drawable(ah)}return aj},add_drawable:function(ae){this.drawables.push(ae);ae.container=this},add_drawable_before:function(ag,ae){var af=this.drawables.indexOf(ae);if(af!=-1){this.drawables.splice(af,0,ag);return true}return false},replace_drawable:function(ag,ae,af){var ah=this.drawables.indexOf(ag);if(ah!==-1){this.drawables[ah]=ae;if(af){ag.container_div.replaceWith(ae.container_div)}}return ah},remove_drawable:function(af){var ae=this.drawables.indexOf(af);if(ae!=-1){this.drawables.splice(ae,1);af.container=null;return true}return false},move_drawable:function(af,ag){var ae=this.drawables.indexOf(af);if(ae!=-1){this.drawables.splice(ae,1);this.drawables.splice(ag,0,af);return true}return false}});var P=function(ah,af,ae,ag){x.call(this,"DrawableGroup",ah,af,ae,ag,"group-handle");this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new Z(this);this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div);this.saved_filters_managers=null};p(P.prototype,q.prototype,x.prototype,{action_icons_def:[q.prototype.action_icons_def[0],q.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ae){$(".tipsy").remove();ae.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(af){if(af.filters_div.is(":visible")){af.filters_manager.clear_filters();for(var ae=0;ae<af.drawables.length;ae++){af.drawables[ae].filters_manager=af.saved_filters_managers[ae]}af.saved_filters_managers=null}else{if(af.filters_manager.filters.length>0){af.saved_filters_managers=[];for(var ae=0;ae<af.drawables.length;ae++){drawable=af.drawables[ae];af.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=af.filters_manager}}af.filters_manager.init_filters();af.request_draw(true)}af.filters_div.toggle()}},q.prototype.action_icons_def[2]],build_container_div:function(){var ae=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ae)}return ae},build_header_div:function(){var ae=$("<div/>").addClass("track-header");ae.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ae);return ae},hide_contents:function(){this.content_div.hide()},show_contents:function(){this.content_div.show();this.request_draw()},update_icons:function(){var ag=this.drawables.length;if(ag===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ag===1){if(this.drawables[0] instanceof h){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aq=true,ai=this.drawables[0].get_type(),ae=0;for(var an=0;an<ag;an++){ak=this.drawables[an];if(ak.get_type()!==ai){can_composite=false;break}if(ak instanceof d){ae++}}if(aq||ae===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}if(ae>1&&ae===this.drawables.length){var ar={},af;ak=this.drawables[0];for(var am=0;am<ak.filters_manager.filters.length;am++){af=ak.filters_manager.filters[am];ar[af.name]=[af]}for(var an=1;an<this.drawables.length;an++){ak=this.drawables[an];for(var am=0;am<ak.filters_manager.filters.length;am++){af=ak.filters_manager.filters[am];if(af.name in ar){ar[af.name].push(af)}}}this.filters_manager.remove_all();var ah,aj,al,ao;for(var ap in ar){ah=ar[ap];if(ah.length===ae){aj=new U(ah[0].name,ah[0].index);this.filters_manager.add_filter(aj)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},show_composite_track:function(){var ai=[];for(var af=0;af<this.drawables.length;af++){ai.push(this.drawables[af].name)}var ag="Composite Track of "+this.drawables.length+" tracks ("+ai.join(", ")+")";var ah=new h(ag,this.view,this.view,this.drawables);var ae=this.container.replace_drawable(this,ah,true);ah.request_draw()},add_drawable:function(ae){x.prototype.add_drawable.call(this,ae);this.update_icons()},remove_drawable:function(ae){x.prototype.remove_drawable.call(this,ae);this.update_icons()},from_dict:function(ah,ae){var ag=x.prototype.from_dict.call(this,ah,ae);for(var af=0;af<ag.drawables.length;af++){ag.content_div.append(ag.drawables[af].container_div)}return ag},request_draw:function(ae,ag){for(var af=0;af<this.drawables.length;af++){this.drawables[af].request_draw(ae,ag)}}});var ab=function(ae,ah,ag,af){x.call(this,"View");this.container=ae;this.chrom=null;this.vis_id=ag;this.dbkey=af;this.title=ah;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ad(ae.get(0).ownerDocument);this.reset()};p(ab.prototype,x.prototype,{init:function(){var ag=this.container,ae=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ag);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ag);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ag);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,ae);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ah=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var af=function(ai){if(ai.type==="focusout"||(ai.keyCode||ai.which)===13||(ai.keyCode||ai.which)===27){if((ai.keyCode||ai.which)!==27){ae.go_to($(this).val())}$(this).hide();$(this).val("");ae.location_span.show();ae.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",af).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){ae.location_span.hide();ae.chrom_select.hide();ae.nav_input.val(ae.chrom+":"+ae.low+"-"+ae.high);ae.nav_input.css("display","inline-block");ae.nav_input.select();ae.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){ae.zoom_out();ae.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){ae.zoom_in();ae.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ae.change_chrom(ae.chrom_select.val())});this.browser_content_div.click(function(ai){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ai){ae.zoom_in(ai.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ai,aj){this.current_x=aj.offsetX}).bind("drag",function(ai,ak){var al=ak.offsetX-this.current_x;this.current_x=ak.offsetX;var aj=Math.round(al/ae.viewport_container.width()*(ae.max_high-ae.max_low));ae.move_delta(-aj)});this.overview_close.click(function(){ae.reset_overview()});this.viewport_container.bind("draginit",function(ai,aj){if(ai.clientX>ae.viewport_container.width()-16){return false}}).bind("dragstart",function(ai,aj){aj.original_low=ae.low;aj.current_height=ai.clientY;aj.current_x=aj.offsetX}).bind("drag",function(ak,am){var ai=$(this);var an=am.offsetX-am.current_x;var aj=ai.scrollTop()-(ak.clientY-am.current_height);ai.scrollTop(aj);am.current_height=ak.clientY;am.current_x=am.offsetX;var al=Math.round(an/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(al)}).bind("mousewheel",function(ak,am,aj,ai){if(aj){aj*=50;var al=Math.round(-aj/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(al)}});this.top_labeltrack.bind("dragstart",function(ai,aj){return $("<div />").css({height:ae.browser_content_div.height()+ae.top_labeltrack.height()+ae.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(am,an){$(an.proxy).css({left:Math.min(am.pageX,an.startX),width:Math.abs(am.pageX-an.startX)});var aj=Math.min(am.pageX,an.startX)-ae.container.offset().left,ai=Math.max(am.pageX,an.startX)-ae.container.offset().left,al=(ae.high-ae.low),ak=ae.viewport_container.width();ae.update_location(Math.round(aj/ak*al)+ae.low,Math.round(ai/ak*al)+ae.low)}).bind("dragend",function(an,ao){var aj=Math.min(an.pageX,ao.startX),ai=Math.max(an.pageX,ao.startX),al=(ae.high-ae.low),ak=ae.viewport_container.width(),am=ae.low;ae.low=Math.round(aj/ak*al)+am;ae.high=Math.round(ai/ak*al)+am;$(ao.proxy).remove();ae.request_redraw()});this.add_label_track(new aa(this,{content_div:this.top_labeltrack}));this.add_label_track(new aa(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ae.resize_window()});$(document).bind("redraw",function(){ae.redraw()});this.reset();$(window).trigger("resize")},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(ae,af){this.location_span.text(commatize(ae)+" - "+commatize(af));this.nav_input.val(this.chrom+":"+commatize(ae)+"-"+commatize(af))},load_chroms:function(ag){ag.num=v;ag.dbkey=this.dbkey;var ae=this,af=$.Deferred();$.ajax({url:chrom_url,data:ag,dataType:"json",success:function(ai){if(ai.chrom_info.length===0){alert("Invalid chromosome: "+ag.chrom);return}if(ai.reference){ae.add_label_track(new z(ae))}ae.chrom_data=ai.chrom_info;var al='<option value="">Select Chrom/Contig</option>';for(var ak=0,ah=ae.chrom_data.length;ak<ah;ak++){var aj=ae.chrom_data[ak].chrom;al+='<option value="'+aj+'">'+aj+"</option>"}if(ai.prev_chroms){al+='<option value="previous">Previous '+v+"</option>"}if(ai.next_chroms){al+='<option value="next">Next '+v+"</option>"}ae.chrom_select.html(al);ae.chrom_start_index=ai.start_index;af.resolve(ai)},error:function(){alert("Could not load chroms for this dbkey:",ae.dbkey)}});return af},change_chrom:function(aj,af,al){if(!aj||aj==="None"){return}var ag=this;if(aj==="previous"){ag.load_chroms({low:this.chrom_start_index-v});return}if(aj==="next"){ag.load_chroms({low:this.chrom_start_index+v});return}var ak=$.grep(ag.chrom_data,function(am,an){return am.chrom===aj})[0];if(ak===undefined){ag.load_chroms({chrom:aj},function(){ag.change_chrom(aj,af,al)});return}else{if(aj!==ag.chrom){ag.chrom=aj;ag.chrom_select.val(ag.chrom);ag.max_high=ak.len-1;ag.reset();ag.request_redraw(true);for(var ai=0,ae=ag.drawables.length;ai<ae;ai++){var ah=ag.drawables[ai];if(ah.init){ah.init()}}if(ag.reference_track){ag.reference_track.init()}}if(af!==undefined&&al!==undefined){ag.low=Math.max(af,0);ag.high=Math.min(al,ag.max_high)}ag.reset_overview();ag.request_redraw()}},go_to:function(ai){ai=ai.replace(/ |,/g,"");var am=this,ae,ah,af=ai.split(":"),ak=af[0],al=af[1];if(al!==undefined){try{var aj=al.split("-");ae=parseInt(aj[0],10);ah=parseInt(aj[1],10)}catch(ag){return false}}am.change_chrom(ak,ae,ah)},move_fraction:function(ag){var ae=this;var af=ae.high-ae.low;this.move_delta(ag*af)},move_delta:function(ag){var ae=this;var af=ae.high-ae.low;if(ae.low-ag<ae.max_low){ae.low=ae.max_low;ae.high=ae.max_low+af}else{if(ae.high-ag>ae.max_high){ae.high=ae.max_high;ae.low=ae.max_high-af}else{ae.high-=ag;ae.low-=ag}}ae.request_redraw()},add_drawable:function(ae){x.prototype.add_drawable.call(this,ae);ae.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ae){ae.view=this;ae.init();this.label_tracks.push(ae)},remove_drawable:function(ag,af){x.prototype.remove_drawable.call(this,ag);if(af){var ae=this;ag.container_div.hide(0,function(){$(this).remove();ae.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(am,ae,al,af){var ak=this,ai=(af?[af]:ak.drawables),ag;var af;for(var aj=0;aj<ai.length;aj++){af=ai[aj];ag=-1;for(var ah=0;ah<ak.tracks_to_be_redrawn.length;ah++){if(ak.tracks_to_be_redrawn[ah][0]===af){ag=ah;break}}if(ag<0){ak.tracks_to_be_redrawn.push([af,ae,al])}else{ak.tracks_to_be_redrawn[aj][1]=ae;ak.tracks_to_be_redrawn[aj][2]=al}}requestAnimationFrame(function(){ak._redraw(am)})},_redraw:function(ao){var al=this.low,ah=this.high;if(al<this.max_low){al=this.max_low}if(ah>this.max_high){ah=this.max_high}var an=this.high-this.low;if(this.high!==0&&an<this.min_separation){ah=al+this.min_separation}this.low=Math.floor(al);this.high=Math.ceil(ah);this.resolution=Math.pow(A,Math.ceil(Math.log((this.high-this.low)/Q)/Math.log(A)));this.zoom_res=Math.pow(u,Math.max(0,Math.ceil(Math.log(this.resolution,u)/Math.log(u))));var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ak=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ap=13;this.overview_box.css({left:ae,width:Math.max(ap,ak)}).show();if(ak<ap){this.overview_box.css("left",ae-(ap-ak)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ak})}this.update_location(this.low,this.high);if(!ao){var ag,af,am;for(var ai=0,aj=this.tracks_to_be_redrawn.length;ai<aj;ai++){ag=this.tracks_to_be_redrawn[ai][0];af=this.tracks_to_be_redrawn[ai][1];am=this.tracks_to_be_redrawn[ai][2];if(ag){ag._draw(af,am)}}this.tracks_to_be_redrawn=[];for(ai=0,aj=this.label_tracks.length;ai<aj;ai++){this.label_tracks[ai]._draw()}}},zoom_in:function(af,ag){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ah=this.high-this.low,ai=ah/2+this.low,ae=(ah/this.zoom_factor)/2;if(af){ai=af/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ai-ae);this.high=Math.round(ai+ae);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var af=this.high-this.low,ag=af/2+this.low,ae=(af*this.zoom_factor)/2;this.low=Math.round(ag-ae);this.high=Math.round(ag+ae);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ag){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ag.dataset_id){return}this.overview_viewport.find(".track").remove()}var af=ag.copy({content_div:this.overview_viewport}),ae=this;af.header_div.hide();af.is_overview=true;ae.overview_drawable=af;this.overview_drawable.postdraw_actions=function(){ae.overview_highlight.show().height(ae.overview_drawable.content_div.height());ae.overview_viewport.height(ae.overview_drawable.content_div.height()+ae.overview_box.outerHeight());ae.overview_close.show();ae.resize_window()};ae.overview_drawable.request_draw();ae.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ag,ak){this.track=ag;this.name=ak.name;this.params=[];var ar=ak.params;for(var ah=0;ah<ar.length;ah++){var am=ar[ah],af=am.name,aq=am.label,ai=unescape(am.html),at=am.value,ao=am.type;if(ao==="number"){this.params[this.params.length]=new f(af,aq,ai,at,am.min,am.max)}else{if(ao=="select"){this.params[this.params.length]=new N(af,aq,ai,at)}else{console.log("WARNING: unrecognized tool parameter type:",af,ao)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(av){av.stopPropagation()}).click(function(av){av.stopPropagation()}).bind("dblclick",function(av){av.stopPropagation()});var ap=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var an=this.params;var al=this;$.each(this.params,function(aw,az){var ay=$("<div>").addClass("param-row").appendTo(al.parent_div);var av=$("<div>").addClass("param-label").text(az.label).appendTo(ay);var ax=$("<div/>").addClass("param-input").html(az.html).appendTo(ay);ax.find(":input").val(az.value);$("<div style='clear: both;'/>").appendTo(ay)});this.parent_div.find("input").click(function(){$(this).select()});var au=$("<div>").addClass("param-row").appendTo(this.parent_div);var aj=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(au);var ae=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(au);var al=this;ae.click(function(){al.run_on_region()});aj.click(function(){al.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var ae={};this.parent_div.find(":input").each(function(){var af=$(this).attr("name"),ag=$(this).val();ae[af]=JSON.stringify(ag)});return ae},get_param_values:function(){var af=[];var ae={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();if(ag){af[af.length]=ah}});return af},run_on_dataset:function(){var ae=this;ae.run({dataset_id:this.track.original_dataset_id,tool_id:ae.name},null,function(af){show_modal(ae.name+" is Running",ae.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var af={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},aj=this.track,ag=af.tool_id+aj.tool_region_and_parameters_str(af.chrom,af.low,af.high),ae;if(aj.container===view){var ai=new P(this.name,this.track.view);var ah=aj.container.replace_drawable(aj,ai,false);ai.container_div.insertBefore(aj.view.content_div.children()[ah]);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);ae=ai}else{ae=aj.container}var ak=new aj.constructor(ag,view,ae,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);ae.add_drawable(ak);ak.content_div.text("Starting job.");this.run(af,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(af,ag,ah){$.extend(af,this.get_param_values_dict());var ae=function(){$.getJSON(rerun_tool_url,af,function(ai){if(ai==="no converter"){ag.container_div.addClass("error");ag.content_div.text(J)}else{if(ai.error){ag.container_div.addClass("error");ag.content_div.text(w+ai.message)}else{if(ai==="pending"){ag.container_div.addClass("pending");ag.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ae,2000)}else{ah(ai)}}}})};ae()}});var N=function(af,ae,ag,ah){this.name=af;this.label=ae;this.html=ag;this.value=ah};var f=function(ag,af,ai,aj,ah,ae){N.call(this,ag,af,ai,aj);this.min=ah;this.max=ae};var g=function(af,ae,ag,ah){this.manager=null;this.name=af;this.index=ae;this.tool_id=ag;this.tool_exp_name=ah};var U=function(af,am,at,ai){g.call(this,af,am,at,ai);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null;var an=function(au,av,aw){au.click(function(){var aB=av.text(),az=parseFloat(aw.slider("option","max")),ay=(az<=1?4:az<=1000000?az.toString().length:6),aA=false,ax=$(this).parents(".slider-row");ax.addClass("input");if(aw.slider("option","values")){ay=2*ay+1;aA=true}av.text("");$("<input type='text'/>").attr("size",ay).attr("maxlength",ay).attr("value",aB).appendTo(av).focus().select().click(function(aC){aC.stopPropagation()}).blur(function(){$(this).remove();av.text(aB);ax.removeClass("input")}).keyup(function(aG){if(aG.keyCode===27){$(this).trigger("blur")}else{if(aG.keyCode===13){var aE=aw.slider("option","min"),aC=aw.slider("option","max"),aF=function(aH){return(isNaN(aH)||aH>aC||aH<aE)},aD=$(this).val();if(!aA){aD=parseFloat(aD);if(aF(aD)){alert("Parameter value must be in the range ["+aE+"-"+aC+"]");return $(this)}}else{aD=aD.split("-");aD=[parseFloat(aD[0]),parseFloat(aD[1])];if(aF(aD[0])||aF(aD[1])){alert("Parameter value must be in the range ["+aE+"-"+aC+"]");return $(this)}}aw.slider((aA?"values":"value"),aD);ax.removeClass("input")}}})})};var ag=this;ag.parent_div=$("<div/>").addClass("filter-row slider-row");var ae=$("<div/>").addClass("elt-label").appendTo(ag.parent_div),aq=$("<span/>").addClass("slider-name").text(ag.name+" ").appendTo(ae),ah=$("<span/>"),aj=$("<span/>").addClass("slider-value").appendTo(ae).append("[").append(ah).append("]");ag.values_span=ah;var ap=$("<div/>").addClass("slider").appendTo(ag.parent_div);ag.control_element=$("<div/>").attr("id",ag.name+"-filter-control").appendTo(ap);var ak=[0,0];ag.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(au,av){ag.slide(au,av)},change:function(au,av){ag.control_element.slider("option","slide").call(ag.control_element,au,av)}});ag.slider=ag.control_element;ag.slider_label=ah;an(aj,ah,ag.control_element);var ar=$("<div/>").addClass("display-controls").appendTo(ag.parent_div),al=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(ag.manager.alpha_filter!==ag){ag.manager.alpha_filter=ag;ag.manager.parent_div.find(".layer-transparent").removeClass("active").hide();al.addClass("active").show()}else{ag.manager.alpha_filter=null;al.removeClass("active")}ag.manager.track.request_draw(true,true)}).appendTo(ar).hide(),ao=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(ag.manager.height_filter!==ag){ag.manager.height_filter=ag;ag.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();ao.addClass("active").show()}else{ag.manager.height_filter=null;ao.removeClass("active")}ag.manager.track.request_draw(true,true)}).appendTo(ar).hide();ag.parent_div.hover(function(){al.show();ao.show()},function(){if(ag.manager.alpha_filter!==ag){al.hide()}if(ag.manager.height_filter!==ag){ao.hide()}});$("<div style='clear: both;'/>").appendTo(ag.parent_div)};p(U.prototype,{get_slider_step:function(ag,ae){var af=ae-ag;return(af<=2?0.01:1)},slide:function(af,ag){var ae=ag.values;this.values_span.text(ae[0]+"-"+ae[1]);this.low=ae[0];this.high=ae[1];this.manager.track.request_draw(true,true)},applies_to:function(ae){if(ae.length>this.index){return true}return false},keep:function(ae){if(!this.applies_to(ae)){return true}var af=ae[this.index];return(isNaN(af)||(af>=this.low&&af<=this.high))},update_attrs:function(af){var ae=false;if(!this.applies_to(af)){return ae}if(af[this.index]<this.min){this.min=Math.floor(af[this.index]);ae=true}if(af[this.index]>this.max){this.max=Math.ceil(af[this.index]);ae=true}return ae},update_ui_elt:function(){if(this.min!=this.max){this.parent_div.show()}else{this.parent_div.hide()}var af=this.slider.slider("option","min"),ae=this.slider.slider("option","max");if(this.min<af||this.max>ae){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var Z=function(ag,aj){this.track=ag;this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aq){aq.stopPropagation()}).click(function(aq){aq.stopPropagation()}).bind("dblclick",function(aq){aq.stopPropagation()}).bind("keydown",function(aq){aq.stopPropagation()});this.filters=[];if(aj){for(var ak=0;ak<aj.length;ak++){var ae=aj[ak],af=ae.name,an=ae.type,am=ae.index,ap=ae.tool_id,ah=ae.tool_exp_name;if(an==="int"||an==="float"){this.add_filter(new U(af,am,ap,ah))}else{console.log("ERROR: unsupported filter: ",af,an)}}}if(this.filters.length!==0){var ao=$("<div/>").addClass("param-row").appendTo(this.parent_div);var al=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ao);var ai=this;al.click(function(){ai.run_on_dataset()})}};p(Z.prototype,{add_filter:function(ae){ae.manager=this;this.parent_div.append(ae.parent_div);this.filters.push(ae)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var ae=0;ae<this.filters.length;ae++){var af=this.filters[ae];af.update_ui_elt()}},clear_filters:function(){for(var ae=0;ae<this.filters.length;ae++){var af=this.filters[ae];af.slider.slider("option","values",[af.min,af.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var am=function(aq,ao,ap){if(!(ao in aq)){aq[ao]=ap}return aq[ao]};var ag={},ae,af,ah;for(var ai=0;ai<this.filters.length;ai++){ae=this.filters[ai];if(ae.tool_id){if(ae.min!=ae.low){af=am(ag,ae.tool_id,[]);af[af.length]=ae.tool_exp_name+" >= "+ae.low}if(ae.max!=ae.high){af=am(ag,ae.tool_id,[]);af[af.length]=ae.tool_exp_name+" <= "+ae.high}}}var ak=[];for(var an in ag){ak[ak.length]=[an,ag[an]]}var al=ak.length;(function aj(av,ar){var ap=ar[0],aq=ap[0],au=ap[1],at="("+au.join(") and (")+")",ao={cond:at,input:av,target_dataset_id:av,tool_id:aq},ar=ar.slice(1);$.getJSON(run_tool_url,ao,function(aw){if(aw.error){show_modal("Filter Dataset","Error running tool "+aq,{Close:hide_modal})}else{if(ar.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{aj(aw.dataset_id,ar)}}})})(this.track.dataset_id,ak)}});var B=function(ae,af){L.Scaler.call(this,af);this.filter=ae};B.prototype.gen_val=function(ae){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ae[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var E=function(ae){this.track=ae.track;this.params=ae.params;this.values={};this.restore_values((ae.saved_values?ae.saved_values:{}));this.onchange=ae.onchange};p(E.prototype,{restore_values:function(ae){var af=this;$.each(this.params,function(ag,ah){if(ae[ah.key]!==undefined){af.values[ah.key]=ae[ah.key]}else{af.values[ah.key]=ah.default_value}})},build_form:function(){var ah=this;var ae=$("<div />");var ag;function af(al,ai){for(var ap=0;ap<al.length;ap++){ag=al[ap];if(ag.hidden){continue}var aj="param_"+ap;var au=ah.values[ag.key];var ax=$("<div class='form-row' />").appendTo(ai);ax.append($("<label />").attr("for",aj).text(ag.label+":"));if(ag.type==="bool"){ax.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",au))}else{if(ag.type==="text"){ax.append($('<input type="text"/>').attr("id",aj).val(au).click(function(){$(this).select()}))}else{if(ag.type=="select"){var ar=$("<select />").attr("id",aj);for(var an=0;an<ag.options.length;an++){$("<option/>").text(ag.options[an].label).attr("value",ag.options[an].value).appendTo(ar)}ar.val(au);ax.append(ar)}else{if(ag.type==="color"){var aw=$("<div/>").appendTo(ax),aq=$("<input />").attr("id",aj).attr("name",aj).val(au).css("float","left").appendTo(aw).click(function(az){$(".tipsy").hide();var ay=$(this).siblings(".tipsy");ay.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ay).height()/2)+($(this).height()/2)}).show();ay.click(function(aA){aA.stopPropagation()});$(document).bind("click.color-picker",function(){ay.hide();$(document).unbind("click.color-picker")});az.stopPropagation()}),ao=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(aw).attr("title","Set new random color").tipsy({gravity:"s"}),at=$("<div class='tipsy tipsy-west' style='position: absolute;' />").appendTo(aw).hide(),ak=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(at),av=$("<div/>").appendTo(ak),am=$.farbtastic(av,{width:100,height:100,callback:aq,color:au});aw.append($("<div/>").css("clear","both"));(function(ay){ao.click(function(){ay.setColor(get_random_color())})})(am)}else{ax.append($("<input />").attr("id",aj).attr("name",aj).val(au))}}}}if(ag.help){ax.append($("<div class='help'/>").text(ag.help))}}}af(this.params,ae);return ae},update_from_form:function(ae){var ag=this;var af=false;$.each(this.params,function(ah,aj){if(!aj.hidden){var ak="param_"+ah;var ai=ae.find("#"+ak).val();if(aj.type==="float"){ai=parseFloat(ai)}else{if(aj.type==="int"){ai=parseInt(ai)}else{if(aj.type==="bool"){ai=ae.find("#"+ak).is(":checked")}}}if(ai!==ag.values[aj.key]){ag.values[aj.key]=ai;af=true}}});if(af){this.onchange()}}});var b=function(ae,ah,ag,af,ai){this.track=ae;this.index=ah;this.low=ah*Q*ag;this.high=(ah+1)*Q*ag;this.resolution=ag;this.html_elt=$("<div class='track-tile'/>").append(af);this.data=ai;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(ae,ah,ag,af,ai,aj){b.call(this,ae,ah,ag,af,ai);this.max_val=aj};p(k.prototype,b.prototype);var O=function(ah,am,ai,ag,ak,ar,al,at,af,ap){b.call(this,ah,am,ai,ag,ak);this.mode=al;this.feature_mapper=ap;this.has_icons=false;if(at||!af){this.has_icons=true;var an=this;ag=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:C-1,width:ag.width}).prependTo(this.html_elt);if(!af){var ao=$("<a href='javascript:void(0);'/>").addClass("icon exclamation").attr("title","To minimize track height, not all features in this region are displayed. Click to display more.").tipsy({gravity:"s"}).appendTo(message_div).click(function(){$(".tipsy").hide();an.track.slotters[ar].max_rows*=2;an.track.request_draw(true)})}if(at){var aq=ak.length,aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+aq+" features in this region were obtained from server. Click to get more data including depth").tipsy({gravity:"s"}).appendTo(message_div),ae=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+aq+" features in this region were obtained from server. Click to get more data excluding depth").tipsy({gravity:"s"}).appendTo(message_div);aj.click(function(){an.stale=true;ah.data_manager.get_more_data(an.low,an.high,ah.mode,an.resolution,{},ah.data_manager.DEEP_DATA_REQ);$(".tipsy").hide();ah.request_draw()}).dblclick(function(au){au.stopPropagation()});ae.click(function(){an.stale=true;ah.data_manager.get_more_data(an.low,an.high,ah.mode,an.resolution,{},ah.data_manager.BROAD_DATA_REQ);$(".tipsy").hide();ah.request_draw()}).dblclick(function(au){au.stopPropagation()})}}};p(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var af=this,ae={};if(af.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).siblings(".feature-popup").remove()}).mousemove(function(aq){if(!this.hovered){return}var al=$(this).offset(),ap=aq.pageX-al.left,ao=aq.pageY-al.top,av=af.feature_mapper.get_feature_data(ap,ao),am=(av?av[0]:null);$(this).siblings(".feature-popup").each(function(){if(!am||$(this).attr("id")!==am.toString()){$(this).remove()}});if(av){var ah=ae[am];if(!ah){var am=av[0],ar={name:av[3],start:av[1],end:av[2],strand:av[4]},ak=af.track.filters_manager.filters,aj;for(var an=0;an<ak.length;an++){aj=ak[an];ar[aj.name]=av[aj.index]}var ah=$("<div/>").attr("id",am).addClass("feature-popup"),aw=$("<table/>"),au,at,ax;for(au in ar){at=ar[au];ax=$("<tr/>").appendTo(aw);$("<th/>").appendTo(ax).text(au);$("<td/>").attr("align","left").appendTo(ax).text(typeof(at)=="number"?Y(at,2):at)}ah.append($("<div class='feature-popup-inner'>").append(aw));ae[am]=ah}ah.appendTo($(af.html_elt).parent());var ai=ap+parseInt(af.html_elt.css("left"))-ah.width()/2,ag=ao+parseInt(af.html_elt.css("top"))+7;ah.css("left",ai+"px").css("top",ag+"px")}else{if(!aq.isPropagationStopped()){aq.stopPropagation();$(this).siblings().each(function(){$(this).trigger(aq)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ah,af,ae,ag,aj,ai,ak){q.call(this,ah,af,ae,{},"draghandle");this.data_url=(ai?ai:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ak?ak:K);this.dataset_check_url=converted_datasets_state_url;this.data_manager=(aj?aj:new S(H,this));this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div)}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ae){ae.view.set_overview(ae)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ae){if(ae.filters_div.is(":visible")){ae.filters_manager.clear_filters()}else{ae.filters_manager.init_filters()}ae.filters_div.toggle()}},{name:"tools_icon",title:"Tools",css_class:"tools-icon",on_click_fn:function(ae){ae.dynamic_tool_div.toggle();if(ae.dynamic_tool_div.is(":visible")){ae.set_name(ae.name+ae.tool_region_and_parameters_str())}else{ae.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ae=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ae)}this.name_div=$("<div/>").addClass("track-name").appendTo(ae).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ae},set_display_modes:function(ah,ak){this.display_modes=ah;this.mode=(ak?ak:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var af=this,ai={};for(var ag=0,ae=af.display_modes.length;ag<ae;ag++){var aj=af.display_modes[ag];ai[aj]=function(al){return function(){af.change_mode(al);af.icons_div.show();af.container_div.mouseleave(function(){af.icons_div.hide()})}}(aj)}make_popupmenu(this.action_icons.mode_icon,ai)},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof aa){return"LabelTrack"}else{if(this instanceof z){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof V){return"ReadTrack"}else{if(this instanceof T){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.content_div.css("height","auto");af.content_div.children().remove();af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}var ae=$.Deferred();$.getJSON(converted_datasets_state_url,{hda_ldda:af.hda_ldda,dataset_id:af.dataset_id,chrom:af.view.chrom},function(ag){if(!ag||ag==="error"||ag.kind==="error"){af.container_div.addClass("error");af.content_div.text(o);if(ag.message){var ah=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})});af.content_div.append(ah)}}else{if(ag==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(D)}else{if(ag==="pending"){af.container_div.addClass("pending");af.content_div.text(t);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ag.status==="data"){if(ag.valid_chroms){af.valid_chroms=ag.valid_chroms;af.update_icons()}af.content_div.text(X);if(af.view.chrom){af.content_div.text("");af.content_div.css("height",af.height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){ae.resolve();af.container_div.removeClass("nodata error pending");af.request_draw()})}else{ae.resolve()}}}}}}});this.update_icons();return ae},predraw_init:function(){}});var M=function(aj,ah,ag,ai,af,al,ak){i.call(this,aj,ah,ag,ai,ak);var ae=this,ah=ae.view;m(ae.container_div,ae.drag_handle_class,".group",ae);this.filters_manager=new Z(this,af);this.filters_available=false;this.tool=(al!==undefined&&obj_length(al)>0?new r(this,al):undefined);this.tile_cache=new c(R);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(M.prototype,q.prototype,i.prototype,{copy:function(ae){var af=new this.constructor(this.name,this.view,ae,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool,this.data_manager);af.change_mode(this.mode);af.enabled=this.enabled;return af},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},from_dict:function(ag,af){var ae=new this.constructor(ag.name,view,af,ag.hda_ldda,ag.dataset_id,ag.prefs,ag.filters,ag.tool);if(ag.mode){ae.change_mode(ag.mode)}return ae},change_mode:function(af){var ae=this;ae.mode=af;ae.config.values.mode=af;ae.tile_cache.clear();ae.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ae.mode+")");return ae},update_icons:function(){var ae=this;if(ae.filters_available){ae.action_icons.filters_icon.show()}else{ae.action_icons.filters_icon.hide()}if(ae.tool){ae.action_icons.tools_icon.show()}else{ae.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(af,ag,ae){return af+"_"+ag+"_"+ae},request_draw:function(af,ae){this.view.request_redraw(false,af,ae,this)},_draw:function(ag,aq){if(!this.can_draw()){return}var ao=this.view.low,ak=this.view.high,am=ak-ao,ah=this.view.container.width(),au=ah/am,aj=this.view.resolution,at=this.content_div;if(this.is_overview){ao=this.view.max_low;ak=this.view.max_high;aj=Math.pow(A,Math.ceil(Math.log((view.max_high-view.max_low)/Q)/Math.log(A)));au=ah/(view.max_high-view.max_low)}this.content_div.children().addClass("remove");this.max_height=0;var af=Math.floor(ao/aj/Q);var an=true;var ar=[];var ae=0;var al=function(av){return(av&&"track" in av)};while((af*Q*aj)<ak){var ap=this.draw_helper(ag,ah,af,aj,at,au);if(al(ap)){ar.push(ap)}else{an=false}af+=1;ae++}if(!aq){this.content_div.children(".remove").remove()}var ai=this;if(an){this.content_div.children(".remove").remove();ai.postdraw_actions(ar,ah,au,aq)}},postdraw_actions:function(ah,ai,ak,ae){var ag=this;var aj=false;for(var af=0;af<ah.length;af++){if(ah[af].has_icons){aj=true;break}}if(aj){for(var af=0;af<ah.length;af++){tile=ah[af];if(!tile.has_icons){tile.html_elt.css("padding-top",C)}}}},draw_helper:function(ae,aq,aw,au,aj,ak,ar){var ap=this,az=this._gen_tile_cache_key(aq,ak,aw),ax=aw*Q*au,af=ax+Q*au;if(!ar){ar={}}var ay=(ae?undefined:ap.tile_cache.get(az));if(ay){ap.show_tile(ay,aj,ak);return ay}var an=true;var av=ap.data_manager.get_data(ax,af,ap.mode,au,ap.data_url_extra_params);if(is_deferred(av)){an=false}var al;if(view.reference_track&&ak>view.canvas_manager.char_width_px){al=view.reference_track.data_manager.get_data(ax,af,ap.mode,au,view.reference_track.data_url_extra_params);if(is_deferred(al)){an=false}}if(an){p(av,ar.more_tile_data);var am=ap.mode;if(am==="Auto"){am=ap.get_mode(av);ap.update_auto_mode(am)}var ag=ap.view.canvas_manager.new_canvas(),ah=ap._get_tile_bounds(aw,au),ax=ah[0],af=ah[1],aq=Math.ceil((af-ax)*ak)+ap.left_offset,ao=ap.get_canvas_height(av,am,ak,aq);ag.width=aq;ag.height=ao;var at=ag.getContext("2d");at.translate(this.left_offset,0);var ay=ap.draw_tile(av,at,am,au,aw,ak,al);if(ay!==undefined){ap.tile_cache.set(az,ay);ap.show_tile(ay,aj,ak)}return ay}var ai=$.Deferred();$.when(av,al).then(function(){view.request_redraw(false,false,false,ap);ai.resolve()});return ai},get_canvas_height:function(ae,ag,ah,af){return this.height_px},draw_tile:function(ae,ag,aj,ai,af,ak,ah){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ag,ai,aj){var af=this,ae=ag.html_elt;ag.predisplay_actions();var ah=(ag.low-(this.is_overview?this.view.max_low:this.view.low))*aj;if(this.left_offset){ah-=this.left_offset}ae.css({position:"absolute",top:0,left:ah,height:""});if(ae.hasClass("remove")){ae.removeClass("remove")}else{ai.append(ae)}af.max_height=Math.max(af.max_height,ae.height());af.content_div.css("height",af.max_height+"px");ai.children().css("height",af.max_height+"px")},_get_tile_bounds:function(ae,af){var ah=ae*Q*af,ai=Q*af,ag=(ah+ai<=this.view.max_high?ah+ai:this.view.max_high);return[ah,ag]},tool_region_and_parameters_str:function(ag,ae,ah){var af=this,ai=(ag!==undefined&&ae!==undefined&&ah!==undefined?ag+":"+ae+"-"+ah:"all");return" - region=["+ai+"], parameters=["+af.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ae,af){return true},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var af=this;var ae=function(){if(af.data_manager.size()===0){setTimeout(ae,300)}else{af.data_url=default_data_url;af.data_query_wait=K;af.dataset_state_url=converted_datasets_state_url;$.getJSON(af.dataset_state_url,{dataset_id:af.dataset_id,hda_ldda:af.hda_ldda},function(ag){})}};ae()}}});var aa=function(af,ae){i.call(this,"label",af,ae,false,{});this.container_div.addClass("label-track")};p(aa.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ag=this.view,ah=ag.high-ag.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ah)/Math.log(10)))),ae=Math.floor(ag.low/ak)*ak,ai=this.view.container.width(),af=$("<div style='position: relative; height: 1.3em;'></div>");while(ae<ag.high){var aj=(ae-ag.low)/ah*ai;af.append($("<div class='label'>"+commatize(ae)+"</div>").css({position:"absolute",left:aj-1}));ae+=ak}this.content_div.children(":first").remove();this.content_div.append(af)}});var h=function(ah,ag,af,ae){M.call(this,ah,ag,af);this.drawables=[];this.left_offset=0;if(ae){var ak=[],aj;for(var ai=0;ai<ae.length;ai++){aj=ae[ai];ak.push(aj.dataset_id);this.drawables[ai]=aj.copy();if(aj.left_offset>this.left_offset){this.left_offset=aj.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,M.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ae){$(".tipsy").remove();ae.show_group()}}].concat(M.prototype.action_icons_def),to_dict:x.prototype.to_dict,add_drawable:x.prototype.add_drawable,from_dict:function(ak,ae){var aj=new this.constructor(ak.name,view,ae,ak.prefs,view.viewport_container,view);var af,ai,ah;for(var ag=0;ag<ak.drawables.length;ag++){af=ak.drawables[ag];ai=af.obj_type;if(!ai){ai=af.track_type}ah=addable_objects[ai].prototype.from_dict(af);aj.add_drawable(ah)}aj.set_display_modes(aj.drawables[0].display_modes,aj.drawables[0].mode);return aj},change_mode:function(ae){M.prototype.change_mode.call(this,ae);for(var af=0;af<this.drawables.length;af++){this.drawables[af].change_mode(ae)}},init:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].init())}var ae=this;$.when.apply($,ag).then(function(){ae.enabled=true;ae.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(af,au,aA,ax,al,an,av){var at=this,aE=this._gen_tile_cache_key(au,an,aA),aB=aA*Q*ax,ag=aB+Q*ax;if(!av){av={}}var aD=(af?undefined:at.tile_cache.get(aE));if(aD){at.show_tile(aD,al,an);return aD}var am=[],at,aq=true,ay,ao;for(var az=0;az<this.drawables.length;az++){at=this.drawables[az];ay=at.data_manager.get_data(aB,ag,at.mode,ax,at.data_url_extra_params);if(is_deferred(ay)){aq=false}am.push(ay);ao=null;if(view.reference_track&&an>view.canvas_manager.char_width_px){ao=view.reference_track.data_manager.get_data(aB,ag,at.mode,ax,view.reference_track.data_url_extra_params);if(is_deferred(ao)){aq=false}}am.push(ao)}if(aq){p(ay,av.more_tile_data);this.tile_predraw_init();var ai=at.view.canvas_manager.new_canvas(),aj=at._get_tile_bounds(aA,ax),aB=aj[0],ag=aj[1],aC=0,au=Math.ceil((ag-aB)*an)+this.left_offset,ar=0,ah=[];var ae=0;for(var az=0;az<this.drawables.length;az++,aC+=2){at=this.drawables[az];ay=am[aC];var ap=at.mode;if(ap==="Auto"){ap=at.get_mode(ay);at.update_auto_mode(ap)}ah.push(ap);ae=at.get_canvas_height(ay,ap,an,au);if(ae>ar){ar=ae}}ai.width=au;ai.height=(av.height?av.height:ar);aC=0;var aw=ai.getContext("2d");aw.translate(this.left_offset,0);aw.globalAlpha=0.5;aw.globalCompositeOperation="source-over";for(var az=0;az<this.drawables.length;az++,aC+=2){at=this.drawables[az];ay=am[aC];ao=am[aC+1];aD=at.draw_tile(ay,aw,ah[az],ax,aA,an,ao)}this.tile_cache.set(aE,aD);this.show_tile(aD,al,an);return aD}var ak=$.Deferred(),at=this;$.when.apply($,am).then(function(){view.request_redraw(false,false,false,at);ak.resolve()});return ak},show_group:function(){var ah=new P(this.name,this.view,this.container),ae;for(var ag=0;ag<this.drawables.length;ag++){ae=this.drawables[ag];ah.add_drawable(ae);ae.container=ah;ah.content_div.append(ae.container_div)}var af=this.container.replace_drawable(this,ah,true);ah.request_draw()},tile_predraw_init:function(){var ah=Number.MAX_VALUE,ae=-ah,af;for(var ag=0;ag<this.drawables.length;ag++){af=this.drawables[ag];if(af instanceof j){if(af.prefs.min_value<ah){ah=af.prefs.min_value}if(af.prefs.max_value>ae){ae=af.prefs.max_value}}}for(var ag=0;ag<this.drawables.length;ag++){af=this.drawables[ag];af.prefs.min_value=ah;af.prefs.max_value=ae}},postdraw_actions:function(ag,aj,al,af){M.prototype.postdraw_actions.call(this,ag,aj,al,af);var ai=-1;for(var ah=0;ah<ag.length;ah++){var ae=ag[ah].html_elt.find("canvas").height();if(ae>ai){ai=ae}}for(var ah=0;ah<ag.length;ah++){var ak=ag[ah];if(ak.html_elt.find("canvas").height()!==ai){this.draw_helper(true,aj,ak.index,ak.resolution,ak.html_elt.parent(),al,{height:ai});ak.html_elt.remove()}}}});var z=function(ae){M.call(this,"reference",ae,{content_div:ae.top_labeltrack},{});ae.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ae.dbkey};this.data_manager=new G(H,this,false)};p(z.prototype,q.prototype,M.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(am,an,aj,ai,af,ao){var ah=this;if(ao>this.view.canvas_manager.char_width_px){if(am.data===null){ah.content_div.css("height","0px");return}var ag=an.canvas;an.font=an.canvas.manager.default_font;an.textAlign="center";am=am.data;for(var ak=0,al=am.length;ak<al;ak++){var ae=Math.round(ak*ao);an.fillText(am[ak],ae,10)}return new b(ah,af,ai,ag,am)}this.content_div.css("height","0px")}});var j=function(ae,al,af,ak,an,am,ai,aj,ag){var ah=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,ae,al,af,am,ai,aj,ag);this.min_height_px=16;this.max_height_px=400;this.height_px=32;this.hda_ldda=ak;this.dataset_id=an;this.original_dataset_id=an;this.left_offset=0;this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ae},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:am,onchange:function(){ah.set_name(ah.prefs.name);ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;$("#linetrack_"+ah.dataset_id+"_minval").text(ah.prefs.min_value);$("#linetrack_"+ah.dataset_id+"_maxval").text(ah.prefs.max_value);ah.tile_cache.clear();ah.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,M.prototype,{add_resize_handle:function(){var ae=this;var ah=false;var ag=false;var af=$("<div class='track-resize'>");$(ae.container_div).hover(function(){if(ae.content_visible){ah=true;af.show()}},function(){ah=false;if(!ag){af.hide()}});af.hide().bind("dragstart",function(ai,aj){ag=true;aj.original_height=$(ae.content_div).height()}).bind("drag",function(aj,ak){var ai=Math.min(Math.max(ak.original_height+ak.deltaY,ae.min_height_px),ae.max_height_px);$(ae.content_div).css("height",ai);ae.height_px=ai;ae.request_draw(true)}).bind("dragend",function(ai,aj){ae.tile_cache.clear();ag=false;if(!ah){af.hide()}ae.config.values.height=ae.height_px}).appendTo(ae.container_div)},predraw_init:function(){var ae=this;ae.vertical_range=undefined;return $.getJSON(ae.data_url,{stats:true,chrom:ae.view.chrom,low:null,high:null,hda_ldda:ae.hda_ldda,dataset_id:ae.dataset_id},function(af){ae.container_div.addClass("line-track");var ai=af.data;if(isNaN(parseFloat(ae.prefs.min_value))||isNaN(parseFloat(ae.prefs.max_value))){var ag=ai.min;var ak=ai.max;ag=Math.floor(Math.min(0,Math.max(ag,ai.mean-2*ai.sd)));ak=Math.ceil(Math.max(0,Math.min(ak,ai.mean+2*ai.sd)));ae.prefs.min_value=ag;ae.prefs.max_value=ak;$("#track_"+ae.dataset_id+"_minval").val(ae.prefs.min_value);$("#track_"+ae.dataset_id+"_maxval").val(ae.prefs.max_value)}ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.total_frequency=ai.total_frequency;ae.container_div.find(".yaxislabel").remove();var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ae.dataset_id+"_minval").text(Y(ae.prefs.min_value,3));var ah=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ae.dataset_id+"_maxval").text(Y(ae.prefs.max_value,3));ah.css({position:"absolute",top:"24px",left:"10px"});ah.prependTo(ae.container_div);aj.css({position:"absolute",bottom:"2px",left:"10px"});aj.prependTo(ae.container_div)})},draw_tile:function(ao,am,aj,ah,af,an){var ag=am.canvas,ae=this._get_tile_bounds(af,ah),ai=ae[0],al=ae[1],ak=new L.LinePainter(ao.data,ai,al,this.prefs,aj);ak.draw(am,ag.width,ag.height,an);return new b(this.track,af,ah,ag,ao.data)}});var d=function(ae,al,af,ak,an,am,ai,aj,ag){var ah=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];M.call(this,ae,al,af,am,ai,aj,ag);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ae},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){ah.set_name(ah.prefs.name);ah.tile_cache.clear();ah.set_painter_from_config();ah.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ak;this.dataset_id=an;this.original_dataset_id=an;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(d.prototype,q.prototype,M.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style=="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(at,ag,av,ar){M.prototype.postdraw_actions.call(this,at,ar);var ai=this;if(ai.mode=="Histogram"){var am=-1;for(var aj=0;aj<at.length;aj++){var aq=at[aj].max_val;if(aq>am){am=aq}}for(var aj=0;aj<at.length;aj++){var ao=at[aj];if(ao.max_val!==am){ao.html_elt.remove();ai.draw_helper(true,ag,ao.index,ao.resolution,ao.html_elt.parent(),av,{more_tile_data:{max:am}})}}}if(ai.filters_manager){var ah=ai.filters_manager.filters;for(var al=0;al<ah.length;al++){ah[al].update_ui_elt()}var ak=false,an,af;for(var aj=0;aj<at.length;aj++){if(at[aj].data.length){an=at[aj].data[0];for(var al=0;al<ah.length;al++){af=ah[al];if(af.applies_to(an)&&af.min!==af.max){ak=true;break}}}}if(ai.filters_available!==ak){ai.filters_available=ak;if(!ai.filters_available){ai.filters_div.hide()}ai.update_icons()}}this.container_div.find(".yaxislabel").remove();var ae=at[0];if(ae instanceof k){var au=(this.prefs.histogram_max?this.prefs.histogram_max:ae.max_val),ap=get_editable_text_elt(au,false,12,0,function(aw){var aw=parseFloat(aw);ai.prefs.histogram_max=(!isNaN(aw)?aw:null);ai.tile_cache.clear();ai.request_draw()}).addClass("yaxislabel histogram-max").css("color",this.prefs.label_color);this.container_div.prepend(ap)}},update_auto_mode:function(ae){var ae;if(this.mode=="Auto"){if(ae=="no_detail"){ae="feature spans"}else{if(ae=="summary_tree"){ae="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ae+")")}},incremental_slots:function(ai,ae,ah){var af=this.view.canvas_manager.dummy_context,ag=this.slotters[ai];if(!ag||(ag.mode!==ah)){ag=new (s.FeatureSlotter)(ai,ah,y,function(aj){return af.measureText(aj)});this.slotters[ai]=ag}return ag.slot_features(ae)},get_summary_tree_data:function(ai,al,ag,au){if(au>ag-al){au=ag-al}var ap=Math.floor((ag-al)/au),at=[],ah=0;var aj=0,ak=0,ao,ar=0,am=[],aq,an;var af=function(ax,aw,ay,av){ax[0]=aw+ay*av;ax[1]=aw+(ay+1)*av};while(ar<au&&aj!==ai.length){var ae=false;for(;ar<au&&!ae;ar++){af(am,al,ar,ap);for(ak=aj;ak<ai.length;ak++){ao=ai[ak].slice(1,3);if(is_overlap(ao,am)){ae=true;break}}if(ae){break}}data_start_index=ak;at[at.length]=aq=[am[0],0];for(;ak<ai.length;ak++){ao=ai[ak].slice(1,3);if(is_overlap(ao,am)){aq[1]++}else{break}}if(aq[1]>ah){ah=aq[1]}ar++}return{max:ah,delta:ap,data:at}},get_mode:function(ae){if(ae.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ae.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ae,ai,aj,af){if(ai==="summary_tree"||ai==="Histogram"){return this.summary_draw_height}else{var ah=this.incremental_slots(aj,ae.data,ai);var ag=new (this.painter)(null,null,null,this.prefs,ai);return Math.max(ac,ag.get_required_height(ah,af))}},draw_tile:function(ap,au,ar,av,az,al,ag){var at=this,af=au.canvas,ai=this._get_tile_bounds(az,av),aC=ai[0],ae=ai[1],aH=25,ah=this.left_offset;if(ar==="summary_tree"||ar==="Histogram"){if(ap.dataset_type!="summary_tree"){var am=this.get_summary_tree_data(ap.data,aC,ae,200);if(ap.max){am.max=ap.max}ap=am}var aE=new L.SummaryTreePainter(ap,aC,ae,this.prefs);aE.draw(au,af.width,af.height,al);return new k(at,az,av,af,ap.data,ap.max)}var ak=[],aq=this.slotters[al].slots;all_slotted=true;if(ap.data){var an=this.filters_manager.filters;for(var aw=0,ay=ap.data.length;aw<ay;aw++){var aj=ap.data[aw];var ax=false;var ao;for(var aB=0,aG=an.length;aB<aG;aB++){ao=an[aB];ao.update_attrs(aj);if(!ao.keep(aj)){ax=true;break}}if(!ax){ak.push(aj);if(!(aj[0] in aq)){all_slotted=false}}}}var aF=(this.filters_manager.alpha_filter?new B(this.filters_manager.alpha_filter):null);var aD=(this.filters_manager.height_filter?new B(this.filters_manager.height_filter):null);var aE=new (this.painter)(ak,aC,ae,this.prefs,ar,aF,aD,ag);var aA=null;au.fillStyle=this.prefs.block_color;au.font=au.canvas.manager.default_font;au.textAlign="right";if(ap.data){aA=aE.draw(au,af.width,af.height,al,aq);aA.translation=-ah}return new O(at,az,av,af,ap.data,al,ar,ap.message,all_slotted,aA)},data_and_mode_compatible:function(ae,af){if(af==="Auto"){return true}else{if(ae.extra_info==="no_detail"||ae.dataset_type==="summary_tree"){return false}else{return true}}},});var T=function(ae,ak,af,aj,am,al,ah,ai,ag){d.call(this,ae,ak,af,aj,am,al,ah,ai,ag);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ae},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:al,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};p(T.prototype,q.prototype,M.prototype,d.prototype);var V=function(ae,ak,af,aj,an,am,ah,ag){d.call(this,ae,ak,af,aj,an,am,ah,ag);var ai=get_random_color(),al=get_random_color([ai,"#ffffff"]);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ae},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ai},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:al},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};p(V.prototype,q.prototype,M.prototype,d.prototype);W.View=ab;W.DrawableGroup=P;W.LineTrack=j;W.FeatureTrack=d;W.ReadTrack=V;W.VcfTrack=T;W.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}else{}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};l.prototype.draw=function(z,A,y,B){};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(L,z,K,M){var E=this.view_start,N=this.view_end-this.view_start,I=this.data.data,G=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),B=K;delta_x_px=Math.ceil(this.data.delta*M);L.save();for(var C=0,D=I.length;C<D;C++){var H=Math.floor((I[C][0]-E)*M);var F=I[C][1];if(!F){continue}var J=F/G*K;if(F!==0&&J<1){J=1}L.fillStyle=this.prefs.block_color;L.fillRect(H,B-J,delta_x_px,J);var A=4;if(this.prefs.show_counts&&(L.measureText(F).width+A)<delta_x_px){L.fillStyle=this.prefs.label_color;L.textAlign="center";L.fillText(F,H+(delta_x_px/2),10)}}L.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(S,Q,N,D){var I=false,K=this.prefs.min_value,F=this.prefs.max_value,M=F-K,B=N,C=this.view_start,P=this.view_end-this.view_start,L=this.mode,aa=this.data;S.save();var 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y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences){if(this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}else{continue}}if(U+af>=L&&U+af<=aa){var 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ac=16,F=9,C=20,y=100,I=12000,Q=200,A=5,u=10,K=5000,v=100,o="There was an error in indexing this dataset. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",D="No data for this chrom/contig.",t="Currently indexing... please wait",w="Tool cannot be rerun: ",a="Loading data...",X="Ready for display",R=10,H=20;function Y(af,ae){if(!ae){ae=0}var ag=Math.pow(10,ae);return Math.round(af*ag)/ag}var c=function(ae){this.num_elements=ae;this.clear()};p(c.prototype,{get:function(af){var ae=this.key_ary.indexOf(af);if(ae!==-1){if(this.obj_cache[af].stale){this.key_ary.splice(ae,1);delete this.obj_cache[af]}else{this.move_key_to_end(af,ae)}}return this.obj_cache[af]},set:function(af,ag){if(!this.obj_cache[af]){if(this.key_ary.length>=this.num_elements){var ae=this.key_ary.shift();delete this.obj_cache[ae]}this.key_ary.push(af)}this.obj_cache[af]=ag;return ag},move_key_to_end:function(af,ae){this.key_ary.splice(ae,1);this.key_ary.push(af)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var S=function(af,ae,ag){c.call(this,af);this.track=ae;this.subset=(ag!==undefined?ag:true)};p(S.prototype,c.prototype,{load_data:function(an,ai,al,af,ak){var am=this.track.view.chrom,ah={chrom:am,low:an,high:ai,mode:al,resolution:af,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ah,ak);if(this.track.filters_manager){var ao=[];var ae=this.track.filters_manager.filters;for(var aj=0;aj<ae.length;aj++){ao.push(ae[aj].name)}ah.filter_cols=JSON.stringify(ao)}var ag=this;return $.getJSON(this.track.data_url,ah,function(ap){ag.set_data(an,ai,ap)})},get_data:function(ae,ai,aj,af,ah){var ag=this.get(ae,ai);if(ag&&(is_deferred(ag)||this.track.data_and_mode_compatible(ag,aj))){return ag}ag=this.load_data(ae,ai,aj,af,ah);this.set_data(ae,ai,ag);return ag},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(am,ah,al,ag,ak,ai){var an=this.get(am,ah);if(!(an&&this.track.data_and_mode_compatible(an,al))){console.log("ERROR: no current data for: ",this.track,am,ah,al,ag,ak);return}an.stale=true;var af=am;if(ai===this.DEEP_DATA_REQ){$.extend(ak,{start_val:an.data.length+1})}else{if(ai===this.BROAD_DATA_REQ){af=(an.max_high?an.max_high:an.data[an.data.length-1][2])+1}}var ae=this,aj=this.load_data(af,ah,al,ag,ak);new_data_available=$.Deferred();this.set_data(am,ah,new_data_available);$.when(aj).then(function(ao){if(ao.data){ao.data=an.data.concat(ao.data);if(ao.max_low){ao.max_low=an.max_low}if(ao.message){ao.message=ao.message.replace(/[0-9]+/,ao.data.length)}}ae.set_data(am,ah,ao);new_data_available.resolve(ao)});return new_data_available},get:function(ae,af){return c.prototype.get.call(this,this.gen_key(ae,af))},set_data:function(af,ag,ae){return this.set(this.gen_key(af,ag),ae)},gen_key:function(ae,ag){var af=ae+"_"+ag;return af},split_key:function(ae){return ae.split("_")}});var G=function(af,ae,ag){S.call(this,af,ae,ag)};p(G.prototype,S.prototype,c.prototype,{get:S.prototype.get,load_data:function(ae,ah,ai,af,ag){if(af>1){return{data:null}}return S.prototype.load_data.call(this,ae,ah,ai,af,ag)}});var q=function(ah,af,ae,ag,aj){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=ah;this.view=af;this.container=ae;this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah}],saved_values:ag,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=aj;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ak){ak.stopPropagation()});var ai=this;this.container_div.hover(function(){ai.icons_div.show()},function(){ai.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ae){if(ae.content_visible){ae.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ae.hide_contents();ae.content_visible=false}else{ae.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ae.content_visible=true;ae.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(af){var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){af.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",ag);show_modal("Configure",af.config.build_form(),{Cancel:ah,OK:ae})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ae){$(".tipsy").remove();ae.remove()}}];p(q.prototype,{init:function(){},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},from_dict:function(ae){},update_icons:function(){},set_name:function(ae){this.old_name=this.name;this.name=ae;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.hide(0,function(){$(this).remove();view.update_intro_div();view.has_changes=true})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(af,aj,ai,ah,ae){var ag=this;this.action_icons[af]=$("<a/>").attr("href","javascript:void(0);").attr("title",aj).addClass("icon-button").addClass(ai).tipsy({gravity:"s"}).click(function(){ah(ag)}).appendTo(this.icons_div)},build_action_icons:function(ae){var ag;for(var af=0;af<ae.length;af++){ag=ae[af];this.add_action_icon(ag.name,ag.title,ag.css_class,ag.on_click_fn,ag.prepend)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var x=function(ai,ah,af,ae,ag,aj){q.call(this,ah,af,ae,ag,aj);this.obj_type=ai;this.drawables=[]};p(x.prototype,q.prototype,{init:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].init()}},_draw:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw()}},to_dict:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:af}},from_dict:function(ak,ae){var aj=new this.constructor(ak.name,view,ae,ak.prefs,view.viewport_container,view);var af,ai,ah;for(var ag=0;ag<ak.drawables.length;ag++){af=ak.drawables[ag];ai=af.obj_type;if(!ai){ai=af.track_type}ah=addable_objects[ai].prototype.from_dict(af,aj);aj.add_drawable(ah)}return aj},add_drawable:function(ae){this.drawables.push(ae);ae.container=this},add_drawable_before:function(ag,ae){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables.splice(af,0,ag);return true}return false},replace_drawable:function(ag,ae,af){var ah=this.drawables.indexOf(ag);if(ah!==-1){this.drawables[ah]=ae;if(af){ag.container_div.replaceWith(ae.container_div)}}return ah},remove_drawable:function(af){var ae=this.drawables.indexOf(af);if(ae!==-1){this.drawables.splice(ae,1);af.container=null;return true}return false},move_drawable:function(af,ag){var ae=this.drawables.indexOf(af);if(ae!==-1){this.drawables.splice(ae,1);this.drawables.splice(ag,0,af);return true}return false}});var P=function(ah,af,ae,ag){x.call(this,"DrawableGroup",ah,af,ae,ag,"group-handle");this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new Z(this);this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div);this.saved_filters_managers=null};p(P.prototype,q.prototype,x.prototype,{action_icons_def:[q.prototype.action_icons_def[0],q.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ae){$(".tipsy").remove();ae.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(af){if(af.filters_div.is(":visible")){af.filters_manager.clear_filters();for(var ae=0;ae<af.drawables.length;ae++){af.drawables[ae].filters_manager=af.saved_filters_managers[ae]}af.saved_filters_managers=null}else{if(af.filters_manager.filters.length>0){af.saved_filters_managers=[];for(var ae=0;ae<af.drawables.length;ae++){drawable=af.drawables[ae];af.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=af.filters_manager}}af.filters_manager.init_filters();af.request_draw(true)}af.filters_div.toggle()}},q.prototype.action_icons_def[2]],build_container_div:function(){var ae=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ae)}return ae},build_header_div:function(){var ae=$("<div/>").addClass("track-header");ae.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ae);return ae},hide_contents:function(){this.content_div.hide()},show_contents:function(){this.content_div.show();this.request_draw()},update_icons:function(){var ag=this.drawables.length;if(ag===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ag===1){if(this.drawables[0] instanceof h){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aq=true,ai=this.drawables[0].get_type(),ae=0;for(var an=0;an<ag;an++){ak=this.drawables[an];if(ak.get_type()!==ai){can_composite=false;break}if(ak instanceof d){ae++}}if(aq||ae===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}if(ae>1&&ae===this.drawables.length){var ar={},af;ak=this.drawables[0];for(var am=0;am<ak.filters_manager.filters.length;am++){af=ak.filters_manager.filters[am];ar[af.name]=[af]}for(var an=1;an<this.drawables.length;an++){ak=this.drawables[an];for(var am=0;am<ak.filters_manager.filters.length;am++){af=ak.filters_manager.filters[am];if(af.name in ar){ar[af.name].push(af)}}}this.filters_manager.remove_all();var ah,aj,al,ao;for(var ap in ar){ah=ar[ap];if(ah.length===ae){aj=new U(ah[0].name,ah[0].index);this.filters_manager.add_filter(aj)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},show_composite_track:function(){var ai=[];for(var af=0;af<this.drawables.length;af++){ai.push(this.drawables[af].name)}var ag="Composite Track of "+this.drawables.length+" tracks ("+ai.join(", ")+")";var ah=new h(ag,this.view,this.view,this.drawables);var ae=this.container.replace_drawable(this,ah,true);ah.request_draw()},add_drawable:function(ae){x.prototype.add_drawable.call(this,ae);this.update_icons()},remove_drawable:function(ae){x.prototype.remove_drawable.call(this,ae);this.update_icons()},from_dict:function(ah,ae){var ag=x.prototype.from_dict.call(this,ah,ae);for(var af=0;af<ag.drawables.length;af++){ag.content_div.append(ag.drawables[af].container_div)}return ag},request_draw:function(ae,ag){for(var af=0;af<this.drawables.length;af++){this.drawables[af].request_draw(ae,ag)}}});var ab=function(ae,ah,ag,af){x.call(this,"View");this.container=ae;this.chrom=null;this.vis_id=ag;this.dbkey=af;this.title=ah;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ad(ae.get(0).ownerDocument);this.reset()};p(ab.prototype,x.prototype,{init:function(){var ag=this.container,ae=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ag);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ag);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ag);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,ae);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ah=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var af=function(ai){if(ai.type==="focusout"||(ai.keyCode||ai.which)===13||(ai.keyCode||ai.which)===27){if((ai.keyCode||ai.which)!==27){ae.go_to($(this).val())}$(this).hide();$(this).val("");ae.location_span.show();ae.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",af).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){ae.location_span.hide();ae.chrom_select.hide();ae.nav_input.val(ae.chrom+":"+ae.low+"-"+ae.high);ae.nav_input.css("display","inline-block");ae.nav_input.select();ae.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){ae.zoom_out();ae.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){ae.zoom_in();ae.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ae.change_chrom(ae.chrom_select.val())});this.browser_content_div.click(function(ai){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ai){ae.zoom_in(ai.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ai,aj){this.current_x=aj.offsetX}).bind("drag",function(ai,ak){var al=ak.offsetX-this.current_x;this.current_x=ak.offsetX;var aj=Math.round(al/ae.viewport_container.width()*(ae.max_high-ae.max_low));ae.move_delta(-aj)});this.overview_close.click(function(){ae.reset_overview()});this.viewport_container.bind("draginit",function(ai,aj){if(ai.clientX>ae.viewport_container.width()-16){return false}}).bind("dragstart",function(ai,aj){aj.original_low=ae.low;aj.current_height=ai.clientY;aj.current_x=aj.offsetX}).bind("drag",function(ak,am){var ai=$(this);var an=am.offsetX-am.current_x;var aj=ai.scrollTop()-(ak.clientY-am.current_height);ai.scrollTop(aj);am.current_height=ak.clientY;am.current_x=am.offsetX;var al=Math.round(an/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(al)}).bind("mousewheel",function(ak,am,aj,ai){if(aj){aj*=50;var al=Math.round(-aj/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(al)}});this.top_labeltrack.bind("dragstart",function(ai,aj){return $("<div />").css({height:ae.browser_content_div.height()+ae.top_labeltrack.height()+ae.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(am,an){$(an.proxy).css({left:Math.min(am.pageX,an.startX),width:Math.abs(am.pageX-an.startX)});var aj=Math.min(am.pageX,an.startX)-ae.container.offset().left,ai=Math.max(am.pageX,an.startX)-ae.container.offset().left,al=(ae.high-ae.low),ak=ae.viewport_container.width();ae.update_location(Math.round(aj/ak*al)+ae.low,Math.round(ai/ak*al)+ae.low)}).bind("dragend",function(an,ao){var aj=Math.min(an.pageX,ao.startX),ai=Math.max(an.pageX,ao.startX),al=(ae.high-ae.low),ak=ae.viewport_container.width(),am=ae.low;ae.low=Math.round(aj/ak*al)+am;ae.high=Math.round(ai/ak*al)+am;$(ao.proxy).remove();ae.request_redraw()});this.add_label_track(new aa(this,{content_div:this.top_labeltrack}));this.add_label_track(new aa(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ae.resize_window()});$(document).bind("redraw",function(){ae.redraw()});this.reset();$(window).trigger("resize")},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(ae,af){this.location_span.text(commatize(ae)+" - "+commatize(af));this.nav_input.val(this.chrom+":"+commatize(ae)+"-"+commatize(af))},load_chroms:function(ag){ag.num=v;ag.dbkey=this.dbkey;var ae=this,af=$.Deferred();$.ajax({url:chrom_url,data:ag,dataType:"json",success:function(ai){if(ai.chrom_info.length===0){alert("Invalid chromosome: "+ag.chrom);return}if(ai.reference){ae.add_label_track(new z(ae))}ae.chrom_data=ai.chrom_info;var al='<option value="">Select Chrom/Contig</option>';for(var ak=0,ah=ae.chrom_data.length;ak<ah;ak++){var aj=ae.chrom_data[ak].chrom;al+='<option value="'+aj+'">'+aj+"</option>"}if(ai.prev_chroms){al+='<option value="previous">Previous '+v+"</option>"}if(ai.next_chroms){al+='<option value="next">Next '+v+"</option>"}ae.chrom_select.html(al);ae.chrom_start_index=ai.start_index;af.resolve(ai)},error:function(){alert("Could not load chroms for this dbkey:",ae.dbkey)}});return af},change_chrom:function(aj,af,al){if(!aj||aj==="None"){return}var ag=this;if(aj==="previous"){ag.load_chroms({low:this.chrom_start_index-v});return}if(aj==="next"){ag.load_chroms({low:this.chrom_start_index+v});return}var ak=$.grep(ag.chrom_data,function(am,an){return am.chrom===aj})[0];if(ak===undefined){ag.load_chroms({chrom:aj},function(){ag.change_chrom(aj,af,al)});return}else{if(aj!==ag.chrom){ag.chrom=aj;ag.chrom_select.val(ag.chrom);ag.max_high=ak.len-1;ag.reset();ag.request_redraw(true);for(var ai=0,ae=ag.drawables.length;ai<ae;ai++){var ah=ag.drawables[ai];if(ah.init){ah.init()}}if(ag.reference_track){ag.reference_track.init()}}if(af!==undefined&&al!==undefined){ag.low=Math.max(af,0);ag.high=Math.min(al,ag.max_high)}ag.reset_overview();ag.request_redraw()}},go_to:function(ai){ai=ai.replace(/ |,/g,"");var am=this,ae,ah,af=ai.split(":"),ak=af[0],al=af[1];if(al!==undefined){try{var aj=al.split("-");ae=parseInt(aj[0],10);ah=parseInt(aj[1],10)}catch(ag){return false}}am.change_chrom(ak,ae,ah)},move_fraction:function(ag){var ae=this;var af=ae.high-ae.low;this.move_delta(ag*af)},move_delta:function(ag){var ae=this;var af=ae.high-ae.low;if(ae.low-ag<ae.max_low){ae.low=ae.max_low;ae.high=ae.max_low+af}else{if(ae.high-ag>ae.max_high){ae.high=ae.max_high;ae.low=ae.max_high-af}else{ae.high-=ag;ae.low-=ag}}ae.request_redraw()},add_drawable:function(ae){x.prototype.add_drawable.call(this,ae);ae.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ae){ae.view=this;ae.init();this.label_tracks.push(ae)},remove_drawable:function(ag,af){x.prototype.remove_drawable.call(this,ag);if(af){var ae=this;ag.container_div.hide(0,function(){$(this).remove();ae.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(am,ae,al,af){var ak=this,ai=(af?[af]:ak.drawables),ag;var af;for(var aj=0;aj<ai.length;aj++){af=ai[aj];ag=-1;for(var ah=0;ah<ak.tracks_to_be_redrawn.length;ah++){if(ak.tracks_to_be_redrawn[ah][0]===af){ag=ah;break}}if(ag<0){ak.tracks_to_be_redrawn.push([af,ae,al])}else{ak.tracks_to_be_redrawn[aj][1]=ae;ak.tracks_to_be_redrawn[aj][2]=al}}requestAnimationFrame(function(){ak._redraw(am)})},_redraw:function(ao){var al=this.low,ah=this.high;if(al<this.max_low){al=this.max_low}if(ah>this.max_high){ah=this.max_high}var an=this.high-this.low;if(this.high!==0&&an<this.min_separation){ah=al+this.min_separation}this.low=Math.floor(al);this.high=Math.ceil(ah);this.resolution=Math.pow(A,Math.ceil(Math.log((this.high-this.low)/Q)/Math.log(A)));this.zoom_res=Math.pow(u,Math.max(0,Math.ceil(Math.log(this.resolution,u)/Math.log(u))));var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ak=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ap=13;this.overview_box.css({left:ae,width:Math.max(ap,ak)}).show();if(ak<ap){this.overview_box.css("left",ae-(ap-ak)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ak})}this.update_location(this.low,this.high);if(!ao){var ag,af,am;for(var ai=0,aj=this.tracks_to_be_redrawn.length;ai<aj;ai++){ag=this.tracks_to_be_redrawn[ai][0];af=this.tracks_to_be_redrawn[ai][1];am=this.tracks_to_be_redrawn[ai][2];if(ag){ag._draw(af,am)}}this.tracks_to_be_redrawn=[];for(ai=0,aj=this.label_tracks.length;ai<aj;ai++){this.label_tracks[ai]._draw()}}},zoom_in:function(af,ag){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ah=this.high-this.low,ai=ah/2+this.low,ae=(ah/this.zoom_factor)/2;if(af){ai=af/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ai-ae);this.high=Math.round(ai+ae);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var af=this.high-this.low,ag=af/2+this.low,ae=(af*this.zoom_factor)/2;this.low=Math.round(ag-ae);this.high=Math.round(ag+ae);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ag){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ag.dataset_id){return}this.overview_viewport.find(".track").remove()}var af=ag.copy({content_div:this.overview_viewport}),ae=this;af.header_div.hide();af.is_overview=true;ae.overview_drawable=af;this.overview_drawable.postdraw_actions=function(){ae.overview_highlight.show().height(ae.overview_drawable.content_div.height());ae.overview_viewport.height(ae.overview_drawable.content_div.height()+ae.overview_box.outerHeight());ae.overview_close.show();ae.resize_window()};ae.overview_drawable.request_draw();ae.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ag,ak){this.track=ag;this.name=ak.name;this.params=[];var ar=ak.params;for(var ah=0;ah<ar.length;ah++){var am=ar[ah],af=am.name,aq=am.label,ai=unescape(am.html),at=am.value,ao=am.type;if(ao==="number"){this.params[this.params.length]=new f(af,aq,ai,at,am.min,am.max)}else{if(ao==="select"){this.params[this.params.length]=new N(af,aq,ai,at)}else{console.log("WARNING: unrecognized tool parameter type:",af,ao)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(av){av.stopPropagation()}).click(function(av){av.stopPropagation()}).bind("dblclick",function(av){av.stopPropagation()});var ap=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var an=this.params;var al=this;$.each(this.params,function(aw,az){var ay=$("<div>").addClass("param-row").appendTo(al.parent_div);var av=$("<div>").addClass("param-label").text(az.label).appendTo(ay);var ax=$("<div/>").addClass("param-input").html(az.html).appendTo(ay);ax.find(":input").val(az.value);$("<div style='clear: both;'/>").appendTo(ay)});this.parent_div.find("input").click(function(){$(this).select()});var au=$("<div>").addClass("param-row").appendTo(this.parent_div);var aj=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(au);var ae=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(au);var al=this;ae.click(function(){al.run_on_region()});aj.click(function(){al.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var ae={};this.parent_div.find(":input").each(function(){var af=$(this).attr("name"),ag=$(this).val();ae[af]=JSON.stringify(ag)});return ae},get_param_values:function(){var af=[];var ae={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();if(ag){af[af.length]=ah}});return af},run_on_dataset:function(){var ae=this;ae.run({dataset_id:this.track.original_dataset_id,tool_id:ae.name},null,function(af){show_modal(ae.name+" is Running",ae.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var af={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},aj=this.track,ag=af.tool_id+aj.tool_region_and_parameters_str(af.chrom,af.low,af.high),ae;if(aj.container===view){var ai=new P(this.name,this.track.view);var ah=aj.container.replace_drawable(aj,ai,false);ai.container_div.insertBefore(aj.view.content_div.children()[ah]);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);ae=ai}else{ae=aj.container}var ak=new aj.constructor(ag,view,ae,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);ae.add_drawable(ak);ak.content_div.text("Starting job.");this.run(af,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(af,ag,ah){$.extend(af,this.get_param_values_dict());var ae=function(){$.getJSON(rerun_tool_url,af,function(ai){if(ai==="no converter"){ag.container_div.addClass("error");ag.content_div.text(J)}else{if(ai.error){ag.container_div.addClass("error");ag.content_div.text(w+ai.message)}else{if(ai==="pending"){ag.container_div.addClass("pending");ag.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ae,2000)}else{ah(ai)}}}})};ae()}});var N=function(af,ae,ag,ah){this.name=af;this.label=ae;this.html=ag;this.value=ah};var f=function(ag,af,ai,aj,ah,ae){N.call(this,ag,af,ai,aj);this.min=ah;this.max=ae};var g=function(af,ae,ag,ah){this.manager=null;this.name=af;this.index=ae;this.tool_id=ag;this.tool_exp_name=ah};var U=function(af,am,at,ai){g.call(this,af,am,at,ai);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null;var an=function(au,av,aw){au.click(function(){var aB=av.text(),az=parseFloat(aw.slider("option","max")),ay=(az<=1?4:az<=1000000?az.toString().length:6),aA=false,ax=$(this).parents(".slider-row");ax.addClass("input");if(aw.slider("option","values")){ay=2*ay+1;aA=true}av.text("");$("<input type='text'/>").attr("size",ay).attr("maxlength",ay).attr("value",aB).appendTo(av).focus().select().click(function(aC){aC.stopPropagation()}).blur(function(){$(this).remove();av.text(aB);ax.removeClass("input")}).keyup(function(aG){if(aG.keyCode===27){$(this).trigger("blur")}else{if(aG.keyCode===13){var aE=aw.slider("option","min"),aC=aw.slider("option","max"),aF=function(aH){return(isNaN(aH)||aH>aC||aH<aE)},aD=$(this).val();if(!aA){aD=parseFloat(aD);if(aF(aD)){alert("Parameter value must be in the range ["+aE+"-"+aC+"]");return $(this)}}else{aD=aD.split("-");aD=[parseFloat(aD[0]),parseFloat(aD[1])];if(aF(aD[0])||aF(aD[1])){alert("Parameter value must be in the range ["+aE+"-"+aC+"]");return $(this)}}aw.slider((aA?"values":"value"),aD);ax.removeClass("input")}}})})};var ag=this;ag.parent_div=$("<div/>").addClass("filter-row slider-row");var ae=$("<div/>").addClass("elt-label").appendTo(ag.parent_div),aq=$("<span/>").addClass("slider-name").text(ag.name+" ").appendTo(ae),ah=$("<span/>"),aj=$("<span/>").addClass("slider-value").appendTo(ae).append("[").append(ah).append("]");ag.values_span=ah;var ap=$("<div/>").addClass("slider").appendTo(ag.parent_div);ag.control_element=$("<div/>").attr("id",ag.name+"-filter-control").appendTo(ap);var ak=[0,0];ag.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(au,av){ag.slide(au,av)},change:function(au,av){ag.control_element.slider("option","slide").call(ag.control_element,au,av)}});ag.slider=ag.control_element;ag.slider_label=ah;an(aj,ah,ag.control_element);var ar=$("<div/>").addClass("display-controls").appendTo(ag.parent_div),al=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(ag.manager.alpha_filter!==ag){ag.manager.alpha_filter=ag;ag.manager.parent_div.find(".layer-transparent").removeClass("active").hide();al.addClass("active").show()}else{ag.manager.alpha_filter=null;al.removeClass("active")}ag.manager.track.request_draw(true,true)}).appendTo(ar).hide(),ao=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(ag.manager.height_filter!==ag){ag.manager.height_filter=ag;ag.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();ao.addClass("active").show()}else{ag.manager.height_filter=null;ao.removeClass("active")}ag.manager.track.request_draw(true,true)}).appendTo(ar).hide();ag.parent_div.hover(function(){al.show();ao.show()},function(){if(ag.manager.alpha_filter!==ag){al.hide()}if(ag.manager.height_filter!==ag){ao.hide()}});$("<div style='clear: both;'/>").appendTo(ag.parent_div)};p(U.prototype,{get_slider_step:function(ag,ae){var af=ae-ag;return(af<=2?0.01:1)},slide:function(af,ag){var ae=ag.values;this.values_span.text(ae[0]+"-"+ae[1]);this.low=ae[0];this.high=ae[1];this.manager.track.request_draw(true,true)},applies_to:function(ae){if(ae.length>this.index){return true}return false},keep:function(ae){if(!this.applies_to(ae)){return true}var af=ae[this.index];return(isNaN(af)||(af>=this.low&&af<=this.high))},update_attrs:function(af){var ae=false;if(!this.applies_to(af)){return ae}if(af[this.index]<this.min){this.min=Math.floor(af[this.index]);ae=true}if(af[this.index]>this.max){this.max=Math.ceil(af[this.index]);ae=true}return ae},update_ui_elt:function(){if(this.min!==this.max){this.parent_div.show()}else{this.parent_div.hide()}var af=this.slider.slider("option","min"),ae=this.slider.slider("option","max");if(this.min<af||this.max>ae){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var Z=function(ag,aj){this.track=ag;this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aq){aq.stopPropagation()}).click(function(aq){aq.stopPropagation()}).bind("dblclick",function(aq){aq.stopPropagation()}).bind("keydown",function(aq){aq.stopPropagation()});this.filters=[];if(aj){for(var ak=0;ak<aj.length;ak++){var ae=aj[ak],af=ae.name,an=ae.type,am=ae.index,ap=ae.tool_id,ah=ae.tool_exp_name;if(an==="int"||an==="float"){this.add_filter(new U(af,am,ap,ah))}else{console.log("ERROR: unsupported filter: ",af,an)}}}if(this.filters.length!==0){var ao=$("<div/>").addClass("param-row").appendTo(this.parent_div);var al=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ao);var ai=this;al.click(function(){ai.run_on_dataset()})}};p(Z.prototype,{add_filter:function(ae){ae.manager=this;this.parent_div.append(ae.parent_div);this.filters.push(ae)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var ae=0;ae<this.filters.length;ae++){var af=this.filters[ae];af.update_ui_elt()}},clear_filters:function(){for(var ae=0;ae<this.filters.length;ae++){var af=this.filters[ae];af.slider.slider("option","values",[af.min,af.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var am=function(aq,ao,ap){if(!(ao in aq)){aq[ao]=ap}return aq[ao]};var ag={},ae,af,ah;for(var ai=0;ai<this.filters.length;ai++){ae=this.filters[ai];if(ae.tool_id){if(ae.min!==ae.low){af=am(ag,ae.tool_id,[]);af[af.length]=ae.tool_exp_name+" >= "+ae.low}if(ae.max!==ae.high){af=am(ag,ae.tool_id,[]);af[af.length]=ae.tool_exp_name+" <= "+ae.high}}}var ak=[];for(var an in ag){ak[ak.length]=[an,ag[an]]}var al=ak.length;(function aj(av,ar){var ap=ar[0],aq=ap[0],au=ap[1],at="("+au.join(") and (")+")",ao={cond:at,input:av,target_dataset_id:av,tool_id:aq},ar=ar.slice(1);$.getJSON(run_tool_url,ao,function(aw){if(aw.error){show_modal("Filter Dataset","Error running tool "+aq,{Close:hide_modal})}else{if(ar.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{aj(aw.dataset_id,ar)}}})})(this.track.dataset_id,ak)}});var B=function(ae,af){L.Scaler.call(this,af);this.filter=ae};B.prototype.gen_val=function(ae){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ae[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var E=function(ae){this.track=ae.track;this.params=ae.params;this.values={};this.restore_values((ae.saved_values?ae.saved_values:{}));this.onchange=ae.onchange};p(E.prototype,{restore_values:function(ae){var af=this;$.each(this.params,function(ag,ah){if(ae[ah.key]!==undefined){af.values[ah.key]=ae[ah.key]}else{af.values[ah.key]=ah.default_value}})},build_form:function(){var ah=this;var ae=$("<div />");var ag;function af(al,ai){for(var ap=0;ap<al.length;ap++){ag=al[ap];if(ag.hidden){continue}var aj="param_"+ap;var au=ah.values[ag.key];var ax=$("<div class='form-row' />").appendTo(ai);ax.append($("<label />").attr("for",aj).text(ag.label+":"));if(ag.type==="bool"){ax.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",au))}else{if(ag.type==="text"){ax.append($('<input type="text"/>').attr("id",aj).val(au).click(function(){$(this).select()}))}else{if(ag.type==="select"){var ar=$("<select />").attr("id",aj);for(var an=0;an<ag.options.length;an++){$("<option/>").text(ag.options[an].label).attr("value",ag.options[an].value).appendTo(ar)}ar.val(au);ax.append(ar)}else{if(ag.type==="color"){var aw=$("<div/>").appendTo(ax),aq=$("<input />").attr("id",aj).attr("name",aj).val(au).css("float","left").appendTo(aw).click(function(az){$(".tipsy").hide();var ay=$(this).siblings(".tipsy");ay.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ay).height()/2)+($(this).height()/2)}).show();ay.click(function(aA){aA.stopPropagation()});$(document).bind("click.color-picker",function(){ay.hide();$(document).unbind("click.color-picker")});az.stopPropagation()}),ao=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(aw).attr("title","Set new random color").tipsy({gravity:"s"}),at=$("<div class='tipsy tipsy-west' style='position: absolute;' />").appendTo(aw).hide(),ak=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(at),av=$("<div/>").appendTo(ak),am=$.farbtastic(av,{width:100,height:100,callback:aq,color:au});aw.append($("<div/>").css("clear","both"));(function(ay){ao.click(function(){ay.setColor(get_random_color())})})(am)}else{ax.append($("<input />").attr("id",aj).attr("name",aj).val(au))}}}}if(ag.help){ax.append($("<div class='help'/>").text(ag.help))}}}af(this.params,ae);return ae},update_from_form:function(ae){var ag=this;var af=false;$.each(this.params,function(ah,aj){if(!aj.hidden){var ak="param_"+ah;var ai=ae.find("#"+ak).val();if(aj.type==="float"){ai=parseFloat(ai)}else{if(aj.type==="int"){ai=parseInt(ai)}else{if(aj.type==="bool"){ai=ae.find("#"+ak).is(":checked")}}}if(ai!==ag.values[aj.key]){ag.values[aj.key]=ai;af=true}}});if(af){this.onchange()}}});var b=function(ae,ah,ag,af,ai){this.track=ae;this.index=ah;this.low=ah*Q*ag;this.high=(ah+1)*Q*ag;this.resolution=ag;this.html_elt=$("<div class='track-tile'/>").append(af);this.data=ai;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(ae,ah,ag,af,ai,aj){b.call(this,ae,ah,ag,af,ai);this.max_val=aj};p(k.prototype,b.prototype);var O=function(ah,am,ai,ag,ak,ar,al,at,af,ap){b.call(this,ah,am,ai,ag,ak);this.mode=al;this.feature_mapper=ap;this.has_icons=false;if(at||!af){this.has_icons=true;var an=this;ag=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:C-1,width:ag.width}).prependTo(this.html_elt);if(!af){var ao=$("<a href='javascript:void(0);'/>").addClass("icon exclamation").attr("title","To minimize track height, not all features in this region are displayed. Click to display more.").tipsy({gravity:"s"}).appendTo(message_div).click(function(){$(".tipsy").hide();an.track.slotters[ar].max_rows*=2;an.track.request_draw(true)})}if(at){var aq=ak.length,aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+aq+" features in this region were obtained from server. Click to get more data including depth").tipsy({gravity:"s"}).appendTo(message_div),ae=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+aq+" features in this region were obtained from server. Click to get more data excluding depth").tipsy({gravity:"s"}).appendTo(message_div);aj.click(function(){an.stale=true;ah.data_manager.get_more_data(an.low,an.high,ah.mode,an.resolution,{},ah.data_manager.DEEP_DATA_REQ);$(".tipsy").hide();ah.request_draw()}).dblclick(function(au){au.stopPropagation()});ae.click(function(){an.stale=true;ah.data_manager.get_more_data(an.low,an.high,ah.mode,an.resolution,{},ah.data_manager.BROAD_DATA_REQ);$(".tipsy").hide();ah.request_draw()}).dblclick(function(au){au.stopPropagation()})}}};p(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var af=this,ae={};if(af.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).siblings(".feature-popup").remove()}).mousemove(function(aq){if(!this.hovered){return}var al=$(this).offset(),ap=aq.pageX-al.left,ao=aq.pageY-al.top,av=af.feature_mapper.get_feature_data(ap,ao),am=(av?av[0]:null);$(this).siblings(".feature-popup").each(function(){if(!am||$(this).attr("id")!==am.toString()){$(this).remove()}});if(av){var ah=ae[am];if(!ah){var am=av[0],ar={name:av[3],start:av[1],end:av[2],strand:av[4]},ak=af.track.filters_manager.filters,aj;for(var an=0;an<ak.length;an++){aj=ak[an];ar[aj.name]=av[aj.index]}var ah=$("<div/>").attr("id",am).addClass("feature-popup"),aw=$("<table/>"),au,at,ax;for(au in ar){at=ar[au];ax=$("<tr/>").appendTo(aw);$("<th/>").appendTo(ax).text(au);$("<td/>").attr("align","left").appendTo(ax).text(typeof(at)==="number"?Y(at,2):at)}ah.append($("<div class='feature-popup-inner'>").append(aw));ae[am]=ah}ah.appendTo($(af.html_elt).parent());var ai=ap+parseInt(af.html_elt.css("left"))-ah.width()/2,ag=ao+parseInt(af.html_elt.css("top"))+7;ah.css("left",ai+"px").css("top",ag+"px")}else{if(!aq.isPropagationStopped()){aq.stopPropagation();$(this).siblings().each(function(){$(this).trigger(aq)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ah,af,ae,ag,aj,ai,ak){q.call(this,ah,af,ae,{},"draghandle");this.data_url=(ai?ai:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ak?ak:K);this.dataset_check_url=converted_datasets_state_url;this.data_manager=(aj?aj:new S(H,this));this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div)}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ae){ae.view.set_overview(ae)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ae){if(ae.filters_div.is(":visible")){ae.filters_manager.clear_filters()}else{ae.filters_manager.init_filters()}ae.filters_div.toggle()}},{name:"tools_icon",title:"Tools",css_class:"tools-icon",on_click_fn:function(ae){ae.dynamic_tool_div.toggle();if(ae.dynamic_tool_div.is(":visible")){ae.set_name(ae.name+ae.tool_region_and_parameters_str())}else{ae.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ae=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ae)}this.name_div=$("<div/>").addClass("track-name").appendTo(ae).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ae},set_display_modes:function(ah,ak){this.display_modes=ah;this.mode=(ak?ak:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var af=this,ai={};for(var ag=0,ae=af.display_modes.length;ag<ae;ag++){var aj=af.display_modes[ag];ai[aj]=function(al){return function(){af.change_mode(al);af.icons_div.show();af.container_div.mouseleave(function(){af.icons_div.hide()})}}(aj)}make_popupmenu(this.action_icons.mode_icon,ai)},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof aa){return"LabelTrack"}else{if(this instanceof z){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof V){return"ReadTrack"}else{if(this instanceof T){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.content_div.css("height","auto");af.content_div.children().remove();af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}var ae=$.Deferred();$.getJSON(converted_datasets_state_url,{hda_ldda:af.hda_ldda,dataset_id:af.dataset_id,chrom:af.view.chrom},function(ag){if(!ag||ag==="error"||ag.kind==="error"){af.container_div.addClass("error");af.content_div.text(o);if(ag.message){var ah=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})});af.content_div.append(ah)}}else{if(ag==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(D)}else{if(ag==="pending"){af.container_div.addClass("pending");af.content_div.text(t);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ag.status==="data"){if(ag.valid_chroms){af.valid_chroms=ag.valid_chroms;af.update_icons()}af.content_div.text(X);if(af.view.chrom){af.content_div.text("");af.content_div.css("height",af.height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){ae.resolve();af.container_div.removeClass("nodata error pending");af.request_draw()})}else{ae.resolve()}}}}}}});this.update_icons();return ae},predraw_init:function(){}});var M=function(aj,ah,ag,ai,af,al,ak){i.call(this,aj,ah,ag,ai,ak);var ae=this,ah=ae.view;m(ae.container_div,ae.drag_handle_class,".group",ae);this.filters_manager=new Z(this,af);this.filters_available=false;this.tool=(al!==undefined&&obj_length(al)>0?new r(this,al):undefined);this.tile_cache=new c(R);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(M.prototype,q.prototype,i.prototype,{copy:function(ae){var af=new this.constructor(this.name,this.view,ae,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool,this.data_manager);af.change_mode(this.mode);af.enabled=this.enabled;return af},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},from_dict:function(ag,af){var ae=new this.constructor(ag.name,view,af,ag.hda_ldda,ag.dataset_id,ag.prefs,ag.filters,ag.tool);if(ag.mode){ae.change_mode(ag.mode)}return ae},change_mode:function(af){var ae=this;ae.mode=af;ae.config.values.mode=af;ae.tile_cache.clear();ae.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ae.mode+")");return ae},update_icons:function(){var ae=this;if(ae.filters_available){ae.action_icons.filters_icon.show()}else{ae.action_icons.filters_icon.hide()}if(ae.tool){ae.action_icons.tools_icon.show()}else{ae.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(af,ag,ae){return af+"_"+ag+"_"+ae},request_draw:function(af,ae){this.view.request_redraw(false,af,ae,this)},_draw:function(ag,aq){if(!this.can_draw()){return}var ao=this.view.low,ak=this.view.high,am=ak-ao,ah=this.view.container.width(),au=ah/am,aj=this.view.resolution,at=this.content_div;if(this.is_overview){ao=this.view.max_low;ak=this.view.max_high;aj=Math.pow(A,Math.ceil(Math.log((view.max_high-view.max_low)/Q)/Math.log(A)));au=ah/(view.max_high-view.max_low)}this.content_div.children().addClass("remove");this.max_height=0;var af=Math.floor(ao/aj/Q);var an=true;var ar=[];var ae=0;var al=function(av){return(av&&"track" in av)};while((af*Q*aj)<ak){var ap=this.draw_helper(ag,ah,af,aj,at,au);if(al(ap)){ar.push(ap)}else{an=false}af+=1;ae++}if(!aq){this.content_div.children(".remove").remove()}var ai=this;if(an){this.content_div.children(".remove").remove();ai.postdraw_actions(ar,ah,au,aq)}},postdraw_actions:function(ah,ai,ak,ae){var ag=this;var aj=false;for(var af=0;af<ah.length;af++){if(ah[af].has_icons){aj=true;break}}if(aj){for(var af=0;af<ah.length;af++){tile=ah[af];if(!tile.has_icons){tile.html_elt.css("padding-top",C)}}}},draw_helper:function(ae,aq,aw,au,aj,ak,ar){var ap=this,az=this._gen_tile_cache_key(aq,ak,aw),ax=aw*Q*au,af=ax+Q*au;if(!ar){ar={}}var ay=(ae?undefined:ap.tile_cache.get(az));if(ay){ap.show_tile(ay,aj,ak);return ay}var an=true;var av=ap.data_manager.get_data(ax,af,ap.mode,au,ap.data_url_extra_params);if(is_deferred(av)){an=false}var al;if(view.reference_track&&ak>view.canvas_manager.char_width_px){al=view.reference_track.data_manager.get_data(ax,af,ap.mode,au,view.reference_track.data_url_extra_params);if(is_deferred(al)){an=false}}if(an){p(av,ar.more_tile_data);var am=ap.mode;if(am==="Auto"){am=ap.get_mode(av);ap.update_auto_mode(am)}var ag=ap.view.canvas_manager.new_canvas(),ah=ap._get_tile_bounds(aw,au),ax=ah[0],af=ah[1],aq=Math.ceil((af-ax)*ak)+ap.left_offset,ao=ap.get_canvas_height(av,am,ak,aq);ag.width=aq;ag.height=ao;var at=ag.getContext("2d");at.translate(this.left_offset,0);var ay=ap.draw_tile(av,at,am,au,aw,ak,al);if(ay!==undefined){ap.tile_cache.set(az,ay);ap.show_tile(ay,aj,ak)}return ay}var ai=$.Deferred();$.when(av,al).then(function(){view.request_redraw(false,false,false,ap);ai.resolve()});return ai},get_canvas_height:function(ae,ag,ah,af){return this.height_px},draw_tile:function(ae,ag,aj,ai,af,ak,ah){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ag,ai,aj){var af=this,ae=ag.html_elt;ag.predisplay_actions();var ah=(ag.low-(this.is_overview?this.view.max_low:this.view.low))*aj;if(this.left_offset){ah-=this.left_offset}ae.css({position:"absolute",top:0,left:ah,height:""});if(ae.hasClass("remove")){ae.removeClass("remove")}else{ai.append(ae)}af.max_height=Math.max(af.max_height,ae.height());af.content_div.css("height",af.max_height+"px");ai.children().css("height",af.max_height+"px")},_get_tile_bounds:function(ae,af){var ah=ae*Q*af,ai=Q*af,ag=(ah+ai<=this.view.max_high?ah+ai:this.view.max_high);return[ah,ag]},tool_region_and_parameters_str:function(ag,ae,ah){var af=this,ai=(ag!==undefined&&ae!==undefined&&ah!==undefined?ag+":"+ae+"-"+ah:"all");return" - region=["+ai+"], parameters=["+af.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ae,af){return true},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var af=this;var ae=function(){if(af.data_manager.size()===0){setTimeout(ae,300)}else{af.data_url=default_data_url;af.data_query_wait=K;af.dataset_state_url=converted_datasets_state_url;$.getJSON(af.dataset_state_url,{dataset_id:af.dataset_id,hda_ldda:af.hda_ldda},function(ag){})}};ae()}}});var aa=function(af,ae){i.call(this,"label",af,ae,false,{});this.container_div.addClass("label-track")};p(aa.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ag=this.view,ah=ag.high-ag.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ah)/Math.log(10)))),ae=Math.floor(ag.low/ak)*ak,ai=this.view.container.width(),af=$("<div style='position: relative; height: 1.3em;'></div>");while(ae<ag.high){var aj=(ae-ag.low)/ah*ai;af.append($("<div class='label'>"+commatize(ae)+"</div>").css({position:"absolute",left:aj-1}));ae+=ak}this.content_div.children(":first").remove();this.content_div.append(af)}});var h=function(ah,ag,af,ae){M.call(this,ah,ag,af);this.drawables=[];this.left_offset=0;if(ae){var ak=[],aj;for(var ai=0;ai<ae.length;ai++){aj=ae[ai];ak.push(aj.dataset_id);this.drawables[ai]=aj.copy();if(aj.left_offset>this.left_offset){this.left_offset=aj.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,M.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ae){$(".tipsy").remove();ae.show_group()}}].concat(M.prototype.action_icons_def),to_dict:x.prototype.to_dict,add_drawable:x.prototype.add_drawable,from_dict:function(ak,ae){var aj=new this.constructor(ak.name,view,ae,ak.prefs,view.viewport_container,view);var af,ai,ah;for(var ag=0;ag<ak.drawables.length;ag++){af=ak.drawables[ag];ai=af.obj_type;if(!ai){ai=af.track_type}ah=addable_objects[ai].prototype.from_dict(af);aj.add_drawable(ah)}aj.set_display_modes(aj.drawables[0].display_modes,aj.drawables[0].mode);return aj},change_mode:function(ae){M.prototype.change_mode.call(this,ae);for(var af=0;af<this.drawables.length;af++){this.drawables[af].change_mode(ae)}},init:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].init())}var ae=this;$.when.apply($,ag).then(function(){ae.enabled=true;ae.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(af,au,aA,ax,al,an,av){var at=this,aE=this._gen_tile_cache_key(au,an,aA),aB=aA*Q*ax,ag=aB+Q*ax;if(!av){av={}}var aD=(af?undefined:at.tile_cache.get(aE));if(aD){at.show_tile(aD,al,an);return aD}var am=[],at,aq=true,ay,ao;for(var az=0;az<this.drawables.length;az++){at=this.drawables[az];ay=at.data_manager.get_data(aB,ag,at.mode,ax,at.data_url_extra_params);if(is_deferred(ay)){aq=false}am.push(ay);ao=null;if(view.reference_track&&an>view.canvas_manager.char_width_px){ao=view.reference_track.data_manager.get_data(aB,ag,at.mode,ax,view.reference_track.data_url_extra_params);if(is_deferred(ao)){aq=false}}am.push(ao)}if(aq){p(ay,av.more_tile_data);this.tile_predraw_init();var ai=at.view.canvas_manager.new_canvas(),aj=at._get_tile_bounds(aA,ax),aB=aj[0],ag=aj[1],aC=0,au=Math.ceil((ag-aB)*an)+this.left_offset,ar=0,ah=[];var ae=0;for(var az=0;az<this.drawables.length;az++,aC+=2){at=this.drawables[az];ay=am[aC];var ap=at.mode;if(ap==="Auto"){ap=at.get_mode(ay);at.update_auto_mode(ap)}ah.push(ap);ae=at.get_canvas_height(ay,ap,an,au);if(ae>ar){ar=ae}}ai.width=au;ai.height=(av.height?av.height:ar);aC=0;var aw=ai.getContext("2d");aw.translate(this.left_offset,0);aw.globalAlpha=0.5;aw.globalCompositeOperation="source-over";for(var az=0;az<this.drawables.length;az++,aC+=2){at=this.drawables[az];ay=am[aC];ao=am[aC+1];aD=at.draw_tile(ay,aw,ah[az],ax,aA,an,ao)}this.tile_cache.set(aE,aD);this.show_tile(aD,al,an);return aD}var ak=$.Deferred(),at=this;$.when.apply($,am).then(function(){view.request_redraw(false,false,false,at);ak.resolve()});return ak},show_group:function(){var ah=new P(this.name,this.view,this.container),ae;for(var ag=0;ag<this.drawables.length;ag++){ae=this.drawables[ag];ah.add_drawable(ae);ae.container=ah;ah.content_div.append(ae.container_div)}var af=this.container.replace_drawable(this,ah,true);ah.request_draw()},tile_predraw_init:function(){var ah=Number.MAX_VALUE,ae=-ah,af;for(var ag=0;ag<this.drawables.length;ag++){af=this.drawables[ag];if(af instanceof j){if(af.prefs.min_value<ah){ah=af.prefs.min_value}if(af.prefs.max_value>ae){ae=af.prefs.max_value}}}for(var ag=0;ag<this.drawables.length;ag++){af=this.drawables[ag];af.prefs.min_value=ah;af.prefs.max_value=ae}},postdraw_actions:function(ag,aj,al,af){M.prototype.postdraw_actions.call(this,ag,aj,al,af);var ai=-1;for(var ah=0;ah<ag.length;ah++){var ae=ag[ah].html_elt.find("canvas").height();if(ae>ai){ai=ae}}for(var ah=0;ah<ag.length;ah++){var ak=ag[ah];if(ak.html_elt.find("canvas").height()!==ai){this.draw_helper(true,aj,ak.index,ak.resolution,ak.html_elt.parent(),al,{height:ai});ak.html_elt.remove()}}}});var z=function(ae){M.call(this,"reference",ae,{content_div:ae.top_labeltrack},{});ae.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ae.dbkey};this.data_manager=new G(H,this,false)};p(z.prototype,q.prototype,M.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(am,an,aj,ai,af,ao){var ah=this;if(ao>this.view.canvas_manager.char_width_px){if(am.data===null){ah.content_div.css("height","0px");return}var ag=an.canvas;an.font=an.canvas.manager.default_font;an.textAlign="center";am=am.data;for(var ak=0,al=am.length;ak<al;ak++){var ae=Math.round(ak*ao);an.fillText(am[ak],ae,10)}return new b(ah,af,ai,ag,am)}this.content_div.css("height","0px")}});var j=function(ae,al,af,ak,an,am,ai,aj,ag){var ah=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,ae,al,af,am,ai,aj,ag);this.min_height_px=16;this.max_height_px=400;this.height_px=32;this.hda_ldda=ak;this.dataset_id=an;this.original_dataset_id=an;this.left_offset=0;this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ae},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:am,onchange:function(){ah.set_name(ah.prefs.name);ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.set_min_value(ah.prefs.min_value);ah.set_max_value(ah.prefs.max_value)}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,M.prototype,{set_min_value:function(ae){this.prefs.min_value=ae;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ae){this.prefs.max_value=ae;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},add_resize_handle:function(){var ae=this;var ah=false;var ag=false;var af=$("<div class='track-resize'>");$(ae.container_div).hover(function(){if(ae.content_visible){ah=true;af.show()}},function(){ah=false;if(!ag){af.hide()}});af.hide().bind("dragstart",function(ai,aj){ag=true;aj.original_height=$(ae.content_div).height()}).bind("drag",function(aj,ak){var ai=Math.min(Math.max(ak.original_height+ak.deltaY,ae.min_height_px),ae.max_height_px);$(ae.content_div).css("height",ai);ae.height_px=ai;ae.request_draw(true)}).bind("dragend",function(ai,aj){ae.tile_cache.clear();ag=false;if(!ah){af.hide()}ae.config.values.height=ae.height_px}).appendTo(ae.container_div)},predraw_init:function(){var ae=this;ae.vertical_range=undefined;return $.getJSON(ae.data_url,{stats:true,chrom:ae.view.chrom,low:null,high:null,hda_ldda:ae.hda_ldda,dataset_id:ae.dataset_id},function(af){ae.container_div.addClass("line-track");var ai=af.data;if(isNaN(parseFloat(ae.prefs.min_value))||isNaN(parseFloat(ae.prefs.max_value))){var ag=ai.min;var ak=ai.max;ag=Math.floor(Math.min(0,Math.max(ag,ai.mean-2*ai.sd)));ak=Math.ceil(Math.max(0,Math.min(ak,ai.mean+2*ai.sd)));ae.prefs.min_value=ag;ae.prefs.max_value=ak;$("#track_"+ae.dataset_id+"_minval").val(ae.prefs.min_value);$("#track_"+ae.dataset_id+"_maxval").val(ae.prefs.max_value)}ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.total_frequency=ai.total_frequency;ae.container_div.find(".yaxislabel").remove();var aj=get_editable_text_elt(Y(ae.prefs.min_value,3),false,6,null,function(al){var al=parseFloat(al);if(!isNaN(al)){ae.set_min_value(al)}}).addClass("yaxislabel bottom").attr("id","linetrack_"+ae.dataset_id+"_minval").prependTo(ae.container_div),ah=get_editable_text_elt(Y(ae.prefs.max_value,3),false,6,null,function(al){var al=parseFloat(al);if(!isNaN(al)){ae.set_max_value(al)}}).addClass("yaxislabel top").attr("id","linetrack_"+ae.dataset_id+"_maxval").prependTo(ae.container_div)})},draw_tile:function(ao,am,aj,ah,af,an){var ag=am.canvas,ae=this._get_tile_bounds(af,ah),ai=ae[0],al=ae[1],ak=new L.LinePainter(ao.data,ai,al,this.prefs,aj);ak.draw(am,ag.width,ag.height,an);return new b(this.track,af,ah,ag,ao.data)}});var d=function(ae,al,af,ak,an,am,ai,aj,ag){var ah=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];M.call(this,ae,al,af,am,ai,aj,ag);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ae},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){ah.set_name(ah.prefs.name);ah.tile_cache.clear();ah.set_painter_from_config();ah.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ak;this.dataset_id=an;this.original_dataset_id=an;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(d.prototype,q.prototype,M.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(at,ag,av,ar){M.prototype.postdraw_actions.call(this,at,ar);var ai=this;if(ai.mode==="Histogram"){var am=-1;for(var aj=0;aj<at.length;aj++){var aq=at[aj].max_val;if(aq>am){am=aq}}for(var aj=0;aj<at.length;aj++){var ao=at[aj];if(ao.max_val!==am){ao.html_elt.remove();ai.draw_helper(true,ag,ao.index,ao.resolution,ao.html_elt.parent(),av,{more_tile_data:{max:am}})}}}if(ai.filters_manager){var ah=ai.filters_manager.filters;for(var al=0;al<ah.length;al++){ah[al].update_ui_elt()}var ak=false,an,af;for(var aj=0;aj<at.length;aj++){if(at[aj].data.length){an=at[aj].data[0];for(var al=0;al<ah.length;al++){af=ah[al];if(af.applies_to(an)&&af.min!==af.max){ak=true;break}}}}if(ai.filters_available!==ak){ai.filters_available=ak;if(!ai.filters_available){ai.filters_div.hide()}ai.update_icons()}}this.container_div.find(".yaxislabel").remove();var ae=at[0];if(ae instanceof k){var au=(this.prefs.histogram_max?this.prefs.histogram_max:ae.max_val),ap=get_editable_text_elt(au,false,12,0,function(aw){var aw=parseFloat(aw);ai.prefs.histogram_max=(!isNaN(aw)?aw:null);ai.tile_cache.clear();ai.request_draw()}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ap)}},update_auto_mode:function(ae){var ae;if(this.mode==="Auto"){if(ae==="no_detail"){ae="feature spans"}else{if(ae==="summary_tree"){ae="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ae+")")}},incremental_slots:function(ai,ae,ah){var af=this.view.canvas_manager.dummy_context,ag=this.slotters[ai];if(!ag||(ag.mode!==ah)){ag=new (s.FeatureSlotter)(ai,ah,y,function(aj){return af.measureText(aj)});this.slotters[ai]=ag}return ag.slot_features(ae)},get_summary_tree_data:function(ai,al,ag,au){if(au>ag-al){au=ag-al}var ap=Math.floor((ag-al)/au),at=[],ah=0;var aj=0,ak=0,ao,ar=0,am=[],aq,an;var af=function(ax,aw,ay,av){ax[0]=aw+ay*av;ax[1]=aw+(ay+1)*av};while(ar<au&&aj!==ai.length){var ae=false;for(;ar<au&&!ae;ar++){af(am,al,ar,ap);for(ak=aj;ak<ai.length;ak++){ao=ai[ak].slice(1,3);if(is_overlap(ao,am)){ae=true;break}}if(ae){break}}data_start_index=ak;at[at.length]=aq=[am[0],0];for(;ak<ai.length;ak++){ao=ai[ak].slice(1,3);if(is_overlap(ao,am)){aq[1]++}else{break}}if(aq[1]>ah){ah=aq[1]}ar++}return{max:ah,delta:ap,data:at}},get_mode:function(ae){if(ae.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ae.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ae,ai,aj,af){if(ai==="summary_tree"||ai==="Histogram"){return this.summary_draw_height}else{var ah=this.incremental_slots(aj,ae.data,ai);var ag=new (this.painter)(null,null,null,this.prefs,ai);return Math.max(ac,ag.get_required_height(ah,af))}},draw_tile:function(ap,au,ar,av,az,al,ag){var at=this,af=au.canvas,ai=this._get_tile_bounds(az,av),aC=ai[0],ae=ai[1],aH=25,ah=this.left_offset;if(ar==="summary_tree"||ar==="Histogram"){if(ap.dataset_type!=="summary_tree"){var am=this.get_summary_tree_data(ap.data,aC,ae,200);if(ap.max){am.max=ap.max}ap=am}var aE=new L.SummaryTreePainter(ap,aC,ae,this.prefs);aE.draw(au,af.width,af.height,al);return new k(at,az,av,af,ap.data,ap.max)}var ak=[],aq=this.slotters[al].slots;all_slotted=true;if(ap.data){var an=this.filters_manager.filters;for(var aw=0,ay=ap.data.length;aw<ay;aw++){var aj=ap.data[aw];var ax=false;var ao;for(var aB=0,aG=an.length;aB<aG;aB++){ao=an[aB];ao.update_attrs(aj);if(!ao.keep(aj)){ax=true;break}}if(!ax){ak.push(aj);if(!(aj[0] in aq)){all_slotted=false}}}}var aF=(this.filters_manager.alpha_filter?new B(this.filters_manager.alpha_filter):null);var aD=(this.filters_manager.height_filter?new B(this.filters_manager.height_filter):null);var aE=new (this.painter)(ak,aC,ae,this.prefs,ar,aF,aD,ag);var aA=null;au.fillStyle=this.prefs.block_color;au.font=au.canvas.manager.default_font;au.textAlign="right";if(ap.data){aA=aE.draw(au,af.width,af.height,al,aq);aA.translation=-ah}return new O(at,az,av,af,ap.data,al,ar,ap.message,all_slotted,aA)},data_and_mode_compatible:function(ae,af){if(af==="Auto"){return true}else{if(ae.extra_info==="no_detail"||ae.dataset_type==="summary_tree"){return false}else{return true}}},});var T=function(ae,ak,af,aj,am,al,ah,ai,ag){d.call(this,ae,ak,af,aj,am,al,ah,ai,ag);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ae},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:al,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};p(T.prototype,q.prototype,M.prototype,d.prototype);var V=function(ae,ak,af,aj,an,am,ah,ag){d.call(this,ae,ak,af,aj,an,am,ah,ag);var ai=get_random_color(),al=get_random_color([ai,"#ffffff"]);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ae},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ai},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:al},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};p(V.prototype,q.prototype,M.prototype,d.prototype);W.View=ab;W.DrawableGroup=P;W.LineTrack=j;W.FeatureTrack=d;W.ReadTrack=V;W.VcfTrack=T;W.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}else{}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};l.prototype.draw=function(z,A,y,B){};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(L,z,K,M){var E=this.view_start,N=this.view_end-this.view_start,I=this.data.data,G=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),B=K;delta_x_px=Math.ceil(this.data.delta*M);L.save();for(var C=0,D=I.length;C<D;C++){var H=Math.floor((I[C][0]-E)*M);var F=I[C][1];if(!F){continue}var J=F/G*K;if(F!==0&&J<1){J=1}L.fillStyle=this.prefs.block_color;L.fillRect(H,B-J,delta_x_px,J);var A=4;if(this.prefs.show_counts&&(L.measureText(F).width+A)<delta_x_px){L.fillStyle=this.prefs.label_color;L.textAlign="center";L.fillText(F,H+(delta_x_px/2),10)}}L.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(S,Q,N,D){var I=false,K=this.prefs.min_value,F=this.prefs.max_value,M=F-K,B=N,C=this.view_start,P=this.view_end-this.view_start,L=this.mode,aa=this.data;S.save();var ac=Math.round(N+K/M*N);if(L!=="Intensity"){S.fillStyle="#aaa";S.fillRect(0,ac,Q,1)}S.beginPath();var Y,G,E;if(aa.length>1){E=Math.ceil((aa[1][0]-aa[0][0])*D)}else{E=10}var A=parseInt(this.prefs.color.slice(1),16),H=(A&16711680)>>16,R=(A&65280)>>8,V=A&255;for(var T=0,U=aa.length;T<U;T++){S.fillStyle=S.strokeStyle=this.prefs.color;Y=Math.round((aa[T][0]-C)*D);G=aa[T][1];var W=false,J=false;if(G===null){if(I&&L==="Filled"){S.lineTo(Y,B)}I=false;continue}if(G<K){J=true;G=K}else{if(G>F){W=true;G=F}}if(L==="Histogram"){G=Math.round(G/M*B);S.fillRect(Y,ac,E,-G)}else{if(L==="Intensity"){var z=(G-K)/M,O=Math.round(H+(255-H)*(1-z)),X=Math.round(R+(255-R)*(1-z)),ab=Math.round(V+(255-V)*(1-z));S.fillStyle="rgb("+O+","+X+","+ab+")";S.fillRect(Y,0,E,B)}else{G=Math.round(B-(G-K)/M*B);if(I){S.lineTo(Y,G)}else{I=true;if(L==="Filled"){S.moveTo(Y,B);S.lineTo(Y,G)}else{S.moveTo(Y,G)}}}}S.fillStyle=this.prefs.overflow_color;if(W||J){var Z;if(L==="Histogram"||L==="Intensity"){Z=E}else{Y-=2;Z=4}if(W){S.fillRect(Y,0,Z,3)}if(J){S.fillRect(Y,B-3,Z,3)}}S.fillStyle=this.prefs.color}if(L==="Filled"){if(I){S.lineTo(Y,ac);S.lineTo(0,ac)}S.fill()}else{S.stroke()}S.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,E,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode==="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2]-1,Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-1-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length===1&&D==="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences){if(this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}else{continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai==="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster: inline editing of LineTrack min and max values.
by Bitbucket 31 Jan '12

31 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/55a4070a62e7/ changeset: 55a4070a62e7 user: jgoecks date: 2012-01-31 21:55:21 summary: Trackster: inline editing of LineTrack min and max values. affected #: 3 files diff -r 115068e367b39bf55a04d9254293d698023f2ab9 -r 55a4070a62e73ddd3ff387cb46a27410a2847110 static/june_2007_style/blue/trackster.css --- a/static/june_2007_style/blue/trackster.css +++ b/static/june_2007_style/blue/trackster.css @@ -18,8 +18,9 @@ .overview-boxback{width:100%;bottom:0px;z-index:50;position:absolute;height:14px;background:#eee;border:solid #999 1px;} .overview-box{cursor:pointer;bottom:0px;z-index:100;position:absolute;margin-top:0px;height:14px;background:#C1C9E5 url(../images/visualization/draggable_horizontal.png) center center no-repeat;border:solid #666 1px;} .viewport-canvas{width:100%;height:100px;} -.yaxislabel{z-index:101;} -.yaxislabel.histogram-max{position:absolute;top:24px;left:10px;} +.yaxislabel{z-index:101;position:absolute;} +.yaxislabel.top{top:24px;left:10px;} +.yaxislabel.bottom{bottom:2px;left:10px;} .line-track .track-content{border-top:1px solid #eee;border-bottom:1px solid #eee;} .group-handle{cursor:move;float:left;background:#eee url('../images/tracks/block.png');width:12px;height:12px;} .group{min-height:20px;border-top:2px solid #888;border-bottom:2px solid #888;} diff -r 115068e367b39bf55a04d9254293d698023f2ab9 -r 55a4070a62e73ddd3ff387cb46a27410a2847110 static/june_2007_style/trackster.css.tmpl --- a/static/june_2007_style/trackster.css.tmpl +++ b/static/june_2007_style/trackster.css.tmpl @@ -123,13 +123,19 @@ .yaxislabel { /* Needs to be > canvas z-index. */ z-index: 101; + position: absolute; } -.yaxislabel.histogram-max { - position: absolute; + +.yaxislabel.top { top: 24px; left: 10px; } +.yaxislabel.bottom { + bottom: 2px; + left: 10px; +} + /* Line track needs borders to show range */ .line-track .track-content { border-top: 1px solid #eee; diff -r 115068e367b39bf55a04d9254293d698023f2ab9 -r 55a4070a62e73ddd3ff387cb46a27410a2847110 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -4032,11 +4032,8 @@ onchange: function() { track.set_name(track.prefs.name); track.vertical_range = track.prefs.max_value - track.prefs.min_value; - // Update the y-axis - $('#linetrack_' + track.dataset_id + '_minval').text(track.prefs.min_value); - $('#linetrack_' + track.dataset_id + '_maxval').text(track.prefs.max_value); - track.tile_cache.clear(); - track.request_draw(); + track.set_min_value(track.prefs.min_value); + track.set_max_value(track.prefs.max_value); } }); @@ -4047,6 +4044,24 @@ this.add_resize_handle(); }; extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, { + /** + * Set track minimum value. + */ + set_min_value: function(new_val) { + this.prefs.min_value = new_val; + $('#linetrack_' + this.dataset_id + '_minval').text(this.prefs.min_value); + this.tile_cache.clear(); + this.request_draw(); + }, + /** + * Set track maximum value. + */ + set_max_value: function(new_val) { + this.prefs.max_value = new_val; + $('#linetrack_' + this.dataset_id + '_maxval').text(this.prefs.max_value); + this.tile_cache.clear(); + this.request_draw(); + }, add_resize_handle: function () { // Add control for resizing // Trickery here to deal with the hovering drag handle, can probably be @@ -4114,14 +4129,21 @@ // Draw y-axis labels if necessary track.container_div.find(".yaxislabel").remove(); - var min_label = $("<div />").addClass('yaxislabel').attr("id", 'linetrack_' + track.dataset_id + '_minval').text(round(track.prefs.min_value, 3)); - var max_label = $("<div />").addClass('yaxislabel').attr("id", 'linetrack_' + track.dataset_id + '_maxval').text(round(track.prefs.max_value, 3)); - - max_label.css({ position: "absolute", top: "24px", left: "10px" }); - max_label.prependTo(track.container_div); - - min_label.css({ position: "absolute", bottom: "2px", left: "10px" }); - min_label.prependTo(track.container_div); + // Add min, max labels. + var min_label = get_editable_text_elt(round(track.prefs.min_value, 3), false, 6, null, function(new_val) { + var new_val = parseFloat(new_val); + if (!isNaN(new_val)) { + track.set_min_value(new_val); + } + } ).addClass('yaxislabel bottom').attr("id", 'linetrack_' + track.dataset_id + '_minval') + .prependTo(track.container_div), + max_label = get_editable_text_elt(round(track.prefs.max_value, 3), false, 6, null, function(new_val) { + var new_val = parseFloat(new_val); + if (!isNaN(new_val)) { + track.set_max_value(new_val); + } + } ).addClass('yaxislabel top').attr("id", 'linetrack_' + track.dataset_id + '_maxval') + .prependTo(track.container_div); }); }, /** @@ -4285,7 +4307,7 @@ track.tile_cache.clear(); track.request_draw(); }) - .addClass('yaxislabel histogram-max') + .addClass('yaxislabel top') .css("color", this.prefs.label_color); this.container_div.prepend(max_label); } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster: more object-specific equality operators.
by Bitbucket 30 Jan '12

30 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/82ee65f9eaa3/ changeset: 82ee65f9eaa3 user: jgoecks date: 2012-01-30 21:10:53 summary: Trackster: more object-specific equality operators. affected #: 1 file diff -r 3d4221462aba3322b7e096a58163db8d7625a216 -r 82ee65f9eaa3878e6e060055818f88ebedd9b5f3 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -1852,7 +1852,7 @@ this.params[this.params.length] = new NumberParameter(name, label, html, value, param_dict.min, param_dict.max); } - else if (type == "select") { + else if (type === "select") { this.params[this.params.length] = new ToolParameter(name, label, html, value); } else { @@ -2598,7 +2598,7 @@ } else if ( param.type === 'text' ) { row.append( $('<input type="text"/>').attr("id", id ).val(value).click( function() { $(this).select() })); // Draw paramter as select area - } else if ( param.type == 'select' ) { + } else if ( param.type === 'select' ) { var select = $('<select />').attr("id", id); for ( var i = 0; i < param.options.length; i++ ) { $("<option/>").text( param.options[i].label ).attr( "value", param.options[i].value ).appendTo( select ); @@ -2866,7 +2866,7 @@ row = $("<tr/>").appendTo(table); $("<th/>").appendTo(row).text(key); $("<td/>").attr("align", "left").appendTo(row) - .text(typeof(value) == 'number' ? round(value, 2) : value); + .text(typeof(value) === 'number' ? round(value, 2) : value); } popup.append( $("<div class='feature-popup-inner'>").append( table ) ); popups[feature_uid] = popup; @@ -4195,7 +4195,7 @@ }; extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, { set_painter_from_config: function() { - if ( this.config.values['connector_style'] == 'arcs' ) { + if ( this.config.values['connector_style'] === 'arcs' ) { this.painter = painters.ArcLinkedFeaturePainter; } else { this.painter = painters.LinkedFeaturePainter; @@ -4211,7 +4211,7 @@ var track = this; // If mode is Histogram and tiles do not share max, redraw tiles as necessary using new max. - if (track.mode == "Histogram") { + if (track.mode === "Histogram") { // Get global max. var global_max = -1; for (var i = 0; i < tiles.length; i++) { @@ -4292,10 +4292,10 @@ }, update_auto_mode: function( mode ) { var mode; - if ( this.mode == "Auto" ) { - if ( mode == "no_detail" ) { + if ( this.mode === "Auto" ) { + if ( mode === "no_detail" ) { mode = "feature spans"; - } else if ( mode == "summary_tree" ) { + } else if ( mode === "summary_tree" ) { mode = "coverage histogram"; } this.action_icons.mode_icon.attr("title", "Set display mode (now: Auto/" + mode + ")"); @@ -5184,7 +5184,7 @@ slot = (slots && slots[feature_uid] !== undefined ? slots[feature_uid] : null); // Draw feature if there's overlap and mode is dense or feature is slotted (as it must be for all non-dense modes). - if ( ( feature_start < view_end && feature_end > view_start ) && (this.mode == "Dense" || slot !== null) ) { + if ( ( feature_start < view_end && feature_end > view_start ) && (this.mode === "Dense" || slot !== null) ) { x_draw_coords = this.draw_element(ctx, this.mode, feature, slot, view_start, view_end, w_scale, y_scale, width); feature_mapper.map_feature_data(feature, slot, x_draw_coords[0], x_draw_coords[1]); } @@ -5389,7 +5389,7 @@ var block_thick_start = Math.max(block_start, thick_start), block_thick_end = Math.min(block_end, thick_end); ctx.fillRect(block_thick_start, y_center + 1, block_thick_end - block_thick_start, thick_height ); - if ( feature_blocks.length == 1 && mode == "Pack") { + if ( feature_blocks.length === 1 && mode === "Pack") { // Exactly one block means we have no introns, but do have a distinct "thick" region, // draw arrows over it if in pack mode if (feature_strand === "+") { @@ -5678,7 +5678,7 @@ ctx.fillText(data[0], data[1], data[2]); ctx.restore(); } - else if (type == "triangle") { + else if (type === "triangle") { drawDownwardEquilateralTriangle(ctx, data[0], data[1], data[2]); } } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Replace None with an empty string when creating tool panel Elements for installed repository tools.
by Bitbucket 30 Jan '12

30 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ebf72cda61e7/ changeset: ebf72cda61e7 user: greg date: 2012-01-30 18:41:17 summary: Replace None with an empty string when creating tool panel Elements for installed repository tools. affected #: 1 file diff -r 8092639dd35b048614cfaa444273a0458b8fa284 -r ebf72cda61e7f28c1f7311d95777902f95776501 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -284,9 +284,18 @@ owner = get_repository_owner( tmp_url ) if tool_section: root_elem = Element( 'section' ) - root_elem.attrib[ 'name' ] = tool_section.name - root_elem.attrib[ 'id' ] = tool_section.id - root_elem.attrib[ 'version' ] = tool_section.version + if tool_section.name is None: + root_elem.attrib[ 'name' ] = '' + else: + root_elem.attrib[ 'name' ] = tool_section.name + if tool_section.id is None: + root_elem.attrib[ 'id' ] = '' + else: + root_elem.attrib[ 'id' ] = tool_section.id + if tool_section.version is None: + root_elem.attrib[ 'version' ] = '' + else: + root_elem.attrib[ 'version' ] = tool_section.version for repository_tool_tup in repository_tools_tups: tool_file_path, guid, tool = repository_tool_tup if tool_section: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guru: added cacao genome to manual builds
by Bitbucket 30 Jan '12

30 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8092639dd35b/ changeset: 8092639dd35b user: guru date: 2012-01-30 18:29:39 summary: added cacao genome to manual builds affected #: 1 file diff -r f8cf58d19ea0bda386ef4cf85a365596a37c3e64 -r 8092639dd35b048614cfaa444273a0458b8fa284 tool-data/shared/ucsc/manual_builds.txt --- a/tool-data/shared/ucsc/manual_builds.txt +++ b/tool-data/shared/ucsc/manual_builds.txt @@ -704,3 +704,4 @@ Homo_sapiens_nuHg19_mtrCRS Homo sapiens (hg19 with mtDNA replaced with rCRS) chr1=249250621,chr2=243199373,chr3=198022430,chr4=191154276,chr5=180915260,chr6=171115067,chr7=159138663,chr8=146364022,chr9=141213431,chr10=135534747,chr11=135006516,chr12=133851895,chr13=115169878,chr14=107349540,chr15=102531392,chr16=90354753,chr17=81195210,chr18=78077248,chr19=59128983,chr20=63025520,chr21=48129895,chr22=51304566,chrX=155270560,chrY=59373566,chrM=16569,chr1_gl000191_random=106433,chr1_gl000192_random=547496,chr4_ctg9_hap1=590426,chr4_gl000193_random=189789,chr4_gl000194_random=191469,chr6_apd_hap1=4622290,chr6_cox_hap2=4795371,chr6_dbb_hap3=4610396,chr6_mann_hap4=4683263,chr6_mcf_hap5=4833398,chr6_qbl_hap6=4611984,chr6_ssto_hap7=4928567,chr7_gl000195_random=182896,chr8_gl000196_random=38914,chr8_gl000197_random=37175,chr9_gl000198_random=90085,chr9_gl000199_random=169874,chr9_gl000200_random=187035,chr9_gl000201_random=36148,chr11_gl000202_random=40103,chr17_ctg5_hap1=1680828,chr17_gl000203_random=37498,chr17_gl000204_random=81310,chr17_gl000205_random=174588,chr17_gl000206_random=41001,chr18_gl000207_random=4262,chr19_gl000208_random=92689,chr19_gl000209_random=159169,chr21_gl000210_random=27682,chrUn_gl000211=166566,chrUn_gl000212=186858,chrUn_gl000213=164239,chrUn_gl000214=137718,chrUn_gl000215=172545,chrUn_gl000216=172294,chrUn_gl000217=172149,chrUn_gl000218=161147,chrUn_gl000219=179198,chrUn_gl000220=161802,chrUn_gl000221=155397,chrUn_gl000222=186861,chrUn_gl000223=180455,chrUn_gl000224=179693,chrUn_gl000225=211173,chrUn_gl000226=15008,chrUn_gl000227=128374,chrUn_gl000228=129120,chrUn_gl000229=19913,chrUn_gl000230=43691,chrUn_gl000231=27386,chrUn_gl000232=40652,chrUn_gl000233=45941,chrUn_gl000234=40531,chrUn_gl000235=34474,chrUn_gl000236=41934,chrUn_gl000237=45867,chrUn_gl000238=39939,chrUn_gl000239=33824,chrUn_gl000240=41933,chrUn_gl000241=42152,chrUn_gl000242=43523,chrUn_gl000243=43341,chrUn_gl000244=39929,chrUn_gl000245=36651,chrUn_gl000246=38154,chrUn_gl000247=36422,chrUn_gl000248=39786,chrUn_gl000249=38502 Arabidopsis_thaliana_TAIR10 Arabidopsis thaliana TAIR10 (Arabidopsis_thaliana_TAIR10) chr1=30427671,chr2=19698289,chr3=23459830,chr4=18585056,chr5=26975502,chrM=366924,chrC=154478 dp4 D. pseudoobscura (dp4) +Tcacao_1.0 Theobroma cacao Dec 2010 (CIRAD/Theobroma cacao Belizian Criollo) Tc01=31268538,Tc02=27754001,Tc03=25475297,Tc04=23504306,Tc05=25651337,Tc06=15484475,Tc07=14169093,Tc08=11535834,Tc09=28459094,Tc10=15164258,Tc00=108886888 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: When storing tool panel section information for installed repository tools, make sure tool section id, name and version values are an empty string rather than None.
by Bitbucket 30 Jan '12

30 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f8cf58d19ea0/ changeset: f8cf58d19ea0 user: greg date: 2012-01-30 18:17:56 summary: When storing tool panel section information for installed repository tools, make sure tool section id, name and version values are an empty string rather than None. affected #: 3 files diff -r 016630d4fb0e9b17b41781613951ae8c89353ca2 -r f8cf58d19ea0bda386ef4cf85a365596a37c3e64 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -192,7 +192,19 @@ else: # The tool_panel_section was introduced late, so set it's value if its missing in the metadata. if section: - tool_panel_section = dict( id=section.id, version=section.version, name=section.name ) + if section.id is None: + section_id = '' + else: + section_id = section.id + if section.version is None: + section_version = '' + else: + section_version = section.version + if section.name is None: + section_name = '' + else: + section_name = section.name + tool_panel_section = dict( id=section_id, version=section_version, name=section_name ) update_needed = True else: tool_panel_section = dict( id='', version='', name='' ) diff -r 016630d4fb0e9b17b41781613951ae8c89353ca2 -r f8cf58d19ea0bda386ef4cf85a365596a37c3e64 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -166,6 +166,9 @@ datatypes_config = None # Keep track of the section in the tool panel in which this repository's tools will be contained. if tool_section_dict: + for k, v in tool_section_dict.items(): + if v is None: + tool_section_dict[ k ] = '' metadata_dict[ 'tool_panel_section' ] = tool_section_dict else: metadata_dict[ 'tool_panel_section' ] = dict( id='', version='', name='' ) @@ -604,9 +607,18 @@ distribution but are now in the main Galaxy tool shed. """ if tool_section: - section_id = tool_section.id - section_version = tool_section.version - section_name = tool_section.name + if tool_section.id is None: + section_id = '' + else: + section_id = tool_section.id + if tool_section.version is None: + section_version = '' + else: + section_version = tool_section.version + if tool_section.name is None: + section_name = '' + else: + section_name = tool_section.name else: section_id = '' section_version = '' diff -r 016630d4fb0e9b17b41781613951ae8c89353ca2 -r f8cf58d19ea0bda386ef4cf85a365596a37c3e64 templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako --- a/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako +++ b/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako @@ -81,11 +81,11 @@ <div class="toolParamHelp" style="clear: both;"> * The repository record's deleted column in the tool_shed_repository database table will be set to True. </div> + <div class="toolParamHelp" style="clear: both;"> + * The repository record's uninstalled column in the tool_shed_repository database table will be set to True. + </div> %if repository.dist_to_shed: <div class="toolParamHelp" style="clear: both;"> - * The repository record's uninstalled column in the tool_shed_repository database table will be set to True. - </div> - <div class="toolParamHelp" style="clear: both;"> * All records associated with this repository will be eliminated from the tool_id_guid_map database table. </div> %endif Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Ensure that the history export dataset is created when the job is created.
by Bitbucket 27 Jan '12

27 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/cb458aca542e/ changeset: cb458aca542e user: natefoo date: 2012-01-27 21:35:57 summary: Ensure that the history export dataset is created when the job is created. affected #: 1 file diff -r 56bdee21dc785c5f941510537978d71c4e9799c5 -r cb458aca542e67c41d1139d0356a6d09d2b12443 lib/galaxy/tools/actions/history_imp_exp.py --- a/lib/galaxy/tools/actions/history_imp_exp.py +++ b/lib/galaxy/tools/actions/history_imp_exp.py @@ -88,8 +88,8 @@ archive_dataset = trans.app.model.Dataset() trans.sa_session.add( archive_dataset ) - trans.sa_session.flush() #ensure job.id and archive_dataset.id are available + trans.app.object_store.create( archive_dataset ) # set the object store id, create dataset (if applicable) # # Setup job and job wrapper. @@ -123,4 +123,4 @@ trans.app.job_queue.put( job.id, tool ) trans.log_event( "Added export history job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id ) - return job, odict() \ No newline at end of file + return job, odict() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Fix unit tests on Python 2.5 (can't load s3_multipart_upload.py).
by Bitbucket 27 Jan '12

27 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/56bdee21dc78/ changeset: 56bdee21dc78 user: natefoo date: 2012-01-27 17:12:56 summary: Fix unit tests on Python 2.5 (can't load s3_multipart_upload.py). affected #: 1 file diff -r f9ca1c23ae7d2614c002257365d67a3eae98228e -r 56bdee21dc785c5f941510537978d71c4e9799c5 lib/galaxy/objectstore/s3_multipart_upload.py --- a/lib/galaxy/objectstore/s3_multipart_upload.py +++ b/lib/galaxy/objectstore/s3_multipart_upload.py @@ -4,13 +4,19 @@ This parallelizes the task over available cores using multiprocessing. Code mostly taken form CloudBioLinux. """ +from __future__ import with_statement + import os +import sys import glob import subprocess import contextlib import functools -import multiprocessing -from multiprocessing.pool import IMapIterator + +if sys.version_info >= (2, 6): + # this is just to prevent unit tests from failing + import multiprocessing + from multiprocessing.pool import IMapIterator from galaxy import eggs eggs.require('boto') Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: GATK: add newly introduced gatkreport datatype, currently used by variant eval.
by Bitbucket 27 Jan '12

27 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f9ca1c23ae7d/ changeset: f9ca1c23ae7d user: dan date: 2012-01-27 16:46:58 summary: GATK: add newly introduced gatkreport datatype, currently used by variant eval. affected #: 2 files diff -r d8af2f7b1f35d9ad654995e52fff6611cdbd0d2d -r f9ca1c23ae7d2614c002257365d67a3eae98228e datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -98,6 +98,7 @@ <converter file="picard_interval_list_to_bed6_converter.xml" target_datatype="bed6"/></datatype><datatype extension="gatk_interval" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/> + <datatype extension="gatk_table" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="True"/><datatype extension="gatk_dbsnp" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/><datatype extension="gatk_tranche" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/><datatype extension="gatk_recal" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"/> diff -r d8af2f7b1f35d9ad654995e52fff6611cdbd0d2d -r f9ca1c23ae7d2614c002257365d67a3eae98228e tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -1,4 +1,4 @@ -<tool id="gatk_variant_eval" name="Eval Variants" version="0.0.6"> +<tool id="gatk_variant_eval" name="Eval Variants" version="0.0.7"><description></description><requirements><requirement type="package" version="1.4">gatk</requirement> @@ -495,7 +495,7 @@ </inputs><outputs> - <data format="tabular" name="output_table" label="${tool.name} on ${on_string} (table)" /> + <data format="gatkreport" name="output_table" label="${tool.name} on ${on_string} (table)" /><data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /></outputs><tests> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Update tool test for GATK Print Reads.
by Bitbucket 26 Jan '12

26 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7d0ea2879bc9/ changeset: 7d0ea2879bc9 user: dan date: 2012-01-26 17:16:30 summary: Update tool test for GATK Print Reads. affected #: 1 file diff -r 8a440d85e13b83697220a2da4bb6f84d58027b60 -r 7d0ea2879bc9746e149e32381ea709a9aea33ff8 tools/gatk/print_reads.xml --- a/tools/gatk/print_reads.xml +++ b/tools/gatk/print_reads.xml @@ -373,7 +373,7 @@ <param name="sample_file_repeat" value="0" /><param name="sample_name_repeat" value="0" /><param name="gatk_param_type_selector" value="basic" /> - <output name="output_bam" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" sort="True"/> + <output name="output_bam" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" compare="contains"/><output name="output_log" file="gatk/gatk_print_reads/gatk_print_reads_out_1.log.contains" compare="contains" /></test></tests> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Update samtools flag stat test data.
by Bitbucket 26 Jan '12

26 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8a440d85e13b/ changeset: 8a440d85e13b user: dan date: 2012-01-26 17:09:59 summary: Update samtools flag stat test data. affected #: 1 file diff -r 8d486ca45a224bf20cca622b0c0f06f72c98ef3c -r 8a440d85e13b83697220a2da4bb6f84d58027b60 test-data/samtools_flagstat_out1.txt --- a/test-data/samtools_flagstat_out1.txt +++ b/test-data/samtools_flagstat_out1.txt @@ -1,12 +1,11 @@ -10 in total -0 QC failure -0 duplicates -10 mapped (100.00%) -0 paired in sequencing -0 read1 -0 read2 -0 properly paired (nan%) -0 with itself and mate mapped -0 singletons (nan%) -0 with mate mapped to a different chr -0 with mate mapped to a different chr (mapQ>=5) +10 + 0 in total (QC-passed reads + QC-failed reads) +0 + 0 duplicates +10 + 0 mapped (100.00%:nan%) +0 + 0 paired in sequencing +0 + 0 read1 +0 + 0 read2 +0 + 0 properly paired (nan%:nan%) +0 + 0 with itself and mate mapped +0 + 0 singletons (nan%:nan%) +0 + 0 with mate mapped to a different chr +0 + 0 with mate mapped to a different chr (mapQ>=5) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: fix bugs to (a) clear reference track when changing chromosomes and (b) to only show differences if reference data is available.
by Bitbucket 26 Jan '12

26 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8d486ca45a22/ changeset: 8d486ca45a22 user: jgoecks date: 2012-01-26 15:02:33 summary: Trackster: fix bugs to (a) clear reference track when changing chromosomes and (b) to only show differences if reference data is available. affected #: 1 file diff -r a741ad5ebd910818153c0a4fdb4331bd76da834f -r 8d486ca45a224bf20cca622b0c0f06f72c98ef3c static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -1549,6 +1549,7 @@ drawable.init(); } } + view.reference_track.init(); } if (low !== undefined && high !== undefined) { view.low = Math.max(low, 0); @@ -3876,8 +3877,9 @@ extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, { build_header_div: function() {}, init: function() { + this.data_manager.clear(); // Enable by default because there should always be data when drawing track. - this.enabled = true; + this.enabled = true; }, can_draw: Drawable.prototype.can_draw, /** @@ -5444,9 +5446,15 @@ // TODO: this can be made much more efficient by computing the complete sequence // to draw and then drawing it. for (var c = 0, str_len = seq.length; c < str_len; c++) { - if (this.prefs.show_differences && this.ref_seq) { - var ref_char = this.ref_seq[seq_start - tile_low + c]; - if (!ref_char || ref_char.toLowerCase() === seq[c].toLowerCase()) { + if (this.prefs.show_differences) { + if (this.ref_seq) { + var ref_char = this.ref_seq[seq_start - tile_low + c]; + if (!ref_char || ref_char.toLowerCase() === seq[c].toLowerCase()) { + continue; + } + } + else { + // No reference so cannot show differences. continue; } } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Add Perform Logistic Regression with vif, Compute partial R square, and Assign weighted-average to tool_conf.xml.main.
by Bitbucket 25 Jan '12

25 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a741ad5ebd91/ changeset: a741ad5ebd91 user: dan date: 2012-01-25 18:56:09 summary: Add Perform Logistic Regression with vif, Compute partial R square, and Assign weighted-average to tool_conf.xml.main. affected #: 1 file diff -r 26920e20157fccbccb7219b48db3e8e57a8e310c -r a741ad5ebd910818153c0a4fdb4331bd76da834f tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -148,6 +148,7 @@ <section name="Regional Variation" id="regVar"><tool file="regVariation/windowSplitter.xml" /><tool file="regVariation/featureCounter.xml" /> + <tool file="regVariation/WeightedAverage.xml" /><tool file="regVariation/quality_filter.xml" /><tool file="regVariation/maf_cpg_filter.xml" /><tool file="regVariation/getIndels_2way.xml" /> @@ -160,8 +161,10 @@ </section><section name="Multiple regression" id="multReg"><tool file="regVariation/linear_regression.xml" /> + <tool file="regVariation/logistic_regression_vif.xml" /><tool file="regVariation/best_regression_subsets.xml" /><tool file="regVariation/rcve.xml" /> + <tool file="regVariation/partialR_square.xml" /></section><section name="Multivariate Analysis" id="multVar"><tool file="multivariate_stats/pca.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Improve language in 'Import workflow' dialog.
by Bitbucket 25 Jan '12

25 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/26920e20157f/ changeset: 26920e20157f user: jgoecks date: 2012-01-25 18:20:50 summary: Improve language in 'Import workflow' dialog. affected #: 1 file diff -r c60760713d26558d6733367709433d8eefbd64ca -r 26920e20157fccbccb7219b48db3e8e57a8e310c templates/workflow/import.mako --- a/templates/workflow/import.mako +++ b/templates/workflow/import.mako @@ -26,24 +26,24 @@ ${render_msg( message, status )} %endif <div class="toolForm"> - <div class="toolFormTitle">Import an exported Galaxy workflow file</div> + <div class="toolFormTitle">Import Galaxy workflow</div><div class="toolFormBody"><form name="import_workflow" id="import_workflow" action="${h.url_for( controller='workflow', action='import_workflow' )}" enctype="multipart/form-data" method="POST"><div class="form-row"> - <label>URL for exported Galaxy workflow:</label> + <label>Galaxy workflow URL:</label><input type="text" name="url" value="${url}" size="40"><div class="toolParamHelp" style="clear: both;"> - If the workflow is accessible via an URL, enter the URL above and click the <b>Import</b> button. + If the workflow is accessible via a URL, enter the URL above and click <b>Import</b>. </div><div style="clear: both"></div></div><div class="form-row"> - <label>Exported Galaxy workflow file:</label> + <label>Galaxy workflow file:</label><div class="form-row-input"><input type="file" name="file_data"/></div><div class="toolParamHelp" style="clear: both;"> - If the workflow is stored locally in a file, browse and select it and then click the <b>Import</b> button. + If the workflow is in a file on your computer, choose it and then click <b>Import</b>. </div><div style="clear: both"></div></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Fix for Input Dataset datatype filtering regression introduced in 6329:ab90893a7cf5.
by Bitbucket 25 Jan '12

25 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c60760713d26/ changeset: c60760713d26 user: dannon date: 2012-01-25 18:12:05 summary: Fix for Input Dataset datatype filtering regression introduced in 6329:ab90893a7cf5. Input Dataset steps will now again properly filter appropriate input datasets based on subsequent tool input types. affected #: 2 files diff -r f9da9ca5ccae7ead780d0331102cda204e38d646 -r c60760713d26558d6733367709433d8eefbd64ca lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -486,7 +486,7 @@ return value def get_initial_value( self, trans, context ): return None - + class HiddenToolParameter( ToolParameter ): """ Parameter that takes one of two values. @@ -816,7 +816,7 @@ for t, v, s in options: if v in value: rval.append( t ) - return "\n".join( rval ) + suffix + return "\n".join( rval ) + suffix def get_dependencies( self ): """ Get the *names* of the other params this param depends on. @@ -1326,7 +1326,7 @@ Nate's next pass at the dataset security stuff will dramatically alter this anyway. """ - def __init__( self, tool, elem ): + def __init__( self, tool, elem, trans=None): ToolParameter.__init__( self, tool, elem ) # Add metadata validator if not string_as_bool( elem.get( 'no_validation', False ) ): @@ -1337,11 +1337,16 @@ for extension in self.extensions: extension = extension.strip() if tool is None: - #This occurs for things such as unit tests - import galaxy.datatypes.registry - datatypes_registry = galaxy.datatypes.registry.Registry() - datatypes_registry.load_datatypes() - formats.append( datatypes_registry.get_datatype_by_extension( extension.lower() ).__class__ ) + if trans: + # Must account for "Input Dataset" types, which while not a tool still need access to the real registry. + # A handle to the transaction (and thus app) will be given by the module. + formats.append( trans.app.datatypes_registry.get_datatype_by_extension( extension.lower() ).__class__ ) + else: + #This occurs for things such as unit tests + import galaxy.datatypes.registry + datatypes_registry = galaxy.datatypes.registry.Registry() + datatypes_registry.load_datatypes() + formats.append( datatypes_registry.get_datatype_by_extension( extension.lower() ).__class__ ) else: formats.append( tool.app.datatypes_registry.get_datatype_by_extension( extension.lower() ).__class__ ) self.formats = tuple( formats ) diff -r f9da9ca5ccae7ead780d0331102cda204e38d646 -r c60760713d26558d6733367709433d8eefbd64ca lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -134,7 +134,7 @@ def get_runtime_inputs( self, filter_set=['data'] ): label = self.state.get( "name", "Input Dataset" ) - return dict( input=DataToolParameter( None, Element( "param", name="input", label=label, multiple=True, type="data", format=', '.join(filter_set) ) ) ) + return dict( input=DataToolParameter( None, Element( "param", name="input", label=label, multiple=True, type="data", format=', '.join(filter_set) ), self.trans ) ) def get_runtime_state( self ): state = DefaultToolState() state.inputs = dict( input=None ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Make additional files output by SamToFastq when using read groups be fastqsanger format instead of just fastq.
by Bitbucket 25 Jan '12

25 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f9da9ca5ccae/ changeset: f9da9ca5ccae user: dan date: 2012-01-25 18:11:27 summary: Make additional files output by SamToFastq when using read groups be fastqsanger format instead of just fastq. affected #: 1 file diff -r fd6f22c072f3b2acbde3311943af004f1094a4fa -r f9da9ca5ccae7ead780d0331102cda204e38d646 tools/picard/picard_SamToFastq_wrapper.py --- a/tools/picard/picard_SamToFastq_wrapper.py +++ b/tools/picard/picard_SamToFastq_wrapper.py @@ -80,13 +80,13 @@ shutil.move( os.path.join( tmp_dir, filename ), fastq_1_name ) fastq_1_name = None else: - shutil.move( os.path.join( tmp_dir, filename ), os.path.join( options.new_files_path, 'primary_%s_%s - 1_visible_fastq' % ( file_id_1, filename[:-len( '_1.fastq' )] ) ) ) + shutil.move( os.path.join( tmp_dir, filename ), os.path.join( options.new_files_path, 'primary_%s_%s - 1_visible_fastqsanger' % ( file_id_1, filename[:-len( '_1.fastq' )] ) ) ) elif filename.endswith( '_2.fastq' ): if fastq_2_name: shutil.move( os.path.join( tmp_dir, filename ), fastq_2_name ) fastq_2_name = None else: - shutil.move( os.path.join( tmp_dir, filename ), os.path.join( options.new_files_path, 'primary_%s_%s - 2_visible_fastq' % ( file_id_2, filename[:-len( '_2.fastq' )] ) ) ) + shutil.move( os.path.join( tmp_dir, filename ), os.path.join( options.new_files_path, 'primary_%s_%s - 2_visible_fastqsanger' % ( file_id_2, filename[:-len( '_2.fastq' )] ) ) ) cleanup_before_exit( tmp_dir ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: In addition to deactivating / reactivating installed tool shed repositories, add the ability to uninstall / reinstall installed tool shed repositories. Uninstalling and reinstalling will affect the repository on disk as well as the tool config files in which the tool shed repostory's tools are defined. Reinstalling a tool shed repository will currently load it's tools into the same location in the tool panel in which the tools were originally located prior to un
by Bitbucket 25 Jan '12

25 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fd6f22c072f3/ changeset: fd6f22c072f3 user: greg date: 2012-01-25 17:17:04 summary: In addition to deactivating / reactivating installed tool shed repositories, add the ability to uninstall / reinstall installed tool shed repositories. Uninstalling and reinstalling will affect the repository on disk as well as the tool config files in which the tool shed repostory's tools are defined. Reinstalling a tool shed repository will currently load it's tools into the same location in the tool panel in which the tools were originally located prior to uninstalling the repository. Installing / uninstalling / deactivating / activating work for tools sheds that were installed either manually be a Galaxy admin or automatically installed by the Galaxy installation manager for those repositories that contain tools tha tused to be in the Galaxy distribution but have since been moved to the main Galaxy tool shed. affected #: 7 files diff -r 9d392eaca847bf26a8383babacc3c94e5a1bab9e -r fd6f22c072f3b2acbde3311943af004f1094a4fa lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2663,7 +2663,8 @@ class ToolShedRepository( object ): def __init__( self, id=None, create_time=None, tool_shed=None, name=None, description=None, owner=None, installed_changeset_revision=None, - changeset_revision=None, metadata=None, includes_datatypes=False, update_available=False, deleted=False ): + changeset_revision=None, metadata=None, includes_datatypes=False, update_available=False, deleted=False, uninstalled=False, + dist_to_shed=False ): self.id = id self.create_time = create_time self.tool_shed = tool_shed @@ -2676,6 +2677,14 @@ self.includes_datatypes = includes_datatypes self.update_available = update_available self.deleted = deleted + self.uninstalled = uninstalled + self.dist_to_shed = dist_to_shed + @property + def includes_tools( self ): + return 'tools' in self.metadata + @property + def includes_workflows( self ): + return 'workflows' in self.metadata class ToolIdGuidMap( object ): def __init__( self, id=None, create_time=None, tool_id=None, tool_version=None, tool_shed=None, repository_owner=None, repository_name=None, guid=None ): diff -r 9d392eaca847bf26a8383babacc3c94e5a1bab9e -r fd6f22c072f3b2acbde3311943af004f1094a4fa lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -378,7 +378,9 @@ Column( "metadata", JSONType, nullable=True ), Column( "includes_datatypes", Boolean, index=True, default=False ), Column( "update_available", Boolean, default=False ), - Column( "deleted", Boolean, index=True, default=False ) ) + Column( "deleted", Boolean, index=True, default=False ), + Column( "uninstalled", Boolean, default=False ), + Column( "dist_to_shed", Boolean, default=False ) ) ToolIdGuidMap.table = Table( "tool_id_guid_map", metadata, Column( "id", Integer, primary_key=True ), diff -r 9d392eaca847bf26a8383babacc3c94e5a1bab9e -r fd6f22c072f3b2acbde3311943af004f1094a4fa lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py @@ -0,0 +1,64 @@ +""" +Migration script to add the uninstalled and dist_to_shed columns to the tool_shed_repository table. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +def upgrade(): + print __doc__ + metadata.reflect() + ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True ) + c = Column( "uninstalled", Boolean, default=False ) + try: + c.create( ToolShedRepository_table ) + assert c is ToolShedRepository_table.c.uninstalled + if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': + default_false = "0" + elif migrate_engine.name == 'postgres': + default_false = "false" + db_session.execute( "UPDATE tool_shed_repository SET uninstalled=%s" % default_false ) + except Exception, e: + print "Adding uninstalled column to the tool_shed_repository table failed: %s" % str( e ) + c = Column( "dist_to_shed", Boolean, default=False ) + try: + c.create( ToolShedRepository_table ) + assert c is ToolShedRepository_table.c.dist_to_shed + if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': + default_false = "0" + elif migrate_engine.name == 'postgres': + default_false = "false" + db_session.execute( "UPDATE tool_shed_repository SET dist_to_shed=%s" % default_false ) + except Exception, e: + print "Adding dist_to_shed column to the tool_shed_repository table failed: %s" % str( e ) + +def downgrade(): + metadata.reflect() + ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True ) + try: + ToolShedRepository_table.c.uninstalled.drop() + except Exception, e: + print "Dropping column uninstalled from the tool_shed_repository table failed: %s" % str( e ) + try: + ToolShedRepository_table.c.dist_to_shed.drop() + except Exception, e: + print "Dropping column dist_to_shed from the tool_shed_repository table failed: %s" % str( e ) diff -r 9d392eaca847bf26a8383babacc3c94e5a1bab9e -r fd6f22c072f3b2acbde3311943af004f1094a4fa lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -94,9 +94,9 @@ tool_shed=self.tool_shed, tool_section=tool_section, shed_tool_conf=self.install_tool_config, - new_install=True ) - # Add a new record to the tool_id_guid_map table for each - # tool in the repository if one doesn't already exist. + new_install=True, + dist_to_shed=True ) + # Add a new record to the tool_id_guid_map table for each tool in the repository if one doesn't already exist. if 'tools' in metadata_dict: tools_mapped = 0 for tool_dict in metadata_dict[ 'tools' ]: diff -r 9d392eaca847bf26a8383babacc3c94e5a1bab9e -r fd6f22c072f3b2acbde3311943af004f1094a4fa lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -79,8 +79,11 @@ tool_dicts=tool_dicts, converter_path=converter_path, display_path=display_path ) -def create_or_update_tool_shed_repository( app, name, description, changeset_revision, repository_clone_url, metadata_dict, owner='' ): - # This method is used by the InstallManager, which does not have access to trans. +def create_or_update_tool_shed_repository( app, name, description, changeset_revision, repository_clone_url, metadata_dict, owner='', dist_to_shed=False ): + # This method is used by the InstallManager, which does not have access to trans. The + # received value for dist_to_shed will be True if the InstallManager is installing a repository + # that contains tools or datatypes that used to be in the Galaxy distribution, but have been + # moved to the main Galaxy tool shed. sa_session = app.model.context.current tmp_url = clean_repository_clone_url( repository_clone_url ) tool_shed = tmp_url.split( 'repos' )[ 0 ].rstrip( '/' ) @@ -94,6 +97,7 @@ tool_shed_repository.metadata = metadata_dict tool_shed_repository.includes_datatypes = includes_datatypes tool_shed_repository.deleted = False + tool_shed_repository.uninstalled = False else: tool_shed_repository = app.model.ToolShedRepository( tool_shed=tool_shed, name=name, @@ -102,7 +106,8 @@ installed_changeset_revision=changeset_revision, changeset_revision=changeset_revision, metadata=metadata_dict, - includes_datatypes=includes_datatypes ) + includes_datatypes=includes_datatypes, + dist_to_shed=dist_to_shed ) sa_session.add( tool_shed_repository ) sa_session.flush() def generate_datatypes_metadata( datatypes_config, metadata_dict ): @@ -584,16 +589,20 @@ app.datatypes_registry.load_datatypes( root_dir=app.config.root, config=datatypes_config, imported_modules=imported_modules, deactivate=deactivate ) return converter_path, display_path def load_repository_contents( app, repository_name, description, owner, changeset_revision, tool_path, repository_clone_url, relative_install_dir, - current_working_dir, tmp_name, tool_shed=None, tool_section=None, shed_tool_conf=None, new_install=True ): - # This method is used by the InstallManager, which does not have access to trans. - # Generate the metadata for the installed tool shed repository. It is imperative that - # the installed repository is updated to the desired changeset_revision before metadata - # is set because the process for setting metadata uses the repository files on disk. This - # method is called when new tools have been installed (in which case values should be received - # for tool_section and shed_tool_conf, and new_install should be left at it's default value) - # and when updates have been pulled to previously installed repositories (in which case the - # default value None is set for tool_section and shed_tool_conf, and the value of new_install - # is passed as False). + current_working_dir, tmp_name, tool_shed=None, tool_section=None, shed_tool_conf=None, new_install=True, dist_to_shed=False ): + """ + This method is used by the InstallManager (which does not have access to trans), to generate the metadata + for the installed tool shed repository, among other things. It is imperative that the installed repository + is updated to the desired changeset_revision before metadata is set because the process for setting metadata + uses the repository files on disk. This method is called when new tools have been installed (in which case + values should be received for tool_section and shed_tool_conf, and new_install should be left at it's default + value) and when updates have been pulled to previously installed repositories (in which case the default value + None is set for tool_section and shed_tool_conf, and the value of new_install is passed as False). When a new + install is being done by the InstallManager (and not a user manually installing a repository from the Admin + perspective), the value of dist_to_shed will be set to True, enabling determinatin of which installed repositories + resulted from the InstallManager installing a repository that contains tools that used to be in the Galaxy + distribution but are now in the main Galaxy tool shed. + """ if tool_section: section_id = tool_section.id section_version = tool_section.version @@ -604,6 +613,17 @@ section_name = '' tool_section_dict = dict( id=section_id, version=section_version, name=section_name ) metadata_dict = generate_metadata( app.toolbox, relative_install_dir, repository_clone_url, tool_section_dict=tool_section_dict ) + # Add a new record to the tool_shed_repository table if one doesn't already exist. If one exists but is marked + # deleted, undelete it. It is imperative that this happens before the call to alter_tool_panel() below because + # tools will not be properly loaded if the repository is marked deleted. + log.debug( "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % repository_name ) + create_or_update_tool_shed_repository( app, + repository_name, + description, + changeset_revision, + repository_clone_url, + metadata_dict, + dist_to_shed=dist_to_shed ) if 'tools' in metadata_dict: repository_tools_tups = get_repository_tools_tups( app, metadata_dict ) if repository_tools_tups: @@ -615,20 +635,22 @@ # Handle tools that use fabric scripts to install dependencies. handle_tool_dependencies( current_working_dir, relative_install_dir, repository_tools_tups ) if new_install: - load_altered_part_of_tool_panel( app=app, - repository_name=repository_name, - repository_clone_url=repository_clone_url, - changeset_revision=changeset_revision, - repository_tools_tups=repository_tools_tups, - tool_section=tool_section, - shed_tool_conf=shed_tool_conf, - tool_path=tool_path, - owner=owner, - deactivate=False ) - else: - if app.toolbox_search.enabled: - # If search support for tools is enabled, index the new installed tools. - app.toolbox_search = ToolBoxSearch( app.toolbox ) + alter_tool_panel( app=app, + repository_name=repository_name, + repository_clone_url=repository_clone_url, + changeset_revision=changeset_revision, + repository_tools_tups=repository_tools_tups, + tool_section=tool_section, + shed_tool_conf=shed_tool_conf, + tool_path=tool_path, + owner=owner, + new_install=new_install, + deactivate=False, + uninstall=False ) + elif app.toolbox_search.enabled: + # If search support for tools is enabled, index the new installed tools. In the + # condition above, this happens in the alter_tool_panel() method. + app.toolbox_search = ToolBoxSearch( app.toolbox ) # Remove the temporary file try: os.unlink( tmp_name ) @@ -653,16 +675,15 @@ if display_path: # Load proprietary datatype display applications app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict ) - # Add a new record to the tool_shed_repository table if one doesn't - # already exist. If one exists but is marked deleted, undelete it. - log.debug( "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % repository_name ) - create_or_update_tool_shed_repository( app, repository_name, description, changeset_revision, repository_clone_url, metadata_dict ) return metadata_dict -def load_altered_part_of_tool_panel( app, repository_name, repository_clone_url, changeset_revision, repository_tools_tups, - tool_section, shed_tool_conf, tool_path, owner, deactivate=False ): - # We'll be changing the contents of the shed_tool_conf file on disk, so we need to - # make the same changes to the in-memory version of that file, which is stored in - # the config_elems entry in the shed_tool_conf_dict associated with the file. +def alter_tool_panel( app, repository_name, repository_clone_url, changeset_revision, repository_tools_tups, tool_section, + shed_tool_conf, tool_path, owner, new_install=True, deactivate=False, uninstall=False ): + """ + A tool shed repository is being installed / updated / deactivated / uninstalled, + so handle tool panel alterations accordingly. + """ + # We need to change the in-memory version of the shed_tool_conf file, which is stored in the config_elems entry + # in the shed_tool_conf_dict associated with the file. for index, shed_tool_conf_dict in enumerate( app.toolbox.shed_tool_confs ): config_filename = shed_tool_conf_dict[ 'config_filename' ] if config_filename == shed_tool_conf: @@ -673,29 +694,91 @@ if tail == shed_tool_conf: config_elems = shed_tool_conf_dict[ 'config_elems' ] break - # Generate a new entry for the tool config. + # Geneate the list of ElementTree Element objects for each section or list of tools. elem_list = generate_tool_panel_elem_list( repository_name, repository_clone_url, changeset_revision, repository_tools_tups, tool_section=tool_section, owner=owner ) - if tool_section: - for section_elem in elem_list: - # Load the section into the tool panel. - app.toolbox.load_section_tag_set( section_elem, app.toolbox.tool_panel, tool_path ) + if deactivate: + # Remove appropriate entries from the shed_tool_conf file on disk. We first create an list of + # guids for all tools that will be removed from the tool config. + tool_elements_removed = 0 + guids_to_remove = [ repository_tool_tup[1] for repository_tool_tup in repository_tools_tups ] + if tool_section: + # Remove all appropriate tool sub-elements from the section element. + for section_elem in elem_list: + section_elem_id = section_elem.get( 'id' ) + section_elem_name = section_elem.get( 'name' ) + section_elem_version = section_elem.get( 'version' ) + for config_elem in config_elems: + config_elems_to_remove = [] + if config_elem.tag == 'section' and \ + config_elem.get( 'id' ) == section_elem_id and \ + config_elem.get( 'name' ) == section_elem_name and \ + config_elem.get( 'version' ) == section_elem_version: + # We've located the section element in the in-memory list of config_elems, so we can remove + # all of the appropriate tools sub-elements from the section. + tool_elems_to_remove = [] + for tool_elem in config_elem: + tool_elem_guid = tool_elem.get( 'guid' ) + if tool_elem_guid in guids_to_remove: + tool_elems_to_remove.append( tool_elem ) + for tool_elem in tool_elems_to_remove: + # Remove all of the appropriate tool sub-elements from the section element. + tool_elem_guid = tool_elem.get( 'guid' ) + config_elem.remove( tool_elem ) + log.debug( "Removed tool with guid '%s'." % str( tool_elem_guid ) ) + tool_elements_removed += 1 + if len( config_elem ) < 1: + # Keep a list of all empty section elements so they can be removed. + config_elems_to_remove.append( config_elem ) + if tool_elements_removed == len( guids_to_remove ): + break + for config_elem in config_elems_to_remove: + # The section element includes no tool sub-elements, so remove it. + config_elems.remove( config_elem ) + log.debug( "Removed section with id '%s'." % str( section_elem_id ) ) + if tool_elements_removed == len( guids_to_remove ): + break + else: + # Remove all appropriate tool elements from the root (tools are outside of any sections). + tool_elems_to_remove = [] + for tool_elem in elem_list: + tool_elem_guid = tool_elem.get( 'guid' ) + for config_elem in config_elems: + if config_elem.tag == 'tool' and config_elem.get( 'guid' ) == tool_elem_guid: + tool_elems_to_remove.append( tool_elem ) + for config_elem in config_elems: + for tool_elem in tool_elems_to_remove: + try: + # Remove the tool element from the in-memory list of config_elems. + config_elem.remove( tool_elem ) + log.debug( "Removed tool with guid '%s'." % str( tool_elem_guid ) ) + except: + # The tool_elem is not a sub-element of the current config_elem. + pass else: - # Load the tools into the tool panel outside of any sections. - for tool_elem in elem_list: - guid = tool_elem.get( 'guid' ) - app.toolbox.load_tool_tag_set( tool_elem, app.toolbox.tool_panel, tool_path=tool_path, guid=guid ) - if not deactivate: - # Append the new entry (either section or list of tools) to the shed_tool_config file, - # and add the xml element to the in-memory list of config_elems. - for elem_entry in elem_list: - config_elems.append( elem_entry ) - shed_tool_conf_dict[ 'config_elems' ] = config_elems - app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict + # Generate a new entry for the tool config. + if tool_section: + for section_elem in elem_list: + # Load the section into the tool panel. + app.toolbox.load_section_tag_set( section_elem, app.toolbox.tool_panel, tool_path ) + else: + # Load the tools into the tool panel outside of any sections. + for tool_elem in elem_list: + guid = tool_elem.get( 'guid' ) + app.toolbox.load_tool_tag_set( tool_elem, app.toolbox.tool_panel, tool_path=tool_path, guid=guid ) + if new_install: + # Append the new entry (either section or list of tools) to the shed_tool_config file, + # and add the xml element to the in-memory list of config_elems. + for elem_entry in elem_list: + config_elems.append( elem_entry ) + shed_tool_conf_dict[ 'config_elems' ] = config_elems + app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict + if uninstall or not deactivate: + # Persist the altered in-memory version of the tool config. config_elems_to_xml_file( app, shed_tool_conf_dict ) if app.toolbox_search.enabled: # If search support for tools is enabled, index the new installed tools. diff -r 9d392eaca847bf26a8383babacc3c94e5a1bab9e -r fd6f22c072f3b2acbde3311943af004f1094a4fa lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -280,7 +280,8 @@ tool_shed=tool_shed, tool_section=tool_section, shed_tool_conf=shed_tool_conf, - new_install=True ) + new_install=True, + dist_to_shed=False ) installed_repository_names.append( name ) else: tmp_stderr = open( tmp_name, 'rb' ) @@ -332,57 +333,81 @@ @web.expose @web.require_admin def deactivate_or_uninstall_repository( self, trans, **kwd ): - # TODO: handle elimination of workflows loaded into the tool panel that are in the repository being deactivated. params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) remove_from_disk = params.get( 'remove_from_disk', '' ) remove_from_disk_checked = CheckboxField.is_checked( remove_from_disk ) repository = get_repository( trans, kwd[ 'id' ] ) + shed_tool_conf, tool_path, relative_install_dir = self.__get_tool_path_and_relative_install_dir( trans, repository ) if params.get( 'deactivate_or_uninstall_repository_button', False ): - # Deatcivate repository tools. - shed_tool_conf, tool_path, relative_install_dir = self.__get_tool_path_and_relative_install_dir( trans, repository ) metadata = repository.metadata - repository_tools_tups = get_repository_tools_tups( trans.app, metadata ) - # Generate the list of tool panel keys derived from the tools included in the repository. - repository_tool_panel_keys = [] - if repository_tools_tups: - repository_tool_panel_keys = [ 'tool_%s' % repository_tools_tup[ 1 ] for repository_tools_tup in repository_tools_tups ] - tool_panel_section = metadata[ 'tool_panel_section' ] - section_id = tool_panel_section[ 'id' ] - if section_id in [ '' ]: - # If the repository includes tools, they were loaded into the tool panel outside of any sections. - tool_section = None - self.__deactivate( trans, repository_tool_panel_keys ) - else: - # If the repository includes tools, they were loaded into the tool panel inside a section. - section_key = 'section_%s' % str( section_id ) - if section_key in trans.app.toolbox.tool_panel: - tool_section = trans.app.toolbox.tool_panel[ section_key ] - self.__deactivate( trans, repository_tool_panel_keys, tool_section=tool_section, section_key=section_key ) + if repository.includes_tools: + # Deactivate repository tools. + repository_tools_tups = get_repository_tools_tups( trans.app, metadata ) + # Generate the list of tool panel keys derived from the tools included in the repository. + repository_tool_panel_keys = [] + if repository_tools_tups: + repository_tool_panel_keys = [ 'tool_%s' % repository_tools_tup[ 1 ] for repository_tools_tup in repository_tools_tups ] + tool_panel_section = metadata[ 'tool_panel_section' ] + section_id = tool_panel_section[ 'id' ] + if section_id in [ '' ]: + # If the repository includes tools, they were loaded into the tool panel outside of any sections. + tool_section = None + self.__remove_tools_from_tool_panel( trans, repository_tool_panel_keys ) else: - # The tool panel section could not be found, so handle deactivating tools - # as if they were loaded into the tool panel outside of any sections. - tool_section = None - self.__deactivate( trans, repository_tool_panel_keys ) + # If the repository includes tools, they were loaded into the tool panel inside a section. + section_key = 'section_%s' % str( section_id ) + if section_key in trans.app.toolbox.tool_panel: + tool_section = trans.app.toolbox.tool_panel[ section_key ] + self.__remove_tools_from_tool_panel( trans, repository_tool_panel_keys, tool_section=tool_section, section_key=section_key ) + else: + # The tool panel section could not be found, so handle deactivating tools + # as if they were loaded into the tool panel outside of any sections. + tool_section = None + self.__remove_tools_from_tool_panel( trans, repository_tool_panel_keys ) + repository_clone_url = self.__generate_clone_url( trans, repository ) + # The repository is either being deactivated or uninstalled, so handle tool panel alterations accordingly. + # If the repository is being uninstalled, the appropriate tools or tool sections will be removed from the + # appropriate tool config file on disk. + alter_tool_panel( app=trans.app, + repository_name=repository.name, + repository_clone_url=repository_clone_url, + changeset_revision=repository.installed_changeset_revision, + repository_tools_tups=repository_tools_tups, + tool_section=tool_section, + shed_tool_conf=shed_tool_conf, + tool_path=tool_path, + owner=repository.owner, + new_install=False, + deactivate=True, + uninstall=remove_from_disk_checked ) + if repository.includes_datatypes: + # Deactivate proprietary datatypes. + load_datatype_items( trans.app, repository, relative_install_dir, deactivate=True ) + if remove_from_disk_checked: + # Remove the repository from disk. + try: + shutil.rmtree( relative_install_dir ) + log.debug( "Removed repository installation directory: %s" % str( relative_install_dir ) ) + except Exception, e: + log.debug( "Error removing repository installation directory %s: %s" % ( str( relative_install_dir ), str( e ) ) ) + # If the repository was installed by the InstallManager, remove + # all appropriate rows from the tool_id_guid_map database table. + if repository.dist_to_shed: + count = 0 + for tool_id_guid_map in trans.sa_session.query( trans.model.ToolIdGuidMap ) \ + .filter( and_( trans.model.ToolIdGuidMap.table.c.tool_shed==repository.tool_shed, + trans.model.ToolIdGuidMap.table.c.repository_owner==repository.owner, + trans.model.ToolIdGuidMap.table.c.repository_name==repository.name ) ): + trans.sa_session.delete( tool_id_guid_map ) + count += 1 + log.debug( "Removed %d rows from the tool_id_guid_map database table." % count ) + repository.uninstalled = True repository.deleted = True trans.sa_session.add( repository ) trans.sa_session.flush() - repository_clone_url = self.__generate_clone_url( trans, repository ) - load_altered_part_of_tool_panel( app=trans.app, - repository_name=repository.name, - repository_clone_url=repository_clone_url, - changeset_revision=repository.installed_changeset_revision, - repository_tools_tups=repository_tools_tups, - tool_section=tool_section, - shed_tool_conf=shed_tool_conf, - tool_path=tool_path, - owner=repository.owner, - deactivate=True ) - # Deactivate proprietary datatypes. - load_datatype_items( trans.app, repository, relative_install_dir, deactivate=True ) if remove_from_disk_checked: - # TODO: Remove repository from disk and alter the shed tool config. message = 'The repository named <b>%s</b> has been uninstalled.' % repository.name else: message = 'The repository named <b>%s</b> has been deactivated.' % repository.name @@ -397,10 +422,10 @@ remove_from_disk_check_box=remove_from_disk_check_box, message=message, status=status ) - def __deactivate( self, trans, repository_tool_panel_keys, tool_section=None, section_key=None ): - # Delete tools loaded into the tool panel. If the tool_panel is received, - # the tools were loaded into the tool panel outside of any sections. If - # the tool_section is received, all tools were loaded into that section. + def __remove_tools_from_tool_panel( self, trans, repository_tool_panel_keys, tool_section=None, section_key=None ): + # Delete tools loaded into the tool panel by altering the in-memory tool_panel dictionary appropriately. If the + # tool_section is not received, the tools were loaded into the tool_panel dictionary outside of any sections. + # Otherwise all tools were loaded into the received tool_section. if tool_section: # The tool_section.elems dictionary looks something like: # {'tool_gvk.bx.psu.edu:9009/repos/test/filter/Filter1/1.0.1': <galaxy.tools.Tool instance at 0x10769ae60>} @@ -418,61 +443,146 @@ @web.expose @web.require_admin def activate_or_reinstall_repository( self, trans, **kwd ): - # TODO: handle re-introduction of workflows loaded into the tool panel that are in the repository being activated. repository = get_repository( trans, kwd[ 'id' ] ) - repository.deleted = False - trans.sa_session.add( repository ) - trans.sa_session.flush() shed_tool_conf, tool_path, relative_install_dir = self.__get_tool_path_and_relative_install_dir( trans, repository ) - metadata = repository.metadata - repository_tools_tups = get_repository_tools_tups( trans.app, metadata ) - tool_panel_section = metadata[ 'tool_panel_section' ] - section_id = tool_panel_section[ 'id' ] - if section_id in [ '' ]: - # If the repository includes tools, reload them into the tool panel outside of any sections. - self.__activate( trans, repository, repository_tools_tups, tool_section=None, section_key=None ) + uninstalled = repository.uninstalled + if uninstalled: + if repository.dist_to_shed: + href = '<a href="http://wiki.g2.bx.psu.edu/Tool%20Shed#Migrating_tools_from_the_Galaxy_distr…" ' + href += 'target="_blank">in this section of the Galaxy Tool Shed wiki</a>' + message = "The <b>%s</b> repository should be reinstalled using the approach described %s. " % ( repository.name, href ) + message += "If <b>enable_tool_shed_install = True</b> and the contents of the file configured for the " + message += "<b>tool_shed_install_config_file</b> setting in your universe_wsgi.ini file enable installation of the " + message += "<b>%s</b> repository, then restarting your Galaxy server will reinstall the repository." % repository.name + new_kwd = {} + new_kwd[ 'sort' ] = 'name' + new_kwd[ 'f-deleted' ] = 'True' + new_kwd[ 'message' ] = message + new_kwd[ 'status' ] = 'error' + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='browse_repositories', + **new_kwd ) ) + else: + current_working_dir = os.getcwd() + repository_clone_url = self.__generate_clone_url( trans, repository ) + clone_dir = os.path.join( tool_path, self.__generate_tool_path( repository_clone_url, repository.installed_changeset_revision ) ) + relative_install_dir = os.path.join( clone_dir, repository.name ) + returncode, tmp_name = clone_repository( repository.name, clone_dir, current_working_dir, repository_clone_url ) + if returncode == 0: + returncode, tmp_name = update_repository( current_working_dir, relative_install_dir, repository.installed_changeset_revision ) + if returncode == 0: + # Get the location in the tool panel in which the tool was originally loaded. + metadata = repository.metadata + tool_panel_section = metadata[ 'tool_panel_section' ] + original_section_id = tool_panel_section[ 'id' ] + original_section_name = tool_panel_section[ 'name' ] + if original_section_id in [ '' ]: + tool_section = None + else: + section_key = 'section_%s' % str( original_section_id ) + if section_key in trans.app.toolbox.tool_panel: + tool_section = trans.app.toolbox.tool_panel[ section_key ] + else: + # The section in which the tool was originally loaded used to be in the tool panel, but no longer is. + elem = Element( 'section' ) + elem.attrib[ 'name' ] = original_section_name + elem.attrib[ 'id' ] = original_section_id + elem.attrib[ 'version' ] = '' + tool_section = tools.ToolSection( elem ) + trans.app.toolbox.tool_panel[ section_key ] = tool_section + metadata_dict = load_repository_contents( app=trans.app, + repository_name=repository.name, + description=repository.description, + owner=repository.owner, + changeset_revision=repository.installed_changeset_revision, + tool_path=tool_path, + repository_clone_url=repository_clone_url, + relative_install_dir=relative_install_dir, + current_working_dir=current_working_dir, + tmp_name=tmp_name, + tool_shed=repository.tool_shed, + tool_section=tool_section, + shed_tool_conf=shed_tool_conf, + new_install=True, + dist_to_shed=False ) + repository.uninstalled = False + repository.deleted = False + trans.sa_session.add( repository ) + trans.sa_session.flush() else: - # If the repository includes tools, reload them into the appropriate tool panel section. - section_key = 'section_%s' % str( section_id ) - if section_key in trans.app.toolbox.tool_panel: - # Load the repository tools into a section that still exists in the tool panel. - tool_section = trans.app.toolbox.tool_panel[ section_key ] - self.__activate( trans, repository, repository_tools_tups, tool_section=tool_section, section_key=section_key ) - else: - # Load the repository tools into a section that no longer exists in the tool panel. - # We first see if the section exists in the tool config, which will be the case if - # the repository was only deactivated and not uninstalled. - section_loaded = False - for tcf in trans.app.config.tool_configs: - # Only inspect tool configs that contain installed tool shed repositories. - if tcf not in [ 'tool_conf.xml' ]: - log.info( "Parsing the tool configuration %s" % tcf ) - tree = util.parse_xml( tcf ) - root = tree.getroot() - tool_path = root.get( 'tool_path' ) - if tool_path is not None: - # Tool configs that contain tools installed from tool shed repositories - # must have a tool_path attribute. - for elem in root: - if elem.tag == 'section': - id_attr = elem.get( 'id' ) - if id_attr == section_id: - tool_section = elem - # Load the tools. - trans.app.toolbox.load_section_tag_set( tool_section, trans.app.toolbox.tool_panel, tool_path ) - section_loaded = True + # The repository was deactivated, but not uninstalled. + repository.deleted = False + trans.sa_session.add( repository ) + trans.sa_session.flush() + if repository.includes_tools: + metadata = repository.metadata + repository_tools_tups = get_repository_tools_tups( trans.app, metadata ) + guids_to_activate = [ repository_tool_tup[1] for repository_tool_tup in repository_tools_tups ] + tool_panel_section = metadata[ 'tool_panel_section' ] + original_section_id = tool_panel_section[ 'id' ] + if original_section_id in [ '' ]: + # If the repository includes tools, reload them into the tool panel outside of any sections. + self.__add_tools_to_tool_panel( trans, repository, repository_tools_tups, tool_section=None, section_key=None ) + else: + original_section_id = tool_panel_section[ 'id' ] + original_section_name = tool_panel_section[ 'name' ] + original_section_version = tool_panel_section[ 'version' ] + # If the repository includes tools, reload them into the appropriate tool panel section. + section_key = 'section_%s' % str( original_section_id ) + if section_key in trans.app.toolbox.tool_panel: + # Load the repository tools into a section that still exists in the tool panel. + tool_section = trans.app.toolbox.tool_panel[ section_key ] + self.__add_tools_to_tool_panel( trans, repository, repository_tools_tups, tool_section=tool_section, section_key=section_key ) + else: + # Load the repository tools into a section that no longer exists in the tool panel. The section must + # still exist in the tool config since the repository was only deactivated and not uninstalled. + sections_to_load = [] + tool_elems_found = 0 + # Only inspect tool configs that contain installed tool shed repositories. + for shed_tool_conf_dict in trans.app.toolbox.shed_tool_confs: + config_filename = shed_tool_conf_dict[ 'config_filename' ] + log.info( "Parsing the tool configuration %s" % config_filename ) + tree = util.parse_xml( config_filename ) + root = tree.getroot() + tool_path = root.get( 'tool_path' ) + if tool_path is not None: + # Tool configs that contain tools installed from tool shed repositories + # must have a tool_path attribute. + for elem in root: + if elem.tag == 'section' and \ + elem.get( 'id' ) == original_section_id and \ + elem.get( 'name' ) == original_section_name and \ + elem.get( 'version' ) == original_section_version: + # We've found the section, but we have to make sure it contains the + # correct tool tag set. This is necessary because the shed tool configs + # can include multiple sections of the same id, name and version, each + # containing one or more tool tag sets. + for tool_elem in elem: + if tool_elem.get( 'guid' ) in guids_to_activate: + tool_elems_found += 1 + if elem not in sections_to_load: + sections_to_load.append( elem ) + if tool_elems_found == len( guids_to_activate ): + break + if tool_elems_found == len( guids_to_activate ): break - if section_loaded: - break - # Load proprietary datatypes. - load_datatype_items( trans.app, repository, relative_install_dir ) - message = 'The repository named <b>%s</b> has been activated.' % repository.name + if tool_elems_found == len( guids_to_activate ): + break + for elem in sections_to_load: + trans.app.toolbox.load_section_tag_set( elem, trans.app.toolbox.tool_panel, tool_path ) + if repository.includes_datatypes: + # Load proprietary datatypes. + load_datatype_items( trans.app, repository, relative_install_dir ) + if uninstalled: + message = 'The <b>%s</b> repository has been reinstalled.' % repository.name + else: + message = 'The <b>%s</b> repository has been activated.' % repository.name status = 'done' return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='browse_repositories', message=message, status=status ) ) - def __activate( self, trans, repository, repository_tools_tups, tool_section=None, section_key=None ): + def __add_tools_to_tool_panel( self, trans, repository, repository_tools_tups, tool_section=None, section_key=None ): # Load tools. if tool_section: elems = tool_section.elems diff -r 9d392eaca847bf26a8383babacc3c94e5a1bab9e -r fd6f22c072f3b2acbde3311943af004f1094a4fa templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako --- a/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako +++ b/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako @@ -43,30 +43,52 @@ ${repository.deleted} </div><div class="form-row"> - ${remove_from_disk_check_box.get_html( disabled=True )} - <label for="repository" style="display: inline;font-weight:normal;">Check to uninstall (not yet implemented) or leave blank to deactivate</label> + ${remove_from_disk_check_box.get_html()} + <label for="repository" style="display: inline;font-weight:normal;">Check to uninstall or leave blank to deactivate</label><br/><br/><label>Deactivating this repository will result in the following:</label><div class="toolParamHelp" style="clear: both;"> - 1. This repository record's deleted column in the tool_shed_repository database table will be set to True. + * The repository and all of it's contents will remain on disk. </div> + %if repository.includes_tools: + <div class="toolParamHelp" style="clear: both;"> + * The repository's tools will not be loaded into the tool panel. + </div> + %endif + %if repository.includes_datatypes: + <div class="toolParamHelp" style="clear: both;"> + * The repository's datatypes, datatype converters and display applications will be eliminated from the datatypes registry. + </div> + %endif <div class="toolParamHelp" style="clear: both;"> - 2. The repository and all of it's contents will remain on disk. - </div> - <div class="toolParamHelp" style="clear: both;"> - 3. If this repository includes tools, they will not be loaded into the tool panel, but the tool config file in which they are defined will not be altered. + * The repository record's deleted column in the tool_shed_repository database table will be set to True. </div><br/> - <label>Uninstalling (not yet implemented) this repository will result in the following:</label> + <label>Uninstalling this repository will result in the following:</label><div class="toolParamHelp" style="clear: both;"> - 1. This repository record's deleted column in the tool_shed_repository database table will be set to True. + * The repository and all of it's contents will be removed from disk. </div> + %if repository.includes_tools: + <div class="toolParamHelp" style="clear: both;"> + * The repository's tool tag sets will be removed from the tool config file in which they are defined. + </div> + %endif + %if repository.includes_datatypes: + <div class="toolParamHelp" style="clear: both;"> + * The repository's datatypes, datatype converters and display applications will be eliminated from the datatypes registry. + </div> + %endif <div class="toolParamHelp" style="clear: both;"> - 2. The repository and all of it's contents will be removed from disk. + * The repository record's deleted column in the tool_shed_repository database table will be set to True. </div> - <div class="toolParamHelp" style="clear: both;"> - 3. If this repository includes tools, they will be removed from the tool config file in which they are defined and they will not be loaded into the tool panel. - </div> + %if repository.dist_to_shed: + <div class="toolParamHelp" style="clear: both;"> + * The repository record's uninstalled column in the tool_shed_repository database table will be set to True. + </div> + <div class="toolParamHelp" style="clear: both;"> + * All records associated with this repository will be eliminated from the tool_id_guid_map database table. + </div> + %endif <div style="clear: both"></div></div><div class="form-row"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Add sort tag to Print Reads test output element.
by Bitbucket 25 Jan '12

25 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/12addb0e91d0/ changeset: 12addb0e91d0 user: dan date: 2012-01-25 14:54:16 summary: Add sort tag to Print Reads test output element. affected #: 1 file diff -r 74343d5f5bda092f0fdad459c391bc0c624dc26e -r 12addb0e91d0911a0553a312497082a4aa395db6 tools/gatk/print_reads.xml --- a/tools/gatk/print_reads.xml +++ b/tools/gatk/print_reads.xml @@ -373,7 +373,7 @@ <param name="sample_file_repeat" value="0" /><param name="sample_name_repeat" value="0" /><param name="gatk_param_type_selector" value="basic" /> - <output name="output_bam" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" /> + <output name="output_bam" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" sort="True"/><output name="output_log" file="gatk/gatk_print_reads/gatk_print_reads_out_1.log.contains" compare="contains" /></test></tests> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0