November 2011 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 3 new changesets
by Bitbucket 10 Nov '11

10 Nov '11

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a807ed5389f4/ changeset: a807ed5389f4 user: fubar date: 2011-11-10 22:23:15 summary: Updates for picard tools 1.56 - they changed the params for CollectInsertSizeMetrics.jar - bless them - so you will need to update your local picard install in tool-data/shared/jars/picard Fixes to picard_wrapper.py so if a picard tool returns a non zero exit code, it will raise an error state. Sadly, this doesn't help the CollectInsertSizeMetrics problem it was meant to address - it will die with no outputs if given an input containing unpaired reads - but the exit code is still zero. Talk about irony. At least it should work right if they ever get around to setting exit codes to indicate a problem. affected #: 6 files diff -r 6ec2d7f4a64dcf6a1c49415bd8f40c8d4ca907c5 -r a807ed5389f4da39f509aa45e5baf7027ceb7a91 test-data/picard_input_sorted_pair.sam --- a/test-data/picard_input_sorted_pair.sam +++ b/test-data/picard_input_sorted_pair.sam @@ -5,11 +5,11 @@ @RG ID:rg1 SM:Z bar:record:1 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 bar:record:1 141 chr1 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:2 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:2 141 chr2 30 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:3 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:3 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:4 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:4 141 chr1 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:5 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:5 141 chr3 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:2 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:2 141 chr1 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:3 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:3 141 chr2 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:4 77 chr2 50 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:4 141 chr2 60 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:5 77 chr3 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:5 141 chr3 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 diff -r 6ec2d7f4a64dcf6a1c49415bd8f40c8d4ca907c5 -r a807ed5389f4da39f509aa45e5baf7027ceb7a91 test-data/picard_output_AsMetrics_indexed_hg18_sorted_pair.html --- a/test-data/picard_output_AsMetrics_indexed_hg18_sorted_pair.html +++ b/test-data/picard_output_AsMetrics_indexed_hg18_sorted_pair.html @@ -6,28 +6,51 @@ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -<meta name="generator" content="Galaxy CollectAlignmentSummaryMetrics tool output - see http://getgalaxy.org/" /> +<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" /><title></title><link rel="stylesheet" href="/static/style/base.css" type="text/css" /></head><body><div class="document"> -Galaxy tool wrapper picard_wrapper at 09/05/2011 11:03:57</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table> +Galaxy tool CollectAlignmentSummaryMetrics run at 11/11/2011 08:07:27</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table><tr><td><a href="CollectAlignmentSummaryMetrics.log">CollectAlignmentSummaryMetrics.log</a></td></tr> +<tr><td><a href="CollectAlignmentSummaryMetrics.metrics.txt">CollectAlignmentSummaryMetrics.metrics.txt</a></td></tr></table><p/> -<b>Picard log</b><hr/> -<pre>## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/5/dataset_5_files/CollectAlignmentSummaryMetrics.metrics.txt R=/udd/rerla/galaxy-central/database/job_working_directory/5/dataset_5_files/hg19.fasta_fake.fasta TMP_DIR=/tmp INPUT=/export/tmp/tmpBrCiH5/database/files/000/dataset_4.dat returned status 1 and stderr: -[Mon May 09 11:03:51 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmpBrCiH5/database/files/000/dataset_4.dat OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/5/dataset_5_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/udd/rerla/galaxy-central/database/job_working_directory/5/dataset_5_files/hg19.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -[Mon May 09 11:03:57 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics done. -Runtime.totalMemory()=912588800 -Exception in thread "main" net.sf.picard.PicardException: Requesting earlier reference sequence: 0 < 1 - at net.sf.picard.reference.ReferenceSequenceFileWalker.get(ReferenceSequenceFileWalker.java:78) - at net.sf.picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:115) - at net.sf.picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:54) - at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:157) - at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:117) - at net.sf.picard.analysis.CollectAlignmentSummaryMetrics.main(CollectAlignmentSummaryMetrics.java:106) - +<b>Picard on line resources</b><ul> +<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li> +<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/> +<b>Picard output (transposed to make it easier to see)</b><hr/> +<table cellpadding="3" > +<tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/data/tmp/tmpLLcl1w/database/files/000/dataset_4.dat OUTPUT=/data/home/rlazarus/galaxy/database/job_working_directory/5/dataset_5_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/data/home/rlazarus/galaxy/database/job_working_directory/5/dataset_5_files/hg19.fa_fake.fasta ASSUME_SORTED=true TMP_DIR=[/tmp] VALIDATION_STRINGENCY=LENIENT METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># Started on: Fri Nov 11 08:07:22 EST 2011</td></tr><tr class="d0"><td colspan="2">## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics</td></tr><tr class="d0"><td>CATEGORY</td><td>FIRST_OF_PAIR </td></tr> +<tr class="d1"><td>TOTAL_READS</td><td>5 </td></tr> +<tr class="d0"><td>PF_READS</td><td>5 </td></tr> +<tr class="d1"><td>PCT_PF_READS</td><td>1 </td></tr> +<tr class="d0"><td>PF_NOISE_READS</td><td>0 </td></tr> +<tr class="d1"><td>PF_READS_ALIGNED</td><td>0 </td></tr> +<tr class="d0"><td>PCT_PF_READS_ALIGNED</td><td>0 </td></tr> +<tr class="d1"><td>PF_ALIGNED_BASES</td><td>0 </td></tr> +<tr class="d0"><td>PF_HQ_ALIGNED_READS</td><td>0 </td></tr> +<tr class="d1"><td>PF_HQ_ALIGNED_BASES</td><td>0 </td></tr> +<tr class="d0"><td>PF_HQ_ALIGNED_Q20_BASES</td><td>0 </td></tr> +<tr class="d1"><td>PF_HQ_MEDIAN_MISMATCHES</td><td>0 </td></tr> +<tr class="d0"><td>PF_MISMATCH_RATE</td><td>0 </td></tr> +<tr class="d1"><td>PF_HQ_ERROR_RATE</td><td>0 </td></tr> +<tr class="d0"><td>PF_INDEL_RATE</td><td>0 </td></tr> +<tr class="d1"><td>MEAN_READ_LENGTH</td><td>13 </td></tr> +<tr class="d0"><td>READS_ALIGNED_IN_PAIRS</td><td>0 </td></tr> +<tr class="d1"><td>PCT_READS_ALIGNED_IN_PAIRS</td><td>0 </td></tr> +<tr class="d0"><td>BAD_CYCLES</td><td>0 </td></tr> +<tr class="d1"><td>STRAND_BALANCE</td><td>0 </td></tr> +<tr class="d0"><td>PCT_CHIMERAS</td><td>0 </td></tr> +<tr class="d1"><td>PCT_ADAPTER</td><td>0 </td></tr> +<tr class="d0"><td>SAMPLE</td><td> </td></tr> +<tr class="d1"><td>LIBRARY</td><td> </td></tr> +<tr class="d0"><td>READ_GROUP +</td><td> + </td></tr> +</table> +<b>Picard Tool Run Log</b><hr/> +<pre>INFO:root:## executing java -Xmx4g -jar /data/home/rlazarus/galaxy/tool-data/shared/jars/picard/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/data/home/rlazarus/galaxy/database/job_working_directory/5/dataset_5_files/CollectAlignmentSummaryMetrics.metrics.txt R=/data/home/rlazarus/galaxy/database/job_working_directory/5/dataset_5_files/hg19.fa_fake.fasta TMP_DIR=/tmp INPUT=/data/tmp/tmpLLcl1w/database/files/000/dataset_4.dat returned status 0 and nothing on stderr </pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html> diff -r 6ec2d7f4a64dcf6a1c49415bd8f40c8d4ca907c5 -r a807ed5389f4da39f509aa45e5baf7027ceb7a91 test-data/picard_output_alignment_summary_metrics.html --- a/test-data/picard_output_alignment_summary_metrics.html +++ b/test-data/picard_output_alignment_summary_metrics.html @@ -12,7 +12,7 @@ </head><body><div class="document"> -Galaxy tool CollectAlignmentSummaryMetrics run at 11/05/2011 23:16:24</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table> +Galaxy tool CollectAlignmentSummaryMetrics run at 11/11/2011 08:07:10</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table><tr><td><a href="CollectAlignmentSummaryMetrics.log">CollectAlignmentSummaryMetrics.log</a></td></tr><tr><td><a href="CollectAlignmentSummaryMetrics.metrics.txt">CollectAlignmentSummaryMetrics.metrics.txt</a></td></tr></table><p/> @@ -21,43 +21,38 @@ <li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/><b>Picard output (transposed to make it easier to see)</b><hr/><table cellpadding="3" > -<tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmp1-mt_l/database/files/000/dataset_2.dat OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsZJS8q6.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># Started on: Wed May 11 23:16:24 EDT 2011</td></tr><tr class="d0"><td colspan="2">## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics</td></tr><tr class="d0"><td>CATEGORY</td><td>FIRST_OF_PAIR </td></tr> +<tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/data/tmp/tmpLLcl1w/database/files/000/dataset_2.dat OUTPUT=/data/home/rlazarus/galaxy/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/data/home/rlazarus/galaxy/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsfq2hit.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=[/tmp] VALIDATION_STRINGENCY=LENIENT METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># Started on: Fri Nov 11 08:07:10 EST 2011</td></tr><tr class="d0"><td colspan="2">## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics</td></tr><tr class="d0"><td>CATEGORY</td><td>FIRST_OF_PAIR </td></tr><tr class="d1"><td>TOTAL_READS</td><td>4 </td></tr><tr class="d0"><td>PF_READS</td><td>4 </td></tr><tr class="d1"><td>PCT_PF_READS</td><td>1 </td></tr><tr class="d0"><td>PF_NOISE_READS</td><td>0 </td></tr><tr class="d1"><td>PF_READS_ALIGNED</td><td>4 </td></tr><tr class="d0"><td>PCT_PF_READS_ALIGNED</td><td>1 </td></tr> -<tr class="d1"><td>PF_HQ_ALIGNED_READS</td><td>4 </td></tr> -<tr class="d0"><td>PF_HQ_ALIGNED_BASES</td><td>404 </td></tr> -<tr class="d1"><td>PF_HQ_ALIGNED_Q20_BASES</td><td>28 </td></tr> -<tr class="d0"><td>PF_HQ_MEDIAN_MISMATCHES</td><td>78 </td></tr> +<tr class="d1"><td>PF_ALIGNED_BASES</td><td>404 </td></tr> +<tr class="d0"><td>PF_HQ_ALIGNED_READS</td><td>4 </td></tr> +<tr class="d1"><td>PF_HQ_ALIGNED_BASES</td><td>404 </td></tr> +<tr class="d0"><td>PF_HQ_ALIGNED_Q20_BASES</td><td>28 </td></tr> +<tr class="d1"><td>PF_HQ_MEDIAN_MISMATCHES</td><td>78 </td></tr> +<tr class="d0"><td>PF_MISMATCH_RATE</td><td>0.777228 </td></tr><tr class="d1"><td>PF_HQ_ERROR_RATE</td><td>0.777228 </td></tr> -<tr class="d0"><td>MEAN_READ_LENGTH</td><td>101 </td></tr> -<tr class="d1"><td>READS_ALIGNED_IN_PAIRS</td><td>3 </td></tr> -<tr class="d0"><td>PCT_READS_ALIGNED_IN_PAIRS</td><td>0.75 </td></tr> -<tr class="d1"><td>BAD_CYCLES</td><td>63 </td></tr> -<tr class="d0"><td>STRAND_BALANCE</td><td>0.25 </td></tr> -<tr class="d1"><td>PCT_CHIMERAS</td><td>0 </td></tr> -<tr class="d0"><td>PCT_ADAPTER -</td><td>0 +<tr class="d0"><td>PF_INDEL_RATE</td><td>0 </td></tr> +<tr class="d1"><td>MEAN_READ_LENGTH</td><td>101 </td></tr> +<tr class="d0"><td>READS_ALIGNED_IN_PAIRS</td><td>3 </td></tr> +<tr class="d1"><td>PCT_READS_ALIGNED_IN_PAIRS</td><td>0.75 </td></tr> +<tr class="d0"><td>BAD_CYCLES</td><td>63 </td></tr> +<tr class="d1"><td>STRAND_BALANCE</td><td>0.25 </td></tr> +<tr class="d0"><td>PCT_CHIMERAS</td><td>0 </td></tr> +<tr class="d1"><td>PCT_ADAPTER</td><td>0 </td></tr> +<tr class="d0"><td>SAMPLE</td><td> </td></tr> +<tr class="d1"><td>LIBRARY</td><td> </td></tr> +<tr class="d0"><td>READ_GROUP +</td><td>  </td></tr></table><b>Picard Tool Run Log</b><hr/> -<pre>Wed, 11 May 2011 23:16:24 INFO - ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/CreateSequenceDictionary.jar REFERENCE=/tmp/CollectAlignmentSummaryMetricsZJS8q6.fasta OUTPUT=/tmp/CollectAlignmentSummaryMetricsZJS8q6.dict URI=dataset_1.dat TRUNCATE_NAMES_AT_WHITESPACE=None returned status 0 and stderr: -[Wed May 11 23:16:24 EDT 2011] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/tmp/CollectAlignmentSummaryMetricsZJS8q6.fasta OUTPUT=/tmp/CollectAlignmentSummaryMetricsZJS8q6.dict URI=dataset_1.dat TRUNCATE_NAMES_AT_WHITESPACE=false NUM_SEQUENCES=2147483647 TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -[Wed May 11 23:16:24 EDT 2011] net.sf.picard.sam.CreateSequenceDictionary done. -Runtime.totalMemory()=9109504 +<pre>INFO:root:## executing java -Xmx4g -jar /data/home/rlazarus/galaxy/tool-data/shared/jars/picard/CreateSequenceDictionary.jar REFERENCE=/tmp/CollectAlignmentSummaryMetricsfq2hit.fasta OUTPUT=/tmp/CollectAlignmentSummaryMetricsfq2hit.dict URI=dataset_1.dat TRUNCATE_NAMES_AT_WHITESPACE=None returned status 0 and nothing on stderr - -Wed, 11 May 2011 23:16:24 INFO - ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt R=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsZJS8q6.fasta_fake.fasta TMP_DIR=/tmp INPUT=/export/tmp/tmp1-mt_l/database/files/000/dataset_2.dat returned status 0 and stderr: -[Wed May 11 23:16:24 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmp1-mt_l/database/files/000/dataset_2.dat OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsZJS8q6.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -WARNING 2011-05-11 23:16:24 SinglePassSamProgram File reports sort order 'queryname', assuming it's coordinate sorted anyway. -[Wed May 11 23:16:24 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics done. -Runtime.totalMemory()=9109504 - +INFO:root:## executing java -Xmx4g -jar /data/home/rlazarus/galaxy/tool-data/shared/jars/picard/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/data/home/rlazarus/galaxy/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt R=/data/home/rlazarus/galaxy/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsfq2hit.fasta_fake.fasta TMP_DIR=/tmp INPUT=/data/tmp/tmpLLcl1w/database/files/000/dataset_2.dat returned status 0 and nothing on stderr </pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html> diff -r 6ec2d7f4a64dcf6a1c49415bd8f40c8d4ca907c5 -r a807ed5389f4da39f509aa45e5baf7027ceb7a91 tools/picard/picard_wrapper.py --- a/tools/picard/picard_wrapper.py +++ b/tools/picard/picard_wrapper.py @@ -125,14 +125,15 @@ tef.close() stderrs = self.readLarge(temperr) stdouts = self.readLarge(templog) - if len(stderrs) > 0: + if rval > 0: s = '## executing %s returned status %d and stderr: \n%s\n' % (cl,rval,stderrs) + stdouts = '%s\n%s' % (stdouts,stderrs) else: s = '## executing %s returned status %d and nothing on stderr\n' % (cl,rval) logging.info(s) os.unlink(templog) # always os.unlink(temperr) # always - return s, stdouts # sometimes this is an output + return s, stdouts, rval # sometimes s is an output def runPic(self, jar, cl): """ @@ -141,8 +142,8 @@ runme = ['java -Xmx%s' % self.opts.maxjheap] runme.append('-jar %s' % jar) runme += cl - s,stdout = self.runCL(cl=runme, output_dir=self.opts.outdir) - return stdout + s,stdouts,rval = self.runCL(cl=runme, output_dir=self.opts.outdir) + return stdouts,rval def samToBam(self,infile=None,outdir=None): """ @@ -150,8 +151,8 @@ """ fd,tempbam = tempfile.mkstemp(dir=outdir,suffix='rgutilsTemp.bam') cl = ['samtools view -h -b -S -o ',tempbam,infile] - tlog,stdouts = self.runCL(cl,outdir) - return tlog,tempbam + tlog,stdouts,rval = self.runCL(cl,outdir) + return tlog,tempbam,rval #def bamToSam(self,infile=None,outdir=None): # """ @@ -167,7 +168,7 @@ """ print '## sortSam got infile=%s,outfile=%s,outdir=%s' % (infile,outfile,outdir) cl = ['samtools sort',infile,outfile] - tlog,stdouts = self.runCL(cl,outdir) + tlog,stdouts,rval = self.runCL(cl,outdir) return tlog def cleanup(self): @@ -243,6 +244,9 @@ if len(pdflist) > 0: # assumes all pdfs come with thumbnail .jpgs for p in pdflist: imghref = '%s.jpg' % os.path.splitext(p)[0] # removes .pdf + mimghref = '%s-0.jpg' % os.path.splitext(p)[0] # multiple pages pdf -> multiple thumbnails without asking! + if mimghref in flist: + imghref=mimghref res.append('<table cellpadding="10"><tr><td>\n') res.append('<a href="%s"><img src="%s" title="Click image preview for a print quality PDF version" hspace="10" align="middle"></a>\n' % (p,imghref)) res.append('</tr></td></table>\n') @@ -383,6 +387,8 @@ op.add_option('', '--taillimit', default="0") op.add_option('', '--histwidth', default="0") op.add_option('', '--minpct', default="0.01") + op.add_option('', '--malevel', default="") + op.add_option('', '--deviations', default="0.0") # CollectAlignmentSummaryMetrics op.add_option('', '--maxinsert', default="20") op.add_option('', '--adaptors', action='append', type="string") @@ -430,7 +436,8 @@ tmp_dir = opts.outdir haveTempout = False # we use this where sam output is an option - + rval = 0 + stdouts = 'Not run yet' # set ref and dict files to use (create if necessary) ref_file_name = opts.ref if opts.ref_file <> None: @@ -453,7 +460,7 @@ pic.delme.append(dict_file_name) pic.delme.append(ref_file_name) pic.delme.append(tmp_ref_name) - s = pic.runPic(jarpath, cl) + stdouts,rval = pic.runPic(jarpath, cl) # run relevant command(s) # define temporary output @@ -486,7 +493,7 @@ cl.append('RGCN="%s"' % opts.rg_seq_center) if opts.rg_desc: cl.append('RGDS="%s"' % opts.rg_desc) - pic.runPic(opts.jar, cl) + stdouts,rval = pic.runPic(opts.jar, cl) haveTempout = True elif pic.picname == 'BamIndexStats': @@ -499,9 +506,9 @@ pic.delme.append(tmp_bam_name) pic.delme.append(tmp_bai_name) pic.delme.append(tmp_name) - s = pic.runPic( opts.jar, cl ) + stdouts,rval = pic.runPic( opts.jar, cl ) f = open(pic.metricsOut,'a') - f.write(s) # got this on stdout from runCl + f.write(stdouts) # got this on stdout from runCl f.write('\n') f.close() doTranspose = False # but not transposed @@ -519,7 +526,7 @@ cl.append('READ_NAME_REGEX="%s"' % opts.readregex) if float(opts.optdupdist) > 0: cl.append('OPTICAL_DUPLICATE_PIXEL_DISTANCE=%s' % opts.optdupdist) - pic.runPic(opts.jar,cl) + stdouts,rval = pic.runPic(opts.jar, cl) elif pic.picname == 'CollectAlignmentSummaryMetrics': # Why do we do this fakefasta thing? Because we need NO fai to be available or picard barfs unless it has the same length as the input data. @@ -532,7 +539,7 @@ info = s shutil.copy(ref_file_name,fakefasta) pic.delme.append(fakefasta) - cl.append('ASSUME_SORTED=%s' % opts.assumesorted) + cl.append('ASSUME_SORTED=true') adaptorseqs = ''.join([' ADAPTER_SEQUENCE=%s' % x for x in opts.adaptors]) cl.append(adaptorseqs) cl.append('IS_BISULFITE_SEQUENCED=%s' % opts.bisulphite) @@ -541,13 +548,24 @@ cl.append('R=%s' % fakefasta) cl.append('TMP_DIR=%s' % opts.tmpdir) if not opts.assumesorted.lower() == 'true': # we need to sort input - fakeinput = '%s.sorted' % opts.input - s = pic.sortSam(opts.input, fakeinput, opts.outdir) - pic.delme.append(fakeinput) - cl.append('INPUT=%s' % fakeinput) + sortedfile = '%s.sorted' % os.path.basename(opts.input) + if opts.datatype == 'sam': # need to work with a bam + tlog,tempbam,rval = pic.samToBam(opts.input,opts.outdir) + pic.delme.append(tempbam) + try: + tlog = pic.sortSam(tempbam,sortedfile,opts.outdir) + except: + print '## exception on sorting sam file %s' % opts.input + else: # is already bam + try: + tlog = pic.sortSam(opts.input,sortedfile,opts.outdir) + except: # bug - [bam_sort_core] not being ignored - TODO fixme + print '## exception on sorting bam file %s' % opts.input + cl.append('INPUT=%s.bam' % os.path.abspath(os.path.join(opts.outdir,sortedfile))) + pic.delme.append(os.path.join(opts.outdir,sortedfile)) else: cl.append('INPUT=%s' % os.path.abspath(opts.input)) - pic.runPic(opts.jar,cl) + stdouts,rval = pic.runPic(opts.jar, cl) elif pic.picname == 'CollectGcBiasMetrics': @@ -575,10 +593,10 @@ cl.append('TMP_DIR=%s' % opts.tmpdir) cl.append('CHART_OUTPUT=%s' % temppdf) cl.append('SUMMARY_OUTPUT=%s' % pic.metricsOut) - pic.runPic(opts.jar,cl) + stdouts,rval = pic.runPic(opts.jar, cl) if os.path.isfile(temppdf): cl2 = ['convert','-resize x400',temppdf,os.path.join(opts.outdir,jpgname)] # make the jpg for fixPicardOutputs to find - s,stdouts = pic.runCL(cl=cl2,output_dir=opts.outdir) + s,stdouts,rval = pic.runCL(cl=cl2,output_dir=opts.outdir) else: s='### runGC: Unable to find pdf %s - please check the log for the causal problem\n' % temppdf lf = open(pic.log_filename,'a') @@ -587,29 +605,39 @@ lf.close() elif pic.picname == 'CollectInsertSizeMetrics': + """ <command interpreter="python"> + picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --deviations "$deviations" + --histwidth "$histWidth" --minpct "$minPct" --malevel "$malevel" + -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file" + </command> + """ isPDF = 'InsertSizeHist.pdf' pdfpath = os.path.join(opts.outdir,isPDF) histpdf = 'InsertSizeHist.pdf' cl.append('I=%s' % opts.input) cl.append('O=%s' % pic.metricsOut) cl.append('HISTOGRAM_FILE=%s' % histpdf) - if opts.taillimit <> '0': - cl.append('TAIL_LIMIT=%s' % opts.taillimit) + #if opts.taillimit <> '0': # this was deprecated although still mentioned in the docs at 1.56 + # cl.append('TAIL_LIMIT=%s' % opts.taillimit) if opts.histwidth <> '0': cl.append('HISTOGRAM_WIDTH=%s' % opts.histwidth) if float( opts.minpct) > 0.0: cl.append('MINIMUM_PCT=%s' % opts.minpct) - pic.runPic(opts.jar,cl) + if float(opts.deviations) > 0.0: + cl.append('DEVIATIONS=%s' % opts.deviations) + if opts.malevel.strip(): + malevels = ['METRIC_ACCUMULATION_LEVEL=%s' % x for x in opts.malevel.split(',')] + cl.append(' '.join(malevels)) + stdouts,rval = pic.runPic(opts.jar, cl) if os.path.exists(pdfpath): # automake thumbnail - will be added to html cl2 = ['mogrify', '-format jpg -resize x400 %s' % pdfpath] - s,stdouts = pic.runCL(cl=cl2,output_dir=opts.outdir) + pic.runCL(cl=cl2,output_dir=opts.outdir) else: s = 'Unable to find expected pdf file %s<br/>\n' % pdfpath s += 'This <b>always happens if single ended data was provided</b> to this tool,\n' s += 'so please double check that your input data really is paired-end NGS data.<br/>\n' s += 'If your input was paired data this may be a bug worth reporting to the galaxy-bugs list\n<br/>' - stdouts = '' - logging.info(s) + logging.info(s) if len(stdouts) > 0: logging.info(stdouts) @@ -627,13 +655,13 @@ cl.append('READ_NAME_REGEX="%s"' % opts.readregex) # maximum offset between two duplicate clusters cl.append('OPTICAL_DUPLICATE_PIXEL_DISTANCE=%s' % opts.optdupdist) - pic.runPic(opts.jar, cl) + stdouts,rval = pic.runPic(opts.jar, cl) elif pic.picname == 'FixMateInformation': cl.append('I=%s' % opts.input) cl.append('O=%s' % tempout) cl.append('SORT_ORDER=%s' % opts.sortorder) - pic.runPic(opts.jar,cl) + stdouts,rval = pic.runPic(opts.jar,cl) haveTempout = True elif pic.picname == 'ReorderSam': @@ -649,14 +677,14 @@ # contig length discordance if opts.allow_contig_len_discord == 'true': cl.append('ALLOW_CONTIG_LENGTH_DISCORDANCE=true') - pic.runPic(opts.jar, cl) + stdouts,rval = pic.runPic(opts.jar, cl) haveTempout = True elif pic.picname == 'ReplaceSamHeader': cl.append('INPUT=%s' % opts.input) cl.append('OUTPUT=%s' % tempout) cl.append('HEADER=%s' % opts.header_file) - pic.runPic(opts.jar, cl) + stdouts,rval = pic.runPic(opts.jar, cl) haveTempout = True elif pic.picname == 'CalculateHsMetrics': @@ -673,7 +701,7 @@ cl.append('INPUT=%s' % os.path.abspath(opts.input)) cl.append('OUTPUT=%s' % pic.metricsOut) cl.append('TMP_DIR=%s' % opts.tmpdir) - pic.runPic(opts.jar,cl) + stdouts,rval = pic.runPic(opts.jar,cl) elif pic.picname == 'ValidateSamFile': import pysam @@ -682,7 +710,7 @@ stf = open(pic.log_filename,'w') tlog = None if opts.datatype == 'sam': # need to work with a bam - tlog,tempbam = pic.samToBam(opts.input,opts.outdir) + tlog,tempbam,rval = pic.samToBam(opts.input,opts.outdir) try: tlog = pic.sortSam(tempbam,sortedfile,opts.outdir) except: @@ -709,7 +737,7 @@ cl.append('IS_BISULFITE_SEQUENCED=true') if opts.ref <> None or opts.ref_file <> None: cl.append('R=%s' % ref_file_name) - pic.runPic(opts.jar,cl) + stdouts,rval = pic.runPic(opts.jar,cl) if opts.datatype == 'sam': pic.delme.append(tempbam) newsam = opts.output @@ -725,10 +753,12 @@ if haveTempout: # Some Picard tools produced a potentially intermediate bam file. # Either just move to final location or create sam - shutil.move(tempout, os.path.abspath(opts.output)) - + if os.path.exists(tempout): + shutil.move(tempout, os.path.abspath(opts.output)) if opts.htmlout <> None or doFix: # return a pretty html page pic.fixPicardOutputs(transpose=doTranspose,maxloglines=maxloglines) - + if rval <> 0: + print >> sys.stderr, '## exit code=%d; stdout=%s' % (rval,stdouts) + # signal failure if __name__=="__main__": __main__() diff -r 6ec2d7f4a64dcf6a1c49415bd8f40c8d4ca907c5 -r a807ed5389f4da39f509aa45e5baf7027ceb7a91 tools/picard/rgPicardASMetrics.xml --- a/tools/picard/rgPicardASMetrics.xml +++ b/tools/picard/rgPicardASMetrics.xml @@ -1,7 +1,7 @@ <tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="0.03.1"><command interpreter="python"> picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" - --assumesorted "$sorted" -b "$bisulphite" --adaptors "$adaptors" --maxinsert "$maxinsert" -n "$out_prefix" + --assumesorted "$sorted" -b "$bisulphite" --adaptors "$adaptors" --maxinsert "$maxinsert" -n "$out_prefix" --datatype "$input_file.ext" -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectAlignmentSummaryMetrics.jar #if $genomeSource.refGenomeSource == "history": --ref-file "$genomeSource.ownFile" diff -r 6ec2d7f4a64dcf6a1c49415bd8f40c8d4ca907c5 -r a807ed5389f4da39f509aa45e5baf7027ceb7a91 tools/picard/rgPicardInsertSize.xml --- a/tools/picard/rgPicardInsertSize.xml +++ b/tools/picard/rgPicardInsertSize.xml @@ -1,9 +1,9 @@ -<tool name="Insertion size metrics" id="PicardInsertSize" version="0.3.1"> +<tool name="Insertion size metrics" id="PicardInsertSize" version="0.3.2"><description>for PAIRED data</description><requirements><requirement type="package">picard</requirement></requirements><command interpreter="python"> - picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --taillimit "$tailLimit" - --histwidth "$histWidth" --minpct "$minPct" + picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --deviations "$deviations" + --histwidth "$histWidth" --minpct "$minPct" --malevel "$malevel" -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file" </command><inputs> @@ -11,15 +11,22 @@ help="If empty, upload or import a SAM/BAM dataset."/><param name="out_prefix" value="Insertion size metrics" type="text" label="Title for the output file" help="Use this remind you what the job was for" size="120" /> - <param name="tailLimit" value="10000" type="integer" - label="Tail limit" size="5" - help="When calculating mean and stdev stop when the bins in the tail of the distribution contain fewer than mode/TAIL_LIMIT items" /> + <param name="deviations" value="10.0" type="float" + label="Deviations" size="5" + help="See Picard documentation: Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION" /><param name="histWidth" value="0" type="integer" label="Histogram width" size="5" - help="Explicitly sets the histogram width, overriding the TAIL_LIMIT option - leave 0 to ignore" /> - <param name="minPct" value="0.01" type="float" + help="Explicitly sets the histogram width option - leave 0 to ignore" /> + <param name="minPct" value="0.05" type="float" label="Minimum percentage" size="5" help="Discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads" /> + <param name="malevel" value="0" type="select" multiple="true" label="Metric Accumulation Level" + help="Level(s) at which metrics will be accumulated"> + <option value="ALL_READS" selected="true">All reads (default)</option> + <option value="SAMPLE" default="true">Sample</option> + <option value="LIBRARY" default="true">Library</option> + <option value="READ_GROUP" default="true">Read group</option> + </param></inputs><outputs><data format="html" name="html_file" label="InsertSize_${out_prefix}.html"/> @@ -28,9 +35,10 @@ <test><param name="input_file" value="picard_input_tiny.sam" /><param name="out_prefix" value="Insertion size metrics" /> - <param name="tailLimit" value="10000" /> + <param name="deviations" value="10.0" /><param name="histWidth" value="0" /><param name="minPct" value="0.01" /> + <param name="malevel" value="ALL_READS" /><output name="html_file" file="picard_output_insertsize_tinysam.html" ftype="html" compare="contains" lines_diff="40" /></test></tests> https://bitbucket.org/galaxy/galaxy-central/changeset/1da4a4a928fb/ changeset: 1da4a4a928fb user: fubar date: 2011-11-11 02:01:07 summary: Some minor additional cleanup to the picard suite affected #: 1 file diff -r a807ed5389f4da39f509aa45e5baf7027ceb7a91 -r 1da4a4a928fb46a7725375a2cb0baa18f32c44b4 tools/picard/picard_wrapper.py --- a/tools/picard/picard_wrapper.py +++ b/tools/picard/picard_wrapper.py @@ -102,7 +102,7 @@ pass tmp.close() except Exception, e: - stop_err( 'Error : %s' % str( e ) ) + stop_err( 'Read Large Exception : %s' % str( e ) ) return s def runCL(self,cl=None,output_dir=None): @@ -154,15 +154,6 @@ tlog,stdouts,rval = self.runCL(cl,outdir) return tlog,tempbam,rval - #def bamToSam(self,infile=None,outdir=None): - # """ - # use samtools view to convert bam to sam - # """ - # fd,tempsam = tempfile.mkstemp(dir=outdir,suffix='rgutilsTemp.sam') - # cl = ['samtools view -h -o ',tempsam,infile] - # tlog,stdouts = self.runCL(cl,outdir) - # return tlog,tempsam - def sortSam(self, infile=None,outfile=None,outdir=None): """ """ @@ -243,10 +234,11 @@ pdflist = [x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'] if len(pdflist) > 0: # assumes all pdfs come with thumbnail .jpgs for p in pdflist: - imghref = '%s.jpg' % os.path.splitext(p)[0] # removes .pdf - mimghref = '%s-0.jpg' % os.path.splitext(p)[0] # multiple pages pdf -> multiple thumbnails without asking! + pbase = os.path.splitext(p)[0] # removes .pdf + imghref = '%s.jpg' % pbase + mimghref = '%s-0.jpg' % pbase # multiple pages pdf -> multiple thumbnails without asking! if mimghref in flist: - imghref=mimghref + imghref=mimghref # only one for thumbnail...it's a multi page pdf res.append('<table cellpadding="10"><tr><td>\n') res.append('<a href="%s"><img src="%s" title="Click image preview for a print quality PDF version" hspace="10" align="middle"></a>\n' % (p,imghref)) res.append('</tr></td></table>\n') @@ -387,7 +379,7 @@ op.add_option('', '--taillimit', default="0") op.add_option('', '--histwidth', default="0") op.add_option('', '--minpct', default="0.01") - op.add_option('', '--malevel', default="") + op.add_option('', '--malevel', action='append', type="string") op.add_option('', '--deviations', default="0.0") # CollectAlignmentSummaryMetrics op.add_option('', '--maxinsert', default="20") @@ -529,13 +521,14 @@ stdouts,rval = pic.runPic(opts.jar, cl) elif pic.picname == 'CollectAlignmentSummaryMetrics': - # Why do we do this fakefasta thing? Because we need NO fai to be available or picard barfs unless it has the same length as the input data. + # Why do we do this fakefasta thing? + # Because we need NO fai to be available or picard barfs unless it matches the input data. # why? Dunno Seems to work without complaining if the .bai file is AWOL.... fakefasta = os.path.join(opts.outdir,'%s_fake.fasta' % os.path.basename(ref_file_name)) try: os.symlink(ref_file_name,fakefasta) except: - s = '## unable to symlink %s to %s - different devices? May need to replace with shutil.copy' + s = '## unable to symlink %s to %s - different devices? Will shutil.copy' info = s shutil.copy(ref_file_name,fakefasta) pic.delme.append(fakefasta) @@ -550,7 +543,7 @@ if not opts.assumesorted.lower() == 'true': # we need to sort input sortedfile = '%s.sorted' % os.path.basename(opts.input) if opts.datatype == 'sam': # need to work with a bam - tlog,tempbam,rval = pic.samToBam(opts.input,opts.outdir) + tlog,tempbam,trval = pic.samToBam(opts.input,opts.outdir) pic.delme.append(tempbam) try: tlog = pic.sortSam(tempbam,sortedfile,opts.outdir) @@ -559,8 +552,8 @@ else: # is already bam try: tlog = pic.sortSam(opts.input,sortedfile,opts.outdir) - except: # bug - [bam_sort_core] not being ignored - TODO fixme - print '## exception on sorting bam file %s' % opts.input + except : # bug - [bam_sort_core] not being ignored - TODO fixme + print '## exception %s on sorting bam file %s' % (sys.exc_info()[0],opts.input) cl.append('INPUT=%s.bam' % os.path.abspath(os.path.join(opts.outdir,sortedfile))) pic.delme.append(os.path.join(opts.outdir,sortedfile)) else: @@ -625,8 +618,8 @@ cl.append('MINIMUM_PCT=%s' % opts.minpct) if float(opts.deviations) > 0.0: cl.append('DEVIATIONS=%s' % opts.deviations) - if opts.malevel.strip(): - malevels = ['METRIC_ACCUMULATION_LEVEL=%s' % x for x in opts.malevel.split(',')] + if opts.malevel: + malevels = ['METRIC_ACCUMULATION_LEVEL=%s' % x for x in opts.malevel] cl.append(' '.join(malevels)) stdouts,rval = pic.runPic(opts.jar, cl) if os.path.exists(pdfpath): # automake thumbnail - will be added to html https://bitbucket.org/galaxy/galaxy-central/changeset/0474dfc4d30f/ changeset: 0474dfc4d30f user: fubar date: 2011-11-11 02:45:25 summary: branch merge affected #: 14 files diff -r 1da4a4a928fb46a7725375a2cb0baa18f32c44b4 -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -19,7 +19,6 @@ from Cheetah.Template import Template - pkg_resources.require( 'elementtree' ) from elementtree import ElementTree, ElementInclude from elementtree.ElementTree import Element @@ -1298,6 +1297,9 @@ group_list_grid = None quota_list_grid = None repository_list_grid = None + delete_operation = None + undelete_operation = None + purge_operation = None @web.expose @web.require_admin @@ -2217,6 +2219,13 @@ **kwd ) ) elif operation == "manage roles and groups": return self.manage_roles_and_groups_for_user( trans, **kwd ) + if trans.app.config.allow_user_deletion: + if self.delete_operation not in self.user_list_grid.operations: + self.user_list_grid.operations.append( self.delete_operation ) + if self.undelete_operation not in self.user_list_grid.operations: + self.user_list_grid.operations.append( self.undelete_operation ) + if self.purge_operation not in self.user_list_grid.operations: + self.user_list_grid.operations.append( self.purge_operation ) # Render the list view return self.user_list_grid( trans, **kwd ) @web.expose diff -r 1da4a4a928fb46a7725375a2cb0baa18f32c44b4 -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py +++ b/lib/galaxy/web/controllers/admin.py @@ -93,11 +93,6 @@ allow_popup=False, url_args=dict( webapp="galaxy", action="reset_user_password" ) ) ] - #TODO: enhance to account for trans.app.config.allow_user_deletion here so that we can eliminate these operations if - # the setting is False - #operations.append( grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True ) ) - #operations.append( grids.GridOperation( "Undelete", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) ) - #operations.append( grids.GridOperation( "Purge", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) ) standard_filters = [ grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), grids.GridColumnFilter( "Deleted", args=dict( deleted=True, purged=False ) ), @@ -443,6 +438,9 @@ group_list_grid = GroupListGrid() quota_list_grid = QuotaListGrid() repository_list_grid = RepositoryListGrid() + delete_operation = grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True ) + undelete_operation = grids.GridOperation( "Undelete", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) + purge_operation = grids.GridOperation( "Purge", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) @web.expose @web.require_admin diff -r 1da4a4a928fb46a7725375a2cb0baa18f32c44b4 -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd lib/galaxy/webapps/community/config.py --- a/lib/galaxy/webapps/community/config.py +++ b/lib/galaxy/webapps/community/config.py @@ -61,6 +61,7 @@ self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None ) self.require_login = string_as_bool( kwargs.get( "require_login", "False" ) ) self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) ) + self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) ) self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) ) self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/community" ), self.root ) diff -r 1da4a4a928fb46a7725375a2cb0baa18f32c44b4 -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd lib/galaxy/webapps/demo_sequencer/config.py --- a/lib/galaxy/webapps/demo_sequencer/config.py +++ b/lib/galaxy/webapps/demo_sequencer/config.py @@ -40,6 +40,7 @@ self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None ) self.require_login = string_as_bool( kwargs.get( "require_login", "False" ) ) self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) ) + self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) ) self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/demo_sequencer" ), self.root ) self.admin_users = kwargs.get( "admin_users", "" ) diff -r 1da4a4a928fb46a7725375a2cb0baa18f32c44b4 -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd lib/galaxy/webapps/reports/config.py --- a/lib/galaxy/webapps/reports/config.py +++ b/lib/galaxy/webapps/reports/config.py @@ -31,6 +31,8 @@ self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/reports" ), self.root ) self.sendmail_path = kwargs.get('sendmail_path',"/usr/sbin/sendmail") + self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) ) + self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) ) self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) self.brand = kwargs.get( 'brand', None ) self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.g2.bx.psu.edu/FrontPage' ) diff -r 1da4a4a928fb46a7725375a2cb0baa18f32c44b4 -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd static/images/fugue/chevron-expand-bw.png Binary file static/images/fugue/chevron-expand-bw.png has changed diff -r 1da4a4a928fb46a7725375a2cb0baa18f32c44b4 -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd static/images/fugue/toggle-bw.png Binary file static/images/fugue/toggle-bw.png has changed diff -r 1da4a4a928fb46a7725375a2cb0baa18f32c44b4 -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd static/images/fugue/toggle-expand-bw.png Binary file static/images/fugue/toggle-expand-bw.png has changed diff -r 1da4a4a928fb46a7725375a2cb0baa18f32c44b4 -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl +++ b/static/june_2007_style/base.css.tmpl @@ -865,10 +865,6 @@ -sprite-group: fugue; -sprite-image: fugue/toggle-expand.png; } -.icon-button.toggle { - -sprite-group: fugue; - -sprite-image: fugue/toggle.png; -} .icon-button.toggle-contract { -sprite-group: fugue; -sprite-image: fugue/toggle.png; diff -r 1da4a4a928fb46a7725375a2cb0baa18f32c44b4 -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -151,9 +151,10 @@ .icon-button.tag{background:url(fugue.png) no-repeat 0px -0px;} .icon-button.tags{background:url(fugue.png) no-repeat 0px -26px;} .icon-button.tag--plus{background:url(fugue.png) no-repeat 0px -52px;} -.icon-button.toggle-expand{background:url(fugue.png) no-repeat 0px -78px;} -.icon-button.toggle{background:url(fugue.png) no-repeat 0px -104px;} -.icon-button.toggle-contract{background:url(fugue.png) no-repeat 0px -104px;} +.icon-button.toggle-expand{background:transparent url(../images/fugue/toggle-expand-bw.png) no-repeat;} +.icon-button.toggle-expand:hover{background:url(fugue.png) no-repeat 0px -78px;} +.icon-button.toggle-contract{background:transparent url(../images/fugue/toggle-bw.png) no-repeat;} +.icon-button.toggle-contract:hover{background:url(fugue.png) no-repeat 0px -104px;} .icon-button.arrow-circle{background:url(fugue.png) no-repeat 0px -130px;} .icon-button.chevron{background:url(fugue.png) no-repeat 0px -156px;} .icon-button.bug{background:url(fugue.png) no-repeat 0px -182px;} diff -r 1da4a4a928fb46a7725375a2cb0baa18f32c44b4 -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd static/june_2007_style/blue/trackster.css --- a/static/june_2007_style/blue/trackster.css +++ b/static/june_2007_style/blue/trackster.css @@ -56,7 +56,9 @@ .tool-name{font-size:110%;font-weight:bold;} .param-row{margin-top:0.2em;margin-left:1em;} .param-label{float:left;font-weight:bold;padding-top:0.2em;} -.menu-button{padding:0px 4px 0px 4px;} +.menu-button{margin:0px 4px 0px 4px;} +.chevron-expand{background:transparent url(../images/fugue/chevron-expand-bw.png) no-repeat;} +.chevron-expand:hover{background:transparent url(../images/fugue/chevron-expand.png) no-repeat;} .settings-icon{background:transparent url(../images/fugue/gear-bw.png) no-repeat;} .settings-icon:hover{background:transparent url(../images/fugue/gear.png) no-repeat;} .overview-icon{background:transparent url(../images/fugue/application-dock-270-bw.png) no-repeat;} diff -r 1da4a4a928fb46a7725375a2cb0baa18f32c44b4 -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd static/june_2007_style/trackster.css.tmpl --- a/static/june_2007_style/trackster.css.tmpl +++ b/static/june_2007_style/trackster.css.tmpl @@ -295,7 +295,13 @@ padding-top: 0.2em; } .menu-button { - padding: 0px 4px 0px 4px; + margin: 0px 4px 0px 4px; +} +.chevron-expand { + background: transparent url(../images/fugue/chevron-expand-bw.png) no-repeat; +} +.chevron-expand:hover { + background:transparent url(../images/fugue/chevron-expand.png) no-repeat; } .settings-icon { background: transparent url(../images/fugue/gear-bw.png) no-repeat; diff -r 1da4a4a928fb46a7725375a2cb0baa18f32c44b4 -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -2381,16 +2381,18 @@ // Create and initialize track header and icons. if (show_header) { - this.header_div = $("<div class='track-header' />").appendTo(this.container_div); + this.header_div = $("<div class='track-header'/>").appendTo(this.container_div); if (this.view.editor) { this.drag_div = $("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div); } this.name_div = $("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name) .attr( "id", this.name.replace(/\s+/g,'-').replace(/[^a-zA-Z0-9\-]/g,'').toLowerCase() ); this.icons_div = $("<div/>").css("float", "left").appendTo(this.header_div).hide(); // Track icons. + this.mode_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Set display mode") + .addClass("icon-button chevron-expand").tipsy( {gravity: 's'} ).appendTo(this.icons_div); this.toggle_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Hide/show track content") - .addClass("icon-button toggle").tipsy( {gravity: 's'} ) - .appendTo(this.icons_div); + .addClass("icon-button toggle-contract").tipsy( {gravity: 's'} ) + .appendTo(this.icons_div); this.settings_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Edit settings") .addClass("icon-button settings-icon").tipsy( {gravity: 's'} ) .appendTo(this.icons_div); @@ -2407,21 +2409,42 @@ .addClass("icon-button remove-icon").tipsy( {gravity: 's'} ) .appendTo(this.icons_div); var track = this; - + // Suppress double clicks in header so that they do not impact viz. this.header_div.dblclick( function(e) { e.stopPropagation(); } ); + + // Set up behavior for modes popup. + if (track.display_modes !== undefined) { + var init_mode = (track.config && track.config.values['mode'] ? + track.config.values['mode'] : track.display_modes[0]); + track.mode = init_mode; + this.mode_icon.attr("title", "Set display mode (now: " + track.mode + ")"); + + var mode_mapping = {}; + for (var i = 0, len = track.display_modes.length; i < len; i++) { + var mode = track.display_modes[i]; + mode_mapping[mode] = function(mode) { + return function() { + track.change_mode(mode); + // HACK: the popup menu messes with the track's hover event, so manually show/hide + // icons div for now. + track.icons_div.show(); + track.container_div.mouseleave(function() { track.icons_div.hide(); } ); }; + }(mode); + } + + make_popupmenu(this.mode_icon, mode_mapping); + } - // Toggle icon hides or shows the track content + // Toggle icon hides or shows the track content. this.toggle_icon.click( function() { if ( track.content_visible ) { - track.toggle_icon.addClass("toggle-expand").removeClass("toggle"); + track.toggle_icon.addClass("toggle-expand").removeClass("toggle-contract"); track.hide_contents(); - track.mode_div.hide(); track.content_visible = false; } else { - track.toggle_icon.addClass("toggle").removeClass("toggle-expand"); + track.toggle_icon.addClass("toggle-contract").removeClass("toggle-expand"); track.content_visible = true; - track.mode_div.show(); track.show_contents(); } }); @@ -2481,35 +2504,12 @@ $(".tipsy").remove(); track.remove(); }); + + // Show icons when users is hovering over track. + this.container_div.hover( function() { track.icons_div.show(); }, function() { track.icons_div.hide(); } ); - // Set up behavior for modes popup. - if (track.display_modes !== undefined) { - if (track.mode_div === undefined) { - track.mode_div = $("<div class='right-float menubutton popup' />").appendTo(track.header_div); - var init_mode = (track.config && track.config.values['mode'] ? - track.config.values['mode'] : track.display_modes[0]); - track.mode = init_mode; - track.mode_div.text(init_mode); - - var mode_mapping = {}; - for (var i = 0, len = track.display_modes.length; i < len; i++) { - var mode = track.display_modes[i]; - mode_mapping[mode] = function(mode) { - return function() { track.change_mode(mode); }; - }(mode); - } - make_popupmenu(track.mode_div, mode_mapping); - } else { - track.mode_div.hide(); - } - - this.header_div.append( $("<div/>").css("clear", "both") ); - - // Set up config icon. - - // Show icons when users is hovering over track. - this.container_div.hover( function() { track.icons_div.show(); }, function() { track.icons_div.hide(); } ); - } + // Needed for floating elts in header. + $("<div style='clear: both'/>").appendTo(this.container_div); } // @@ -2696,12 +2696,12 @@ */ change_mode: function(name) { var track = this; - track.mode_div.text(name); // TODO: is it necessary to store the mode in two places (.mode and track_config)? track.mode = name; track.config.values['mode'] = name; track.tile_cache.clear(); track.request_draw(); + this.mode_icon.attr("title", "Set display mode (now: " + track.mode + ")"); return track; }, /** @@ -3405,13 +3405,14 @@ } }, update_auto_mode: function( mode ) { + var mode; if ( this.mode == "Auto" ) { if ( mode == "no_detail" ) { mode = "feature spans"; } else if ( mode == "summary_tree" ) { mode = "coverage histogram"; } - this.mode_div.text( "Auto (" + mode + ")" ); + this.mode_icon.attr("title", "Set display mode (now: Auto/" + mode + ")"); } }, /** diff -r 1da4a4a928fb46a7725375a2cb0baa18f32c44b4 -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd tools/picard/picard_wrapper.py --- a/tools/picard/picard_wrapper.py +++ b/tools/picard/picard_wrapper.py @@ -379,11 +379,11 @@ op.add_option('', '--taillimit', default="0") op.add_option('', '--histwidth', default="0") op.add_option('', '--minpct', default="0.01") - op.add_option('', '--malevel', action='append', type="string") + op.add_option('', '--malevel', default='') op.add_option('', '--deviations', default="0.0") # CollectAlignmentSummaryMetrics op.add_option('', '--maxinsert', default="20") - op.add_option('', '--adaptors', action='append', type="string") + op.add_option('', '--adaptors', default='') # FixMateInformation and validate # CollectGcBiasMetrics op.add_option('', '--windowsize', default='100') @@ -533,8 +533,9 @@ shutil.copy(ref_file_name,fakefasta) pic.delme.append(fakefasta) cl.append('ASSUME_SORTED=true') - adaptorseqs = ''.join([' ADAPTER_SEQUENCE=%s' % x for x in opts.adaptors]) - cl.append(adaptorseqs) + adaptlist = opts.adaptors.split(',') + adaptorseqs = ['ADAPTER_SEQUENCE=%s' % x for x in adaptlist] + cl += adaptorseqs cl.append('IS_BISULFITE_SEQUENCED=%s' % opts.bisulphite) cl.append('MAX_INSERT_SIZE=%s' % opts.maxinsert) cl.append('OUTPUT=%s' % pic.metricsOut) @@ -619,8 +620,9 @@ if float(opts.deviations) > 0.0: cl.append('DEVIATIONS=%s' % opts.deviations) if opts.malevel: - malevels = ['METRIC_ACCUMULATION_LEVEL=%s' % x for x in opts.malevel] - cl.append(' '.join(malevels)) + malists = opts.malevel.split(',') + malist = ['METRIC_ACCUMULATION_LEVEL=%s' % x for x in malists] + cl += malist stdouts,rval = pic.runPic(opts.jar, cl) if os.path.exists(pdfpath): # automake thumbnail - will be added to html cl2 = ['mogrify', '-format jpg -resize x400 %s' % pdfpath] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix grid operations for use in UserListGrid to allow for Delete, Undelete, Purge of users if the allow_user_deletion config setting is true.
by Bitbucket 10 Nov '11

10 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/26da65326612/ changeset: 26da65326612 user: greg date: 2011-11-11 01:23:44 summary: Fix grid operations for use in UserListGrid to allow for Delete, Undelete, Purge of users if the allow_user_deletion config setting is true. affected #: 5 files diff -r 52bf302e209ed6890e37fa49215d8875af7ab1f1 -r 26da65326612232bfc7a0a9beddaeb176c9974ae lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -19,7 +19,6 @@ from Cheetah.Template import Template - pkg_resources.require( 'elementtree' ) from elementtree import ElementTree, ElementInclude from elementtree.ElementTree import Element @@ -1298,6 +1297,9 @@ group_list_grid = None quota_list_grid = None repository_list_grid = None + delete_operation = None + undelete_operation = None + purge_operation = None @web.expose @web.require_admin @@ -2217,6 +2219,13 @@ **kwd ) ) elif operation == "manage roles and groups": return self.manage_roles_and_groups_for_user( trans, **kwd ) + if trans.app.config.allow_user_deletion: + if self.delete_operation not in self.user_list_grid.operations: + self.user_list_grid.operations.append( self.delete_operation ) + if self.undelete_operation not in self.user_list_grid.operations: + self.user_list_grid.operations.append( self.undelete_operation ) + if self.purge_operation not in self.user_list_grid.operations: + self.user_list_grid.operations.append( self.purge_operation ) # Render the list view return self.user_list_grid( trans, **kwd ) @web.expose diff -r 52bf302e209ed6890e37fa49215d8875af7ab1f1 -r 26da65326612232bfc7a0a9beddaeb176c9974ae lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py +++ b/lib/galaxy/web/controllers/admin.py @@ -93,11 +93,6 @@ allow_popup=False, url_args=dict( webapp="galaxy", action="reset_user_password" ) ) ] - #TODO: enhance to account for trans.app.config.allow_user_deletion here so that we can eliminate these operations if - # the setting is False - #operations.append( grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True ) ) - #operations.append( grids.GridOperation( "Undelete", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) ) - #operations.append( grids.GridOperation( "Purge", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) ) standard_filters = [ grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), grids.GridColumnFilter( "Deleted", args=dict( deleted=True, purged=False ) ), @@ -443,6 +438,9 @@ group_list_grid = GroupListGrid() quota_list_grid = QuotaListGrid() repository_list_grid = RepositoryListGrid() + delete_operation = grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True ) + undelete_operation = grids.GridOperation( "Undelete", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) + purge_operation = grids.GridOperation( "Purge", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) @web.expose @web.require_admin diff -r 52bf302e209ed6890e37fa49215d8875af7ab1f1 -r 26da65326612232bfc7a0a9beddaeb176c9974ae lib/galaxy/webapps/community/config.py --- a/lib/galaxy/webapps/community/config.py +++ b/lib/galaxy/webapps/community/config.py @@ -61,6 +61,7 @@ self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None ) self.require_login = string_as_bool( kwargs.get( "require_login", "False" ) ) self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) ) + self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) ) self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) ) self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/community" ), self.root ) diff -r 52bf302e209ed6890e37fa49215d8875af7ab1f1 -r 26da65326612232bfc7a0a9beddaeb176c9974ae lib/galaxy/webapps/demo_sequencer/config.py --- a/lib/galaxy/webapps/demo_sequencer/config.py +++ b/lib/galaxy/webapps/demo_sequencer/config.py @@ -40,6 +40,7 @@ self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None ) self.require_login = string_as_bool( kwargs.get( "require_login", "False" ) ) self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) ) + self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) ) self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/demo_sequencer" ), self.root ) self.admin_users = kwargs.get( "admin_users", "" ) diff -r 52bf302e209ed6890e37fa49215d8875af7ab1f1 -r 26da65326612232bfc7a0a9beddaeb176c9974ae lib/galaxy/webapps/reports/config.py --- a/lib/galaxy/webapps/reports/config.py +++ b/lib/galaxy/webapps/reports/config.py @@ -31,6 +31,8 @@ self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/reports" ), self.root ) self.sendmail_path = kwargs.get('sendmail_path',"/usr/sbin/sendmail") + self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) ) + self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) ) self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) self.brand = kwargs.get( 'brand', None ) self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.g2.bx.psu.edu/FrontPage' ) 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: use icon to set track mode.
by Bitbucket 10 Nov '11

10 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/52bf302e209e/ changeset: 52bf302e209e user: jgoecks date: 2011-11-11 01:01:31 summary: Trackster: use icon to set track mode. affected #: 6 files diff -r 9dbc82483bd2c72f2def795bf2a7cd5f13886a24 -r 52bf302e209ed6890e37fa49215d8875af7ab1f1 static/images/fugue/chevron-expand-bw.png Binary file static/images/fugue/chevron-expand-bw.png has changed diff -r 9dbc82483bd2c72f2def795bf2a7cd5f13886a24 -r 52bf302e209ed6890e37fa49215d8875af7ab1f1 static/images/fugue/toggle-bw.png Binary file static/images/fugue/toggle-bw.png has changed diff -r 9dbc82483bd2c72f2def795bf2a7cd5f13886a24 -r 52bf302e209ed6890e37fa49215d8875af7ab1f1 static/images/fugue/toggle-expand-bw.png Binary file static/images/fugue/toggle-expand-bw.png has changed diff -r 9dbc82483bd2c72f2def795bf2a7cd5f13886a24 -r 52bf302e209ed6890e37fa49215d8875af7ab1f1 static/june_2007_style/blue/trackster.css --- a/static/june_2007_style/blue/trackster.css +++ b/static/june_2007_style/blue/trackster.css @@ -57,6 +57,8 @@ .param-row{margin-top:0.2em;margin-left:1em;} .param-label{float:left;font-weight:bold;padding-top:0.2em;} .menu-button{margin:0px 4px 0px 4px;} +.chevron-expand{background:transparent url(../images/fugue/chevron-expand-bw.png) no-repeat;} +.chevron-expand:hover{background:transparent url(../images/fugue/chevron-expand.png) no-repeat;} .settings-icon{background:transparent url(../images/fugue/gear-bw.png) no-repeat;} .settings-icon:hover{background:transparent url(../images/fugue/gear.png) no-repeat;} .overview-icon{background:transparent url(../images/fugue/application-dock-270-bw.png) no-repeat;} diff -r 9dbc82483bd2c72f2def795bf2a7cd5f13886a24 -r 52bf302e209ed6890e37fa49215d8875af7ab1f1 static/june_2007_style/trackster.css.tmpl --- a/static/june_2007_style/trackster.css.tmpl +++ b/static/june_2007_style/trackster.css.tmpl @@ -297,6 +297,12 @@ .menu-button { margin: 0px 4px 0px 4px; } +.chevron-expand { + background: transparent url(../images/fugue/chevron-expand-bw.png) no-repeat; +} +.chevron-expand:hover { + background:transparent url(../images/fugue/chevron-expand.png) no-repeat; +} .settings-icon { background: transparent url(../images/fugue/gear-bw.png) no-repeat; } diff -r 9dbc82483bd2c72f2def795bf2a7cd5f13886a24 -r 52bf302e209ed6890e37fa49215d8875af7ab1f1 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -2381,16 +2381,18 @@ // Create and initialize track header and icons. if (show_header) { - this.header_div = $("<div class='track-header' />").appendTo(this.container_div); + this.header_div = $("<div class='track-header'/>").appendTo(this.container_div); if (this.view.editor) { this.drag_div = $("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div); } this.name_div = $("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name) .attr( "id", this.name.replace(/\s+/g,'-').replace(/[^a-zA-Z0-9\-]/g,'').toLowerCase() ); this.icons_div = $("<div/>").css("float", "left").appendTo(this.header_div).hide(); // Track icons. + this.mode_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Set display mode") + .addClass("icon-button chevron-expand").tipsy( {gravity: 's'} ).appendTo(this.icons_div); this.toggle_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Hide/show track content") - .addClass("icon-button toggle-contract").tipsy( {gravity: 's'} ) - .appendTo(this.icons_div); + .addClass("icon-button toggle-contract").tipsy( {gravity: 's'} ) + .appendTo(this.icons_div); this.settings_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Edit settings") .addClass("icon-button settings-icon").tipsy( {gravity: 's'} ) .appendTo(this.icons_div); @@ -2407,21 +2409,42 @@ .addClass("icon-button remove-icon").tipsy( {gravity: 's'} ) .appendTo(this.icons_div); var track = this; - + // Suppress double clicks in header so that they do not impact viz. this.header_div.dblclick( function(e) { e.stopPropagation(); } ); + + // Set up behavior for modes popup. + if (track.display_modes !== undefined) { + var init_mode = (track.config && track.config.values['mode'] ? + track.config.values['mode'] : track.display_modes[0]); + track.mode = init_mode; + this.mode_icon.attr("title", "Set display mode (now: " + track.mode + ")"); + + var mode_mapping = {}; + for (var i = 0, len = track.display_modes.length; i < len; i++) { + var mode = track.display_modes[i]; + mode_mapping[mode] = function(mode) { + return function() { + track.change_mode(mode); + // HACK: the popup menu messes with the track's hover event, so manually show/hide + // icons div for now. + track.icons_div.show(); + track.container_div.mouseleave(function() { track.icons_div.hide(); } ); }; + }(mode); + } + + make_popupmenu(this.mode_icon, mode_mapping); + } - // Toggle icon hides or shows the track content + // Toggle icon hides or shows the track content. this.toggle_icon.click( function() { if ( track.content_visible ) { track.toggle_icon.addClass("toggle-expand").removeClass("toggle-contract"); track.hide_contents(); - track.mode_div.hide(); track.content_visible = false; } else { track.toggle_icon.addClass("toggle-contract").removeClass("toggle-expand"); track.content_visible = true; - track.mode_div.show(); track.show_contents(); } }); @@ -2481,35 +2504,12 @@ $(".tipsy").remove(); track.remove(); }); + + // Show icons when users is hovering over track. + this.container_div.hover( function() { track.icons_div.show(); }, function() { track.icons_div.hide(); } ); - // Set up behavior for modes popup. - if (track.display_modes !== undefined) { - if (track.mode_div === undefined) { - track.mode_div = $("<div class='right-float menubutton popup' />").appendTo(track.header_div); - var init_mode = (track.config && track.config.values['mode'] ? - track.config.values['mode'] : track.display_modes[0]); - track.mode = init_mode; - track.mode_div.text(init_mode); - - var mode_mapping = {}; - for (var i = 0, len = track.display_modes.length; i < len; i++) { - var mode = track.display_modes[i]; - mode_mapping[mode] = function(mode) { - return function() { track.change_mode(mode); }; - }(mode); - } - make_popupmenu(track.mode_div, mode_mapping); - } else { - track.mode_div.hide(); - } - - this.header_div.append( $("<div/>").css("clear", "both") ); - - // Set up config icon. - - // Show icons when users is hovering over track. - this.container_div.hover( function() { track.icons_div.show(); }, function() { track.icons_div.hide(); } ); - } + // Needed for floating elts in header. + $("<div style='clear: both'/>").appendTo(this.container_div); } // @@ -2696,12 +2696,12 @@ */ change_mode: function(name) { var track = this; - track.mode_div.text(name); // TODO: is it necessary to store the mode in two places (.mode and track_config)? track.mode = name; track.config.values['mode'] = name; track.tile_cache.clear(); track.request_draw(); + this.mode_icon.attr("title", "Set display mode (now: " + track.mode + ")"); return track; }, /** @@ -3405,13 +3405,14 @@ } }, update_auto_mode: function( mode ) { + var mode; if ( this.mode == "Auto" ) { if ( mode == "no_detail" ) { mode = "feature spans"; } else if ( mode == "summary_tree" ) { mode = "coverage histogram"; } - this.mode_div.text( "Auto (" + mode + ")" ); + this.mode_icon.attr("title", "Set display mode (now: Auto/" + mode + ")"); } }, /** Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Make toggle icons use black and white and color on hover to match other Trackster icons.
by Bitbucket 10 Nov '11

10 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9dbc82483bd2/ changeset: 9dbc82483bd2 user: jgoecks date: 2011-11-10 22:16:26 summary: Make toggle icons use black and white and color on hover to match other Trackster icons. affected #: 5 files diff -r 6ec2d7f4a64dcf6a1c49415bd8f40c8d4ca907c5 -r 9dbc82483bd2c72f2def795bf2a7cd5f13886a24 static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl +++ b/static/june_2007_style/base.css.tmpl @@ -865,10 +865,6 @@ -sprite-group: fugue; -sprite-image: fugue/toggle-expand.png; } -.icon-button.toggle { - -sprite-group: fugue; - -sprite-image: fugue/toggle.png; -} .icon-button.toggle-contract { -sprite-group: fugue; -sprite-image: fugue/toggle.png; diff -r 6ec2d7f4a64dcf6a1c49415bd8f40c8d4ca907c5 -r 9dbc82483bd2c72f2def795bf2a7cd5f13886a24 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -151,9 +151,10 @@ .icon-button.tag{background:url(fugue.png) no-repeat 0px -0px;} .icon-button.tags{background:url(fugue.png) no-repeat 0px -26px;} .icon-button.tag--plus{background:url(fugue.png) no-repeat 0px -52px;} -.icon-button.toggle-expand{background:url(fugue.png) no-repeat 0px -78px;} -.icon-button.toggle{background:url(fugue.png) no-repeat 0px -104px;} -.icon-button.toggle-contract{background:url(fugue.png) no-repeat 0px -104px;} +.icon-button.toggle-expand{background:transparent url(../images/fugue/toggle-expand-bw.png) no-repeat;} +.icon-button.toggle-expand:hover{background:url(fugue.png) no-repeat 0px -78px;} +.icon-button.toggle-contract{background:transparent url(../images/fugue/toggle-bw.png) no-repeat;} +.icon-button.toggle-contract:hover{background:url(fugue.png) no-repeat 0px -104px;} .icon-button.arrow-circle{background:url(fugue.png) no-repeat 0px -130px;} .icon-button.chevron{background:url(fugue.png) no-repeat 0px -156px;} .icon-button.bug{background:url(fugue.png) no-repeat 0px -182px;} diff -r 6ec2d7f4a64dcf6a1c49415bd8f40c8d4ca907c5 -r 9dbc82483bd2c72f2def795bf2a7cd5f13886a24 static/june_2007_style/blue/trackster.css --- a/static/june_2007_style/blue/trackster.css +++ b/static/june_2007_style/blue/trackster.css @@ -56,7 +56,7 @@ .tool-name{font-size:110%;font-weight:bold;} .param-row{margin-top:0.2em;margin-left:1em;} .param-label{float:left;font-weight:bold;padding-top:0.2em;} -.menu-button{padding:0px 4px 0px 4px;} +.menu-button{margin:0px 4px 0px 4px;} .settings-icon{background:transparent url(../images/fugue/gear-bw.png) no-repeat;} .settings-icon:hover{background:transparent url(../images/fugue/gear.png) no-repeat;} .overview-icon{background:transparent url(../images/fugue/application-dock-270-bw.png) no-repeat;} diff -r 6ec2d7f4a64dcf6a1c49415bd8f40c8d4ca907c5 -r 9dbc82483bd2c72f2def795bf2a7cd5f13886a24 static/june_2007_style/trackster.css.tmpl --- a/static/june_2007_style/trackster.css.tmpl +++ b/static/june_2007_style/trackster.css.tmpl @@ -295,7 +295,7 @@ padding-top: 0.2em; } .menu-button { - padding: 0px 4px 0px 4px; + margin: 0px 4px 0px 4px; } .settings-icon { background: transparent url(../images/fugue/gear-bw.png) no-repeat; diff -r 6ec2d7f4a64dcf6a1c49415bd8f40c8d4ca907c5 -r 9dbc82483bd2c72f2def795bf2a7cd5f13886a24 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -2389,7 +2389,7 @@ // Track icons. this.toggle_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Hide/show track content") - .addClass("icon-button toggle").tipsy( {gravity: 's'} ) + .addClass("icon-button toggle-contract").tipsy( {gravity: 's'} ) .appendTo(this.icons_div); this.settings_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Edit settings") .addClass("icon-button settings-icon").tipsy( {gravity: 's'} ) @@ -2414,12 +2414,12 @@ // Toggle icon hides or shows the track content this.toggle_icon.click( function() { if ( track.content_visible ) { - track.toggle_icon.addClass("toggle-expand").removeClass("toggle"); + track.toggle_icon.addClass("toggle-expand").removeClass("toggle-contract"); track.hide_contents(); track.mode_div.hide(); track.content_visible = false; } else { - track.toggle_icon.addClass("toggle").removeClass("toggle-expand"); + track.toggle_icon.addClass("toggle-contract").removeClass("toggle-expand"); track.content_visible = true; track.mode_div.show(); track.show_contents(); 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 slug check flag pointed out by Andrew Warren.
by Bitbucket 10 Nov '11

10 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6ec2d7f4a64d/ changeset: 6ec2d7f4a64d user: dannon date: 2011-11-10 20:56:35 summary: Fix for slug check flag pointed out by Andrew Warren. affected #: 1 file diff -r 429f6b869c71b2aa2df8d6b61b6e12cd22fc8a4d -r 6ec2d7f4a64dcf6a1c49415bd8f40c8d4ca907c5 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -149,7 +149,8 @@ # Legacy issue: all shared workflows must have slugs. slug_set = False for workflow_assoc in shared_by_others: - slug_set = self.create_item_slug( trans.sa_session, workflow_assoc.stored_workflow ) + if self.create_item_slug( trans.sa_session, workflow_assoc.stored_workflow ): + slug_set = True if slug_set: trans.sa_session.flush() 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 an exception class that doesn't exist. Thanks Oleksandr Moskalenko.
by Bitbucket 10 Nov '11

10 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/429f6b869c71/ changeset: 429f6b869c71 user: natefoo date: 2011-11-10 18:49:44 summary: Fix an exception class that doesn't exist. Thanks Oleksandr Moskalenko. affected #: 1 file diff -r d9408bcb3cf4bcb81e9dac4ddeda74cbc164e123 -r 429f6b869c71b2aa2df8d6b61b6e12cd22fc8a4d lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -607,7 +607,7 @@ log.error( "The server didn't accept the username/password combination: %s" % e ) s.close() raise - except smtplib.SMTPError, e: + except smtplib.SMTPException, e: log.error( "No suitable authentication method was found: %s" % e ) s.close() raise Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Eliminate the non-functional PacBio tools from the distribution and the sample tool config.
by Bitbucket 10 Nov '11

10 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d9408bcb3cf4/ changeset: d9408bcb3cf4 user: greg date: 2011-11-10 18:09:45 summary: Eliminate the non-functional PacBio tools from the distribution and the sample tool config. affected #: 14 files diff -r 3565ae97160f4a70b3910b54bcd98c0f4c7d1796 -r d9408bcb3cf4bcb81e9dac4ddeda74cbc164e123 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -477,17 +477,6 @@ <tool file="vcf_tools/filter.xml" /><tool file="vcf_tools/extract.xml" /></section> - <section name="PacBio/Illumina Assembly" id="hybrid"> - <tool file="ilmn_pacbio/quake.xml"/> - <tool file="ilmn_pacbio/quake_pe.xml"/> - <tool file="ilmn_pacbio/soap_denovo.xml"/> -  - <tool file="ilmn_pacbio/smrtpipe_hybrid.xml"/> - <tool file="ilmn_pacbio/assembly_stats.xml"/> - </section> - <inputs> - <param name="contigs" format="fasta" type="data" label="Starting Contigs"/> - <param name="reads" format="fasta" type="data" label="PacBio Reads"/> - <param name="schedule" type="text" value="6,3,75;6,3,75;5,3,75;5,3,75;6,2,75;6,2,75;5,2,75;5,2,75" label="Parameter Schedule" size="60"/> - </inputs> - <configfiles> - <configfile name="iniFile"> -[input] -assembled_contigs:${contigs} -file:${reads} - -[HybridAssembly] -instrumentModel=RS -cleanup=False -untangler=pacbio -#set $schedule2 = $schedule.replace('X',';') -paramSchedule=${schedule2} -dontFillin=False -longReadsAsStrobe=True -exactQueryIds=True -rm4Opts=-minMatch 7 -minFrac 0.1 -minPctIdentity 65 -bestn 10 -noSplitSubreads -numberProcesses=16 -cluster=False -minRepeatLength=100000 - </configfile> - </configfiles> - <outputs> - <data name="outfile" format="fasta" label="Hybrid assembly contigs from ${on_string}"/> - </outputs> - <help> - -**What it does** - -The AHA assembly algorithm is an AMOS_-based pipeline -for finishing bacterial-sized -genomes using draft contigs and PacBio reads. - -.. _AMOS: http://sourceforge.net/apps/mediawiki/amos - -**Parameter list** - -Parameter schedule - The parameter schedule is a semi-colon delimited list of triples. Each triple represents an iteration of hybrid assembly (alignment/scaffolding/gap-filling). The three paremeters for each iteration are the Z-score, number of reads required to define a link, and the minimum length of subreads used in links. - -**Output** - -FASTA file containing scaffolded and gap-filled contigs resulting from the -hybrid assembly. - - </help> -</tool> diff -r 3565ae97160f4a70b3910b54bcd98c0f4c7d1796 -r d9408bcb3cf4bcb81e9dac4ddeda74cbc164e123 tools/ilmn_pacbio/soap_denovo.xml --- a/tools/ilmn_pacbio/soap_denovo.xml +++ /dev/null @@ -1,73 +0,0 @@ -<tool id="soap_denovo" name="SOAPdenovo" version="1.0.0"> - <description>Short-read de novo assembly</description> -  - <command> - SOAPdenovo-127mer all -s ${soap_config} -o assembly -K ${k} -p 24 -d -D -R - </command> - <inputs> - <conditional name="inputs"> - <param name="read_type" type="select" label="Illumina read type"> - <option value="single">Single fragment</option> - <option value="paired">Paired-end</option> - </param> - <when value="single"> - <param name="input1" format="fastq" type="data" label="FASTQ file for reads"/> - </when> - <when value="paired"> - <param name="input1" format="fastq" type="data" label="FASTQ file for forward reads"/> - <param name="input2" format="fastq" type="data" label="FASTQ file for reverse reads"/> - <param name="d" type="integer" value="500" label="Estimated insert size for paired-end reads" /> - </when> - </conditional> - <param name="k" type="integer" value="23" label="Size of k for forming the de Bruijn overlap graph" /> - </inputs> - <configfiles> - <configfile name="soap_config">max_rd_len=105 -[LIB] -#if $inputs.read_type == "single" -q=${inputs.input1.file_name} -#else -avg_ins=${inputs.d} -asm_flags=3 -reverse_seq=0 -q1=${inputs.input1.file_name} -q2=${inputs.input2.file_name} -#end if - </configfile> - </configfiles> - <outputs> - <data name="assembled_contigs" format="fasta" from_work_dir="assembly.scafSeq" label="Assembled contigs from ${on_string}" /> - </outputs> - <help> - -**What it does** - -Runs SOAPdenovo_ to generate a genome assembly -using single-fragment or paired-end short reads. - -Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J. -"De novo assembly of human genomes with massively parallel short read sequencing." -*Genome Res.* 2010 Feb;20(2):265-72. - -.. _SOAPdenovo: http://soap.genomics.org.cn/soapdenovo.html - -**Parameter list** - -k - k-mer size for constructing the de Bruijn graph. The appropriate size of k is genome and data set dependent, but a good starting choice might be 75% of the read length. - -Insert size - For paired-end libraries, the expected insert size. - -**Output** - -assembly - - </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: dan: Update GeneTrack help.
by Bitbucket 10 Nov '11

10 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3565ae97160f/ changeset: 3565ae97160f user: dan date: 2011-11-10 17:54:50 summary: Update GeneTrack help. affected #: 2 files diff -r b62855bbd52e68b7ecac586e3bc329c7e472bc47 -r 3565ae97160f4a70b3910b54bcd98c0f4c7d1796 tools/genetrack/genetrack_indexer.xml --- a/tools/genetrack/genetrack_indexer.xml +++ b/tools/genetrack/genetrack_indexer.xml @@ -49,10 +49,14 @@ When shifting the averaging process in GeneTrack is able correct for longer or shorter than expected fragment sizes as long as the errors are reasonably random. +See http://genetrack.bx.psu.edu/ for more information on GeneTrack. + ------ **Citation** +For the underlying tool, please cite `Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics. 2008 May 15;24(10):1305-6. <http://www.ncbi.nlm.nih.gov/pubmed/18388141>`_ + If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* </help> diff -r b62855bbd52e68b7ecac586e3bc329c7e472bc47 -r 3565ae97160f4a70b3910b54bcd98c0f4c7d1796 tools/genetrack/genetrack_peak_prediction.xml --- a/tools/genetrack/genetrack_peak_prediction.xml +++ b/tools/genetrack/genetrack_peak_prediction.xml @@ -54,10 +54,14 @@ - **Prediction method** the function used to average nearby values +See http://genetrack.bx.psu.edu/ for more information on GeneTrack. + ------ **Citation** +For the underlying tool, please cite `Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics. 2008 May 15;24(10):1305-6. <http://www.ncbi.nlm.nih.gov/pubmed/18388141>`_ + If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* </help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add the ability to enter a new tool panel section label when installing repositories with tools from a tool shed in addition to being able to choose an existing tool panel section for containing the tools. Also clean up code related to message displayed when a local Galaxy instance is missing tools required by an imported workflow.
by Bitbucket 10 Nov '11

10 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b62855bbd52e/ changeset: b62855bbd52e user: greg date: 2011-11-10 16:57:39 summary: Add the ability to enter a new tool panel section label when installing repositories with tools from a tool shed in addition to being able to choose an existing tool panel section for containing the tools. Also clean up code related to message displayed when a local Galaxy instance is missing tools required by an imported workflow. affected #: 5 files diff -r 23198e766859394108d48de1489be7052530d38b -r b62855bbd52e68b7ecac586e3bc329c7e472bc47 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -22,6 +22,7 @@ pkg_resources.require( 'elementtree' ) from elementtree import ElementTree, ElementInclude +from elementtree.ElementTree import Element log = logging.getLogger( __name__ ) diff -r 23198e766859394108d48de1489be7052530d38b -r b62855bbd52e68b7ecac586e3bc329c7e472bc47 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py +++ b/lib/galaxy/web/controllers/admin.py @@ -3,7 +3,7 @@ from galaxy.model.orm import * from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.tools.search import ToolBoxSearch -from galaxy.tools import json_fix +from galaxy.tools import ToolSection, json_fix import logging log = logging.getLogger( __name__ ) @@ -403,7 +403,7 @@ def get_value( self, trans, grid, tool_shed_repository ): return tool_shed_repository.tool_shed # Grid definition - title = "Tool shed repositories" + title = "Installed tool shed repositories" model_class = model.ToolShedRepository template='/admin/tool_shed_repository/grid.mako' default_sort_key = "name" @@ -807,28 +807,45 @@ status = kwd.get( 'status', 'done' ) tool_shed_url = kwd[ 'tool_shed_url' ] repo_info_dict = kwd[ 'repo_info_dict' ] + new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' ) + tool_panel_section = kwd.get( 'tool_panel_section', '' ) if kwd.get( 'select_tool_panel_section_button', False ): shed_tool_conf = kwd[ 'shed_tool_conf' ] # Get the tool path. for k, tool_path in trans.app.toolbox.shed_tool_confs.items(): if k == shed_tool_conf: break - if 'tool_panel_section' in kwd: - section_key = 'section_%s' % kwd[ 'tool_panel_section' ] - tool_section = trans.app.toolbox.tool_panel[ section_key ] + if new_tool_panel_section or tool_panel_section: + if new_tool_panel_section: + section_id = new_tool_panel_section.lower().replace( ' ', '_' ) + new_section_key = 'section_%s' % str( section_id ) + if new_section_key in trans.app.toolbox.tool_panel: + # Appending a tool to an existing section in trans.app.toolbox.tool_panel + log.debug( "Appending to tool panel section: %s" % new_tool_panel_section ) + tool_section = trans.app.toolbox.tool_panel[ new_section_key ] + else: + # Appending a new section to trans.app.toolbox.tool_panel + log.debug( "Loading new tool panel section: %s" % new_tool_panel_section ) + elem = Element( 'section' ) + elem.attrib[ 'name' ] = new_tool_panel_section + elem.attrib[ 'id' ] = section_id + tool_section = ToolSection( elem ) + trans.app.toolbox.tool_panel[ new_section_key ] = tool_section + else: + section_key = 'section_%s' % tool_panel_section + tool_section = trans.app.toolbox.tool_panel[ section_key ] # Decode the encoded repo_info_dict param value. repo_info_dict = tool_shed_decode( repo_info_dict ) # Clone the repository to the configured location. current_working_dir = os.getcwd() + installed_repository_names = [] for name, repo_info_tuple in repo_info_dict.items(): description, repository_clone_url, changeset_revision = repo_info_tuple clone_dir = os.path.join( tool_path, self.__generate_tool_path( repository_clone_url, changeset_revision ) ) if os.path.exists( clone_dir ): # Repository and revision has already been cloned. # TODO: implement the ability to re-install or revert an existing repository. - message += 'Revision <b>%s</b> of repository <b>%s</b> has already been installed. Updating an existing repository is not yet supported.<br/>' % \ - ( changeset_revision, name ) - status = 'error' + message += 'Revision <b>%s</b> of repository <b>%s</b> was previously installed.<br/>' % ( changeset_revision, name ) else: os.makedirs( clone_dir ) log.debug( 'Cloning %s...' % repository_clone_url ) @@ -892,9 +909,7 @@ if trans.app.toolbox_search.enabled: # If search support for tools is enabled, index the new installed tools. trans.app.toolbox_search = ToolBoxSearch( trans.app.toolbox ) - message += 'Revision <b>%s</b> of repository <b>%s</b> has been loaded into tool panel section <b>%s</b>.<br/>' % \ - ( changeset_revision, name, tool_section.name ) - #return trans.show_ok_message( message ) + installed_repository_names.append( name ) else: tmp_stderr = open( tmp_name, 'rb' ) message += '%s<br/>' % tmp_stderr.read() @@ -905,6 +920,19 @@ message += '%s<br/>' % tmp_stderr.read() tmp_stderr.close() status = 'error' + if installed_repository_names: + installed_repository_names.sort() + message += 'These %d repositories were installed and all tools were loaded into tool panel section <b>%s</b>:<br/>' % \ + ( len( installed_repository_names ), tool_section.name ) + for i, repo_name in enumerate( installed_repository_names ): + if i == len( installed_repository_names ) -1: + message += '%s.<br/>' % repo_name + else: + message += '%s, ' % repo_name + return trans.response.send_redirect( web.url_for( controller='admin', + action='browse_tool_shed_repositories', + message=message, + status=status ) ) else: message = 'Choose the section in your tool panel to contain the installed tools.' status = 'error' @@ -921,6 +949,7 @@ shed_tool_conf=shed_tool_conf, shed_tool_conf_select_field=shed_tool_conf_select_field, tool_panel_section_select_field=tool_panel_section_select_field, + new_tool_panel_section=new_tool_panel_section, message=message, status=status ) @web.expose diff -r 23198e766859394108d48de1489be7052530d38b -r b62855bbd52e68b7ecac586e3bc329c7e472bc47 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -1115,10 +1115,10 @@ workflow_name = tool_shed_decode( workflow_name ) # The following parameters will have a value only if the import originated # from a tool shed repository installed locally. - local_file = kwd.get( 'local_file', '' ) + installed_repository_file = kwd.get( 'installed_repository_file', '' ) repository_id = kwd.get( 'repository_id', '' ) - if local_file and not import_button: - workflow_file = open( local_file, 'rb' ) + if installed_repository_file and not import_button: + workflow_file = open( installed_repository_file, 'rb' ) workflow_text = workflow_file.read() workflow_file.close() import_button = True @@ -1197,27 +1197,26 @@ if shed_url.endswith( '/' ): shed_url = shed_url.rstrip( '/' ) url = '%s/repository/find_tools?galaxy_url=%s&webapp=%s' % ( shed_url, trans.request.host, webapp ) + if missing_tool_tups: + url += '&tool_id=' for missing_tool_tup in missing_tool_tups: missing_tool_id = missing_tool_tup[0] - url += '&tool_id=%s' % missing_tool_id + url += '%s,' % missing_tool_id message += '<a href="%s">%s</a><br/>' % ( url, shed_name ) status = 'error' - if local_file or tool_shed_url: + if installed_repository_file or tool_shed_url: # Another Galaxy panels Hack: The request did not originate from the Galaxy # workflow view, so we don't need to render the Galaxy panels. - return trans.response.send_redirect( web.url_for( controller='admin', - action='center', - webapp='galaxy', - message=message, - status=status ) ) + action = 'center' else: # Another Galaxy panels hack: The request originated from the Galaxy # workflow view, so we need to render the Galaxy panels. - return trans.response.send_redirect( web.url_for( controller='admin', - action='index', - webapp='galaxy', - message=message, - status=status ) ) + action = 'index' + return trans.response.send_redirect( web.url_for( controller='admin', + action=action, + webapp='galaxy', + message=message, + status=status ) ) else: # TODO: Figure out what to do here... pass @@ -1228,7 +1227,7 @@ url = 'http://%s/workflow/view_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&message=%s' % \ ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp, message ) return trans.response.send_redirect( url ) - elif local_file: + elif installed_repository_file: # The workflow was read from a file included with an installed tool shed repository. message = "Workflow <b>%s</b> imported successfully." % workflow.name return trans.response.send_redirect( web.url_for( controller='admin', diff -r 23198e766859394108d48de1489be7052530d38b -r b62855bbd52e68b7ecac586e3bc329c7e472bc47 templates/admin/select_tool_panel_section.mako --- a/templates/admin/select_tool_panel_section.mako +++ b/templates/admin/select_tool_panel_section.mako @@ -23,7 +23,7 @@ <br/><div class="toolForm"> - <div class="toolFormTitle">Load tools into tool panel</div> + <div class="toolFormTitle">Choose section to load tools into tool panel</div><div class="toolFormBody"><form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin', action='install_tool_shed_repository', tool_shed_url=tool_shed_url, repo_info_dict=repo_info_dict )}" method="post" > %if shed_tool_conf_select_field: @@ -40,10 +40,17 @@ <input type="hidden" name="shed_tool_conf" value="${shed_tool_conf}"/> %endif <div class="form-row"> - <label>Tool panel section:</label> + <label>Add new tool panel section:</label> + <input name="new_tool_panel_section" type="textfield" value="${new_tool_panel_section}" size="40"/> + <div class="toolParamHelp" style="clear: both;"> + Add a new tool panel section or choose an existing section in your tool panel below to contain the installed tools. + </div> + </div> + <div class="form-row"> + <label>Select existing tool panel section:</label> ${tool_panel_section_select_field.get_html()} <div class="toolParamHelp" style="clear: both;"> - Choose the section in your tool panel to contain the installed tools. + Choose an existing section in your tool panel to contain the installed tools. </div></div><div class="form-row"> diff -r 23198e766859394108d48de1489be7052530d38b -r b62855bbd52e68b7ecac586e3bc329c7e472bc47 templates/admin/tool_shed_repository/browse_repository.mako --- a/templates/admin/tool_shed_repository/browse_repository.mako +++ b/templates/admin/tool_shed_repository/browse_repository.mako @@ -103,7 +103,7 @@ <div class="menubutton" style="float: left;" id="workflow-${index}-popup"> ${workflow_name} <div popupmenu="workflow-${index}-popup"> - <a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', local_file=full_path, repository_id=trans.security.encode_id( repository.id ) )}">Import to Galaxy</a> + <a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', installed_repository_file=full_path, repository_id=trans.security.encode_id( repository.id ) )}">Import to Galaxy</a></div></div></td> 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: Repack of .js
by Bitbucket 10 Nov '11

10 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/23198e766859/ changeset: 23198e766859 user: dannon date: 2011-11-10 14:54:23 summary: Repack of .js affected #: 3 files diff -r a4df07ccecdb70ae45982e596d2e360bdc9ab217 -r 23198e766859394108d48de1489be7052530d38b static/scripts/packed/galaxy.panels.js --- a/static/scripts/packed/galaxy.panels.js +++ b/static/scripts/packed/galaxy.panels.js @@ -1,1 +1,1 @@ -function ensure_dd_helper(){if($("#DD-helper").length==0){$("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}var MIN_PANEL_WIDTH=100,MAX_PANEL_WIDTH=1000;function make_left_panel(h,c,e){var g=false;var f=null;var d=function(i){var j=i;if(i<0){i=0}$(h).css("width",i);$(e).css("left",j);$(c).css("left",i+7);if(document.recalc){document.recalc()}};var 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a=c.scroll||"auto";$("#overlay-background").bind("click.overlay",function(){hide_modal();$("#overlay-background").unbind("click.overlay")});show_modal(null,$("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+image_path+"/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+c.url+"' width='"+d+"' height='"+b+"' scrolling='"+a+"' frameborder='0'></iframe></div>"));$("#close_button").bind("click",function(){hide_modal()})}$(function(){$(".tab").each(function(){var a=$(this).children(".submenu");if(a.length>0){if($.browser.msie){a.prepend("<iframe style=\"position: absolute; top: 0; left: 0; width: 100%; height: 100%; z-index: -1; filter:Alpha(Opacity='0');\"></iframe>")}$(this).hover(function(){a.show()},function(){a.hide()});a.click(function(){a.hide()})}})});function user_changed(a,b){if(a){$(".loggedin-only").show();$(".loggedout-only").hide();$("#user-email").text(a);if(b){$(".admin-only").show()}}else{$(".loggedin-only").hide();$(".loggedout-only").show();$(".admin-only").hide()}}; \ No newline at end of file diff -r a4df07ccecdb70ae45982e596d2e360bdc9ab217 -r 23198e766859394108d48de1489be7052530d38b 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 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 m=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(u,t,v,r,i,s){return(Math.max(u,r)-Math.min(u,r))+(Math.max(t,i)-Math.min(t,i))+(Math.max(v,s)-Math.min(v,s))};var g,n,f,k,p,h,q,c,d,b,o,l=false;do{g=Math.random()*16777215;n=g|16711680;f=g|65280;k=g|255;d=m(n,f,k);l=true;for(var j=0;j<a.length;j++){p=a[j];h=p|16711680;q=p|65280;c=p|255;b=m(h,q,c);o=e(n,f,k,h,q,c);if((Math.abs(d-b)<125)||(o<500)){l=false;break}}}while(!l);return"#"+(16777216+g).toString(16).substr(1,6)};var trackster_module=function(f,X){var p=f("class").extend,s=f("slotting"),M=f("painters");var ae=function(af,ag){this.document=af;this.default_font=ag!==undefined?ag:"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(ae.prototype,{load_pattern:function(af,aj){var ag=this.patterns,ah=this.dummy_context,ai=new 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av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable(ap);return}}}al=null;for(ao=0;ao<an.length;ao++){am=$(an.get(ao));au=am.position().top;ak=au+am.outerHeight();if(am.is(aj)&&this!==am.get(0)&&at.offsetY>=au&&at.offsetY<=ak){if(at.offsetY-au<ak-at.offsetY){am.find(".content-div").prepend(this)}else{am.find(".content-div").append(this)}if(ap.container){ap.container.remove_drawable(ap)}n[am.attr("id")].add_drawable(ap);return}}for(ao=0;ao<an.length;ao++){if(at.offsetY<$(an.get(ao)).position().top){break}}if(ao===an.length){if(this!==an.get(ao-1)){aw.append(this);n[aw.attr("id")].move_drawable(ap,ao)}}else{if(this!==an.get(ao)){$(this).insertBefore(an.get(ao));n[aw.attr("id")].move_drawable(ap,(at.deltaY>0?ao-1:ao))}}}).bind("dragstart",function(){ag["border-top"]=af.css("border-top");ag["border-bottom"]=af.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ag)})};X.moveable=m;var ad=16,H=9,E=20,T=H+2,z=100,J=12000,R=200,C=5,v=10,L=5000,w=100,o="There was an error in indexing this dataset. ",K="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",F="No data for this chrom/contig.",t="Currently indexing... please wait",x="Tool cannot be rerun: ",a="Loading data...",Y="Ready for display",d=10,u=5,B=5;function Z(ag,af){if(!af){af=0}var ah=Math.pow(10,af);return Math.round(ag*ah)/ah}var c=function(af){this.num_elements=af;this.clear()};p(c.prototype,{get:function(ag){var af=this.key_ary.indexOf(ag);if(af!==-1){if(this.obj_cache[ag].stale){this.key_ary.splice(af,1);delete this.obj_cache[ag]}else{this.move_key_to_end(ag,af)}}return this.obj_cache[ag]},set:function(ag,ah){if(!this.obj_cache[ag]){if(this.key_ary.length>=this.num_elements){var af=this.key_ary.shift();delete this.obj_cache[af]}this.key_ary.push(ag)}this.obj_cache[ag]=ah;return ah},move_key_to_end:function(ag,af){this.key_ary.splice(af,1);this.key_ary.push(ag)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var 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ag=an;if(aj===this.DEEP_DATA_REQ){$.extend(al,{start_val:ao.data.length+1})}else{if(aj===this.BROAD_DATA_REQ){ag=(ao.max_high?ao.max_high:ao.data[ao.data.length-1][2])+1}}var af=this,ak=this.load_data(ag,ai,am,ah,al);new_data_available=$.Deferred();this.set_data(an,ai,am,new_data_available);$.when(ak).then(function(ap){if(ap.data){ap.data=ao.data.concat(ap.data);if(ap.max_low){ap.max_low=ao.max_low}if(ap.message){ap.message=ap.message.replace(/[0-9]+/,ap.data.length)}}af.set_data(an,ai,am,ap);new_data_available.resolve(ap)});return new_data_available},get_data_from_cache:function(af,ag,ah){return this.get(this.gen_key(af,ag,ah))},set_data:function(ag,ah,ai,af){return this.set(this.gen_key(ag,ah,ai),af)},gen_key:function(af,ah,ai){var ag=af+"_"+ah+"_"+ai;return ag},split_key:function(af){return af.split("_")}});var I=function(ag,af,ah){S.call(this,ag,af,ah)};p(I.prototype,S.prototype,c.prototype,{load_data:function(af,ai,aj,ag,ah){if(ag>1){return{data:null}}return S.prototype.load_data.call(this,af,ai,aj,ag,ah)}});var q=function(ai,ag,af,ah,aj){this.name=ai;this.view=ag;this.container=af;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ai}],saved_values:ah,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=aj;this.is_overview=false};p(q.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_track_icons:function(){},set_name:function(af){this.old_name=this.name;this.name=af;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var y=function(aj,ai,ag,af,ah,ak){q.call(this,ai,ag,af,ah,ak);this.obj_type=aj;this.drawables=[]};p(y.prototype,q.prototype,{init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_json:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},add_drawable:function(af){this.drawables.push(af);af.container=this},add_drawable_before:function(ah,af){var ag=this.drawables.indexOf(af);if(ag!=-1){this.drawables.splice(ag,0,ah);return true}return false},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);ag.container=null;return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);return true}return false}});var Q=function(ai,ag,af,ah){y.call(this,"DrawableGroup",ai,ag,af,ah,"group-handle");if(!Q.id_counter){Q.id_counter=0}var aj=Q.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+aj).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+aj+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.update_track_icons()};p(Q.prototype,q.prototype,y.prototype,{update_track_icons:function(){var ag=this;var af={};af["Edit configuration"]=function(){var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){ah()}}};$(window).bind("keypress.check_enter_esc",ai);show_modal("Configure Group",ag.config.build_form(),{Cancel:aj,OK:ah})};af.Remove=function(){ag.remove()};make_popupmenu(ag.name_div,af)}});var ac=function(af,ai,ah,ag){y.call(this,"View");this.container=af;this.chrom=null;this.vis_id=ah;this.dbkey=ag;this.title=ai;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ae(af.get(0).ownerDocument);this.reset()};p(ac.prototype,y.prototype,{init:function(){var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);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,af);this.intro_div=$("<div/>").addClass("intro");var ai=$("<div/>").text("Add Datasets to 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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=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.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 id='zoom-out' />").click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX),width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new ab(this,{content_div:this.top_labeltrack}));this.add_label_track(new ab(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){af.resize_window()});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(af,ag){this.location_span.text(commatize(af)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ag))},load_chroms:function(ah){ah.num=w;$.extend(ah,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var af=this,ag=$.Deferred();$.ajax({url:chrom_url,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){alert("Invalid chromosome: "+ah.chrom);return}if(aj.reference){af.add_label_track(new A(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+w+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+w+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){if(!ak||ak==="None"){return}var ah=this;if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-w});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+w});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ah){var af=this;var ag=af.high-af.low;if(af.low-ah<af.max_low){af.low=af.max_low;af.high=af.max_low+ag}else{if(af.high-ah>af.max_high){af.high=af.max_high;af.low=af.max_high-ag}else{af.high-=ah;af.low-=ah}}af.request_redraw()},add_drawable:function(af){y.prototype.add_drawable.call(this,af);af.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){y.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.fadeOut("slow",function(){$(this).remove();af.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(an,af,am,ag){var al=this,aj=(ag?[ag]:al.drawables),ah;var ag;for(var ak=0;ak<aj.length;ak++){ag=aj[ak];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[ak][1]=af;al.tracks_to_be_redrawn[ak][2]=am}}requestAnimationFrame(function(){al._redraw(an)})},_redraw:function(ap){var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.resolution=Math.pow(C,Math.ceil(Math.log((this.high-this.low)/R)/Math.log(C)));this.zoom_res=Math.pow(v,Math.max(0,Math.ceil(Math.log(this.resolution,v)/Math.log(v))));var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}this.update_location(this.low,this.high);if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};this.overview_drawable.init();af.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ah,al){this.track=ah;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],ag=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params[this.params.length]=new g(ag,ar,aj,au,an.min,an.max)}else{if(ap=="select"){this.params[this.params.length]=new O(ag,ar,aj,au)}else{console.log("WARNING: unrecognized tool parameter type:",ag,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("slider").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);var am=this;af.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=JSON.stringify(ah)});return af},get_param_values:function(){var ag=[];var af={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();if(ah){ag[ag.length]=ai}});return ag},run_on_dataset:function(){var af=this;af.run({dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={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,ah=ag.tool_id+aj.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(aj.container===view){var ai=new Q(this.name,this.track.view,this.track.container);aj.container.add_drawable(ai);aj.container.remove_drawable(aj);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);af=ai}else{af=aj.container}var ak=new aj.constructor(ah,view,af,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);af.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ag,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ag,ah,ai){$.extend(ag,this.get_param_values_dict());var af=function(){$.getJSON(rerun_tool_url,ag,function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(x+aj.message)}else{if(aj==="pending"){ah.container_div.addClass("pending");ah.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(af,2000)}else{ai(aj)}}}})};af()}});var O=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=ah;this.value=ai};var g=function(ah,ag,aj,ak,ai,af){O.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};var h=function(ag,af,ah,ai){this.name=ag;this.index=af;this.tool_id=ah;this.tool_exp_name=ai};var V=function(ag,af,ah,ai){h.call(this,ag,af,ah,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};p(V.prototype,{applies_to:function(af){if(af.length>this.index){return true}return false},keep:function(af){if(!this.applies_to(af)){return true}var ag=af[this.index];return(isNaN(ag)||(ag>=this.low&&ag<=this.high))},update_attrs:function(ag){var af=false;if(!this.applies_to(ag)){return af}if(ag[this.index]<this.min){this.min=Math.floor(ag[this.index]);af=true}if(ag[this.index]>this.max){this.max=Math.ceil(ag[this.index]);af=true}return af},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ah=function(ak,ai){var aj=ai-ak;return(aj<=2?0.01:1)};var ag=this.slider.slider("option","min"),af=this.slider.slider("option","max");if(this.min<ag||this.max>af){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ah(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var aa=function(aq,ay){this.track=aq;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,af=au.type,ah=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(af==="int"||af==="float"){this.filters[at]=new V(az,ah,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,af)}}var ai=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var an=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("filter-row slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+" ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];an.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;ai(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var ak=$("<div/>").addClass("param-row").appendTo(av);var am=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ak);var ag=this;am.click(function(){ag.run_on_dataset()})}var ap=$("<div/>").addClass("display-controls").appendTo(this.parent_div),ar,al,ao,aj={Transparency:function(aA){an.alpha_filter=aA},Height:function(aA){an.height_filter=aA}};$.each(aj,function(aC,aB){ar=$("<div/>").addClass("filter-row").appendTo(ap),al=$("<span/>").addClass("elt-label").text(aC+":").appendTo(ar),ao=$("<select/>").attr("name",aC+"_dropdown").css("float","right").appendTo(ar);$("<option/>").attr("value",-1).text("== None ==").appendTo(ao);for(var aA=0;aA<an.filters.length;aA++){$("<option/>").attr("value",aA).text(an.filters[aA].name).appendTo(ao)}ao.change(function(){$(this).children("option:selected").each(function(){var aD=parseInt($(this).val());aj[aC]((aD>=0?an.filters[aD]:null));an.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(ar)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};p(aa.prototype,{reset_filters:function(){for(var af=0;af<this.filters.length;af++){filter=this.filters[af];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var an=function(ar,ap,aq){if(!(ap in ar)){ar[ap]=aq}return ar[ap]};var ah={},af,ag,ai;for(var aj=0;aj<this.filters.length;aj++){af=this.filters[aj];if(af.tool_id){if(af.min!=af.low){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" >= "+af.low}if(af.max!=af.high){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" <= "+af.high}}}var al=[];for(var ao in ah){al[al.length]=[ao,ah[ao]]}var am=al.length;(function ak(aw,at){var aq=at[0],ar=aq[0],av=aq[1],au="("+av.join(") and (")+")",ap={cond:au,input:aw,target_dataset_id:aw,tool_id:ar},at=at.slice(1);$.getJSON(run_tool_url,ap,function(ax){if(ax.error){show_modal("Filter Dataset","Error running tool "+ar,{Close:hide_modal})}else{if(at.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ak(ax.dataset_id,at)}}})})(this.track.dataset_id,al)}});var D=function(af,ag){M.Scaler.call(this,ag);this.filter=af};D.prototype.gen_val=function(af){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(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};p(G.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ag=this;var af=$("<div />");$.each(this.params,function(ak,ai){if(!ai.hidden){var ah="param_"+ak;var am=ag.values[ai.key];var ap=$("<div class='form-row' />").appendTo(af);ap.append($("<label />").attr("for",ah).text(ai.label+":"));if(ai.type==="bool"){ap.append($('<input type="checkbox" />').attr("id",ah).attr("name",ah).attr("checked",am))}else{if(ai.type==="text"){ap.append($('<input type="text"/>').attr("id",ah).val(am).click(function(){$(this).select()}))}else{if(ai.type==="color"){var al=$("<input />").attr("id",ah).attr("name",ah).val(am);var an=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var aj=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(an);var ao=$("<div/>").appendTo(aj).farbtastic({width:100,height:100,callback:al,color:am});$("<div />").append(al).append(an).appendTo(ap).bind("click",function(aq){an.css({left:$(this).position().left+($(al).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){an.hide();$(document).unbind("click.color-picker")});aq.stopPropagation()})}else{ap.append($("<input />").attr("id",ah).attr("name",ah).val(am))}}}}});return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange()}}});var b=function(af,ai,ah,ag,aj){this.track=af;this.index=ai;this.low=ai*R*ah;this.high=(ai+1)*R*ah;this.resolution=ah;this.canvas=$("<div class='track-tile'/>").append(ag);this.data=aj;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(af,ai,ah,ag,aj,ak){b.call(this,af,ai,ah,ag,aj);this.max_val=ak};p(k.prototype,b.prototype);var P=function(af,aj,ai,ah,al,am,ak,ag){b.call(this,af,aj,ai,ah,al);this.mode=am;this.message=ak;this.feature_mapper=ag};p(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.canvas).mousemove(function(ar){var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).siblings(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),av,au,ax=$("<table/>").appendTo(ai),ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)=="number"?Z(au,2):au)}af[an]=ai}ai.appendTo($(ag.canvas).parent());var aj=aq+parseInt(ag.canvas.css("left"))+7,ah=ap+parseInt(ag.canvas.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ai,aq,aj,am,ar,ah,ag){q.call(this,ai,aq,aj,{},"draghandle");this.data_url=(ah?ah:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ag?ag:L);this.dataset_check_url=converted_datasets_state_url;if(!i.id_counter){i.id_counter=0}this.id=i.id_counter++;this.container_div=$("<div />").addClass("track").attr("id","track_"+this.id).css("position","relative");if(am){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("<div/>").css("float","left").appendTo(this.header_div).hide();this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.overview_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var ak=this;this.header_div.dblclick(function(at){at.stopPropagation()});this.settings_icon.click(function(){var av=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},at=function(){ak.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},au=function(aw){if((aw.keyCode||aw.which)===27){av()}else{if((aw.keyCode||aw.which)===13){at()}}};$(window).bind("keypress.check_enter_esc",au);show_modal("Configure Track",ak.config.build_form(),{Cancel:av,OK:at})});this.overview_icon.click(function(){ak.view.set_overview(ak)});this.filters_icon.click(function(){ak.filters_div.toggle();ak.filters_manager.reset_filters()});this.tools_icon.click(function(){ak.dynamic_tool_div.toggle();if(ak.dynamic_tool_div.is(":visible")){ak.set_name(ak.name+ak.tool_region_and_parameters_str())}else{ak.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();ak.remove()});if(ak.display_modes!==undefined){if(ak.mode_div===undefined){ak.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ak.header_div);var al=(ak.config&&ak.config.values.mode?ak.config.values.mode:ak.display_modes[0]);ak.mode=al;ak.mode_div.text(al);var af={};for(var an=0,ap=ak.display_modes.length;an<ap;an++){var ao=ak.display_modes[an];af[ao]=function(at){return function(){ak.change_mode(at)}}(ao)}make_popupmenu(ak.mode_div,af)}else{ak.mode_div.hide()}this.header_div.append($("<div/>").css("clear","both"));this.container_div.hover(function(){ak.icons_div.show()},function(){ak.icons_div.hide()})}}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};p(i.prototype,q.prototype,{get_type:function(){if(this instanceof ab){return"LabelTrack"}else{if(this instanceof A){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof W){return"ReadTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.initial_canvas=undefined;af.content_div.css("height","auto");af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}$.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=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})});af.content_div.append(ah)}}else{if(ag==="no converter"){af.container_div.addClass("error");af.content_div.text(K)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(F)}else{if(ag==="pending"){af.container_div.addClass("pending");af.content_div.text(t);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ag.status==="data"){if(ag.valid_chroms){af.valid_chroms=ag.valid_chroms;af.update_track_icons()}af.content_div.text(Y);if(af.view.chrom){af.content_div.text("");af.content_div.css("height",af.height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){af.container_div.removeClass("nodata error pending");af.request_draw()})}}}}}}});this.update_track_icons()},predraw_init:function(){}});var N=function(aj,ah,ag,am,ai,al,ak){i.call(this,aj,ah,ag,am,ai);var af=this,ah=af.view;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new aa(this,(al!==undefined?al:{}));this.filters_available=false;this.filters_visible=false;this.tool=(ak!==undefined&&obj_length(ak)>0?new r(this,ak):undefined);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(N.prototype,q.prototype,i.prototype,{copy:function(af){return new this.constructor(this.name,this.view,af,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json: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,}},change_mode:function(ag){var af=this;af.mode_div.text(ag);af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();return af},update_track_icons:function(){var af=this;if(af.filters_available>0){af.filters_icon.show()}else{af.filters_icon.hide()}if(af.tool){af.tools_icon.show()}else{af.tools_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},_draw:function(ah,ap){if(!this.enabled){return}if(!(this instanceof A)&&(!this.dataset_id)){return}var ao=this.view.low,al=this.view.high,am=al-ao,ai=this.view.container.width(),at=ai/am,ak=this.view.resolution,ar=$("<div style='position: relative;'></div>");if(this.is_overview){ao=this.view.max_low;al=this.view.max_high;ak=Math.pow(C,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(C)));at=ai/(view.max_high-view.max_low)}if(!ap){this.content_div.children().remove()}this.content_div.append(ar);this.max_height=0;var ag=Math.floor(ao/ak/R);var an=true;var aq=[];var af=0;while((ag*R*ak)<al){tile=this.draw_helper(ah,ai,ag,ak,ar,at);if(tile){aq.push(tile)}else{an=false}ag+=1;af++}var aj=this;if(an){aj.postdraw_actions(aq,ai,at,ap)}},postdraw_actions:function(aj,ak,al,af){var ah=this;var ai=false;for(var ag=0;ag<aj.length;ag++){if(aj[ag].message){ai=true;break}}if(ai){for(var ag=0;ag<aj.length;ag++){tile=aj[ag];if(!tile.message){tile.canvas.css("padding-top",E)}}}},draw_helper:function(ag,ah,ai,al,ar,aw,at,am){var aj=this,aq=this._gen_tile_cache_key(ah,aw,ai),an=ai*R*al,av=an+R*al;var ao=(ag?undefined:aj.tile_cache.get(aq));if(ao){aj.show_tile(ao,ar,aw);return ao}var ap=function(ax){return("isResolved" in ax)};var ak=true;var af=aj.data_manager.get_data(an,av,aj.mode,al,aj.data_url_extra_params);if(ap(af)){ak=false}var au;if(view.reference_track&&aw>view.canvas_manager.char_width_px){au=view.reference_track.data_manager.get_data(an,av,aj.mode,al,view.reference_track.data_url_extra_params);if(ap(au)){ak=false}}if(ak){p(af,am);var ao=aj.draw_tile(af,aj.mode,al,ai,aw,au);if(ao!==undefined){aj.tile_cache.set(aq,ao);aj.show_tile(ao,ar,aw)}return ao}$.when(af,au).then(function(){view.request_redraw(false,false,false,aj)});return null},show_tile:function(al,an,ao){var ah=this,ag=al.canvas,ak=ag;if(al.message){var ap=$("<div/>"),am=$("<div/>").addClass("tile-message").text(al.message).css({height:E-1,width:al.canvas.width}).appendTo(ap),aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(am),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(am);ap.append(ag);ak=ap;aj.click(function(){al.stale=true;ah.data_manager.get_more_data(al.low,al.high,ah.mode,al.resolution,{},ah.data_manager.DEEP_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()});af.click(function(){al.stale=true;ah.data_manager.get_more_data(al.low,al.high,ah.mode,al.resolution,{},ah.data_manager.BROAD_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}al.predisplay_actions();var ai=(al.low-(this.is_overview?this.view.max_low:this.view.low))*ao;if(this.left_offset){ai-=this.left_offset}ak.css({position:"absolute",top:0,left:ai,height:""});an.append(ak);ah.max_height=Math.max(ah.max_height,ak.height());ah.content_div.css("height",ah.max_height+"px");an.children().css("height",ah.max_height+"px")},_get_tile_bounds:function(af,ag){var ai=af*R*ag,aj=R*ag,ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return[ai,ah]},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},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 ag=this;var af=function(){if(ag.data_manager.size()===0){setTimeout(af,300)}else{ag.data_url=default_data_url;ag.data_query_wait=L;ag.dataset_state_url=converted_datasets_state_url;$.getJSON(ag.dataset_state_url,{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},function(ah){})}};af()}}});var ab=function(ag,af){i.call(this,"label",ag,af,false,{});this.container_div.addClass("label-track")};p(ab.prototype,i.prototype,{init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var A=function(af){N.call(this,"reference",af,{content_div:af.top_labeltrack},false,{});af.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:af.dbkey};this.data_manager=new I(B,this,false);this.tile_cache=new c(u)};p(A.prototype,q.prototype,N.prototype,{init:function(){this.enabled=true},draw_tile:function(ap,al,ak,ag,aq){var aj=this,ah=R*ak;if(aq>this.view.canvas_manager.char_width_px){if(ap.data===null){aj.content_div.css("height","0px");return}var ai=this.view.canvas_manager.new_canvas();var ao=ai.getContext("2d");ai.width=Math.ceil(ah*aq+aj.left_offset);ai.height=aj.height_px;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";ap=ap.data;for(var am=0,an=ap.length;am<an;am++){var af=Math.round(am*aq);ao.fillText(ap[am],af+aj.left_offset,10)}return new b(aj,ag,ak,ai,ap)}this.content_div.css("height","0px")}});var j=function(ak,ai,ah,al,af,aj){var ag=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";N.call(this,ak,ai,ah,true,aj);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=al;this.dataset_id=af;this.original_dataset_id=af;this.data_manager=new S(B,this);this.tile_cache=new c(u);this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{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:aj,onchange:function(){ag.set_name(ag.prefs.name);ag.vertical_range=ag.prefs.max_value-ag.prefs.min_value;$("#linetrack_"+ag.dataset_id+"_minval").text(ag.prefs.min_value);$("#linetrack_"+ag.dataset_id+"_maxval").text(ag.prefs.max_value);ag.tile_cache.clear();ag.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,N.prototype,{add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){ai=true;ag.show()},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.content_div).css("height",aj);af.height_px=aj;af.request_draw(true)}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.height_px}).appendTo(af.container_div)},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.data_url,{stats:true,chrom:af.view.chrom,low:null,high:null,hda_ldda:af.hda_ldda,dataset_id:af.dataset_id},function(ag){af.container_div.addClass("line-track");var ai=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){af.prefs.min_value=ai.min;af.prefs.max_value=ai.max;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=ai.total_frequency;af.container_div.find(".yaxislabel").remove();var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_minval").text(Z(af.prefs.min_value,3));var ah=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_maxval").text(Z(af.prefs.max_value,3));ah.css({position:"absolute",top:"24px",left:"10px"});ah.prependTo(af.container_div);aj.css({position:"absolute",bottom:"2px",left:"10px"});aj.prependTo(af.container_div)})},draw_tile:function(ar,ak,aj,ah,aq){if(this.vertical_range===undefined){return}var af=this._get_tile_bounds(ah,aj),al=af[0],ap=af[1],ag=Math.ceil((ap-al)*aq),an=this.height_px;var ai=this.view.canvas_manager.new_canvas();ai.width=ag,ai.height=an;var ao=ai.getContext("2d");var am=new M.LinePainter(ar.data,al,ap,this.prefs,ak);am.draw(ao,ag,an);return new b(this.track,ah,aj,ai,ar.data)}});var e=function(af,al,ag,ak,an,am,ai,aj){var ah=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];N.call(this,af,al,ag,true,am,ai,aj);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){ah.set_name(ah.prefs.name);ah.tile_cache.clear();ah.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ak;this.dataset_id=an;this.original_dataset_id=an;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new S(20,this);this.left_offset=200;this.painter=M.LinkedFeaturePainter};p(e.prototype,q.prototype,N.prototype,{postdraw_actions:function(av,af,aw,au){N.prototype.postdraw_actions.call(this,av,au);var ai=this;if(au){var ak=ai.content_div.children();var al=false;for(var aj=ak.length-1,ap=0;aj>=ap;aj--){var ah=$(ak[aj]);if(al){ah.remove()}else{if(ah.children().length!==0){al=true}}}}if(ai.mode=="Histogram"){var ao=-1;for(var aj=0;aj<av.length;aj++){var at=av[aj].max_val;if(at>ao){ao=at}}for(var aj=0;aj<av.length;aj++){var ar=av[aj];if(ar.max_val!==ao){ar.canvas.remove();ai.draw_helper(true,af,ar.index,ar.resolution,ar.canvas.parent(),aw,[],{max:ao})}}}if(ai.filters_manager){var ag=ai.filters_manager.filters;for(var an=0;an<ag.length;an++){ag[an].update_ui_elt()}var am=false,aq;for(var aj=0;aj<av.length;aj++){if(av[aj].data.length){aq=av[aj].data[0];for(var an=0;an<ag.length;an++){if(ag[an].applies_to(aq)){am=true;break}}}}if(ai.filters_available!==am){ai.filters_available=am;if(!ai.filters_available){ai.filters_div.hide()}ai.update_track_icons()}}},update_auto_mode:function(af){if(this.mode=="Auto"){if(af=="no_detail"){af="feature spans"}else{if(af=="summary_tree"){af="coverage histogram"}}this.mode_div.text("Auto ("+af+")")}},incremental_slots:function(aj,ag,ai){var ah=this.view.canvas_manager.dummy_context,af=this.inc_slots[aj];if(!af||(af.mode!==ai)){af=new (s.FeatureSlotter)(aj,ai==="Pack",z,function(ak){return ah.measureText(ak)});af.mode=ai;this.inc_slots[aj]=af}return af.slot_features(ag)},get_summary_tree_data:function(aj,am,ah,av){if(av>ah-am){av=ah-am}var aq=Math.floor((ah-am)/av),au=[],ai=0;var ak=0,al=0,ap,at=0,an=[],ar,ao;var ag=function(ay,ax,az,aw){ay[0]=ax+az*aw;ay[1]=ax+(az+1)*aw};while(at<av&&ak!==aj.length){var af=false;for(;at<av&&!af;at++){ag(an,am,at,aq);for(al=ak;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){af=true;break}}if(af){break}}data_start_index=al;au[au.length]=ar=[an[0],0];for(;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){ar[1]++}else{break}}if(ar[1]>ai){ai=ar[1]}at++}return{max:ai,delta:aq,data:au}},draw_tile:function(au,ax,aB,aF,ap,ai){var ay=this,ak=ay._get_tile_bounds(aF,aB),aI=ak[0],ag=ak[1],aw=ag-aI,az=Math.ceil(aw*ap),aO=25,aj=this.left_offset,av,al;if(ax==="Auto"){if(au.dataset_type==="summary_tree"){ax=au.dataset_type}else{if(au.extra_info==="no_detail"||ay.is_overview){ax="no_detail"}else{var aN=au.data;if(this.view.high-this.view.low>J){ax="Squish"}else{ax="Pack"}}}this.update_auto_mode(ax)}if(ax==="summary_tree"||ax==="Histogram"){al=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel");af.text(au.max);af.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});af.prependTo(this.container_div);var ah=this.view.canvas_manager.new_canvas();ah.width=az+aj;ah.height=al+T;if(au.dataset_type!="summary_tree"){var aq=this.get_summary_tree_data(au.data,aI,ag,200);if(au.max){aq.max=au.max}au=aq}var aK=new M.SummaryTreePainter(au,aI,ag,this.prefs);var aA=ah.getContext("2d");aA.translate(aj,T);aK.draw(aA,az,al);return new k(ay,aF,aB,ah,au.data,au.max)}var av,an=1;if(ax==="no_detail"||ax==="Squish"||ax==="Pack"){an=this.incremental_slots(ap,au.data,ax);av=this.inc_slots[ap].slots}var ao=[];if(au.data){var ar=this.filters_manager.filters;for(var aC=0,aE=au.data.length;aC<aE;aC++){var am=au.data[aC];var aD=false;var at;for(var aH=0,aM=ar.length;aH<aM;aH++){at=ar[aH];at.update_attrs(am);if(!at.keep(am)){aD=true;break}}if(!aD){ao.push(am)}}}var aL=(this.filters_manager.alpha_filter?new D(this.filters_manager.alpha_filter):null);var aJ=(this.filters_manager.height_filter?new D(this.filters_manager.height_filter):null);var aK=new (this.painter)(ao,aI,ag,this.prefs,ax,aL,aJ,ai);var al=Math.max(ad,aK.get_required_height(an));var ah=this.view.canvas_manager.new_canvas();var aG=null;ah.width=az+aj;ah.height=al;var aA=ah.getContext("2d");aA.fillStyle=this.prefs.block_color;aA.font=aA.canvas.manager.default_font;aA.textAlign="right";this.container_div.find(".yaxislabel").remove();if(au.data){aA.translate(aj,0);aG=aK.draw(aA,az,al,av);aG.translation=-aj}return new P(ay,aF,aB,ah,au.data,ax,au.message,aG)}});var U=function(ak,ah,ag,am,af,aj,al,ai){e.call(this,ak,ah,ag,am,af,aj,al,ai);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{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:aj,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=M.ReadPainter};p(U.prototype,q.prototype,N.prototype,e.prototype);var W=function(aj,ah,ag,al,af,ai,ak){e.call(this,aj,ah,ag,al,af,ai,ak);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:aj},{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_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ai,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=M.ReadPainter;this.update_track_icons()};p(W.prototype,q.prototype,N.prototype,e.prototype);X.View=ac;X.DrawableGroup=Q;X.LineTrack=j;X.FeatureTrack=e;X.ReadTrack=W;X.VcfTrack=U};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.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(F,G){for(var E=0;E<=z;E++){var C=false,H=h[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var i=H[B];if(G>i[0]&&F<i[1]){C=true;break}}}if(!C){return E}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(i,w){var t=i("class").extend;var o=function(H,z,F,y,E,C){if(C===undefined){C=4}var B=y-z;var A=E-F;var D=Math.floor(Math.sqrt(B*B+A*A)/C);var I=B/D;var G=A/D;var x;for(x=0;x<D;x++,z+=I,F+=G){if(x%2!==0){continue}H.fillRect(z,F,C,1)}};var p=function(A,z,x,D){var C=z-D/2,B=z+D/2,E=x-Math.sqrt(D*3/2);A.beginPath();A.moveTo(C,E);A.lineTo(B,E);A.lineTo(z,x);A.lineTo(C,E);A.strokeStyle=this.fillStyle;A.fill();A.stroke();A.closePath()};var d=function(x){this.default_val=(x?x:1)};d.prototype.gen_val=function(x){return this.default_val};var l=function(z,B,x,y,A){this.data=z;this.view_start=B;this.view_end=x;this.prefs=t({},this.default_prefs,y);this.mode=A};l.prototype.default_prefs={};var u=function(z,B,x,y,A){l.call(this,z,B,x,y,A)};u.prototype.default_prefs={show_counts:false};u.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var b=function(x,B,D,E,z){l.call(this,x,B,D,E,z);if(this.prefs.min_value===undefined){var F=Infinity;for(var y=0,A=this.data.length;y<A;y++){F=Math.min(F,this.data[y][1])}this.prefs.min_value=F}if(this.prefs.max_value===undefined){var C=-Infinity;for(var y=0,A=this.data.length;y<A;y++){C=Math.max(C,this.data[y][1])}this.prefs.max_value=C}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(M,L,J){var E=false,G=this.prefs.min_value,C=this.prefs.max_value,I=C-G,x=J,z=this.view_start,K=this.view_end-this.view_start,A=L/K,H=this.mode,S=this.data;M.save();var T=Math.round(J+G/I*J);if(H!=="Intensity"){M.fillStyle="#aaa";M.fillRect(0,T,L,1)}M.beginPath();var Q,D,B;if(S.length>1){B=Math.ceil((S[1][0]-S[0][0])*A)}else{B=10}for(var N=0,O=S.length;N<O;N++){M.fillStyle=this.prefs.color;Q=Math.round((S[N][0]-z)*A);D=S[N][1];var P=false,F=false;if(D===null){if(E&&H==="Filled"){M.lineTo(Q,x)}E=false;continue}if(D<G){F=true;D=G}else{if(D>C){P=true;D=C}}if(H==="Histogram"){D=Math.round(D/I*x);M.fillRect(Q,T,B,-D)}else{if(H==="Intensity"){D=255-Math.floor((D-G)/I*255);M.fillStyle="rgb("+D+","+D+","+D+")";M.fillRect(Q,0,B,x)}else{D=Math.round(x-(D-G)/I*x);if(E){M.lineTo(Q,D)}else{E=true;if(H==="Filled"){M.moveTo(Q,x);M.lineTo(Q,D)}else{M.moveTo(Q,D)}}}}M.fillStyle=this.prefs.overflow_color;if(P||F){var R;if(H==="Histogram"||H==="Intensity"){R=B}else{Q-=2;R=4}if(P){M.fillRect(Q,0,R,3)}if(F){M.fillRect(Q,x-3,R,3)}}M.fillStyle=this.prefs.color}if(H==="Filled"){if(E){M.lineTo(Q,T);M.lineTo(0,T)}M.fill()}else{M.stroke()}M.restore()};var m=function(x){this.feature_positions={};this.slot_height=x;this.translation=0};m.prototype.map_feature_data=function(y,A,x,z){if(!this.feature_positions[A]){this.feature_positions[A]=[]}this.feature_positions[A].push({data:y,x_start:x,x_end:z})};m.prototype.get_feature_data=function(z,D){var C=Math.floor(D/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 n=function(z,C,x,y,B,D,A){l.call(this,z,C,x,y,B);this.alpha_scaler=(D?D:new d());this.height_scaler=(A?A:new d())};n.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};t(n.prototype,{get_required_height:function(y){var x=y_scale=this.get_row_height(),z=this.mode;if(z==="no_detail"||z==="Squish"||z==="Pack"){x=y*y_scale}return x+Math.max(Math.round(y_scale/2),5)},draw:function(J,H,F,E){var P=this.data,C=this.view_start,L=this.view_end;J.save();J.fillStyle=this.prefs.block_color;J.textAlign="right";var G=this.view_end-this.view_start,D=H/G,K=this.get_row_height(),O=new m(K),A;for(var M=0,N=P.length;M<N;M++){var z=P[M],B=z[0],I=z[1],x=z[2],y=(E&&E[B]!==undefined?E[B]:null);if((I<L&&x>C)&&(this.mode=="Dense"||y!==null)){A=this.draw_element(J,this.mode,z,y,C,L,D,K,H);O.map_feature_data(z,y,A[0],A[1])}}J.restore();return O},draw_element:function(D,z,F,B,A,C,E,y,x){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,v=10,f=1,r=3,e=3,a=9,j=2,g="#ccc";var q=function(z,C,x,y,B,D,A){n.call(this,z,C,x,y,B,D,A)};t(q.prototype,n.prototype,{get_row_height:function(){var y=this.mode,x;if(y==="Dense"){x=c}else{if(y==="no_detail"){x=h}else{if(y==="Squish"){x=k}else{x=v}}}return x},draw_element:function(L,C,U,G,N,af,aj,al,x){var R=U[0],ah=U[1],Z=U[2],P=U[3],aa=Math.floor(Math.max(0,(ah-N)*aj)),M=Math.ceil(Math.min(x,Math.max(0,(Z-N)*aj))),Y=aa,ak=M,X=(C==="Dense"?0:(0+G))*al,K,ad,Q=null,an=null,A=this.prefs.block_color,ac=this.prefs.label_color;L.globalAlpha=this.alpha_scaler.gen_val(U);if(C==="Dense"){G=1}if(C==="no_detail"){L.fillStyle=A;L.fillRect(aa,X+5,M-aa,f)}else{var J=U[4],W=U[5],ab=U[6],B=U[7];if(W&&ab){Q=Math.floor(Math.max(0,(W-N)*aj));an=Math.ceil(Math.min(x,Math.max(0,(ab-N)*aj)))}var ai,S;if(C==="Squish"||C==="Dense"){ai=1;S=e}else{ai=5;S=a}if(!B){if(U.strand){if(U.strand==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(U.strand==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}}else{L.fillStyle=A}L.fillRect(aa,X,M-aa,S)}else{var I,T;if(C==="Squish"||C==="Dense"){L.fillStyle=g;I=X+Math.floor(e/2)+1;T=1}else{if(J){var I=X;var T=S;if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand")}}}else{L.fillStyle=g;I+=(e/2)+1;T=1}}L.fillRect(aa,I,M-aa,T);var D;for(var ag=0,z=B.length;ag<z;ag++){var E=B[ag],y=Math.floor(Math.max(0,(E[0]-N)*aj)),V=Math.ceil(Math.min(x,Math.max((E[1]-N)*aj)));if(y>V){continue}L.fillStyle=A;L.fillRect(y,X+(S-ai)/2+1,V-y,ai);if(Q!==undefined&&ab>W&&!(y>an||V<Q)){var ae=Math.max(y,Q),H=Math.min(V,an);L.fillRect(ae,X+1,H-ae,S);if(B.length==1&&C=="Pack"){if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}if(ae+14<H){ae+=2;H-=2}L.fillRect(ae,X+1,H-ae,S)}}}if(C==="Pack"){L.globalAlpha=1;L.fillStyle="white";var F=this.height_scaler.gen_val(U),O=Math.ceil(S*F),am=Math.round((S-O)/2);if(F!==1){L.fillRect(aa,I+1,M-aa,am);L.fillRect(aa,I+S-am+1,M-aa,am)}}}L.globalAlpha=1;if(C==="Pack"&&ah>N){L.fillStyle=ac;if(N===0&&aa-L.measureText(P).width<0){L.textAlign="left";L.fillText(P,M+j,X+8);ak+=L.measureText(P).width+j}else{L.textAlign="right";L.fillText(P,aa-j,X+8);Y-=L.measureText(P).width+j}}}L.globalAlpha=1;return[Y,ak]}});var s=function(A,D,x,z,C,E,B,y){n.call(this,A,D,x,z,C,E,B);this.ref_seq=(y?y.data:null)};s.prototype.default_prefs=t({},n.prototype.default_prefs,{show_insertions:false});t(s.prototype,n.prototype,{get_row_height:function(){var x,y=this.mode;if(y==="Dense"){x=c}else{if(y==="Squish"){x=k}else{x=v;if(this.prefs.show_insertions){x*=2}}}return x},draw_read:function(U,P,L,Z,A,T,I,F,E){U.textAlign="center";var S=this,z=[Z,A],O=0,V=0,R=0,x=U.canvas.manager.char_width_px;var ae=[];if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>x){R=Math.round(L/2)}if(!I){I=[[0,F.length]]}for(var M=0,X=I.length;M<X;M++){var J=I[M],B="MIDNSHP=X"[J[0]],N=J[1];if(B==="H"||B==="S"){O-=N}var G=T+O,ad=Math.floor(Math.max(0,(G-Z)*L)),H=Math.floor(Math.max(0,(G+N-Z)*L));if(ad===H){H+=1}switch(B){case"H":break;case"S":case"M":case"=":if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(R>0){U.fillStyle=this.prefs.block_color;U.fillRect(ad-R,E+1,H-ad,9);U.fillStyle=g;for(var ab=0,y=Q.length;ab<y;ab++){if(this.prefs.show_differences&&this.ref_seq){var K=this.ref_seq[G-Z+ab];if(!K||K.toLowerCase()===Q[ab].toLowerCase()){continue}}if(G+ab>=Z&&G+ab<=A){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac,E+9)}}}else{U.fillStyle=this.prefs.block_color;U.fillRect(ad,E+4,H-ad,e)}}V+=N;O+=N;break;case"N":U.fillStyle=g;U.fillRect(ad-R,E+5,H-ad,1);O+=N;break;case"D":U.fillStyle="red";U.fillRect(ad-R,E+4,H-ad,3);O+=N;break;case"P":break;case"I":var Y=ad-R;if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(this.prefs.show_insertions){var D=ad-(H-ad)/2;if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>x){U.fillStyle="yellow";U.fillRect(D-R,E-9,H-ad,9);ae[ae.length]={type:"triangle",data:[Y,E+4,5]};U.fillStyle=g;switch(compute_overlap([G,G+N],z)){case (OVERLAP_START):Q=Q.slice(Z-G);break;case (OVERLAP_END):Q=Q.slice(0,G-A);break;case (CONTAINED_BY):break;case (CONTAINS):Q=Q.slice(Z-G,G-A);break}for(var ab=0,y=Q.length;ab<y;ab++){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac-(H-ad)/2,E)}}else{U.fillStyle="yellow";U.fillRect(D,E+(this.mode!=="Dense"?2:5),H-ad,(P!=="Dense"?e:r))}}else{if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>x){ae.push({type:"text",data:[Q.length,Y,E+9]})}else{}}}V+=N;break;case"X":V+=N;break}}U.fillStyle="yellow";var aa,C,af;for(var W=0;W<ae.length;W++){aa=ae[W];C=aa.type;af=aa.data;if(C==="text"){U.save();U.font="bold "+U.font;U.fillText(af[0],af[1],af[2]);U.restore()}else{if(C=="triangle"){p(U,af[0],af[1],af[2])}}}},draw_element:function(Q,L,D,A,T,y,H,R,O){var G=D[0],P=D[1],z=D[2],I=D[3],C=Math.floor(Math.max(0,(P-T)*H)),E=Math.ceil(Math.min(O,Math.max(0,(z-T)*H))),B=(L==="Dense"?0:(0+A))*R,U=this.prefs.block_color,F=this.prefs.label_color,N=0;if((L==="Pack"||this.mode==="Auto")&&H>Q.canvas.manager.char_width_px){var N=Math.round(H/2)}Q.fillStyle=U;if(D[5] instanceof Array){var M=Math.floor(Math.max(0,(D[4][0]-T)*H)),K=Math.ceil(Math.min(O,Math.max(0,(D[4][1]-T)*H))),J=Math.floor(Math.max(0,(D[5][0]-T)*H)),x=Math.ceil(Math.min(O,Math.max(0,(D[5][1]-T)*H)));if(D[4][1]>=T&&D[4][0]<=y&&D[4][2]){this.draw_read(Q,L,H,T,y,D[4][0],D[4][2],D[4][3],B)}if(D[5][1]>=T&&D[5][0]<=y&&D[5][2]){this.draw_read(Q,L,H,T,y,D[5][0],D[5][2],D[5][3],B)}if(J>K){Q.fillStyle=g;o(Q,K-N,B+5,J-N,B+5)}}else{Q.fillStyle=U;this.draw_read(Q,L,H,T,y,P,D[4],D[5],B)}if(L==="Pack"&&P>T&&I!=="."){Q.fillStyle=this.prefs.label_color;var S=1;if(S===0&&C-Q.measureText(I).width<0){Q.textAlign="left";Q.fillText(I,E+j-N,B+8)}else{Q.textAlign="right";Q.fillText(I,C-j-N,B+8)}Q.fillStyle=U}return[0,0]}});w.Scaler=d;w.SummaryTreePainter=u;w.LinePainter=b;w.LinkedFeaturePainter=q;w.ReadPainter=s};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file +var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var 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 m=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(u,t,v,r,i,s){return(Math.max(u,r)-Math.min(u,r))+(Math.max(t,i)-Math.min(t,i))+(Math.max(v,s)-Math.min(v,s))};var g,n,f,k,p,h,q,c,d,b,o,l=false;do{g=Math.random()*16777215;n=g|16711680;f=g|65280;k=g|255;d=m(n,f,k);l=true;for(var j=0;j<a.length;j++){p=a[j];h=p|16711680;q=p|65280;c=p|255;b=m(h,q,c);o=e(n,f,k,h,q,c);if((Math.abs(d-b)<125)||(o<500)){l=false;break}}}while(!l);return"#"+(16777216+g).toString(16).substr(1,6)};var trackster_module=function(f,X){var p=f("class").extend,s=f("slotting"),M=f("painters");var ae=function(af,ag){this.document=af;this.default_font=ag!==undefined?ag:"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(ae.prototype,{load_pattern:function(af,aj){var ag=this.patterns,ah=this.dummy_context,ai=new Image();ai.src=image_path+aj;ai.onload=function(){ag[af]=ah.createPattern(ai,"repeat")}},get_pattern:function(af){return this.patterns[af]},new_canvas:function(){var af=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(af)}af.manager=this;return af}});var n={};var l=function(af,ag){n[af.attr("id")]=ag};var m=function(af,ah,aj,ai){aj=".group";var ag={};n[af.attr("id")]=ai;af.bind("drag",{handle:"."+ah,relative:true},function(ar,at){var aq=$(this);var aw=$(this).parent(),an=aw.children(),ap=n[$(this).attr("id")],am,al,au,ak,ao;al=$(this).parents(aj);if(al.length!==0){au=al.position().top;ak=au+al.outerHeight();if(at.offsetY<au){$(this).insertBefore(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable_before(ap,av);return}else{if(at.offsetY>ak){$(this).insertAfter(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable(ap);return}}}al=null;for(ao=0;ao<an.length;ao++){am=$(an.get(ao));au=am.position().top;ak=au+am.outerHeight();if(am.is(aj)&&this!==am.get(0)&&at.offsetY>=au&&at.offsetY<=ak){if(at.offsetY-au<ak-at.offsetY){am.find(".content-div").prepend(this)}else{am.find(".content-div").append(this)}if(ap.container){ap.container.remove_drawable(ap)}n[am.attr("id")].add_drawable(ap);return}}for(ao=0;ao<an.length;ao++){if(at.offsetY<$(an.get(ao)).position().top){break}}if(ao===an.length){if(this!==an.get(ao-1)){aw.append(this);n[aw.attr("id")].move_drawable(ap,ao)}}else{if(this!==an.get(ao)){$(this).insertBefore(an.get(ao));n[aw.attr("id")].move_drawable(ap,(at.deltaY>0?ao-1:ao))}}}).bind("dragstart",function(){ag["border-top"]=af.css("border-top");ag["border-bottom"]=af.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ag)})};X.moveable=m;var ad=16,H=9,E=20,T=H+2,z=100,J=12000,R=200,C=5,v=10,L=5000,w=100,o="There was an error in indexing this dataset. ",K="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",F="No data for this chrom/contig.",t="Currently indexing... please wait",x="Tool cannot be rerun: ",a="Loading data...",Y="Ready for display",d=10,u=5,B=5;function Z(ag,af){if(!af){af=0}var ah=Math.pow(10,af);return Math.round(ag*ah)/ah}var c=function(af){this.num_elements=af;this.clear()};p(c.prototype,{get:function(ag){var af=this.key_ary.indexOf(ag);if(af!==-1){if(this.obj_cache[ag].stale){this.key_ary.splice(af,1);delete this.obj_cache[ag]}else{this.move_key_to_end(ag,af)}}return this.obj_cache[ag]},set:function(ag,ah){if(!this.obj_cache[ag]){if(this.key_ary.length>=this.num_elements){var af=this.key_ary.shift();delete this.obj_cache[af]}this.key_ary.push(ag)}this.obj_cache[ag]=ah;return ah},move_key_to_end:function(ag,af){this.key_ary.splice(af,1);this.key_ary.push(ag)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var S=function(ag,af,ah){c.call(this,ag);this.track=af;this.subset=(ah!==undefined?ah:true)};p(S.prototype,c.prototype,{load_data:function(ao,aj,am,ag,al){var an=this.track.view.chrom,ai={chrom:an,low:ao,high:aj,mode:am,resolution:ag,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ai,al);if(this.track.filters_manager){var ap=[];var af=this.track.filters_manager.filters;for(var ak=0;ak<af.length;ak++){ap[ap.length]=af[ak].name}ai.filter_cols=JSON.stringify(ap)}var ah=this;return $.getJSON(this.track.data_url,ai,function(aq){ah.set_data(ao,aj,am,aq)})},get_data:function(af,aj,ak,ag,ai){var ah=this.get_data_from_cache(af,aj,ak);if(ah){return ah}ah=this.load_data(af,aj,ak,ag,ai);this.set_data(af,aj,ak,ah);return ah},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(an,ai,am,ah,al,aj){var ao=this.get_data_from_cache(an,ai,am);if(!ao){console.log("ERROR: no current data for: ",this.track,an,ai,am,ah,al);return}ao.stale=true;var ag=an;if(aj===this.DEEP_DATA_REQ){$.extend(al,{start_val:ao.data.length+1})}else{if(aj===this.BROAD_DATA_REQ){ag=(ao.max_high?ao.max_high:ao.data[ao.data.length-1][2])+1}}var af=this,ak=this.load_data(ag,ai,am,ah,al);new_data_available=$.Deferred();this.set_data(an,ai,am,new_data_available);$.when(ak).then(function(ap){if(ap.data){ap.data=ao.data.concat(ap.data);if(ap.max_low){ap.max_low=ao.max_low}if(ap.message){ap.message=ap.message.replace(/[0-9]+/,ap.data.length)}}af.set_data(an,ai,am,ap);new_data_available.resolve(ap)});return new_data_available},get_data_from_cache:function(af,ag,ah){return this.get(this.gen_key(af,ag,ah))},set_data:function(ag,ah,ai,af){return this.set(this.gen_key(ag,ah,ai),af)},gen_key:function(af,ah,ai){var ag=af+"_"+ah+"_"+ai;return ag},split_key:function(af){return af.split("_")}});var I=function(ag,af,ah){S.call(this,ag,af,ah)};p(I.prototype,S.prototype,c.prototype,{load_data:function(af,ai,aj,ag,ah){if(ag>1){return{data:null}}return S.prototype.load_data.call(this,af,ai,aj,ag,ah)}});var q=function(ai,ag,af,ah,aj){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=ai;this.view=ag;this.container=af;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ai}],saved_values:ah,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};p(q.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_icons:function(){},set_name:function(af){this.old_name=this.name;this.name=af;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(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var y=function(aj,ai,ag,af,ah,ak){q.call(this,ai,ag,af,ah,ak);this.obj_type=aj;this.drawables=[]};p(y.prototype,q.prototype,{init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_json:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},add_drawable:function(af){this.drawables.push(af);af.container=this},add_drawable_before:function(ah,af){var ag=this.drawables.indexOf(af);if(ag!=-1){this.drawables.splice(ag,0,ah);return true}return false},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);ag.container=null;return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);return true}return false}});var Q=function(ai,ag,af,ah){y.call(this,"DrawableGroup",ai,ag,af,ah,"group-handle");this.container_div=$("<div/>").addClass("group").attr("id","group_"+this.id).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<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.update_icons()};p(Q.prototype,q.prototype,y.prototype,{update_icons:function(){var ag=this;var af={};af["Edit configuration"]=function(){var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){ah()}}};$(window).bind("keypress.check_enter_esc",ai);show_modal("Configure Group",ag.config.build_form(),{Cancel:aj,OK:ah})};af.Remove=function(){ag.remove()};make_popupmenu(ag.name_div,af)}});var ac=function(af,ai,ah,ag){y.call(this,"View");this.container=af;this.chrom=null;this.vis_id=ah;this.dbkey=ag;this.title=ai;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 ae(af.get(0).ownerDocument);this.reset()};p(ac.prototype,y.prototype,{init:function(){var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro");var ai=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<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 ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){ak*=50;var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX),width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new ab(this,{content_div:this.top_labeltrack}));this.add_label_track(new ab(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){af.resize_window()});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize")},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(af,ag){this.location_span.text(commatize(af)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ag))},load_chroms:function(ah){ah.num=w;$.extend(ah,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var af=this,ag=$.Deferred();$.ajax({url:chrom_url,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){alert("Invalid chromosome: "+ah.chrom);return}if(aj.reference){af.add_label_track(new A(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+w+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+w+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){if(!ak||ak==="None"){return}var ah=this;if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-w});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+w});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ah){var af=this;var ag=af.high-af.low;if(af.low-ah<af.max_low){af.low=af.max_low;af.high=af.max_low+ag}else{if(af.high-ah>af.max_high){af.high=af.max_high;af.low=af.max_high-ag}else{af.high-=ah;af.low-=ah}}af.request_redraw()},add_drawable:function(af){y.prototype.add_drawable.call(this,af);af.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){y.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.hide(0,function(){$(this).remove();af.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(an,af,am,ag){var al=this,aj=(ag?[ag]:al.drawables),ah;var ag;for(var ak=0;ak<aj.length;ak++){ag=aj[ak];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[ak][1]=af;al.tracks_to_be_redrawn[ak][2]=am}}requestAnimationFrame(function(){al._redraw(an)})},_redraw:function(ap){var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.resolution=Math.pow(C,Math.ceil(Math.log((this.high-this.low)/R)/Math.log(C)));this.zoom_res=Math.pow(v,Math.max(0,Math.ceil(Math.log(this.resolution,v)/Math.log(v))));var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}this.update_location(this.low,this.high);if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};this.overview_drawable.init();af.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ah,al){this.track=ah;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],ag=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params[this.params.length]=new g(ag,ar,aj,au,an.min,an.max)}else{if(ap=="select"){this.params[this.params.length]=new O(ag,ar,aj,au)}else{console.log("WARNING: unrecognized tool parameter type:",ag,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("slider").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);var am=this;af.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=JSON.stringify(ah)});return af},get_param_values:function(){var ag=[];var af={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();if(ah){ag[ag.length]=ai}});return ag},run_on_dataset:function(){var af=this;af.run({dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={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,ah=ag.tool_id+aj.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(aj.container===view){var ai=new Q(this.name,this.track.view,this.track.container);aj.container.add_drawable(ai);aj.container.remove_drawable(aj);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);af=ai}else{af=aj.container}var ak=new aj.constructor(ah,view,af,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);af.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ag,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ag,ah,ai){$.extend(ag,this.get_param_values_dict());var af=function(){$.getJSON(rerun_tool_url,ag,function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(x+aj.message)}else{if(aj==="pending"){ah.container_div.addClass("pending");ah.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(af,2000)}else{ai(aj)}}}})};af()}});var O=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=ah;this.value=ai};var g=function(ah,ag,aj,ak,ai,af){O.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};var h=function(ag,af,ah,ai){this.name=ag;this.index=af;this.tool_id=ah;this.tool_exp_name=ai};var V=function(ag,af,ah,ai){h.call(this,ag,af,ah,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};p(V.prototype,{applies_to:function(af){if(af.length>this.index){return true}return false},keep:function(af){if(!this.applies_to(af)){return true}var ag=af[this.index];return(isNaN(ag)||(ag>=this.low&&ag<=this.high))},update_attrs:function(ag){var af=false;if(!this.applies_to(ag)){return af}if(ag[this.index]<this.min){this.min=Math.floor(ag[this.index]);af=true}if(ag[this.index]>this.max){this.max=Math.ceil(ag[this.index]);af=true}return af},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ah=function(ak,ai){var aj=ai-ak;return(aj<=2?0.01:1)};var ag=this.slider.slider("option","min"),af=this.slider.slider("option","max");if(this.min<ag||this.max>af){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ah(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var aa=function(aq,ay){this.track=aq;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,af=au.type,ah=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(af==="int"||af==="float"){this.filters[at]=new V(az,ah,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,af)}}var ai=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var an=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("filter-row slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+" ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];an.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;ai(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var ak=$("<div/>").addClass("param-row").appendTo(av);var am=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ak);var ag=this;am.click(function(){ag.run_on_dataset()})}var ap=$("<div/>").addClass("display-controls").appendTo(this.parent_div),ar,al,ao,aj={Transparency:function(aA){an.alpha_filter=aA},Height:function(aA){an.height_filter=aA}};$.each(aj,function(aC,aB){ar=$("<div/>").addClass("filter-row").appendTo(ap),al=$("<span/>").addClass("elt-label").text(aC+":").appendTo(ar),ao=$("<select/>").attr("name",aC+"_dropdown").css("float","right").appendTo(ar);$("<option/>").attr("value",-1).text("== None ==").appendTo(ao);for(var aA=0;aA<an.filters.length;aA++){$("<option/>").attr("value",aA).text(an.filters[aA].name).appendTo(ao)}ao.change(function(){$(this).children("option:selected").each(function(){var aD=parseInt($(this).val());aj[aC]((aD>=0?an.filters[aD]:null));an.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(ar)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};p(aa.prototype,{reset_filters:function(){for(var af=0;af<this.filters.length;af++){filter=this.filters[af];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var an=function(ar,ap,aq){if(!(ap in ar)){ar[ap]=aq}return ar[ap]};var ah={},af,ag,ai;for(var aj=0;aj<this.filters.length;aj++){af=this.filters[aj];if(af.tool_id){if(af.min!=af.low){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" >= "+af.low}if(af.max!=af.high){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" <= "+af.high}}}var al=[];for(var ao in ah){al[al.length]=[ao,ah[ao]]}var am=al.length;(function ak(aw,at){var aq=at[0],ar=aq[0],av=aq[1],au="("+av.join(") and (")+")",ap={cond:au,input:aw,target_dataset_id:aw,tool_id:ar},at=at.slice(1);$.getJSON(run_tool_url,ap,function(ax){if(ax.error){show_modal("Filter Dataset","Error running tool "+ar,{Close:hide_modal})}else{if(at.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ak(ax.dataset_id,at)}}})})(this.track.dataset_id,al)}});var D=function(af,ag){M.Scaler.call(this,ag);this.filter=af};D.prototype.gen_val=function(af){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(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};p(G.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ai=this;var af=$("<div />");var ah;function ag(am,aj){for(var ao=0;ao<am.length;ao++){ah=am[ao];if(ah.hidden){continue}var ak="param_"+ao;var at=ai.values[ah.key];var av=$("<div class='form-row' />").appendTo(aj);av.append($("<label />").attr("for",ak).text(ah.label+":"));if(ah.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ak).attr("name",ak).attr("checked",at))}else{if(ah.type==="text"){av.append($('<input type="text"/>').attr("id",ak).val(at).click(function(){$(this).select()}))}else{if(ah.type=="select"){var aq=$("<select />").attr("id",ak);for(var an=0;an<ah.options.length;an++){$("<option/>").text(ah.options[an].label).attr("value",ah.options[an].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ah.type==="color"){var ap=$("<input />").attr("id",ak).attr("name",ak).val(at);var ar=$("<div class='tipsy tipsy-west' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ar);var au=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:ap,color:at});$("<div />").append(ap).append(ar).appendTo(av).bind("click",function(aw){ar.css({left:$(this).position().left+$(ap).width()+5,top:$(this).position().top-($(ar).height()/2)+($(ap).height()/2)}).show();$(document).bind("click.color-picker",function(){ar.hide();$(document).unbind("click.color-picker")});aw.stopPropagation()})}else{av.append($("<input />").attr("id",ak).attr("name",ak).val(at))}}}}if(ah.help){av.append($("<div class='help'/>").text(ah.help))}}}ag(this.params,af);return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange()}}});var b=function(af,ai,ah,ag,aj){this.track=af;this.index=ai;this.low=ai*R*ah;this.high=(ai+1)*R*ah;this.resolution=ah;this.canvas=$("<div class='track-tile'/>").append(ag);this.data=aj;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(af,ai,ah,ag,aj,ak){b.call(this,af,ai,ah,ag,aj);this.max_val=ak};p(k.prototype,b.prototype);var P=function(af,aj,ai,ah,al,am,ak,ag){b.call(this,af,aj,ai,ah,al);this.mode=am;this.message=ak;this.feature_mapper=ag};p(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.canvas).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).siblings(".feature-popup").remove()}).mousemove(function(ar){if(!this.hovered){return}var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).siblings(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),ax=$("<table/>"),av,au,ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)=="number"?Z(au,2):au)}ai.append($("<div class='feature-popup-inner'>").append(ax));af[an]=ai}ai.appendTo($(ag.canvas).parent());var aj=aq+parseInt(ag.canvas.css("left"))-ai.width()/2,ah=ap+parseInt(ag.canvas.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ai,aq,aj,am,ar,ah,ag){q.call(this,ai,aq,aj,{},"draghandle");this.data_url=(ah?ah:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ag?ag:L);this.dataset_check_url=converted_datasets_state_url;this.content_visible=true;if(!i.id_counter){i.id_counter=0}this.id=i.id_counter++;this.container_div=$("<div />").addClass("track").attr("id","track_"+this.id).css("position","relative");if(am){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("<div/>").css("float","left").appendTo(this.header_div).hide();this.toggle_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Hide/show track content").addClass("icon-button toggle").tipsy({gravity:"s"}).appendTo(this.icons_div);this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.overview_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var ak=this;this.header_div.dblclick(function(at){at.stopPropagation()});this.toggle_icon.click(function(){if(ak.content_visible){ak.toggle_icon.addClass("toggle-expand").removeClass("toggle");ak.hide_contents();ak.mode_div.hide();ak.content_visible=false}else{ak.toggle_icon.addClass("toggle").removeClass("toggle-expand");ak.content_visible=true;ak.mode_div.show();ak.show_contents()}});this.settings_icon.click(function(){var av=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},at=function(){ak.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},au=function(aw){if((aw.keyCode||aw.which)===27){av()}else{if((aw.keyCode||aw.which)===13){at()}}};$(window).bind("keypress.check_enter_esc",au);show_modal("Configure Track",ak.config.build_form(),{Cancel:av,OK:at})});this.overview_icon.click(function(){ak.view.set_overview(ak)});this.filters_icon.click(function(){ak.filters_div.toggle();ak.filters_manager.reset_filters()});this.tools_icon.click(function(){ak.dynamic_tool_div.toggle();if(ak.dynamic_tool_div.is(":visible")){ak.set_name(ak.name+ak.tool_region_and_parameters_str())}else{ak.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();ak.remove()});if(ak.display_modes!==undefined){if(ak.mode_div===undefined){ak.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ak.header_div);var al=(ak.config&&ak.config.values.mode?ak.config.values.mode:ak.display_modes[0]);ak.mode=al;ak.mode_div.text(al);var af={};for(var an=0,ap=ak.display_modes.length;an<ap;an++){var ao=ak.display_modes[an];af[ao]=function(at){return function(){ak.change_mode(at)}}(ao)}make_popupmenu(ak.mode_div,af)}else{ak.mode_div.hide()}this.header_div.append($("<div/>").css("clear","both"));this.container_div.hover(function(){ak.icons_div.show()},function(){ak.icons_div.hide()})}}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};p(i.prototype,q.prototype,{get_type:function(){if(this instanceof ab){return"LabelTrack"}else{if(this instanceof A){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof W){return"ReadTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.initial_canvas=undefined;af.content_div.css("height","auto");af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:af.hda_ldda,dataset_id:af.dataset_id,chrom:af.view.chrom},function(ag){if(!ag||ag==="error"||ag.kind==="error"){af.container_div.addClass("error");af.content_div.text(o);if(ag.message){var ah=$(" <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(K)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(F)}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(Y);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(){af.container_div.removeClass("nodata error pending");af.request_draw()})}}}}}}});this.update_icons()},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()},predraw_init:function(){}});var N=function(aj,ah,ag,am,ai,al,ak){i.call(this,aj,ah,ag,am,ai);var af=this,ah=af.view;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new aa(this,(al!==undefined?al:{}));this.filters_available=false;this.filters_visible=false;this.tool=(ak!==undefined&&obj_length(ak)>0?new r(this,ak):undefined);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(N.prototype,q.prototype,i.prototype,{copy:function(af){return new this.constructor(this.name,this.view,af,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json: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,}},change_mode:function(ag){var af=this;af.mode_div.text(ag);af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();return af},update_icons:function(){var af=this;if(af.filters_available>0){af.filters_icon.show()}else{af.filters_icon.hide()}if(af.tool){af.tools_icon.show()}else{af.tools_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},_draw:function(ah,ap){if(!this.enabled){return}if(!this.content_visible){return}if(!(this instanceof A)&&(!this.dataset_id)){return}var ao=this.view.low,al=this.view.high,am=al-ao,ai=this.view.container.width(),at=ai/am,ak=this.view.resolution,ar=$("<div style='position: relative;'></div>");if(this.is_overview){ao=this.view.max_low;al=this.view.max_high;ak=Math.pow(C,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(C)));at=ai/(view.max_high-view.max_low)}if(!ap){this.content_div.children().remove()}this.content_div.append(ar);this.max_height=0;var ag=Math.floor(ao/ak/R);var an=true;var aq=[];var af=0;while((ag*R*ak)<al){tile=this.draw_helper(ah,ai,ag,ak,ar,at);if(tile){aq.push(tile)}else{an=false}ag+=1;af++}var aj=this;if(an){aj.postdraw_actions(aq,ai,at,ap)}},postdraw_actions:function(aj,ak,al,af){var ah=this;var ai=false;for(var ag=0;ag<aj.length;ag++){if(aj[ag].message){ai=true;break}}if(ai){for(var ag=0;ag<aj.length;ag++){tile=aj[ag];if(!tile.message){tile.canvas.css("padding-top",E)}}}},draw_helper:function(ag,ah,ai,al,ar,aw,at,am){var aj=this,aq=this._gen_tile_cache_key(ah,aw,ai),an=ai*R*al,av=an+R*al;var ao=(ag?undefined:aj.tile_cache.get(aq));if(ao){aj.show_tile(ao,ar,aw);return ao}var ap=function(ax){return("isResolved" in ax)};var ak=true;var af=aj.data_manager.get_data(an,av,aj.mode,al,aj.data_url_extra_params);if(ap(af)){ak=false}var au;if(view.reference_track&&aw>view.canvas_manager.char_width_px){au=view.reference_track.data_manager.get_data(an,av,aj.mode,al,view.reference_track.data_url_extra_params);if(ap(au)){ak=false}}if(ak){p(af,am);var ao=aj.draw_tile(af,aj.mode,al,ai,aw,au);if(ao!==undefined){aj.tile_cache.set(aq,ao);aj.show_tile(ao,ar,aw)}return ao}$.when(af,au).then(function(){view.request_redraw(false,false,false,aj)});return null},show_tile:function(al,an,ao){var ah=this,ag=al.canvas,ak=ag;if(al.message){var ap=$("<div/>"),am=$("<div/>").addClass("tile-message").text(al.message).css({height:E-1,width:al.canvas.width}).appendTo(ap),aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(am),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(am);ap.append(ag);ak=ap;aj.click(function(){al.stale=true;ah.data_manager.get_more_data(al.low,al.high,ah.mode,al.resolution,{},ah.data_manager.DEEP_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()});af.click(function(){al.stale=true;ah.data_manager.get_more_data(al.low,al.high,ah.mode,al.resolution,{},ah.data_manager.BROAD_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}al.predisplay_actions();var ai=(al.low-(this.is_overview?this.view.max_low:this.view.low))*ao;if(this.left_offset){ai-=this.left_offset}ak.css({position:"absolute",top:0,left:ai,height:""});an.append(ak);ah.max_height=Math.max(ah.max_height,ak.height());ah.content_div.css("height",ah.max_height+"px");an.children().css("height",ah.max_height+"px")},_get_tile_bounds:function(af,ag){var ai=af*R*ag,aj=R*ag,ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return[ai,ah]},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ag=this;var af=function(){if(ag.data_manager.size()===0){setTimeout(af,300)}else{ag.data_url=default_data_url;ag.data_query_wait=L;ag.dataset_state_url=converted_datasets_state_url;$.getJSON(ag.dataset_state_url,{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},function(ah){})}};af()}}});var ab=function(ag,af){i.call(this,"label",ag,af,false,{});this.container_div.addClass("label-track")};p(ab.prototype,i.prototype,{init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var A=function(af){N.call(this,"reference",af,{content_div:af.top_labeltrack},false,{});af.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:af.dbkey};this.data_manager=new I(B,this,false);this.tile_cache=new c(u)};p(A.prototype,q.prototype,N.prototype,{init:function(){this.enabled=true},draw_tile:function(ap,al,ak,ag,aq){var aj=this,ah=R*ak;if(aq>this.view.canvas_manager.char_width_px){if(ap.data===null){aj.content_div.css("height","0px");return}var ai=this.view.canvas_manager.new_canvas();var ao=ai.getContext("2d");ai.width=Math.ceil(ah*aq+aj.left_offset);ai.height=aj.height_px;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";ap=ap.data;for(var am=0,an=ap.length;am<an;am++){var af=Math.round(am*aq);ao.fillText(ap[am],af+aj.left_offset,10)}return new b(aj,ag,ak,ai,ap)}this.content_div.css("height","0px")}});var j=function(ak,ai,ah,al,af,aj){var ag=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";N.call(this,ak,ai,ah,true,aj);this.min_height_px=16;this.max_height_px=400;this.height_px=32;this.hda_ldda=al;this.dataset_id=af;this.original_dataset_id=af;this.data_manager=new S(B,this);this.tile_cache=new c(u);this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{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:aj,onchange:function(){ag.set_name(ag.prefs.name);ag.vertical_range=ag.prefs.max_value-ag.prefs.min_value;$("#linetrack_"+ag.dataset_id+"_minval").text(ag.prefs.min_value);$("#linetrack_"+ag.dataset_id+"_maxval").text(ag.prefs.max_value);ag.tile_cache.clear();ag.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,N.prototype,{add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){if(af.content_visible){ai=true;ag.show()}},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.content_div).css("height",aj);af.height_px=aj;af.request_draw(true)}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.height_px}).appendTo(af.container_div)},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.data_url,{stats:true,chrom:af.view.chrom,low:null,high:null,hda_ldda:af.hda_ldda,dataset_id:af.dataset_id},function(ag){af.container_div.addClass("line-track");var aj=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){var ah=aj.min;var al=aj.max;ah=Math.floor(Math.min(0,Math.max(ah,aj.mean-2*aj.sd)));al=Math.ceil(Math.max(0,Math.min(al,aj.mean+2*aj.sd)));af.prefs.min_value=ah;af.prefs.max_value=al;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=aj.total_frequency;af.container_div.find(".yaxislabel").remove();var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_minval").text(Z(af.prefs.min_value,3));var ai=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_maxval").text(Z(af.prefs.max_value,3));ai.css({position:"absolute",top:"24px",left:"10px"});ai.prependTo(af.container_div);ak.css({position:"absolute",bottom:"2px",left:"10px"});ak.prependTo(af.container_div)})},draw_tile:function(ar,ak,aj,ah,aq){if(this.vertical_range===undefined){return}var af=this._get_tile_bounds(ah,aj),al=af[0],ap=af[1],ag=Math.ceil((ap-al)*aq),an=this.height_px;var ai=this.view.canvas_manager.new_canvas();ai.width=ag,ai.height=an;var ao=ai.getContext("2d");var am=new M.LinePainter(ar.data,al,ap,this.prefs,ak);am.draw(ao,ag,an);return new b(this.track,ah,aj,ai,ar.data)}});var e=function(af,al,ag,ak,an,am,ai,aj){var ah=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];N.call(this,af,al,ag,true,am,ai,aj);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{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:"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.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new S(20,this);this.left_offset=200;this.set_painter_from_config()};p(e.prototype,q.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style=="arcs"){this.painter=M.ArcLinkedFeaturePainter}else{this.painter=M.LinkedFeaturePainter}},postdraw_actions:function(av,af,aw,au){N.prototype.postdraw_actions.call(this,av,au);var ai=this;if(au){var ak=ai.content_div.children();var al=false;for(var aj=ak.length-1,ap=0;aj>=ap;aj--){var ah=$(ak[aj]);if(al){ah.remove()}else{if(ah.children().length!==0){al=true}}}}if(ai.mode=="Histogram"){var ao=-1;for(var aj=0;aj<av.length;aj++){var at=av[aj].max_val;if(at>ao){ao=at}}for(var aj=0;aj<av.length;aj++){var ar=av[aj];if(ar.max_val!==ao){ar.canvas.remove();ai.draw_helper(true,af,ar.index,ar.resolution,ar.canvas.parent(),aw,[],{max:ao})}}}if(ai.filters_manager){var ag=ai.filters_manager.filters;for(var an=0;an<ag.length;an++){ag[an].update_ui_elt()}var am=false,aq;for(var aj=0;aj<av.length;aj++){if(av[aj].data.length){aq=av[aj].data[0];for(var an=0;an<ag.length;an++){if(ag[an].applies_to(aq)){am=true;break}}}}if(ai.filters_available!==am){ai.filters_available=am;if(!ai.filters_available){ai.filters_div.hide()}ai.update_icons()}}},update_auto_mode:function(af){if(this.mode=="Auto"){if(af=="no_detail"){af="feature spans"}else{if(af=="summary_tree"){af="coverage histogram"}}this.mode_div.text("Auto ("+af+")")}},incremental_slots:function(aj,ag,ai){var ah=this.view.canvas_manager.dummy_context,af=this.inc_slots[aj];if(!af||(af.mode!==ai)){af=new (s.FeatureSlotter)(aj,ai==="Pack",z,function(ak){return ah.measureText(ak)});af.mode=ai;this.inc_slots[aj]=af}return af.slot_features(ag)},get_summary_tree_data:function(aj,am,ah,av){if(av>ah-am){av=ah-am}var aq=Math.floor((ah-am)/av),au=[],ai=0;var ak=0,al=0,ap,at=0,an=[],ar,ao;var ag=function(ay,ax,az,aw){ay[0]=ax+az*aw;ay[1]=ax+(az+1)*aw};while(at<av&&ak!==aj.length){var af=false;for(;at<av&&!af;at++){ag(an,am,at,aq);for(al=ak;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){af=true;break}}if(af){break}}data_start_index=al;au[au.length]=ar=[an[0],0];for(;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){ar[1]++}else{break}}if(ar[1]>ai){ai=ar[1]}at++}return{max:ai,delta:aq,data:au}},draw_tile:function(au,ax,aB,aF,ap,ai){var ay=this,ak=ay._get_tile_bounds(aF,aB),aI=ak[0],ag=ak[1],aw=ag-aI,az=Math.ceil(aw*ap),aO=25,aj=this.left_offset,av,al;if(ax==="Auto"){if(au.dataset_type==="summary_tree"){ax=au.dataset_type}else{if(au.extra_info==="no_detail"||ay.is_overview){ax="no_detail"}else{var aN=au.data;if(this.view.high-this.view.low>J){ax="Squish"}else{ax="Pack"}}}this.update_auto_mode(ax)}if(ax==="summary_tree"||ax==="Histogram"){al=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel");af.text(au.max);af.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});af.prependTo(this.container_div);var ah=this.view.canvas_manager.new_canvas();ah.width=az+aj;ah.height=al+T;if(au.dataset_type!="summary_tree"){var aq=this.get_summary_tree_data(au.data,aI,ag,200);if(au.max){aq.max=au.max}au=aq}var aK=new M.SummaryTreePainter(au,aI,ag,this.prefs);var aA=ah.getContext("2d");aA.translate(aj,T);aK.draw(aA,az,al);return new k(ay,aF,aB,ah,au.data,au.max)}var av,an=1;if(ax==="no_detail"||ax==="Squish"||ax==="Pack"){an=this.incremental_slots(ap,au.data,ax);av=this.inc_slots[ap].slots}var ao=[];if(au.data){var ar=this.filters_manager.filters;for(var aC=0,aE=au.data.length;aC<aE;aC++){var am=au.data[aC];var aD=false;var at;for(var aH=0,aM=ar.length;aH<aM;aH++){at=ar[aH];at.update_attrs(am);if(!at.keep(am)){aD=true;break}}if(!aD){ao.push(am)}}}var aL=(this.filters_manager.alpha_filter?new D(this.filters_manager.alpha_filter):null);var aJ=(this.filters_manager.height_filter?new D(this.filters_manager.height_filter):null);var aK=new (this.painter)(ao,aI,ag,this.prefs,ax,aL,aJ,ai);var al=Math.max(ad,aK.get_required_height(an,az));var ah=this.view.canvas_manager.new_canvas();var aG=null;ah.width=az+aj;ah.height=al;var aA=ah.getContext("2d");aA.fillStyle=this.prefs.block_color;aA.font=aA.canvas.manager.default_font;aA.textAlign="right";this.container_div.find(".yaxislabel").remove();if(au.data){aA.translate(aj,0);aG=aK.draw(aA,az,al,av);aG.translation=-aj}return new P(ay,aF,aB,ah,au.data,ax,au.message,aG)}});var U=function(ak,ah,ag,am,af,aj,al,ai){e.call(this,ak,ah,ag,am,af,aj,al,ai);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{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:aj,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=M.ReadPainter};p(U.prototype,q.prototype,N.prototype,e.prototype);var W=function(af,ak,ag,aj,an,am,ah){e.call(this,af,ak,ag,aj,an,am,ah);var ai=get_random_color(),al=get_random_color([ai,"#ffffff"]);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{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:"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=M.ReadPainter;this.update_icons()};p(W.prototype,q.prototype,N.prototype,e.prototype);X.View=ac;X.DrawableGroup=Q;X.LineTrack=j;X.FeatureTrack=e;X.ReadTrack=W;X.VcfTrack=U};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.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(F,G){for(var E=0;E<=z;E++){var C=false,H=h[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var i=H[B];if(G>i[0]&&F<i[1]){C=true;break}}}if(!C){return E}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}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={};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(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.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(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.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,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,E=I/H,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],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]-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&&this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){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 diff -r a4df07ccecdb70ae45982e596d2e360bdc9ab217 -r 23198e766859394108d48de1489be7052530d38b static/scripts/packed/trackster_ui.js --- a/static/scripts/packed/trackster_ui.js +++ b/static/scripts/packed/trackster_ui.js @@ -1,1 +1,1 @@ -var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,VcfTrack:VcfTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d<f.drawables.length;d++){var b=f.drawables[d],c;if(b.track_type){c=track_from_dict(b,e)}else{c=drawable_collection_from_dict(b)}e.add_drawable(c);e.content_div.append(c.container_div)}return e};var drawable_from_dict=function(b,a){return(b.track_type?track_from_dict(b,a):drawable_collection_from_dict(b,a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o,view))}}var n;for(var j=0;j<view.drawables.length;j++){if(view.drawables[j].name===m){view.set_overview(view.drawables[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})}; \ No newline at end of file +var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,VcfTrack:VcfTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d<f.drawables.length;d++){var b=f.drawables[d],c;if(b.track_type){c=track_from_dict(b,e)}else{c=drawable_collection_from_dict(b)}e.add_drawable(c);e.content_div.append(c.container_div)}return e};var drawable_from_dict=function(b,a){return(b.track_type?track_from_dict(b,a):drawable_collection_from_dict(b,a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o,view))}}view.update_intro_div();var n;for(var j=0;j<view.drawables.length;j++){if(view.drawables[j].name===m){view.set_overview(view.drawables[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTop(a.viewport_container.scrollTop()-20);break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTop(a.viewport_container.scrollTop()+20);break}})}; \ No newline at end of file Repository URL: 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