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commit/galaxy-central: jgoecks: Fix hyperlinks in Cuffcompare and Cuffdiff documentation.
by Bitbucket 07 Apr '11

07 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8a43c7a39dd1/ changeset: r5356:8a43c7a39dd1 user: jgoecks date: 2011-04-07 22:28:56 summary: Fix hyperlinks in Cuffcompare and Cuffdiff documentation. affected #: 2 files (36 bytes) --- a/tools/ngs_rna/cuffcompare_wrapper.xml Thu Apr 07 08:39:07 2011 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.xml Thu Apr 07 16:28:56 2011 -0400 @@ -130,9 +130,9 @@ **Input format** -Cuffcompare takes Cufflinks' GTF output as input, and optionally can take a "reference" annotation (such as from Ensembl___) +Cuffcompare takes Cufflinks' GTF output as input, and optionally can take a "reference" annotation (such as from Ensembl_) -.. ___: http://www.todo.org +.. _Ensembl: http://www.ensembl.org ------ --- a/tools/ngs_rna/cuffdiff_wrapper.xml Thu Apr 07 08:39:07 2011 -0400 +++ b/tools/ngs_rna/cuffdiff_wrapper.xml Thu Apr 07 16:28:56 2011 -0400 @@ -198,8 +198,6 @@ Cuffdiff takes Cufflinks or Cuffcompare GTF files as input along with two SAM files containing the fragment alignments for two or more samples. -.. ___: http://www.todo.org - ------ **Outputs** 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: Additional fix for typo propagated from manual_builds, which was updated in 5350:cd2aff5b117c.
by Bitbucket 07 Apr '11

07 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/50e249442c5a/ changeset: r5355:50e249442c5a user: dan date: 2011-04-07 14:39:07 summary: Additional fix for typo propagated from manual_builds, which was updated in 5350:cd2aff5b117c. affected #: 1 file (0 bytes) --- a/tool-data/shared/gbrowse/gbrowse_build_sites.txt Wed Apr 06 16:28:33 2011 -0400 +++ b/tool-data/shared/gbrowse/gbrowse_build_sites.txt Thu Apr 07 08:39:07 2011 -0400 @@ -10,5 +10,5 @@ modencode_fly http://modencode.oicr.on.ca/fgb2/gbrowse/fly dm2 #SGD -sgd_yeast http://browse.yeastgenome.org/fgb2/gbrowse/scgenome Saccharomcyes_cerevisiae_S288C_SGD2010 +sgd_yeast http://browse.yeastgenome.org/fgb2/gbrowse/scgenome Saccharomyces_cerevisiae_S288C_SGD2010 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: kellyv: Added BWA for SOLiD to tool_conf.xml.main
by Bitbucket 06 Apr '11

06 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b1657489f16c/ changeset: r5354:b1657489f16c user: kellyv date: 2011-04-06 22:28:33 summary: Added BWA for SOLiD to tool_conf.xml.main affected #: 1 file (53 bytes) --- a/tool_conf.xml.main Wed Apr 06 12:44:58 2011 -0400 +++ b/tool_conf.xml.main Wed Apr 06 16:28:33 2011 -0400 @@ -358,6 +358,7 @@ <tool file="metag_tools/megablast_xml_parser.xml" /><label text="AB-SOLiD" id="ab_solid"/><tool file="sr_mapping/bowtie_color_wrapper.xml" /> + <tool file="sr_mapping/bwa_color_wrapper.xml" /></section><section name="NGS: SAM Tools" id="samtools"><tool file="samtools/sam_bitwise_flag_filter.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Disable eagerloading of a job's datasets. This results in more queries but does away with a join that was returning a far bigger result than it should've.
by Bitbucket 06 Apr '11

06 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d44244ed570a/ changeset: r5353:d44244ed570a user: natefoo date: 2011-04-06 18:44:58 summary: Disable eagerloading of a job's datasets. This results in more queries but does away with a join that was returning a far bigger result than it should've. affected #: 1 file (36 bytes) --- a/lib/galaxy/model/mapping.py Wed Apr 06 12:40:20 2011 -0400 +++ b/lib/galaxy/model/mapping.py Wed Apr 06 12:44:58 2011 -0400 @@ -1392,10 +1392,10 @@ history=relation( History ), library_folder=relation( LibraryFolder ), parameters=relation( JobParameter, lazy=False ), - input_datasets=relation( JobToInputDatasetAssociation, lazy=False ), - output_datasets=relation( JobToOutputDatasetAssociation, lazy=False ), + input_datasets=relation( JobToInputDatasetAssociation ), + output_datasets=relation( JobToOutputDatasetAssociation ), post_job_actions=relation( PostJobActionAssociation, lazy=False ), - output_library_datasets=relation( JobToOutputLibraryDatasetAssociation, lazy=False ), + output_library_datasets=relation( JobToOutputLibraryDatasetAssociation ), external_output_metadata = relation( JobExternalOutputMetadata, lazy = False ) ) ) assign_mapper( context, Task, Task.table, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 06 Apr '11

06 Apr '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/73d12ac49c2a/ changeset: r5351:73d12ac49c2a user: kanwei date: 2011-04-06 18:38:00 summary: More BLAST tests affected #: 20 files (155.6 KB) Diff too large to display. http://bitbucket.org/galaxy/galaxy-central/changeset/420ddcb0be8c/ changeset: r5352:420ddcb0be8c user: kanwei date: 2011-04-06 18:40:20 summary: Delete unused BLAST tests affected #: 2 files (0 bytes) --- a/test-data/blastp_four_human_vs_rhodopsin_22c.tabular Wed Apr 06 12:38:00 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| 96.55 348 12 0 1 348 1 348 0.0 660 gi|57163783|ref|NP_001009242.1| 1704 336 343 0 98.56 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA -sp|P08100|OPSD_HUMAN gi|3024260|sp|P56514.1|OPSD_BUFBU 84.80 342 51 1 1 341 1 342 8e-170 578 gi|3024260|sp|P56514.1|OPSD_BUFBU 1489 290 322 1 94.15 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE -sp|P08100|OPSD_HUMAN gi|283855846|gb|ADB45242.1| 94.82 328 17 0 11 338 1 328 4e-180 612 gi|283855846|gb|ADB45242.1| 1578 311 321 0 97.87 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS -sp|P08100|OPSD_HUMAN gi|283855823|gb|ADB45229.1| 94.82 328 17 0 11 338 1 328 1e-173 591 gi|283855823|gb|ADB45229.1| 1523 311 323 0 98.48 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS -sp|P08100|OPSD_HUMAN gi|223523|prf||0811197A 93.10 348 23 1 1 348 1 347 0.0 634 gi|223523|prf||0811197A 1634 324 336 1 96.55 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA -sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| 82.16 342 60 1 1 341 1 342 2e-165 563 gi|12583665|dbj|BAB21486.1| 1451 281 314 1 91.81 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE --- a/test-data/blastp_human_vs_pdb_seg_no_converted_x22.tabular Wed Apr 06 12:38:00 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -sp|Q9BS26|ERP44_HUMAN gi|193885198|pdb|2R2J|A 97.11 381 11 0 26 406 2 382 0.0 768 gi|193885198|pdb|2R2J|A 1982 370 372 0 97.64 1 1 PVTTEITSLDTENIDEILNNADVALVNFYADWCRFSQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMKREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHADCDKFRHPLLHIQKTPADCPVIAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREFHHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL PLGSEITSLDTENIDEILNNADVALVNFYADWCRFSQXLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGXXXKREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDXVYLGAXTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHXKEDTESLEIFQNEVARQLISEKGTINFLHADCDKFRHPLLHIQKTPADCPVIAIDSFRHXYVFGDFKDVLIPGKLKQFVFDLHSGKLHREFHHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL -sp|Q9BS26|ERP44_HUMAN gi|88192228|pdb|2B5E|A 25.17 290 193 8 25 306 10 283 4e-20 95.1 gi|88192228|pdb|2B5E|A;gi|206581884|pdb|3BOA|A 235 73 133 24 45.86 1 1 TPVTTEITSLDTENIDEILNNADVALVNFYADWCRFSQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMKR-EYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNI---IYKPPGHSAPDMVYLGA---MTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHADCDKF-RH APEDSAVVKLATDSFNEYIQSHDLVLAEFFAPWCGHCKNMAPEYVKAAETLVEK-----NITLAQIDCTENQDLCMEHNIPGFPSLKIFKNSDVNNSIDYEGPRTAEAIVQFMIKQSQPAVAVVADLPAYLANETFVTPVIVQSGKIDADFNATFYSMANKHFNDYDFVSA--------ENADDDFKLSIYLPSAMDEP-VVYNGKKADIADADVFEKWLQVEALPYFGEIDGSVFAQYVESGLPLGYLFY--NDEEELEEYKPLFTELAKKNRGLMNFVSIDARKFGRH -sp|Q9NSY1|BMP2K_HUMAN gi|73536291|pdb|2BUJ|A 29.39 279 182 8 40 308 21 294 1e-22 105 gi|73536291|pdb|2BUJ|A;gi|73536292|pdb|2BUJ|B 262 82 130 15 46.59 1 1 GVRVFAVGRHQVTLEESLAEGGFSTVFLVR-THGGIRCALKRMYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSISDNVWEVLILMEYCRAGQVVNQMNKKLQTG--FTEPEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLNDGGNYVLCDFGSATNKFLNPQKDG-VNVVEEEIKKYTTLSYRAPEMINLYGGKPITTKADIWALGCLLYKLCFFTLPF------GESQVAICDGNFTIPDNSRYSRNIHCLIRFMLEPDPEHRPDI GHMVIIDNKHYLFIQK-LGEGGFSYVDLVEGLHDGHFYALKRILCHEQQDREEAQREAD-MHRLFNHPNILRLVAYCLRERGAKH-EAWLLLPFFKRGTLWNEIERLKDKGNFLTEDQILWLLLGICRGLEAIH--AKGYAHRDLKPTNILLGDEGQPVLMDLGSMNQACIHVEGSRQALTLQDWAAQRCTISYRAPELFSVQSHCVIDERTDVWSLGCVLYAMMFGEGPYDMVFQKGDSVALAVQNQLSIPQSPRHSSALWQLLNSMMTVDPHQRPHI -sp|Q9NSY1|BMP2K_HUMAN gi|270346335|pdb|2WQM|A 27.21 272 166 12 53 311 36 288 6e-17 86.3 gi|270346335|pdb|2WQM|A;gi|270346336|pdb|2WQN|A 212 74 129 32 47.43 1 1 LEESLAEGGFSTVFLVRTH-GGIRCALKRMYVNNMPDLNV---CKREITIMKELSGHKNIVGYLDCAVNSISDNVWEVLILMEYCRAGQVVNQMN--KKLQTGFTEPEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLNDGGNYVLCDFGSATNKFLNPQKDGVNVVEEEIKKYTTLSYRAPEMINLYGGKPITTKADIWALGCLLYKLCFFTLPFGESQV---AICD----GNFTIPDNSRYSRNIHCLIRFMLEPDPEHRPDIFQV IEKKIGRGQFSEVYRAACLLDGVPVALKKVQIFDLMDAKARADCIKEIDLLKQLN-HPNVIKYY---ASFIEDN--ELNIVLELADAGDLSRMIKHFKKQKRLIPERTVWKYFVQLCSALEHMHSRR--VMHRDIKPANVFITATGVVKLGDLG--LGRFFSSKTTAAHSL------VGTPYYMSPERIHENG---YNFKSDIWSLGCLLYEMAALQSPFYGDKMNLYSLCKKIEQCDYPPLPSDHYSEELRQLVNMCINPDPEKRPDVTYV -sp|P06213|INSR_HUMAN gi|116667097|pdb|2DTG|E 95.91 928 7 2 28 955 1 897 0.0 1846 gi|116667097|pdb|2DTG|E 4781 890 893 31 96.23 1 1 HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWERQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQILKELEESSFRKTFEDYLHNVVFVPRKTSSGTGAEDPRPSRKRRSLGDVGNVTVAVPTVAAFPNTSSTSVPTSPEEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCVSRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIA HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNHIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWERQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQILKELEESSFRKTFEDYLHNVVFV------------PRPSRKRRSLGDVGNA-------------------GNNEEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCDTRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIA -sp|P06213|INSR_HUMAN gi|114794482|pdb|2HR7|A 99.59 485 2 0 28 512 1 485 0.0 1016 gi|114794482|pdb|2HR7|A;gi|114794483|pdb|2HR7|B 2628 483 485 0 100.00 1 1 HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKI HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNHIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDKASCENELLKFSYIRTSFDKI -sp|P08100|OPSD_HUMAN gi|16975387|pdb|1JFP|A 93.39 348 23 0 1 348 1 348 0.0 681 gi|16975387|pdb|1JFP|A;gi|22219255|pdb|1LN6|A;gi|157878065|pdb|1GZM|A;gi|157878066|pdb|1GZM|B;gi|157878298|pdb|1HZX|A;gi|157878299|pdb|1HZX|B;gi|157878979|pdb|1L9H|A;gi|157878980|pdb|1L9H|B;gi|157880263|pdb|1U19|A;gi|157880264|pdb|1U19|B;gi|157883606|pdb|2G87|A;gi|157883607|pdb|2G87|B;gi|157883830|pdb|2HPY|A;gi|157883831|pdb|2HPY|B;gi|157883860|pdb|2I35|A;gi|157883861|pdb|2I36|A;gi|157883862|pdb|2I36|B;gi|157883863|pdb|2I36|C;gi|157883864|pdb|2I37|A;gi|157883865|pdb|2I37|B;gi|157883866|pdb|2I37|C;gi|159795066|pdb|2PED|A;gi|159795067|pdb|2PED|B;gi|192988480|pdb|3CAP|A;gi|192988481|pdb|3CAP|B;gi|195927457|pdb|3C9L|A;gi|197107530|pdb|1F88|A;gi|197107531|pdb|1F88|B;gi|206582030|pdb|3DQB|A 1756 325 337 0 96.84 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA -sp|P08100|OPSD_HUMAN gi|195927458|pdb|3C9M|A 93.10 348 24 0 1 348 1 348 0.0 674 gi|195927458|pdb|3C9M|A 1738 324 335 0 96.26 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MCGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSCFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: kellyv: Corrected typo in manual build name
by Bitbucket 06 Apr '11

06 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/cd2aff5b117c/ changeset: r5350:cd2aff5b117c user: kellyv date: 2011-04-06 16:16:30 summary: Corrected typo in manual build name affected #: 1 file (0 bytes) --- a/tool-data/shared/ucsc/manual_builds.txt Tue Apr 05 17:59:43 2011 -0400 +++ b/tool-data/shared/ucsc/manual_builds.txt Wed Apr 06 10:16:30 2011 -0400 @@ -692,7 +692,7 @@ eschColi_TW14359 Escherichia coli TW14359 chr=5528136,plasmid_pO157=94601 pUC18 pUC18 Plasmid plasmid=2686 nomLeu1 Gibbon chr1=245538060,chr10=135320619,chr10_random=51011,chr11=134551115,chr12=132397767,chr12_random=336702,chr13=114140689,chr14=106383727,chr15=100373758,chr15_random=814500,chr16=88836341,chr16_random=121782,chr17=78641643,chr17_random=2617017,chr18=76124575,chr19=63791437,chr19_random=297341,chr1_random=3502083,chr2=242756806,chr20=62432189,chr21=47019833,chr22=49520868,chr22_random=31530,chr2_random=335351,chr3=199337376,chr3_random=950829,chr4=191633586,chr4_random=923474,chr5=180612635,chr5_random=150620,chr6=170839170,chr6_random=1837487,chr7=158619002,chr7_random=805938,chr8=146283503,chr8_random=649034,chr9=138402467,chr9_random=1315712,chrUn=217400297,chrX=154793867,chrX_random=1690203,chrY=57470892 -Saccharomcyes_cerevisiae_S288C_SGD2010 S. cerevisae str. S288C chr1=230218,chr2=813184,chr3=316620,chr4=1531933,chr5=576874,chr6=270161,chr7=1090940,chr8=562643,chr9=439888,chr10=745751,chr11=666816,chr12=1078177,chr13=924431,chr14=784333,chr15=1091291,chr16=948066,chrM=85779 +Saccharomyces_cerevisiae_S288C_SGD2010 S. cerevisae str. S288C chr1=230218,chr2=813184,chr3=316620,chr4=1531933,chr5=576874,chr6=270161,chr7=1090940,chr8=562643,chr9=439888,chr10=745751,chr11=666816,chr12=1078177,chr13=924431,chr14=784333,chr15=1091291,chr16=948066,chrM=85779 Spur_v2.6 Purple Sea Urchin (Strongylocentrotus purpuratus) v2.6 Ptrichocarpa_156 Poplar (Populus trichocarpa) Hydra_JCVI Hydra magnipapillata str. 105 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: ensure that reads are drawn in squish and pack modes even when view area is large by setting a minimum width of 1px.
by Bitbucket 05 Apr '11

05 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/dd604de40ac4/ changeset: r5349:dd604de40ac4 user: jgoecks date: 2011-04-05 23:59:43 summary: Trackster: ensure that reads are drawn in squish and pack modes even when view area is large by setting a minimum width of 1px. affected #: 1 file (317 bytes) --- a/static/scripts/trackster.js Tue Apr 05 14:16:26 2011 -0400 +++ b/static/scripts/trackster.js Tue Apr 05 17:59:43 2011 -0400 @@ -1126,10 +1126,9 @@ /** * Tiles for TiledTracks. */ -var Tile = function(track, canvas, histo_max) { +var Tile = function(track, canvas) { this.track = track; this.canvas = canvas; - this.histo_max = histo_max; }; /** @@ -2192,7 +2191,7 @@ // Start dealing with row-by-row tracks - // If working with a mode where slotting is neccesary, update the incremental slotting + // If working with a mode where slotting is necessary, update the incremental slotting var slots, slots_required = 1; if ( mode === "no_detail" || mode === "Squish" || mode === "Pack" ) { slots_required = this.incremental_slots(w_scale, result.data, mode); @@ -3164,6 +3163,14 @@ var seq_start = feature_start + base_offset, s_start = Math.floor( Math.max(0, (seq_start - tile_low) * w_scale) ), s_end = Math.floor( Math.max(0, (seq_start + cig_len - tile_low) * w_scale) ); + + // Make sure that read is drawn even if it too small to be rendered officially; in this case, + // read is drawn at 1px. + // TODO: need to ensure that s_start, s_end are calcuated the same for both slotting + // and drawing. + if (s_start === s_end) { + s_end += 1; + } switch (cig_op) { case "H": // Hard clipping. 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: 3 new changesets
by Bitbucket 05 Apr '11

05 Apr '11

3 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/63e0cc9ca457/ changeset: r5346:63e0cc9ca457 user: jgoecks date: 2011-04-05 20:12:39 summary: Trackster: mode is not reduced if in auto mode. affected #: 1 file (22 bytes) --- a/static/scripts/trackster.js Tue Apr 05 12:08:42 2011 -0400 +++ b/static/scripts/trackster.js Tue Apr 05 14:12:39 2011 -0400 @@ -2092,9 +2092,9 @@ update_auto_mode: function( mode ) { if ( this.mode == "Auto" ) { if ( mode == "no_detail" ) { - mode = "reduced to feature spans"; + mode = "feature spans"; } else if ( mode == "summary_tree" ) { - mode = "reduced to coverage histogram"; + mode = "coverage histogram"; } this.mode_div.text( "Auto (" + mode + ")" ); } http://bitbucket.org/galaxy/galaxy-central/changeset/6131f91bad52/ changeset: r5347:6131f91bad52 user: jgoecks date: 2011-04-05 20:14:32 summary: Merge. affected #: 3 files (740 bytes) --- a/tool_conf.xml.main Tue Apr 05 14:12:39 2011 -0400 +++ b/tool_conf.xml.main Tue Apr 05 14:14:32 2011 -0400 @@ -169,12 +169,6 @@ <tool file="evolution/mutate_snp_codon.xml" /></section> - <section name="Motif Tools" id="motifs"> - <tool file="rgenetics/rgWebLogo3.xml" /> - </section> - <section name="Multiple Alignments" id="clustal"> - <tool file="rgenetics/rgClustalw.xml" /> - </section><section name="Metagenomic analyses" id="tax_manipulation"><tool file="taxonomy/gi2taxonomy.xml" /><tool file="taxonomy/t2t_report.xml" /> --- a/tools/rgenetics/rgCaCo.py Tue Apr 05 14:12:39 2011 -0400 +++ b/tools/rgenetics/rgCaCo.py Tue Apr 05 14:14:32 2011 -0400 @@ -53,28 +53,26 @@ resfl = resfl[1:] headl = [x.strip().upper() for x in headl] headIndex = dict(zip(headl,range(0,len(headl)))) - chrpos = headIndex.get('CHR',None) - rspos = headIndex.get('RS',None) - offspos = headIndex.get('OFFSET',None) - ppos = headIndex.get('LOG10ARMITAGEP',None) - wewant = [chrpos,rspos,offspos,ppos] + whatwewant = ['CHR','RS','OFFSET','LOG10ARMITAGEP'] + wewant = [headIndex.get(x,None) for x in whatwewant] if None in wewant: # missing something - logf.write('### Error missing a required header in makeGFF - headIndex=%s\n' % headIndex) + logf.write('### Error missing a required header from %s in makeGFF - headIndex=%s\n' % (whatwewant,headIndex)) return - resfl = [x for x in resfl if x[ppos] > ''] + ppos = wewant[3] # last in list + resfl = [x for x in resfl if x[ppos] > '' and x[ppos] <> 'NA'] resfl = [(float(x[ppos]),x) for x in resfl] # decorate resfl.sort() resfl.reverse() # using -log10 so larger is better - resfl = resfl[:topn] # truncate pvals = [x[0] for x in resfl] # need to scale resfl = [x[1] for x in resfl] # drop decoration + resfl = resfl[:topn] # truncate maxp = max(pvals) # need to scale minp = min(pvals) prange = abs(maxp-minp) + 0.5 # fudge scalefact = 1000.0/prange logf.write('###maxp=%f,minp=%f,prange=%f,scalefact=%f\n' % (maxp,minp,prange,scalefact)) for i,row in enumerate(resfl): - row[ppos] = '%d' % (int(scalefact*pvals[i])) + row[ppos] = '%d' % (int(scalefact*pvals[i])) resfl[i] = row # replace outf = file(outfname,'w') outf.write(header) --- a/tools/rgenetics/rgWebLogo3.xml Tue Apr 05 14:12:39 2011 -0400 +++ b/tools/rgenetics/rgWebLogo3.xml Tue Apr 05 14:14:32 2011 -0400 @@ -5,7 +5,7 @@ #if $range.mode == 'part' -l "$range.seqstart" -u "$range.seqend" #end if - </command> + </command><inputs><page><param format="fasta" name="input" type="data" label="Fasta File" /> @@ -71,7 +71,7 @@ <param name = "mode" value="complete" /><param name = "size" value="medium" /><param name = "colours" value="auto" /> - <output name="output" file="rgWebLogo3_test.jpg" ftype="jpg" /> + <output name="output" file="rgWebLogo3_test.jpg" ftype="jpg" compare="sim_size" delta="10000" /></test></tests> @@ -90,6 +90,15 @@ ---- +**Warning about input Fasta format files** + +The Weblogo3 program used by this tool will fail if your fasta sequences are not all EXACTLY the same length. + +Fasta alignments from the companion ClustalW Galaxy tool will work but many other fasta files may cause this tool to fail - please do not file +a Galaxy bug report - this is a feature of the tool and a problem with your source data - not a tool error - please make certain all your fasta +sequences are the same length! + +---- **Attribution** http://bitbucket.org/galaxy/galaxy-central/changeset/79021bb57c1f/ changeset: r5348:79021bb57c1f user: jgoecks date: 2011-04-05 20:16:26 summary: Merge. affected #: 1 file (207 bytes) --- a/tool_conf.xml.main Tue Apr 05 14:14:32 2011 -0400 +++ b/tool_conf.xml.main Tue Apr 05 14:16:26 2011 -0400 @@ -169,6 +169,12 @@ <tool file="evolution/mutate_snp_codon.xml" /></section> + <section name="Motif Tools" id="motifs"> + <tool file="rgenetics/rgWebLogo3.xml" /> + </section> + <section name="Multiple Alignments" id="clustal"> + <tool file="rgenetics/rgClustalw.xml" /> + </section><section name="Metagenomic analyses" id="tax_manipulation"><tool file="taxonomy/gi2taxonomy.xml" /><tool file="taxonomy/t2t_report.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: fubar: reverted unintended changes to tool_conf.xml.main
by Bitbucket 05 Apr '11

05 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4257de2ebdd0/ changeset: r5345:4257de2ebdd0 user: fubar date: 2011-04-05 20:14:08 summary: reverted unintended changes to tool_conf.xml.main affected #: 1 file (207 bytes) --- a/tool_conf.xml.main Tue Apr 05 14:07:10 2011 -0400 +++ b/tool_conf.xml.main Tue Apr 05 14:14:08 2011 -0400 @@ -169,6 +169,12 @@ <tool file="evolution/mutate_snp_codon.xml" /></section> + <section name="Motif Tools" id="motifs"> + <tool file="rgenetics/rgWebLogo3.xml" /> + </section> + <section name="Multiple Alignments" id="clustal"> + <tool file="rgenetics/rgClustalw.xml" /> + </section><section name="Metagenomic analyses" id="tax_manipulation"><tool file="taxonomy/gi2taxonomy.xml" /><tool file="taxonomy/t2t_report.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by Bitbucket 05 Apr '11

05 Apr '11

3 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/232df3fff6b3/ changeset: r5342:232df3fff6b3 user: fubar date: 2011-03-28 01:50:50 summary: minor tweaks to rgCaCo.py affected #: 1 file (17 bytes) --- a/tools/rgenetics/rgCaCo.py Fri Mar 25 13:26:40 2011 -0400 +++ b/tools/rgenetics/rgCaCo.py Sun Mar 27 19:50:50 2011 -0400 @@ -53,28 +53,26 @@ resfl = resfl[1:] headl = [x.strip().upper() for x in headl] headIndex = dict(zip(headl,range(0,len(headl)))) - chrpos = headIndex.get('CHR',None) - rspos = headIndex.get('RS',None) - offspos = headIndex.get('OFFSET',None) - ppos = headIndex.get('LOG10ARMITAGEP',None) - wewant = [chrpos,rspos,offspos,ppos] + whatwewant = ['CHR','RS','OFFSET','LOG10ARMITAGEP'] + wewant = [headIndex.get(x,None) for x in whatwewant] if None in wewant: # missing something - logf.write('### Error missing a required header in makeGFF - headIndex=%s\n' % headIndex) + logf.write('### Error missing a required header from %s in makeGFF - headIndex=%s\n' % (whatwewant,headIndex)) return - resfl = [x for x in resfl if x[ppos] > ''] + ppos = wewant[3] # last in list + resfl = [x for x in resfl if x[ppos] > '' and x[ppos] <> 'NA'] resfl = [(float(x[ppos]),x) for x in resfl] # decorate resfl.sort() resfl.reverse() # using -log10 so larger is better - resfl = resfl[:topn] # truncate pvals = [x[0] for x in resfl] # need to scale resfl = [x[1] for x in resfl] # drop decoration + resfl = resfl[:topn] # truncate maxp = max(pvals) # need to scale minp = min(pvals) prange = abs(maxp-minp) + 0.5 # fudge scalefact = 1000.0/prange logf.write('###maxp=%f,minp=%f,prange=%f,scalefact=%f\n' % (maxp,minp,prange,scalefact)) for i,row in enumerate(resfl): - row[ppos] = '%d' % (int(scalefact*pvals[i])) + row[ppos] = '%d' % (int(scalefact*pvals[i])) resfl[i] = row # replace outf = file(outfname,'w') outf.write(header) http://bitbucket.org/galaxy/galaxy-central/changeset/be1accb7a6d0/ changeset: r5343:be1accb7a6d0 user: fubar date: 2011-04-05 19:57:14 summary: merge affected #: 33 files (24.1 KB) --- a/cron/add_manual_builds.py Sun Mar 27 19:50:50 2011 -0400 +++ b/cron/add_manual_builds.py Tue Apr 05 13:57:14 2011 -0400 @@ -21,12 +21,12 @@ build_file_out = open(build_file,'a') for line in open(input_file): try: - fields = line.split("\t") + fields = line.replace("\n","").replace("\r","").split("\t") build = fields.pop(0) if build in existing_builds: continue # if build exists, leave alone name = fields.pop(0) try: # get chrom lens if included in file, otherwise still add build - chrs = fields.pop(0).replace("\n","").replace("\r","").split(",") + chrs = fields.pop(0).split(",") except: chrs = [] print>>build_file_out, build+"\t"+name+" ("+build+")" --- a/datatypes_conf.xml.sample Sun Mar 27 19:50:50 2011 -0400 +++ b/datatypes_conf.xml.sample Tue Apr 05 13:57:14 2011 -0400 @@ -128,9 +128,9 @@ <converter file="wiggle_to_simple_converter.xml" target_datatype="interval"/></datatype> - <datatype extension="array_tree" type="galaxy.datatypes.data:Data" /><datatype extension="summary_tree" type="galaxy.datatypes.data:Data" /><datatype extension="interval_index" type="galaxy.datatypes.data:Data" /> + <datatype extension="tabix" type="galaxy.datatypes.data:Data" /><datatype extension="acedb" type="galaxy.datatypes.data:Text"/><datatype extension="asn1" type="galaxy.datatypes.data:Text"/> --- a/lib/galaxy/config.py Sun Mar 27 19:50:50 2011 -0400 +++ b/lib/galaxy/config.py Tue Apr 05 13:57:14 2011 -0400 @@ -2,7 +2,7 @@ Universe configuration builder. """ -import sys, os +import sys, os, tempfile import logging, logging.config import ConfigParser from galaxy.util import string_as_bool @@ -39,6 +39,7 @@ # Where dataset files are stored self.file_path = resolve_path( kwargs.get( "file_path", "database/files" ), self.root ) self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root ) + tempfile.tempdir = self.new_file_path self.openid_consumer_cache_path = resolve_path( kwargs.get( "openid_consumer_cache_path", "database/openid_consumer_cache" ), self.root ) self.cookie_path = kwargs.get( "cookie_path", "/" ) # web API --- a/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py Sun Mar 27 19:50:50 2011 -0400 +++ b/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py Tue Apr 05 13:57:14 2011 -0400 @@ -32,7 +32,7 @@ convert_gff_coords_to_bed( feature ) index.add( feature.chrom, feature.start, feature.end, offset ) - offset += feature.raw_size() + offset += feature.raw_size index.write( open(out_fname, "w") ) --- a/lib/galaxy/datatypes/data.py Sun Mar 27 19:50:50 2011 -0400 +++ b/lib/galaxy/datatypes/data.py Tue Apr 05 13:57:14 2011 -0400 @@ -354,6 +354,7 @@ class Text( Data ): file_ext = 'txt' + line_class = 'line' """Add metadata elements""" MetadataElement( name="data_lines", default=0, desc="Number of data lines", readonly=True, optional=True, visible=False, no_value=0 ) @@ -417,26 +418,30 @@ data_lines += 1 return data_lines def set_peek( self, dataset, line_count=None, is_multi_byte=False ): + """ + Set the peek. This method is used by various subclasses of Text. + """ if not dataset.dataset.purged: # The file must exist on disk for the get_file_peek() method dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) if line_count is None: # See if line_count is stored in the metadata - if dataset.metadata.data_lines is not None: - dataset.blurb = "%s %s" % ( util.commaify( str(dataset.metadata.data_lines) ), inflector.cond_plural(dataset.metadata.data_lines, "line") ) + if dataset.metadata.data_lines: + dataset.blurb = "%s %s" % ( util.commaify( str(dataset.metadata.data_lines) ), inflector.cond_plural(dataset.metadata.data_lines, self.line_class) ) else: # Number of lines is not known ( this should not happen ), and auto-detect is # needed to set metadata # This can happen when the file is larger than max_optional_metadata_filesize. if int(dataset.get_size()) <= 1048576: #Small dataset, recount all lines and reset peek afterward. - dataset.metadata.data_lines = self.count_data_lines(dataset) - self.set_peek(dataset) + lc = self.count_data_lines(dataset) + dataset.metadata.data_lines = lc + dataset.blurb = "%s %s" % ( util.commaify( str(lc) ), inflector.cond_plural(lc, self.line_class) ) else: est_lines = self.estimate_file_lines(dataset) - dataset.blurb = "~%s %s" % ( util.commaify(util.roundify(str(est_lines))), inflector.cond_plural(est_lines, "line") ) + dataset.blurb = "~%s %s" % ( util.commaify(util.roundify(str(est_lines))), inflector.cond_plural(est_lines, self.line_class) ) else: - dataset.blurb = "%s %s" % util.commaify( str(line_count) ), inflector.cond_plural(line_count, "line") + dataset.blurb = "%s %s" % ( util.commaify( str(line_count) ), inflector.cond_plural(line_count, self.line_class) ) else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' --- a/lib/galaxy/datatypes/interval.py Sun Mar 27 19:50:50 2011 -0400 +++ b/lib/galaxy/datatypes/interval.py Tue Apr 05 13:57:14 2011 -0400 @@ -45,6 +45,7 @@ class Interval( Tabular ): """Tab delimited data containing interval information""" file_ext = "interval" + line_class = "region" """Add metadata elements""" MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter ) @@ -60,23 +61,6 @@ self.add_display_app ( 'ucsc', 'display at UCSC', 'as_ucsc_display_file', 'ucsc_links' ) def init_meta( self, dataset, copy_from=None ): Tabular.init_meta( self, dataset, copy_from=copy_from ) - def set_peek( self, dataset, line_count=None, is_multi_byte=False ): - """Set the peek and blurb text""" - if not dataset.dataset.purged: - dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) - if line_count is None: - # See if line_count is stored in the metadata - if dataset.metadata.data_lines is not None: - dataset.blurb = "%s regions" % util.commaify( str( dataset.metadata.data_lines ) ) - else: - # Number of lines is not known ( this should not happen ), and auto-detect is - # needed to set metadata - dataset.blurb = "~%s regions" % util.commaify(util.roundify(str(self.estimate_file_lines(dataset)))) - else: - dataset.blurb = "%s regions" % util.commaify( str( line_count ) ) - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' def set_meta( self, dataset, overwrite = True, first_line_is_header = False, **kwd ): """Tries to guess from the line the location number of the column for the chromosome, region start-end and strand""" Tabular.set_meta( self, dataset, overwrite = overwrite, skip = 0 ) --- a/lib/galaxy/datatypes/tabular.py Sun Mar 27 19:50:50 2011 -0400 +++ b/lib/galaxy/datatypes/tabular.py Tue Apr 05 13:57:14 2011 -0400 @@ -223,8 +223,8 @@ out.append( '<tr><td>' ) out.append( '%s</td></tr>' % escape( comments.pop(0) ) ) return "".join( out ) - def set_peek( self, dataset, line_count=None, is_multi_byte=False ): - data.Text.set_peek( self, dataset, line_count=line_count, is_multi_byte=is_multi_byte ) + def set_peek( self, dataset, line_count=None, is_multi_byte=False): + super(Tabular, self).set_peek( dataset, line_count=line_count, is_multi_byte=is_multi_byte) if dataset.metadata.comment_lines: dataset.blurb = "%s, %s comments" % ( dataset.blurb, util.commaify( str( dataset.metadata.comment_lines ) ) ) def display_peek( self, dataset ): @@ -383,6 +383,7 @@ class Pileup( Tabular ): """Tab delimited data in pileup (6- or 10-column) format""" file_ext = "pileup" + line_class = "genomic coordinate" """Add metadata elements""" MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter ) @@ -392,24 +393,6 @@ def init_meta( self, dataset, copy_from=None ): Tabular.init_meta( self, dataset, copy_from=copy_from ) - def set_peek( self, dataset, line_count=None, is_multi_byte=False ): - """Set the peek and blurb text""" - if not dataset.dataset.purged: - dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) - if line_count is None: - # See if line_count is stored in the metadata - if dataset.metadata.data_lines is not None: - dataset.blurb = "%s genomic coordinates" % util.commaify( str( dataset.metadata.data_lines ) ) - else: - # Number of lines is not known ( this should not happen ), and auto-detect is - # needed to set metadata - dataset.blurb = "? genomic coordinates" - else: - dataset.blurb = "%s genomic coordinates" % util.commaify( str( line_count ) ) - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' - def make_html_table( self, dataset, skipchars=[] ): """Create HTML table, used for displaying peek""" out = ['<table cellspacing="0" cellpadding="3">'] --- a/lib/galaxy/datatypes/util/gff_util.py Sun Mar 27 19:50:50 2011 -0400 +++ b/lib/galaxy/datatypes/util/gff_util.py Tue Apr 05 13:57:14 2011 -0400 @@ -11,7 +11,7 @@ only attribute is 'group.' """ def __init__( self, reader, fields, chrom_col, feature_col, start_col, end_col, \ - strand_col, score_col, default_strand, fix_strand=False, raw_line='' ): + strand_col, score_col, default_strand, fix_strand=False ): # HACK: GFF format allows '.' for strand but GenomicInterval does not. To get around this, # temporarily set strand and then unset after initing GenomicInterval. unknown_strand = False @@ -34,8 +34,7 @@ raise MissingFieldError( "No field for score_col (%d)" % score_col ) self.score = self.fields[ self.score_col ] - # Attributes specific to GFF. - self.raw_line = raw_line + # GFF attributes. self.attributes = parse_gff_attributes( fields[8] ) class GFFFeature( GFFInterval ): @@ -43,11 +42,13 @@ A GFF feature, which can include multiple intervals. """ def __init__( self, reader, chrom_col, feature_col, start_col, end_col, \ - strand_col, score_col, default_strand, fix_strand=False, intervals=[] ): + strand_col, score_col, default_strand, fix_strand=False, intervals=[], \ + raw_size=0 ): GFFInterval.__init__( self, reader, intervals[0].fields, chrom_col, feature_col, \ start_col, end_col, strand_col, score_col, default_strand, \ fix_strand=fix_strand ) self.intervals = intervals + self.raw_size = raw_size # Use intervals to set feature attributes. for interval in self.intervals: # Error checking. NOTE: intervals need not share the same strand. @@ -68,20 +69,6 @@ if not name: name = self.attributes.get( 'group', None ) return name - - def raw_size( self ): - """ - Returns raw size of feature; raw size is the number of bytes that - comprise feature. - """ - # Feature length is all intervals/lines that comprise feature. - feature_len = 0 - for interval in self.intervals: - # HACK: +1 for EOL char. Need bx-python to provide raw_line itself - # b/c TableReader strips EOL characters, thus changing the line - # length. - feature_len += len( interval.raw_line ) + 1 - return feature_len class GFFIntervalToBEDReaderWrapper( NiceReaderWrapper ): """ @@ -124,7 +111,7 @@ def parse_row( self, line ): interval = GFFInterval( self, line.split( "\t" ), self.chrom_col, self.feature_col, \ self.start_col, self.end_col, self.strand_col, self.score_col, \ - self.default_strand, fix_strand=self.fix_strand, raw_line=line ) + self.default_strand, fix_strand=self.fix_strand ) return interval def next( self ): @@ -151,7 +138,8 @@ # # Get next GFFFeature - # + # + raw_size = 0 # If there is no seed interval, set one. Also, if there are no more # intervals to read, this is where iterator dies. @@ -161,6 +149,8 @@ self.seed_interval = GenomicIntervalReader.next( self ) except ParseError, e: handle_parse_error( e ) + finally: + raw_size += len( self.current_line ) # If header or comment, clear seed interval and return it. if isinstance( self.seed_interval, ( Header, Comment ) ): @@ -187,6 +177,9 @@ break except ParseError, e: handle_parse_error( e ) + continue + finally: + raw_size += len( self.current_line ) # If interval not associated with feature, break. group = interval.attributes.get( 'group', None ) @@ -214,7 +207,7 @@ return GFFFeature( self, self.chrom_col, self.feature_col, self.start_col, \ self.end_col, self.strand_col, self.score_col, \ self.default_strand, fix_strand=self.fix_strand, \ - intervals=feature_intervals ) + intervals=feature_intervals, raw_size=raw_size ) def convert_bed_coords_to_gff( interval ): --- a/lib/galaxy/model/__init__.py Sun Mar 27 19:50:50 2011 -0400 +++ b/lib/galaxy/model/__init__.py Tue Apr 05 13:57:14 2011 -0400 @@ -103,14 +103,14 @@ # For historical reasons state propogates down to datasets for da in self.output_datasets: da.dataset.state = state - def get_param_values( self, app ): + def get_param_values( self, app, ignore_errors=False ): """ Read encoded parameter values from the database and turn back into a dict of tool parameter values. """ param_dict = dict( [ ( p.name, p.value ) for p in self.parameters ] ) tool = app.toolbox.tools_by_id[self.tool_id] - param_dict = tool.params_from_strings( param_dict, app ) + param_dict = tool.params_from_strings( param_dict, app, ignore_errors=ignore_errors ) return param_dict def check_if_output_datasets_deleted( self ): """ --- a/lib/galaxy/model/mapping.py Sun Mar 27 19:50:50 2011 -0400 +++ b/lib/galaxy/model/mapping.py Tue Apr 05 13:57:14 2011 -0400 @@ -1268,7 +1268,7 @@ assign_mapper( context, Library, Library.table, properties=dict( root_folder=relation( LibraryFolder, backref=backref( "library_root" ) ) - ) + ) ) assign_mapper( context, LibraryInfoAssociation, LibraryInfoAssociation.table, @@ -1281,26 +1281,26 @@ ) ) assign_mapper( context, LibraryFolder, LibraryFolder.table, - properties=dict( - folders=relation( - LibraryFolder, + properties=dict( + folders=relation( + LibraryFolder, primaryjoin=( LibraryFolder.table.c.parent_id == LibraryFolder.table.c.id ), order_by=asc( LibraryFolder.table.c.name ), backref=backref( "parent", primaryjoin=( LibraryFolder.table.c.parent_id == LibraryFolder.table.c.id ), remote_side=[LibraryFolder.table.c.id] ) ), - active_folders=relation( LibraryFolder, - primaryjoin=( ( LibraryFolder.table.c.parent_id == LibraryFolder.table.c.id ) & ( not_( LibraryFolder.table.c.deleted ) ) ), - order_by=asc( LibraryFolder.table.c.name ), + active_folders=relation( LibraryFolder, + primaryjoin=( ( LibraryFolder.table.c.parent_id == LibraryFolder.table.c.id ) & ( not_( LibraryFolder.table.c.deleted ) ) ), + order_by=asc( LibraryFolder.table.c.name ), lazy=True, #"""sqlalchemy.exceptions.ArgumentError: Error creating eager relationship 'active_folders' on parent class '<class 'galaxy.model.LibraryFolder'>' to child class '<class 'galaxy.model.LibraryFolder'>': Cant use eager loading on a self referential relationship.""" viewonly=True ), datasets=relation( LibraryDataset, - primaryjoin=( ( LibraryDataset.table.c.folder_id == LibraryFolder.table.c.id ) ), - order_by=asc( LibraryDataset.table.c._name ), - lazy=False, + primaryjoin=( ( LibraryDataset.table.c.folder_id == LibraryFolder.table.c.id ) ), + order_by=asc( LibraryDataset.table.c._name ), + lazy=True, viewonly=True ), active_datasets=relation( LibraryDataset, primaryjoin=( ( LibraryDataset.table.c.folder_id == LibraryFolder.table.c.id ) & ( not_( LibraryDataset.table.c.deleted ) ) ), - order_by=asc( LibraryDataset.table.c._name ), - lazy=False, + order_by=asc( LibraryDataset.table.c._name ), + lazy=True, viewonly=True ) ) ) --- a/lib/galaxy/tools/__init__.py Sun Mar 27 19:50:50 2011 -0400 +++ b/lib/galaxy/tools/__init__.py Tue Apr 05 13:57:14 2011 -0400 @@ -1252,7 +1252,21 @@ for input in inputs.itervalues(): # No value, insert the default if input.name not in values: - messages[ input.name ] = "No value found for '%s%s', used default" % ( prefix, input.label ) + if isinstance( input, Conditional ): + messages[ input.name ] = { input.test_param.name: "No value found for '%s%s', used default" % ( prefix, input.label ) } + test_value = input.test_param.get_initial_value( trans, context ) + current_case = input.get_current_case( test_value, trans ) + self.check_and_update_param_values_helper( input.cases[ current_case ].inputs, {}, trans, messages[ input.name ], context, prefix ) + elif isinstance( input, Repeat ): + if input.min: + messages[ input.name ] = [] + for i in range( input.min ): + rep_prefix = prefix + "%s %d > " % ( input.title, i + 1 ) + rep_dict = dict() + messages[ input.name ].append( rep_dict ) + self.check_and_update_param_values_helper( input.inputs, {}, trans, rep_dict, context, rep_prefix ) + else: + messages[ input.name ] = "No value found for '%s%s', used default" % ( prefix, input.label ) values[ input.name ] = input.get_initial_value( trans, context ) # Value, visit recursively as usual else: --- a/lib/galaxy/tools/actions/__init__.py Sun Mar 27 19:50:50 2011 -0400 +++ b/lib/galaxy/tools/actions/__init__.py Tue Apr 05 13:57:14 2011 -0400 @@ -133,16 +133,18 @@ else: new_list.append( value ) return new_list - def wrap_values( inputs, input_values ): + def wrap_values( inputs, input_values, skip_missing_values = False ): # Wrap tool inputs as necessary for input in inputs.itervalues(): + if input.name not in input_values and skip_missing_values: + continue if isinstance( input, Repeat ): for d in input_values[ input.name ]: - wrap_values( input.inputs, d ) + wrap_values( input.inputs, d, skip_missing_values = skip_missing_values ) elif isinstance( input, Conditional ): values = input_values[ input.name ] current = values[ "__current_case__" ] - wrap_values( input.cases[current].inputs, values ) + wrap_values( input.cases[current].inputs, values, skip_missing_values = skip_missing_values ) elif isinstance( input, DataToolParameter ): input_values[ input.name ] = \ galaxy.tools.DatasetFilenameWrapper( input_values[ input.name ], @@ -254,7 +256,7 @@ if output.change_format: if params is None: params = make_dict_copy( incoming ) - wrap_values( tool.inputs, params ) + wrap_values( tool.inputs, params, skip_missing_values = not tool.check_values ) for change_elem in output.change_format: for when_elem in change_elem.findall( 'when' ): check = when_elem.get( 'input', None ) @@ -304,7 +306,7 @@ # <outputs> # <data format="input" name="output" label="Blat on ${<input_param>.name}" /> # </outputs> - wrap_values( tool.inputs, params ) + wrap_values( tool.inputs, params, skip_missing_values = not tool.check_values ) #tool (only needing to be set once) and on_string (set differently for each label) are overwritten for each output dataset label being determined params['tool'] = tool params['on_string'] = on_text --- a/lib/galaxy/visualization/tracks/data_providers.py Sun Mar 27 19:50:50 2011 -0400 +++ b/lib/galaxy/visualization/tracks/data_providers.py Tue Apr 05 13:57:14 2011 -0400 @@ -11,13 +11,16 @@ pkg_resources.require( "pysam" ) pkg_resources.require( "numpy" ) from galaxy.datatypes.util.gff_util import * +from galaxy.util.json import from_json_string from bx.interval_index_file import Indexes from bx.arrays.array_tree import FileArrayTreeDict from bx.bbi.bigwig_file import BigWigFile from galaxy.util.lrucache import LRUCache from galaxy.visualization.tracks.summary import * from galaxy.datatypes.tabular import Vcf -from galaxy.datatypes.interval import Bed, Gff +from galaxy.datatypes.interval import Bed, Gff, Gtf +from galaxy.datatypes.util.gff_util import parse_gff_attributes + from pysam import csamtools MAX_VALS = 5000 # only display first MAX_VALS features @@ -126,7 +129,7 @@ return st.chrom_blocks.keys() - def get_summary( self, chrom, start, end, **kwargs): + def get_summary( self, chrom, start, end, **kwargs ): filename = self.converted_dataset.file_name st = self.CACHE[filename] if st is None: @@ -170,7 +173,7 @@ self.CACHE[filename] = st # Check for data. - return st.chrom_blocks.get(chrom, None) is not None or st.chrom_blocks.get(chrom[3:], None) is not None + return st.chrom_blocks.get(chrom, None) is not None or (chrom and st.chrom_blocks.get(chrom[3:], None) is not None) class VcfDataProvider( TracksDataProvider ): """ @@ -303,12 +306,12 @@ if read.is_proper_pair: if qname in paired_pending: # one in dict is always first pair = paired_pending[qname] - results.append( [ "%i_%s" % ( read.pos, qname ), + results.append( [ "%i_%s" % ( pair['start'], qname ), pair['start'], read.pos + read_len, qname, [ pair['start'], pair['end'], pair['cigar'], pair['seq'] ], - [ read.pos, read.pos + read_len, read.cigar, seq] + [ read.pos, read.pos + read_len, read.cigar, seq ] ] ) del paired_pending[qname] else: @@ -484,9 +487,76 @@ col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } } def write_data_to_file( self, chrom, start, end, filename ): - # TODO: write function. - pass - + source = open( self.original_dataset.file_name ) + index = Indexes( self.converted_dataset.file_name ) + out = open( filename, 'w' ) + for start, end, offset in index.find(chrom, start, end): + source.seek( offset ) + if isinstance( self.original_dataset.datatype, Gff ): + reader = GFFReaderWrapper( source, fix_strand=True ) + feature = reader.next() + for interval in feature.intervals: + out.write(interval.raw_line + '\n') + elif isinstance( self.original_dataset.datatype, Bed ): + out.write( source.readline() ) + out.close() + + def get_filters( self ): + """ Returns a dataset's filters. """ + + # is_ functions taken from Tabular.set_meta + def is_int( column_text ): + try: + int( column_text ) + return True + except: + return False + def is_float( column_text ): + try: + float( column_text ) + return True + except: + if column_text.strip().lower() == 'na': + return True #na is special cased to be a float + return False + + # + # Get filters. + # TODOs: + # (a) might be useful to move this into each datatype's set_meta method; + # (b) could look at first N lines to ensure GTF attribute types are consistent. + # + filters = [] + # HACK: first 8 fields are for drawing, so start filter column index at 9. + filter_col = 8 + if isinstance( self.original_dataset.datatype, Gff ): + # Can filter by score and GTF attributes. + filters = [ { 'name': 'Score', 'type': 'int', 'index': filter_col } ] + filter_col += 1 + if isinstance( self.original_dataset.datatype, Gtf ): + for i, line in enumerate( open(self.original_dataset.file_name) ): + if not line.startswith('#'): + # Look at first line for attributes and types. + attributes = parse_gff_attributes( line.split('\t')[8] ) + for attr, value in attributes.items(): + # Get attribute type. + if is_int( value ): + attr_type = 'int' + elif is_float( value ): + attr_type = 'float' + else: + attr_type = 'str' + # Add to filters. + if attr_type is not 'str': + filters.append( { 'name': attr, 'type': attr_type, 'index': filter_col } ) + filter_col += 1 + break + elif isinstance( self.original_dataset.datatype, Bed ): + # Can filter by score column only. + filters = [ { 'name': 'Score', 'type': 'int', 'index': filter_col } ] + + return filters + def get_data( self, chrom, start, end, **kwargs ): start, end = int(start), int(end) source = open( self.original_dataset.file_name ) @@ -509,6 +579,7 @@ # # First three entries are mandatory, others are optional. # + filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) no_detail = ( "no_detail" in kwargs ) for start, end, offset in index.find(chrom, start, end): if count >= MAX_VALS: @@ -522,7 +593,7 @@ # GFF dataset. reader = GFFReaderWrapper( source, fix_strand=True ) feature = reader.next() - payload = package_gff_feature( feature, no_detail ) + payload = package_gff_feature( feature, no_detail, filter_cols ) payload.insert( 0, offset ) elif isinstance( self.original_dataset.datatype, Bed ): # BED dataset. @@ -536,15 +607,11 @@ #end = min( len( feature ), 8 ) #payload.extend( feature[ 3:end ] ) - # Name, score, strand, thick start, thick end. + # Name, strand, thick start, thick end. if length >= 4: payload.append(feature[3]) - if length >= 5: - payload.append( float(feature[4]) ) if length >= 6: payload.append(feature[5]) - - # Thick start, end. if length >= 8: payload.append(int(feature[6])) payload.append(int(feature[7])) @@ -555,7 +622,11 @@ block_starts = [ int(n) for n in feature[11].split(',') if n != '' ] blocks = zip( block_sizes, block_starts ) payload.append( [ ( start + block[1], start + block[1] + block[0] ) for block in blocks ] ) - + + # Score (filter data) + if length >= 5 and filter_cols and filter_cols[0] == "Score": + payload.append( float(feature[4]) ) + results.append( payload ) return { 'data': results, 'message': message } @@ -587,7 +658,7 @@ payload = package_gff_feature( feature ) payload.insert( 0, offset ) results.append( payload ) - offset += feature.raw_size() + offset += feature.raw_size return { 'data': results, 'message': message } @@ -644,7 +715,7 @@ pass return data_provider -def package_gff_feature( feature, no_detail=False ): +def package_gff_feature( feature, no_detail=False, filter_cols=[] ): """ Package a GFF feature in an array for data providers. """ feature = convert_gff_coords_to_bed( feature ) @@ -656,7 +727,6 @@ payload = [ feature.start, feature.end, feature.name(), - feature.score, feature.strand, # No notion of thick start, end in GFF, so make everything # thick. @@ -677,4 +747,13 @@ blocks = zip( block_sizes, block_starts ) payload.append( [ ( feature.start + block[1], feature.start + block[1] + block[0] ) for block in blocks ] ) + # Add filter data to payload. + for col in filter_cols: + if col == "Score": + payload.append( feature.score ) + elif col in feature.attributes: + payload.append( feature.attributes[col] ) + else: + # Dummy value. + payload.append( "na" ) return payload --- a/lib/galaxy/visualization/tracks/visual_analytics.py Sun Mar 27 19:50:50 2011 -0400 +++ b/lib/galaxy/visualization/tracks/visual_analytics.py Tue Apr 05 13:57:14 2011 -0400 @@ -1,5 +1,7 @@ -from galaxy.tools.parameters.basic import IntegerToolParameter, FloatToolParameter +import urllib +from galaxy.tools.parameters.basic import IntegerToolParameter, FloatToolParameter, SelectToolParameter +from galaxy.tools.parameters.dynamic_options import DynamicOptions def get_dataset_job( hda ): # Get dataset's job. @@ -28,14 +30,19 @@ tool_param_values = dict( [ ( p.name, p.value ) for p in job.parameters ] ) tool_param_values = tool.params_from_strings( tool_param_values, trans.app, ignore_errors=True ) for name, input in tool.inputs.items(): - if type( input ) == IntegerToolParameter: - tool_params.append( { 'name' : name, 'label': input.label, 'type': 'int', \ - 'value': tool_param_values.get( name, input.value ), \ - 'min' : input.min, 'max' : input.max } ) - elif type( input ) == FloatToolParameter: - tool_params.append( { 'name' : name, 'label': input.label, 'type': 'float', \ - 'value': tool_param_values.get( name, input.value ), \ - 'min' : input.min, 'max' : input.max } ) + if type( input ) == IntegerToolParameter or type( input ) == FloatToolParameter: + param_dict = { 'name' : name, 'label' : input.label, \ + 'value' : tool_param_values.get( name, input.value ), \ + 'type' : 'number', 'init_value' : input.value, + 'html' : urllib.quote( input.get_html() ) } + if input.min: + param_dict['min'] = input.min + if input.max: + param_dict['max'] = input.max + tool_params.append( param_dict ) + elif type( input ) == SelectToolParameter and type( input.options ) != DynamicOptions: + tool_params.append( { 'name' : name, 'label' : input.label, 'type' : 'select', \ + 'html' : urllib.quote( input.get_html() ) } ) # If tool has parameters that can be interactively modified, return tool. # Return empty set otherwise. --- a/lib/galaxy/web/api/workflows.py Sun Mar 27 19:50:50 2011 -0400 +++ b/lib/galaxy/web/api/workflows.py Tue Apr 05 13:57:14 2011 -0400 @@ -57,7 +57,7 @@ inputs = {} for step in latest_workflow.steps: if step.type == 'data_input': - inputs[step.id] = {'label':"Input Dataset", 'value':""} + inputs[step.id] = {'label':step.tool_inputs['name'], 'value':""} else: pass # Eventually, allow regular tool parameters to be inserted and modified at runtime. --- a/lib/galaxy/web/controllers/tool_runner.py Sun Mar 27 19:50:50 2011 -0400 +++ b/lib/galaxy/web/controllers/tool_runner.py Tue Apr 05 13:57:14 2011 -0400 @@ -120,7 +120,7 @@ error( "The '%s' tool does not currently support rerunning." % tool.name ) # Get the job's parameters try: - params_objects = job.get_param_values( trans.app ) + params_objects = job.get_param_values( trans.app, ignore_errors = True ) except: raise Exception( "Failed to get parameters for dataset id %d " % data.id ) upgrade_messages = tool.check_and_update_param_values( params_objects, trans ) --- a/lib/galaxy/web/controllers/tracks.py Sun Mar 27 19:50:50 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Tue Apr 05 13:57:14 2011 -0400 @@ -2,7 +2,7 @@ Support for constructing and viewing custom "track" browsers within Galaxy. """ -import re, time, pkg_resources +import re, pkg_resources pkg_resources.require( "bx-python" ) from bx.seq.twobit import TwoBitFile @@ -13,7 +13,6 @@ from galaxy.web.framework import simplejson from galaxy.web.framework.helpers import time_ago, grids from galaxy.util.bunch import Bunch -from galaxy import util from galaxy.datatypes.interval import Gff from galaxy.visualization.tracks.data_providers import * @@ -202,7 +201,6 @@ return trans.fill_template( "tracks/new_browser.mako", dbkeys=self._get_dbkeys( trans ), default_dbkey=kwargs.get("default_dbkey", None) ) @web.json - @web.require_login() def add_track_async(self, trans, hda_id=None, ldda_id=None): if hda_id: hda_ldda = "hda" @@ -671,6 +669,8 @@ if not tool: return messages.NO_TOOL tool_params = dict( [ ( p.name, p.value ) for p in original_job.parameters ] ) + # TODO: need to handle updates to conditional parameters; conditional + # params are stored in dicts (and dicts within dicts). tool_params.update( dict( [ ( key, value ) for key, value in kwargs.items() if key in tool.inputs ] ) ) tool_params = tool.params_from_strings( tool_params, self.app ) @@ -686,13 +686,16 @@ messages_list = [] for jida in original_job.input_datasets: input_dataset = jida.dataset - track_type, data_sources = input_dataset.datatype.get_track_type() - # Convert to datasource that provides 'data' because we need to - # extract the original data. - data_source = data_sources[ 'data' ] - msg = self._convert_dataset( trans, input_dataset, data_source ) - if msg is not None: - messages_list.append( msg ) + # TODO: put together more robust way to determine if a dataset can be indexed. + if hasattr( input_dataset, 'get_track_type' ): + # Can index dataset. + track_type, data_sources = input_dataset.datatype.get_track_type() + # Convert to datasource that provides 'data' because we need to + # extract the original data. + data_source = data_sources[ 'data' ] + msg = self._convert_dataset( trans, input_dataset, data_source ) + if msg is not None: + messages_list.append( msg ) # Return any messages generated during conversions. return_message = _get_highest_priority_msg( messages_list ) @@ -703,51 +706,67 @@ # Set input datasets for tool. Input datasets are subsets of full # datasets and are based on chrom, low, high. # - hda_permissions = trans.app.security_agent.history_get_default_permissions( original_dataset.history ) + + # If user is rerunning own tool, put new data in original dataset's + # history. If another user is running tool, put new data in current + # history. + if original_dataset.history.user == trans.user: + working_history = original_dataset.history + else: + working_history = trans.get_history( create=True ) + hda_permissions = trans.app.security_agent.history_get_default_permissions( working_history ) messages_list = [] for jida in original_job.input_datasets: input_dataset = jida.dataset - track_type, data_sources = input_dataset.datatype.get_track_type() - data_source = data_sources[ 'data' ] - converted_dataset = input_dataset.get_converted_dataset( trans, data_source ) + if hasattr( input_dataset, 'get_track_type' ): + # + # Dataset can be indexed and hence a subset can be extracted. + # + track_type, data_sources = input_dataset.datatype.get_track_type() + data_source = data_sources[ 'data' ] + converted_dataset = input_dataset.get_converted_dataset( trans, data_source ) - # - # Create new HDA for input dataset's subset. - # - subset_dataset = trans.app.model.HistoryDatasetAssociation( extension=input_dataset.ext, \ - dbkey=input_dataset.dbkey, \ - create_dataset=True, \ - sa_session=trans.sa_session, - name="Subset [%s:%i-%i] of data %i" % \ - ( chrom, low, high, input_dataset.hid ), - visible=False ) - input_dataset.history.add_dataset( subset_dataset ) - trans.sa_session.add( subset_dataset ) - trans.app.security_agent.set_all_dataset_permissions( subset_dataset.dataset, hda_permissions ) - if input_dataset.extension == 'bam': - data_provider = BamDataProvider( original_dataset=input_dataset, converted_dataset=converted_dataset ) - data_provider.write_data_to_file( chrom, low, high, subset_dataset.file_name ) - # TODO: size not working. - subset_dataset.set_size() - subset_dataset.info = "Data subset for trackster" - subset_dataset.set_dataset_state( trans.app.model.Dataset.states.OK ) - trans.sa_session.flush() + # + # Create new HDA for input dataset's subset. + # + new_dataset = trans.app.model.HistoryDatasetAssociation( extension=input_dataset.ext, \ + dbkey=input_dataset.dbkey, \ + create_dataset=True, \ + sa_session=trans.sa_session, + name="Subset [%s:%i-%i] of data %i" % \ + ( chrom, low, high, input_dataset.hid ), + visible=False ) + working_history.add_dataset( new_dataset ) + trans.sa_session.add( new_dataset ) + trans.app.security_agent.set_all_dataset_permissions( new_dataset.dataset, hda_permissions ) - # Add dataset to tool's parameters. - tool_params[ jida.name ] = subset_dataset + # Write subset of data to new dataset + data_provider_class = get_data_provider( original_dataset=input_dataset ) + data_provider = data_provider_class( original_dataset=input_dataset, + converted_dataset=converted_dataset ) + data_provider.write_data_to_file( chrom, low, high, new_dataset.file_name ) + + # TODO: size not working. + new_dataset.set_size() + new_dataset.info = "Data subset for trackster" + new_dataset.set_dataset_state( trans.app.model.Dataset.states.OK ) + trans.sa_session.flush() + + # Add dataset to tool's parameters. + tool_params[ jida.name ] = new_dataset # # Start tool and handle outputs. # try: - subset_job, subset_job_outputs = tool.execute( trans, incoming=tool_params, history=original_dataset.history ) + subset_job, subset_job_outputs = tool.execute( trans, incoming=tool_params, history=working_history ) except Exception, e: # Lots of things can go wrong when trying to execute tool. return to_json_string( { "error" : True, "message" : e.__class__.__name__ + ": " + str(e) } ) for output in subset_job_outputs.values(): output.visible = False trans.sa_session.flush() - + # Return new track that corresponds to the original dataset. output_name = None for joda in original_job.output_datasets: --- a/static/june_2007_style/blue/trackster.css Sun Mar 27 19:50:50 2011 -0400 +++ b/static/june_2007_style/blue/trackster.css Tue Apr 05 13:57:14 2011 -0400 @@ -22,7 +22,7 @@ .track{background:white;} .track-header{text-align:left;padding:4px 0px;color:#666;} .track-header .menubutton{margin-left:0px;} -.track-content{overflow:hidden;text-align:center;border-bottom:1px solid #bbb;background:#eee url('/static/images/tracks/diag_bg.gif');min-height:16px;} +.track-content{overflow:hidden;text-align:center;border-top:1px solid #eee;border-bottom:1px solid #eee;background:#eee url('/static/images/tracks/diag_bg.gif');min-height:16px;} .label-track .track-content{background:white;} .track-tile{background:white;} .track-tile canvas{position:relative;z-index:100;border:solid white;border-width:2px 0px 0px 0px;} @@ -38,11 +38,12 @@ .top-labeltrack{position:relative;border-bottom:solid #999 1px;} .nav-labeltrack{border-top:solid #999 1px;border-bottom:solid #333 1px;} input{font:10px verdana;} -.values{padding-left:0.25em;} -.dynamic-tool,.filters{width:400px;margin-left:0.25em;padding-bottom:0.5em;} +.dynamic-tool,.filters{width:410px;margin-left:0.25em;padding-bottom:0.5em;} .slider-row{margin-top:0.4em;margin-left:1em;} .slider-label{float:left;font-weight:bold;} .slider{float:right;width:200px;position:relative;} .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;} .child-track-icon{background:url('../images/fugue/arrow-000-small-bw.png') no-repeat;width:30px;cursor:move;} .track-resize{background:white url('../images/visualization/draggable_vertical.png') no-repeat top center;position:absolute;right:3px;bottom:-4px;width:14px;height:7px;border:solid #999 1px;z-index:100;} --- a/static/june_2007_style/trackster.css.tmpl Sun Mar 27 19:50:50 2011 -0400 +++ b/static/june_2007_style/trackster.css.tmpl Tue Apr 05 13:57:14 2011 -0400 @@ -146,8 +146,8 @@ .track-content { overflow: hidden; text-align: center; -/* border-top: 1px solid #eee; */ - border-bottom: 1px solid #bbb; + border-top: 1px solid #eee; + border-bottom: 1px solid #eee; background: #eee url('/static/images/tracks/diag_bg.gif'); min-height: 16px; } @@ -228,11 +228,8 @@ input { font: 10px verdana; } -.values { - padding-left: 0.25em; -} .dynamic-tool, .filters { - width: 400px; + width: 410px; margin-left: 0.25em; padding-bottom:0.5em; } @@ -240,7 +237,7 @@ margin-top: 0.4em; margin-left: 1em; } -.slider-label { +.param-label, .slider-label { float: left; font-weight: bold; } @@ -253,6 +250,15 @@ 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; +} .child-track-icon { background:url('../images/fugue/arrow-000-small-bw.png') no-repeat; width: 30px; --- a/static/scripts/packed/trackster.js Sun Mar 27 19:50:50 2011 -0400 +++ b/static/scripts/packed/trackster.js Tue Apr 05 13:57:14 2011 -0400 @@ -1,1 +1,1 @@ -CanvasRenderingContext2D.prototype.dashedLine=function(c,j,b,h,f){if(f===undefined){f=4}var e=b-c;var d=h-j;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var l=e/g;var k=d/g;var a;for(a=0;a<g;a++,c+=l,j+=k){if(a%2!==0){continue}this.fillRect(c,j,f,1)}};CanvasRenderingContext2D.prototype.drawDownwardEquilateralTriangle=function(b,a,e){var d=b-e/2,c=b+e/2,f=a-Math.sqrt(e*3/2);this.beginPath();this.moveTo(d,f);this.lineTo(c,f);this.lineTo(b,a);this.lineTo(d,f);this.strokeStyle=this.fillStyle;this.fill();this.stroke();this.closePath()};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();var c;for(c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c===f.length){if(this!==f.get(c-1)){g.append(this)}}else{if(this!==f.get(c)){$(this).insertBefore(f.get(c))}}})}var NO_OVERLAP=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005;function compute_overlap(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=NO_OVERLAP}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=NO_OVERLAP}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a}function is_overlap(b,a){return(compute_overlap(b,a)!==NO_OVERLAP)}var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=1,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,ERROR_PADDING=10,LABEL_SPACING=2,PACK_SPACING=5,MIN_SQUISH_VIEW_WIDTH=12000,DEFAULT_FONT="9px Monaco, Lucida Console, monospace",DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}var CONTEXT=DUMMY_CANVAS.getContext("2d");CONTEXT.font=DEFAULT_FONT;var CHAR_WIDTH_PX=CONTEXT.measureText("A").width,CHAR_HEIGHT_PX=9;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!==-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataManager=function(b,a,c){Cache.call(this,b);this.track=a;this.subset=(c!==undefined?c:true)};$.extend(DataManager.prototype,Cache.prototype,{load_data:function(d,a,f,h,b,e){var g={chrom:d,low:a,high:f,mode:h,resolution:b,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(g,e);var c=this;return $.getJSON(this.track.data_url,g,function(j){c.set_data(a,f,h,j)})},get_data:function(j,k,c,h,b,f){var l=this.get(this.gen_key(k,c,h));if(l){return l}if(this.subset){var m,g,a,e,h,l;for(var d=0;d<this.key_ary.length;d++){m=this.key_ary[d];g=this.split_key(m);a=g[0];e=g[1];if(k>=a&&c<=e){l=this.obj_cache[m];if(l.dataset_type!=="summary_tree"&&l.extra_info!=="no_detail"){this.move_key_to_end(m,d);return l}}}}return this.load_data(j,k,c,h,b,f)},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c+"_"+d;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_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 href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();$(this).val("");a.location_span.show();a.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",b).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.val(a.chrom+":"+a.low+"-"+a.high);a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var j=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(j/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,k){var f=$(this);var l=k.offsetX-k.current_x;var g=f.scrollTop()-(h.clientY-k.current_height);f.scrollTop(g);k.current_height=h.clientY;k.current_x=k.offsetX;var j=Math.round(l/a.viewport_container.width()*(a.high-a.low));a.move_delta(j)}).bind("mousewheel",function(h,k,g,f){if(g){var j=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(j)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(k,l){$(l.proxy).css({left:Math.min(k.pageX,l.startX),width:Math.abs(k.pageX-l.startX)});var g=Math.min(k.pageX,l.startX)-a.container.offset().left,f=Math.max(k.pageX,l.startX)-a.container.offset().left,j=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*j)+a.low,Math.round(f/h*j)+a.low)}).bind("dragend",function(l,m){var g=Math.min(l.pageX,m.startX),f=Math.max(l.pageX,m.startX),j=(a.high-a.low),h=a.viewport_container.width(),k=a.low;a.low=Math.round(g/h*j)+k;a.high=Math.round(f/h*j)+k;$(m.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.chrom_info.length===0){alert("Invalid chromosome: "+b.chrom);return}if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e==="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e==="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len-1;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var k=this,a,d,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}k.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},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.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").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()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)===0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e==="int"||e==="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(f,d){if(!d.hidden){var c="param_"+f;var l=$("<div class='form-row' />").appendTo(a);l.append($("<label />").attr("for",c).text(d.label+":"));if(d.type==="bool"){l.append($('<input type="checkbox" />').attr("id",c).attr("name",c).attr("checked",b.values[d.key]))}else{if(d.type==="color"){var h=b.values[d.key];var g=$("<input />").attr("id",c).attr("name",c).val(h);var j=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var e=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(j);var k=$("<div/>").appendTo(e).farbtastic({width:100,height:100,callback:g,color:h});$("<div />").append(g).append(j).appendTo(l).bind("click",function(m){j.css({left:$(this).position().left+($(g).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){j.hide();$(document).unbind("click.color-picker")});m.stopPropagation()})}else{l.append($("<input />").attr("id",c).attr("name",c).val(b.values[d.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type==="float"){e=parseFloat(e)}else{if(f.type==="int"){e=parseInt(e)}else{if(f.type==="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_url_extra_params={};this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b.status==="data"){if(b.valid_chroms){a.valid_chroms=b.valid_chroms;a.make_name_popup_menu()}a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;$.when(a.predraw_init()).done(function(){a.draw()})}}}}}}})},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(b,j,n){var c=this,o=c.view;this.filters=(b!==undefined?get_filters_from_dict(b):[]);this.filters_available=false;this.filters_visible=false;this.tool=(j!==undefined?get_tool_from_dict(j):undefined);this.parent_track=n;this.child_tracks=[];if(c.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filters_div=$("<div/>").addClass("filters").hide();this.header_div.after(this.filters_div);this.filters_div.bind("drag",function(q){q.stopPropagation()}).bind("dblclick",function(q){q.stopPropagation()});$.each(this.filters,function(t,w){var u=$("<div/>").addClass("slider-row").appendTo(c.filters_div);var v=$("<div/>").addClass("slider-label").appendTo(u);var s=$("<span/>").addClass("name").appendTo(v);s.text(w.name+" ");var r=$("<span/>").addClass("values").appendTo(v);var q=$("<div/>").addClass("slider").appendTo(u);w.control_element=$("<div/>").attr("id",w.name+"-filter-control").appendTo(q);w.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(y,z){var x=z.values;r.text("["+x[0]+"-"+x[1]+"]");w.low=x[0];w.high=x[1];c.draw(true,true)},change:function(x,y){w.control_element.slider("option","slide").call(w.control_element,x,y)}});w.slider=w.control_element;w.slider_label=r;$("<div style='clear: both;'/>").appendTo(u)});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(q){q.stopPropagation()}).bind("click",function(q){q.stopPropagation()}).bind("dblclick",function(q){q.stopPropagation()});var m=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var l=this.tool.params;var c=this;$.each(this.tool.params,function(x,s){var v=$("<div>").addClass("slider-row").appendTo(c.dynamic_tool_div);var u=$("<div>").addClass("slider-label").appendTo(v);var z=$("<span class='param-name'>").text(s.label+" ").appendTo(u);var t=$("<span/>").text(s.value);var w=$("<span class='param-value'>").appendTo(u).append("[").append(t).append("]");var y=$("<div/>").addClass("slider").appendTo(v);var q=$("<div id='"+s.name+"-param-control'>").appendTo(y);var r=(s.max<=1?0.01:(s.max<=1000?1:5));q.slider({min:s.min,max:s.max,step:r,value:s.value,slide:function(A,C){var B=C.value;s.value=B;if(0<B&&B<1){B=parseFloat(B).toFixed(2)}t.text(B)},change:function(A,B){s.value=B.value}});w.click(function(){var C=t,B=C.text(),A=(s.max<=1?4:s.max.length);C.text("");$("<input type='text'/>").attr("size",A).attr("maxlength",A).attr("value",B).appendTo(C).focus().select().click(function(D){D.stopPropagation()}).blur(function(){$(this).remove();C.text(B)}).keyup(function(F){if(F.keyCode===27){$(this).trigger("blur")}else{if(F.keyCode===13){var D=$(this),E=parseFloat(D.val());if(isNaN(E)||E>s.max||E<s.min){alert("Parameter value must be in the range ["+s.min+"-"+s.max+"]");return $(this)}C.text(E);q.slider("value",E);s.value=E}}})});$("<div style='clear: both;'/>").appendTo(v)});var p=$("<div>").addClass("slider-row").appendTo(this.dynamic_tool_div);var k=$("<input type='submit'>").attr("value","Run").appendTo(p);var c=this;k.click(function(){c.run_tool()})}c.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();c.container_div.append(c.child_tracks_container);if(c.display_modes!==undefined){if(c.mode_div===undefined){c.mode_div=$("<div class='right-float menubutton popup' />").appendTo(c.header_div);var e=(c.track_config&&c.track_config.values.mode?c.track_config.values.mode:c.display_modes[0]);c.mode=e;c.mode_div.text(e);var d=function(q){c.mode_div.text(q);c.mode=q;c.track_config.values.mode=q;c.tile_cache.clear();c.draw()};var a={};for(var f=0,h=c.display_modes.length;f<h;f++){var g=c.display_modes[f];a[g]=function(q){return function(){d(q)}}(g)}make_popupmenu(c.mode_div,a)}else{c.mode_div.hide()}}this.make_name_popup_menu()};$.extend(TiledTrack.prototype,Track.prototype,{make_name_popup_menu:function(){var b=this;var a={};a["Edit configuration"]=function(){var h=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},f=function(){b.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},g=function(j){if((j.keyCode||j.which)===27){h()}else{if((j.keyCode||j.which)===13){f()}}};$(window).bind("keypress.check_enter_esc",g);show_modal("Configure Track",b.track_config.build_form(),{Cancel:h,OK:f})};if(b.filters_available>0){var e=(b.filters_div.is(":visible")?"Hide filters":"Show filters");a[e]=function(){b.filters_visible=(b.filters_div.is(":visible"));b.filters_div.toggle();b.make_name_popup_menu()}}if(b.tool){var e=(b.dynamic_tool_div.is(":visible")?"Hide Tool":"Show Tool");a[e]=function(){if(!b.dynamic_tool_div.is(":visible")){b.update_name(b.name+b.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";b.revert_name()}b.dynamic_tool_div.toggle();b.make_name_popup_menu()}}if(b.valid_chroms){a["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+b.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var c=view;var d=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;d=function(){}}a.Remove=function(){c.remove_track(b);if(c.num_tracks===0){d()}};make_popupmenu(b.name_div,a)},draw:function(a,d){var s=this.view.low,g=this.view.high,j=g-s,l=this.view.container.width(),m=this.view.resolution;var e=$("<div style='position: relative;'></div>"),f=l/j;if(!d){this.content_div.children().remove()}this.content_div.append(e);this.max_height=0;var o=Math.floor(s/m/DENSITY);var c={};while((o*DENSITY*m)<g){var r=l+"_"+f+"_"+o;var h=this.tile_cache.get(r);var p=o*DENSITY*this.view.resolution;var b=p+DENSITY*this.view.resolution;if(!a&&h){this.show_tile(h,e,p,f)}else{this.delayed_draw(a,r,p,b,o,m,e,f,c)}o+=1}if(d){var k=this;var q=setInterval(function(){if(obj_length(c)===0){var v=k.content_div.children();var u=false;for(var w=v.length-1,t=0;w>=t;w--){var x=$(v[w]);if(u){x.remove()}else{if(x.children().length!==0){u=true}}}clearInterval(q)}},50)}for(var n=0;n<this.child_tracks.length;n++){this.child_tracks[n].draw(a,d)}},delayed_draw:function(b,j,g,l,c,e,k,m,f){var d=this;var h=function(u,n,p,o,s,t,q){returned_tile=d.draw_tile(n,p,o,s,t,q);var r=$("<div class='track-tile'>").prepend(returned_tile);tile_element=r;d.tile_cache.set(j,tile_element);d.show_tile(tile_element,s,g,t);delete f[u]};var a=setTimeout(function(){if(g<=d.view.high&&l>=d.view.low){var n=(b?undefined:d.tile_cache.get(j));if(n){d.show_tile(n,k,g,m);delete f[a]}else{$.when(d.data_cache.get_data(view.chrom,g,l,d.mode,e,d.data_url_extra_params)).then(function(){var o=d.data_cache.get_data(view.chrom,g,l,d.mode,e,d.data_url_extra_params);if(view.reference_track&&m>CHAR_WIDTH_PX){$.when(view.reference_track.data_cache.get_data(view.chrom,g,l,d.mode,e,view.reference_track.data_url_extra_params)).then(function(){var p=view.reference_track.data_cache.get_data(view.chrom,g,l,d.mode,e,view.reference_track.data_url_extra_params);h(a,o,e,c,k,m,p)})}else{h(a,o,e,c,k,m)}})}}},50);f[a]=true},show_tile:function(h,j,e,k){var a=this;var c=this.view.high-this.view.low,b=(e-this.view.low)*k;if(this.left_offset){b-=this.left_offset}h.css({position:"absolute",top:0,left:b,height:""});j.append(h);a.max_height=Math.max(a.max_height,h.height());a.content_div.css("height",a.max_height+"px");j.children().css("height",a.max_height+"px");if(a.hidden){return}for(var g=0;g<a.filters.length;g++){a.filters[g].update_ui_elt()}var d=false;if(a.example_feature){for(var g=0;g<a.filters.length;g++){if(a.filters[g].applies_to(a.example_feature)){d=true;break}}}if(a.filters_available!==d){a.filters_available=d;if(!a.filters_available){a.filters_div.hide()}a.make_name_popup_menu()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type==="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,d.hda_ldda,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f==="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f==="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.view.container.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);a.reference_track=this;this.left_offset=200;this.height_px=12;this.font=DEFAULT_FONT;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:a.dbkey};this.data_cache=new DataManager(CACHED_DATA,this,false);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{draw_tile:function(m,g,b,j,n){var f=this,d=DENSITY*g;if(n>CHAR_WIDTH_PX){if(m===null){f.content_div.css("height","0px");return}var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var l=e.get(0).getContext("2d");e.get(0).width=Math.ceil(d*n+f.left_offset);e.get(0).height=f.height_px;l.font=DEFAULT_FONT;l.textAlign="center";for(var h=0,k=m.length;h<k;h++){var a=Math.round(h*n);l.fillText(m[h],a+f.left_offset,10)}return e}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataManager(CACHED_DATA,this);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;(function(g){var k=false;var j=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){k=true;h.show()},function(){k=false;if(!j){h.hide()}});h.hide().bind("dragstart",function(l,m){j=true;m.original_height=$(g.content_div).height()}).bind("drag",function(m,n){var l=Math.min(Math.max(n.original_height+n.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",l);g.height_px=l;g.draw(true)}).bind("dragend",function(l,m){g.tile_cache.clear();j=false;if(!k){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;return $.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},draw_tile:function(j,q,t,c,e){if(this.vertical_range===undefined){return}var o=this,u=t*DENSITY*q,a=DENSITY*q,B=q+"_"+t,v={hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution};var b=document.createElement("canvas"),z=j.data;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);b.get(0).width=Math.ceil(a*e);b.get(0).height=o.height_px;var p=b.get(0).getContext("2d"),k=false,l=o.prefs.min_value,g=o.prefs.max_value,n=o.vertical_range,w=o.total_frequency,d=o.height_px,m=o.mode;var A=Math.round(d+l/n*d);p.beginPath();p.moveTo(0,A);p.lineTo(a*e,A);p.fillStyle="#aaa";p.stroke();p.beginPath();p.fillStyle=o.prefs.color;var x,h,f;if(z.length>1){f=Math.ceil((z[1][0]-z[0][0])*e)}else{f=10}for(var r=0,s=z.length;r<s;r++){x=Math.round((z[r][0]-u)*e);h=z[r][1];if(h===null){if(k&&m==="Filled"){p.lineTo(x,d)}k=false;continue}if(h<l){h=l}else{if(h>g){h=g}}if(m==="Histogram"){h=Math.round(h/n*d);p.fillRect(x,A,f,-h)}else{if(m==="Intensity"){h=255-Math.floor((h-l)/n*255);p.fillStyle="rgb("+h+","+h+","+h+")";p.fillRect(x,0,f,d)}else{h=Math.round(d-(h-l)/n*d);if(k){p.lineTo(x,h)}else{k=true;if(m==="Filled"){p.moveTo(x,d);p.lineTo(x,h)}else{p.moveTo(x,h)}}}}}if(m==="Filled"){if(k){p.lineTo(x,A);p.lineTo(0,A)}p.fill()}else{p.stroke()}return b}});var FeatureTrack=function(a,f,e,j,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{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:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=j;this.original_dataset_id=j;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.default_font=DEFAULT_FONT;this.inc_slots={};this.start_end_dct={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataManager(20,this);this.left_offset=200};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{incremental_slots:function(a,h,p){var q=this.inc_slots[a];if(!q||(q.mode!==p)){q={};q.w_scale=a;q.mode=p;this.inc_slots[a]=q;this.start_end_dct[a]={}}var l=q.w_scale,w=[],x=[],j=0,n=this.view.max_low;for(var u=0,v=h.length;u<v;u++){var g=h[u],k=g[0];if(q[k]!==undefined){j=Math.max(j,q[k]);x.push(q[k])}else{w.push(u)}}var d=this.start_end_dct[a];var m=function(D,E){for(var C=0;C<=MAX_FEATURE_DEPTH;C++){var A=false,F=d[C];if(F!==undefined){for(var z=0,B=F.length;z<B;z++){var y=F[z];if(E>y[0]&&D<y[1]){A=true;break}}}if(!A){return C}}return -1};for(var u=0,v=w.length;u<v;u++){var g=h[w[u]],k=g[0],s=g[1],b=g[2],o=g[3],c=Math.floor((s-n)*l),f=Math.ceil((b-n)*l),t=CONTEXT.measureText(o).width,e;if(o!==undefined&&p==="Pack"){t+=(LABEL_SPACING+PACK_SPACING);if(c-t>=0){c-=t;e="left"}else{f+=t;e="right"}}var r=m(c,f);if(r>=0){if(d[r]===undefined){d[r]=[]}d[r].push([c,f]);q[k]=r;j=Math.max(j,r)}else{}}return j+1},draw_summary_tree:function(b,o,n,l,r,j,f,e){var c=j+LABEL_SPACING+CHAR_HEIGHT_PX;delta_x_px=Math.ceil(n*r);var h=$("<div />").addClass("yaxislabel");h.text(l);h.css({position:"absolute",top:"22px",left:"10px"});h.prependTo(this.container_div);var q=b.get(0).getContext("2d");for(var d=0,g=o.length;d<g;d++){var m=Math.floor((o[d][0]-f)*r);var k=o[d][1];if(!k){continue}var p=k/l*j;q.fillStyle="black";q.fillRect(m+e,c-p,delta_x_px,p);var a=4;if(this.prefs.show_counts&&(q.measureText(k).width+a)<delta_x_px){q.fillStyle="#666";q.textAlign="center";q.fillText(k,m+e+(delta_x_px/2),10)}}},draw_element:function(p,f,g,x,j,r,I,M,N,a,A){var u=x[0],K=x[1],C=x[2]-1,s=x[3],D=Math.floor(Math.max(0,(K-r)*M)),q=Math.ceil(Math.min(a,Math.max(0,(C-r)*M))),B=ERROR_PADDING+(g==="Dense"?0:(0+j))*N,o,G,t=null,O=null,d=this.prefs.block_color,F=this.prefs.label_color;if(g==="Dense"){p.fillStyle=d;p.fillRect(D+A,B,q-D,DENSE_FEATURE_HEIGHT)}else{if(g==="no_detail"){p.fillStyle=d;p.fillRect(D+A,B+5,q-D,DENSE_FEATURE_HEIGHT)}else{var n=x[5],z=x[6],E=x[7],e=x[8];if(z&&E){t=Math.floor(Math.max(0,(z-r)*M));O=Math.ceil(Math.min(a,Math.max(0,(E-r)*M)))}var L,v;if(g==="Squish"){L=1;v=SQUISH_FEATURE_HEIGHT}else{L=5;v=PACK_FEATURE_HEIGHT}if(!e){if(x.strand){if(x.strand==="+"){p.fillStyle=RIGHT_STRAND_INV}else{if(x.strand==="-"){p.fillStyle=LEFT_STRAND_INV}}}else{p.fillStyle=d}p.fillRect(D+A,B,q-D,v)}else{var m,w;if(g==="Squish"){p.fillStyle=CONNECTOR_COLOR;m=B+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;w=1}else{if(n){var m=B;var w=v;if(n==="+"){p.fillStyle=RIGHT_STRAND}else{if(n==="-"){p.fillStyle=LEFT_STRAND}}}else{p.fillStyle=CONNECTOR_COLOR;m+=(SQUISH_FEATURE_HEIGHT/2)+1;w=1}}p.fillRect(D+A,m,q-D,w);for(var J=0,c=e.length;J<c;J++){var h=e[J],b=Math.floor(Math.max(0,(h[0]-r)*M)),y=Math.ceil(Math.min(a,Math.max((h[1]-1-r)*M)));if(b>y){continue}p.fillStyle=d;p.fillRect(b+A,B+(v-L)/2+1,y-b,L);if(t!==undefined&&!(b>O||y<t)){var H=Math.max(b,t),l=Math.min(y,O);p.fillRect(H+A,B+1,l-H,v)}}}if(g==="Pack"&&K>r){p.fillStyle=F;if(f===0&&D-p.measureText(s).width<0){p.textAlign="left";p.fillText(s,q+A+LABEL_SPACING,B+8)}else{p.textAlign="right";p.fillText(s,D+A-LABEL_SPACING,B+8)}p.fillStyle=d}}}},get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="no_detail"){a=NO_DETAIL_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT}}}return a},draw_tile:function(o,x,C,k,m,d){var t=this;var E=C*DENSITY*x,a=(C+1)*DENSITY*x,q=a-E,F={hda_ldda:t.hda_ldda,dataset_id:t.dataset_id,resolution:this.view.resolution,mode:this.mode};var v=Math.ceil(q*m),s=this.mode,H=25,g=this.left_offset,p,h;var c=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(c)}c=$(c);if(s==="Auto"){if(o.dataset_type==="summary_tree"){s=o.dataset_type}else{if(o.extra_info==="no_detail"){s="no_detail"}else{var G=o.data;if((G.length&&G.length<4)||(this.view.high-this.view.low>MIN_SQUISH_VIEW_WIDTH)){s="Squish"}else{s="Pack"}}}}var y=this.get_y_scale(s);if(s==="summary_tree"){h=this.summary_draw_height}if(s==="Dense"){h=H}else{if(s==="no_detail"||s==="Squish"||s==="Pack"){h=this.incremental_slots(m,o.data,s)*y+H;p=this.inc_slots[m]}}c.get(0).width=v+g;c.get(0).height=h;if(o.dataset_type==="summary_tree"){c.get(0).height+=LABEL_SPACING+CHAR_HEIGHT_PX}k.parent().css("height",Math.max(this.height_px,h)+"px");var w=c.get(0).getContext("2d");w.fillStyle=this.prefs.block_color;w.font=this.default_font;w.textAlign="right";this.container_div.find(".yaxislabel").remove();if(s==="summary_tree"){this.draw_summary_tree(c,o.data,o.delta,o.max,m,h,E,g);return c}if(o.message){c.css({"border-top":"1px solid red"});w.fillStyle="red";w.textAlign="left";var r=w.textBaseline;w.textBaseline="top";w.fillText(o.message,g,0);w.textBaseline=r;if(!o.data){return c}}this.example_feature=(o.data.length?o.data[0]:undefined);var G=o.data;for(var z=0,B=G.length;z<B;z++){var j=G[z],l=j[0],u=j[1],b=j[2],e=(p&&p[l]!==undefined?p[l]:null);var A=false;var n;for(var D=0;D<this.filters.length;D++){n=this.filters[D];n.update_attrs(j);if(!n.keep(j)){A=true;break}}if(A){continue}if(is_overlap([u,b],[E,a])&&(s=="Dense"||e!==null)){this.draw_element(w,C,s,j,e,E,a,m,y,v,g,d)}}return c}});var VcfTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="VcfTrack"};$.extend(VcfTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_element:function(u,p,j,e,x,c,m,v,s){var j=data[i],l=j[0],t=j[1],d=j[2]-1,o=j[3],g=Math.floor(Math.max(0,(t-x)*m)),k=Math.ceil(Math.min(s,Math.max(0,(d-x)*m))),f=ERROR_PADDING+(p==="Dense"?0:(0+e))*v,a,y,b=null,n=null;if(no_label){u.fillStyle=block_color;u.fillRect(g+left_offset,f+5,k-g,1)}else{var w=j[4],r=j[5],h=j[6];a=9;y=1;u.fillRect(g+left_offset,f,k-g,a);if(p!=="Dense"&&o!==undefined&&t>x){u.fillStyle=label_color;if(tile_index===0&&g-u.measureText(o).width<0){u.textAlign="left";u.fillText(o,k+2+left_offset,f+8)}else{u.textAlign="right";u.fillText(o,g-2+left_offset,f+8)}u.fillStyle=block_color}var q=w+" / "+r;if(t>x&&u.measureText(q).width<(k-g)){u.fillStyle="white";u.textAlign="center";u.fillText(q,left_offset+g+(k-g)/2,f+8);u.fillStyle=block_color}}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{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:c,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.track_type="ReadTrack";this.make_name_popup_menu()};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT;if(this.track_config.values.show_insertions){a*=2}}}return a},draw_read:function(m,d,J,n,D,G,e,o,y,a){m.textAlign="center";var l=this,u=[n,D],C=0,z=0,f=0;var r=[];if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){f=Math.round(J/2)}if(!e){e=[[0,o.length]]}for(var h=0,k=e.length;h<k;h++){var b=e[h],g="MIDNSHP=X"[b[0]],v=b[1];if(g==="H"||g==="S"){C-=v}var x=G+C,B=Math.floor(Math.max(0,(x-n)*J)),E=Math.floor(Math.max(0,(x+v-n)*J));switch(g){case"H":break;case"S":case"M":case"=":var p=compute_overlap([x,x+v],u);if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(f>0){m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset-f,y+1,E-B,9);m.fillStyle=CONNECTOR_COLOR;for(var I=0,j=q.length;I<j;I++){if(this.track_config.values.show_differences&&a){var s=a[x-n+I];if(!s||s.toLowerCase()===q[I].toLowerCase()){continue}}if(x+I>=n&&x+I<=D){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset,y+9)}}}else{m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset,y+(this.mode!=="Dense"?4:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}z+=v;C+=v;break;case"N":m.fillStyle=CONNECTOR_COLOR;m.fillRect(B+this.left_offset-f,y+5,E-B,1);C+=v;break;case"D":m.fillStyle="red";m.fillRect(B+this.left_offset-f,y+4,E-B,3);C+=v;break;case"P":break;case"I":var p=compute_overlap([x,x+v],u),K=this.left_offset+B-f;if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(this.track_config.values.show_insertions){var w=this.left_offset+B-(E-B)/2;if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){m.fillStyle="yellow";m.fillRect(w-f,y-9,E-B,9);r[r.length]={type:"triangle",data:[K,y+4,5]};m.fillStyle=CONNECTOR_COLOR;switch(p){case (OVERLAP_START):q=q.slice(n-x);break;case (OVERLAP_END):q=q.slice(0,x-D);break;case (CONTAINED_BY):break;case (CONTAINS):q=q.slice(n-x,x-D);break}for(var I=0,j=q.length;I<j;I++){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset-(E-B)/2,y)}}else{m.fillStyle="yellow";m.fillRect(w,y+(this.mode!=="Dense"?2:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){r[r.length]={type:"text",data:[q.length,K,y+9]}}else{}}}z+=v;break;case"X":z+=v;break}}m.fillStyle="yellow";var t,L,H;for(var F=0;F<r.length;F++){t=r[F];L=t.type;H=t.data;if(L==="text"){m.font="bold "+DEFAULT_FONT;m.fillText(H[0],H[1],H[2]);m.font=DEFAULT_FONT}else{if(L=="triangle"){m.drawDownwardEquilateralTriangle(H[0],H[1],H[2])}}}},draw_element:function(w,y,r,k,e,A,b,n,x,u,f,c){var m=k[0],v=k[1],d=k[2],o=k[3],h=Math.floor(Math.max(0,(v-A)*n)),j=Math.ceil(Math.min(u,Math.max(0,(d-A)*n))),g=(r==="Dense"?1:(1+e))*x,z=this.prefs.block_color,l=this.prefs.label_color;t=0;w.fillStyle=z;if(k[5] instanceof Array){var s=Math.floor(Math.max(0,(k[4][0]-A)*n)),q=Math.ceil(Math.min(u,Math.max(0,(k[4][1]-A)*n))),p=Math.floor(Math.max(0,(k[5][0]-A)*n)),a=Math.ceil(Math.min(u,Math.max(0,(k[5][1]-A)*n)));if(k[4][1]>=A&&k[4][0]<=b&&k[4][2]){this.draw_read(w,r,n,A,b,k[4][0],k[4][2],k[4][3],g,c)}if(k[5][1]>=A&&k[5][0]<=b&&k[5][2]){this.draw_read(w,r,n,A,b,k[5][0],k[5][2],k[5][3],g,c)}if(p>q){w.fillStyle=CONNECTOR_COLOR;w.dashedLine(q+f,g+5,f+p,g+5)}}else{w.fillStyle=z;this.draw_read(w,r,n,A,b,v,k[4],k[5],g,c)}if(r==="Pack"&&v>A){w.fillStyle=this.prefs.label_color;if((r==="Pack"||this.mode==="Auto")&&n>CHAR_WIDTH_PX){var t=Math.round(n/2)}if(y===0&&h-w.measureText(o).width<0){w.textAlign="left";w.fillText(o,j+f+LABEL_SPACING-t,g+8)}else{w.textAlign="right";w.fillText(o,h+f-LABEL_SPACING-t,g+8)}w.fillStyle=z}}});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()===0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id,hda_ldda:b.hda_ldda},function(c){})}};a()}}); \ No newline at end of file +var extend=function(){var c=arguments[0];for(var b=1;b<arguments.length;b++){var a=arguments[b];for(key in a){c[key]=a[key]}}};var trackster_module=function(f,Q){var o=f("slotting"),G=f("painters");var V=function(W,X){this.document=W;this.default_font=X!==undefined?X:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};extend(V.prototype,{load_pattern:function(W,aa){var X=this.patterns,Y=this.dummy_context,Z=new Image();Z.src=image_path+aa;Z.onload=function(){X[W]=Y.createPattern(Z,"repeat")}},get_pattern:function(W){return this.patterns[W]},new_canvas:function(){var W=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(W)}W.manager=this;return W}});var B=function(W,X){W.bind("drag",{handle:X,relative:true},function(ab,ac){var aa=$(this).parent();var Z=aa.children();var Y;for(Y=0;Y<Z.length;Y++){if(ac.offsetY<$(Z.get(Y)).position().top){break}}if(Y===Z.length){if(this!==Z.get(Y-1)){aa.append(this)}}else{if(this!==Z.get(Y)){$(this).insertBefore(Z.get(Y))}}})};var h=function(Y,W){var X=W-Y;return(X<=2?0.01:(X<=100?1:(X<=1000?5:10)))};var C=9,z=10,L=C+2,w=100,D=12000,J=200,r=10,F=5000,s=100,m="There was an error in indexing this dataset. ",E="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",A="No data for this chrom/contig.",p="Currently indexing... please wait",u="Tool cannot be rerun: ",a="Loading data...",R="Ready for display",d=10,q=5,y=5;function t(W){return Math.round(W*1000)/1000}var c=function(W){this.num_elements=W;this.clear()};extend(c.prototype,{get:function(X){var W=this.key_ary.indexOf(X);if(W!==-1){this.move_key_to_end(X,W)}return this.obj_cache[X]},set:function(X,Y){if(!this.obj_cache[X]){if(this.key_ary.length>=this.num_elements){var W=this.key_ary.shift();delete this.obj_cache[W]}this.key_ary.push(X)}this.obj_cache[X]=Y;return Y},move_key_to_end:function(X,W){this.key_ary.splice(W,1);this.key_ary.push(X)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var K=function(X,W,Y){c.call(this,X);this.track=W;this.subset=(Y!==undefined?Y:true)};extend(K.prototype,c.prototype,{load_data:function(ad,ae,Z,ac,W,ab){var Y={chrom:ad,low:ae,high:Z,mode:ac,resolution:W,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(Y,ab);var af=[];for(var aa=0;aa<this.track.filters.length;aa++){af[af.length]=this.track.filters[aa].name}Y.filter_cols=JSON.stringify(af);var X=this;return $.getJSON(this.track.data_url,Y,function(ag){X.set_data(ae,Z,ac,ag)})},get_data:function(Y,W,ab,ac,X,aa){var Z=this.get(this.gen_key(W,ab,ac));if(Z){return Z}Z=this.load_data(Y,W,ab,ac,X,aa);this.set_data(W,ab,ac,Z);return Z},set_data:function(X,Y,Z,W){return this.set(this.gen_key(X,Y,Z),W)},gen_key:function(W,Y,Z){var X=W+"_"+Y+"_"+Z;return X},split_key:function(W){return W.split("_")}});var U=function(W,Z,Y,X,aa){this.container=W;this.chrom=null;this.vis_id=Y;this.dbkey=X;this.title=Z;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(aa);this.canvas_manager=new V(W.get(0).ownerDocument);this.reset()};extend(U.prototype,{init:function(Z){var Y=this.container,W=this;this.top_container=$("<div/>").addClass("top-container").appendTo(Y);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(Y);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(Y);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<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=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var X=function(aa){if(aa.type==="focusout"||(aa.keyCode||aa.which)===13||(aa.keyCode||aa.which)===27){if((aa.keyCode||aa.which)!==27){W.go_to($(this).val())}$(this).hide();$(this).val("");W.location_span.show();W.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",X).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){W.location_span.hide();W.chrom_select.hide();W.nav_input.val(W.chrom+":"+W.low+"-"+W.high);W.nav_input.css("display","inline-block");W.nav_input.select();W.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){W.zoom_out();W.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){W.zoom_in();W.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},Z);this.chrom_select.bind("change",function(){W.change_chrom(W.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(aa){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(aa){W.zoom_in(aa.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aa,ab){this.current_x=ab.offsetX}).bind("drag",function(aa,ac){var ad=ac.offsetX-this.current_x;this.current_x=ac.offsetX;var ab=Math.round(ad/W.viewport_container.width()*(W.max_high-W.max_low));W.move_delta(-ab)});this.overview_close.bind("click",function(){for(var ab=0,aa=W.tracks.length;ab<aa;ab++){W.tracks[ab].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",W.overview_box.height());W.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(aa,ab){if(aa.clientX>W.viewport_container.width()-16){return false}}).bind("dragstart",function(aa,ab){ab.original_low=W.low;ab.current_height=aa.clientY;ab.current_x=ab.offsetX}).bind("drag",function(ac,ae){var aa=$(this);var af=ae.offsetX-ae.current_x;var ab=aa.scrollTop()-(ac.clientY-ae.current_height);aa.scrollTop(ab);ae.current_height=ac.clientY;ae.current_x=ae.offsetX;var ad=Math.round(af/W.viewport_container.width()*(W.high-W.low));W.move_delta(ad)}).bind("mousewheel",function(ac,ae,ab,aa){if(ab){var ad=Math.round(-ab/W.viewport_container.width()*(W.high-W.low));W.move_delta(ad)}});this.top_labeltrack.bind("dragstart",function(aa,ab){return $("<div />").css({height:W.content_div.height()+W.top_labeltrack.height()+W.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ae,af){$(af.proxy).css({left:Math.min(ae.pageX,af.startX),width:Math.abs(ae.pageX-af.startX)});var ab=Math.min(ae.pageX,af.startX)-W.container.offset().left,aa=Math.max(ae.pageX,af.startX)-W.container.offset().left,ad=(W.high-W.low),ac=W.viewport_container.width();W.update_location(Math.round(ab/ac*ad)+W.low,Math.round(aa/ac*ad)+W.low)}).bind("dragend",function(af,ag){var ab=Math.min(af.pageX,ag.startX),aa=Math.max(af.pageX,ag.startX),ad=(W.high-W.low),ac=W.viewport_container.width(),ae=W.low;W.low=Math.round(ab/ac*ad)+ae;W.high=Math.round(aa/ac*ad)+ae;$(ag.proxy).remove();W.redraw()});this.add_label_track(new T(this,this.top_labeltrack));this.add_label_track(new T(this,this.nav_labeltrack));$(window).bind("resize",function(){W.resize_window()});$(document).bind("redraw",function(){W.redraw()});this.reset();$(window).trigger("resize")},update_location:function(W,X){this.location_span.text(commatize(W)+" - "+commatize(X));this.nav_input.val(this.chrom+":"+commatize(W)+"-"+commatize(X))},load_chroms:function(X,Y){X.num=s;$.extend(X,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var W=this;$.ajax({url:chrom_url,data:X,dataType:"json",success:function(aa){if(aa.chrom_info.length===0){alert("Invalid chromosome: "+X.chrom);return}if(aa.reference){W.add_label_track(new x(W))}W.chrom_data=aa.chrom_info;var ad='<option value="">Select Chrom/Contig</option>';for(var ac=0,Z=W.chrom_data.length;ac<Z;ac++){var ab=W.chrom_data[ac].chrom;ad+='<option value="'+ab+'">'+ab+"</option>"}if(aa.prev_chroms){ad+='<option value="previous">Previous '+s+"</option>"}if(aa.next_chroms){ad+='<option value="next">Next '+s+"</option>"}W.chrom_select.html(ad);if(Y){Y()}W.chrom_start_index=aa.start_index},error:function(){alert("Could not load chroms for this dbkey:",W.dbkey)}})},change_chrom:function(aa,X,ac){if(!aa||aa==="None"){return}var Z=this;if(aa==="previous"){Z.load_chroms({low:this.chrom_start_index-s});return}if(aa==="next"){Z.load_chroms({low:this.chrom_start_index+s});return}var ab=$.grep(Z.chrom_data,function(ae,af){return ae.chrom===aa})[0];if(ab===undefined){Z.load_chroms({chrom:aa},function(){Z.change_chrom(aa,X,ac)});return}else{if(aa!==Z.chrom){Z.chrom=aa;if(!Z.chrom){Z.intro_div.show()}else{Z.intro_div.hide()}Z.chrom_select.val(Z.chrom);Z.max_high=ab.len-1;Z.reset();Z.redraw(true);for(var ad=0,W=Z.tracks.length;ad<W;ad++){var Y=Z.tracks[ad];if(Y.init){Y.init()}}}if(X!==undefined&&ac!==undefined){Z.low=Math.max(X,0);Z.high=Math.min(ac,Z.max_high)}Z.reset_overview();Z.redraw()}},go_to:function(aa){var ae=this,W,Z,X=aa.split(":"),ac=X[0],ad=X[1];if(ad!==undefined){try{var ab=ad.split("-");W=parseInt(ab[0].replace(/,/g,""),10);Z=parseInt(ab[1].replace(/,/g,""),10)}catch(Y){return false}}ae.change_chrom(ac,W,Z)},move_fraction:function(Y){var W=this;var X=W.high-W.low;this.move_delta(Y*X)},move_delta:function(Y){var W=this;var X=W.high-W.low;if(W.low-Y<W.max_low){W.low=W.max_low;W.high=W.max_low+X}else{if(W.high-Y>W.max_high){W.high=W.max_high;W.low=W.max_high-X}else{W.high-=Y;W.low-=Y}}W.redraw()},add_track:function(W){W.view=this;W.track_id=this.track_id_counter;this.tracks.push(W);if(W.init){W.init()}W.container_div.attr("id","track_"+W.track_id);B(W.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(W){W.view=this;this.label_tracks.push(W)},remove_track:function(W){this.has_changes=true;W.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(W)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(ad){var ac=this.high-this.low,ab=this.low,X=this.high;if(ab<this.max_low){ab=this.max_low}if(X>this.max_high){X=this.max_high}if(this.high!==0&&ac<this.min_separation){X=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(X);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(r,Math.max(0,Math.ceil(Math.log(this.resolution,r)/Math.log(r))));var W=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aa=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:W,width:Math.max(ae,aa)}).show();if(aa<ae){this.overview_box.css("left",W-(ae-aa)/2)}if(this.overview_highlight){this.overview_highlight.css({left:W,width:aa})}this.update_location(this.low,this.high);if(!ad){for(var Y=0,Z=this.tracks.length;Y<Z;Y++){if(this.tracks[Y]&&this.tracks[Y].enabled){this.tracks[Y].draw()}}for(Y=0,Z=this.label_tracks.length;Y<Z;Y++){this.label_tracks[Y].draw()}}},zoom_in:function(X,Y){if(this.max_high===0||this.high-this.low<this.min_separation){return}var Z=this.high-this.low,aa=Z/2+this.low,W=(Z/this.zoom_factor)/2;if(X){aa=X/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aa-W);this.high=Math.round(aa+W);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var X=this.high-this.low,Y=X/2+this.low,W=(X*this.zoom_factor)/2;this.low=Math.round(Y-W);this.high=Math.round(Y+W);this.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.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").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()}});var n=function(X,aa){this.track=X;this.name=aa.name;this.params=[];var ai=aa.params;for(var Y=0;Y<ai.length;Y++){var ad=ai[Y],W=ad.name,ah=ad.label,Z=unescape(ad.html),af=ad.type;if(af==="number"){this.params[this.params.length]=new g(W,ah,Z,ad.min,ad.max)}else{if(af=="select"){this.params[this.params.length]=new I(W,ah,Z)}else{console.log("WARNING: unrecognized tool parameter type:",W,af)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ak){ak.stopPropagation()}).bind("click",function(ak){ak.stopPropagation()}).bind("dblclick",function(ak){ak.stopPropagation()});var ag=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ae=this.params;var ab=this;$.each(this.params,function(al,ao){var an=$("<div>").addClass("param-row").appendTo(ab.parent_div);var ak=$("<div>").addClass("param-label").text(ao.label).appendTo(an);var am=$("<div/>").addClass("slider").html(ao.html).appendTo(an);$("<div style='clear: both;'/>").appendTo(an)});this.parent_div.find("input").click(function(){$(this).select()});var aj=$("<div>").addClass("slider-row").appendTo(this.parent_div);var ac=$("<input type='submit'>").attr("value","Run").appendTo(aj);var ab=this;ac.click(function(){ab.run()})};extend(n.prototype,{get_param_values_dict:function(){var W={};this.parent_div.find(":input").each(function(){var X=$(this).attr("name"),Y=$(this).val();W[X]=JSON.stringify(Y)});return W},get_param_values:function(){var X=[];var W={};this.parent_div.find(":input").each(function(){var Y=$(this).attr("name"),Z=$(this).val();if(Y){X[X.length]=Z}});return X},run:function(){var X={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name};$.extend(X,this.get_param_values_dict());var Z=this.track,Y=X.tool_id+Z.tool_region_and_parameters_str(X.chrom,X.low,X.high),aa;if(Z.track_type==="FeatureTrack"){aa=new N(Y,view,Z.hda_ldda,undefined,{},{},Z)}this.track.add_track(aa);aa.content_div.text("Starting job.");var W=function(){$.getJSON(run_tool_url,X,function(ab){if(ab==="no converter"){aa.container_div.addClass("error");aa.content_div.text(E)}else{if(ab.error){aa.container_div.addClass("error");aa.content_div.text(u+ab.message)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.content_div.text("Converting input data so that it can be easily reused.");setTimeout(W,2000)}else{aa.dataset_id=ab.dataset_id;aa.content_div.text("Running job.");aa.init()}}}})};W()}});var I=function(X,W,Y){this.name=X;this.label=W;this.html=Y};var g=function(Y,X,aa,Z,W){I.call(this,Y,X,aa);this.min=Z;this.max=W};var j=function(X,W,Y){this.name=X;this.index=W;this.value=Y};var O=function(X,W){this.name=X;this.index=W;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};extend(O.prototype,{applies_to:function(W){if(W.length>this.index){return true}return false},keep:function(W){if(!this.applies_to(W)){return true}return(W[this.index]>=this.low&&W[this.index]<=this.high)},update_attrs:function(X){var W=false;if(!this.applies_to(X)){return W}if(X[this.index]<this.min){this.min=Math.floor(X[this.index]);W=true}if(X[this.index]>this.max){this.max=Math.ceil(X[this.index]);W=true}return W},update_ui_elt:function(){var X=this.slider.slider("option","min"),W=this.slider.slider("option","max");if(this.min<X||this.max>W){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",h(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var v=function(W){var ac=[];for(var Z=0;Z<W.length;Z++){var ab=W[Z];var Y=ab.name,aa=ab.type,X=ab.index;if(aa==="int"||aa==="float"){ac[Z]=new O(Y,X)}else{ac[Z]=new j(Y,X,aa)}}return ac};var S=function(W){this.track=W.track;this.params=W.params;this.values={};if(W.saved_values){this.restore_values(W.saved_values)}this.onchange=W.onchange};extend(S.prototype,{restore_values:function(W){var X=this;$.each(this.params,function(Y,Z){if(W[Z.key]!==undefined){X.values[Z.key]=W[Z.key]}else{X.values[Z.key]=Z.default_value}})},build_form:function(){var X=this;var W=$("<div />");$.each(this.params,function(ab,Z){if(!Z.hidden){var Y="param_"+ab;var ag=$("<div class='form-row' />").appendTo(W);ag.append($("<label />").attr("for",Y).text(Z.label+":"));if(Z.type==="bool"){ag.append($('<input type="checkbox" />').attr("id",Y).attr("name",Y).attr("checked",X.values[Z.key]))}else{if(Z.type==="color"){var ad=X.values[Z.key];var ac=$("<input />").attr("id",Y).attr("name",Y).val(ad);var ae=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var aa=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ae);var af=$("<div/>").appendTo(aa).farbtastic({width:100,height:100,callback:ac,color:ad});$("<div />").append(ac).append(ae).appendTo(ag).bind("click",function(ah){ae.css({left:$(this).position().left+($(ac).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ae.hide();$(document).unbind("click.color-picker")});ah.stopPropagation()})}else{ag.append($("<input />").attr("id",Y).attr("name",Y).val(X.values[Z.key]))}}}});return W},update_from_form:function(W){var Y=this;var X=false;$.each(this.params,function(Z,ab){if(!ab.hidden){var ac="param_"+Z;var aa=W.find("#"+ac).val();if(ab.type==="float"){aa=parseFloat(aa)}else{if(ab.type==="int"){aa=parseInt(aa)}else{if(ab.type==="bool"){aa=W.find("#"+ac).is(":checked")}}}if(aa!==Y.values[ab.key]){Y.values[ab.key]=aa;X=true}}});if(X){this.onchange()}}});var b=function(W,X,Y){this.track=W;this.canvas=X;this.histo_max=Y};var k=function(X,W,aa,Y,Z){this.name=X;this.view=W;this.parent_element=aa;this.data_url=(Y?Y:default_data_url);this.data_url_extra_params={};this.data_query_wait=(Z?Z:F);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};extend(k.prototype,{init:function(){var W=this;W.enabled=false;W.tile_cache.clear();W.data_cache.clear();W.initial_canvas=undefined;W.content_div.css("height","auto");W.container_div.removeClass("nodata error pending");if(!W.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:W.hda_ldda,dataset_id:W.dataset_id,chrom:W.view.chrom},function(X){if(!X||X==="error"||X.kind==="error"){W.container_div.addClass("error");W.content_div.text(m);if(X.message){var Z=W.view.tracks.indexOf(W);var Y=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+X.message+"</pre>",{Close:hide_modal})});W.content_div.append(Y)}}else{if(X==="no converter"){W.container_div.addClass("error");W.content_div.text(E)}else{if(X==="no data"||(X.data!==undefined&&(X.data===null||X.data.length===0))){W.container_div.addClass("nodata");W.content_div.text(A)}else{if(X==="pending"){W.container_div.addClass("pending");W.content_div.text(p);setTimeout(function(){W.init()},W.data_query_wait)}else{if(X.status==="data"){if(X.valid_chroms){W.valid_chroms=X.valid_chroms;W.make_name_popup_menu()}W.content_div.text(R);if(W.view.chrom){W.content_div.text("");W.content_div.css("height",W.height_px+"px");W.enabled=true;$.when(W.predraw_init()).done(function(){W.draw()})}}}}}}})},predraw_init:function(){},update_name:function(W){this.old_name=this.name;this.name=W;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var H=function(X,ad,ag){var Y=this,ah=Y.view;this.filters=(X!==undefined?v(X):[]);this.filters_available=false;this.filters_visible=false;this.tool=(ad!==undefined&&obj_length(ad)>0?new n(this,ad):undefined);this.parent_track=ag;this.child_tracks=[];if(Y.hidden){return}var af=function(ai,aj,ak){ai.click(function(){var al=aj.text();max=parseFloat(ak.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(ak.slider("option","values")){input_size=2*input_size+1;multi_value=true}aj.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",al).appendTo(aj).focus().select().click(function(am){am.stopPropagation()}).blur(function(){$(this).remove();aj.text(al)}).keyup(function(aq){if(aq.keyCode===27){$(this).trigger("blur")}else{if(aq.keyCode===13){var ao=ak.slider("option","min"),am=ak.slider("option","max"),ap=function(ar){return(isNaN(ar)||ar>am||ar<ao)},an=$(this).val();if(!multi_value){an=parseFloat(an);if(ap(an)){alert("Parameter value must be in the range ["+ao+"-"+am+"]");return $(this)}}else{an=an.split("-");an=[parseFloat(an[0]),parseFloat(an[1])];if(ap(an[0])||ap(an[1])){alert("Parameter value must be in the range ["+ao+"-"+am+"]");return $(this)}}ak.slider((multi_value?"values":"value"),an)}}})})};if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filters_div=$("<div/>").addClass("filters").hide();this.header_div.after(this.filters_div);this.filters_div.bind("drag",function(ai){ai.stopPropagation()}).bind("click",function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()});$.each(this.filters,function(ao,aj){var al=$("<div/>").addClass("slider-row").appendTo(Y.filters_div);var ai=$("<div/>").addClass("slider-label").appendTo(al);var aq=$("<span/>").addClass("slider-name").text(aj.name+" ").appendTo(ai);var ak=$("<span/>");var am=$("<span/>").addClass("slider-value").appendTo(ai).append("[").append(ak).append("]");var ap=$("<div/>").addClass("slider").appendTo(al);aj.control_element=$("<div/>").attr("id",aj.name+"-filter-control").appendTo(ap);var an=[0,0];aj.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(ar,at){an=at.values;ak.text(at.values[0]+"-"+at.values[1]);setTimeout(function(){if(at.values[0]==an[0]&&at.values[1]==an[1]){var au=at.values;ak.text(au[0]+"-"+au[1]);aj.low=au[0];aj.high=au[1];Y.draw(true,true)}},50)},change:function(ar,at){aj.control_element.slider("option","slide").call(aj.control_element,ar,at)}});aj.slider=aj.control_element;aj.slider_label=ak;af(am,ak,aj.control_element);$("<div style='clear: both;'/>").appendTo(al)});if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}Y.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();Y.container_div.append(Y.child_tracks_container);if(Y.display_modes!==undefined){if(Y.mode_div===undefined){Y.mode_div=$("<div class='right-float menubutton popup' />").appendTo(Y.header_div);var aa=(Y.track_config&&Y.track_config.values.mode?Y.track_config.values.mode:Y.display_modes[0]);Y.mode=aa;Y.mode_div.text(aa);var Z=function(ai){Y.mode_div.text(ai);Y.mode=ai;Y.track_config.values.mode=ai;Y.tile_cache.clear();Y.draw()};var W={};for(var ab=0,ae=Y.display_modes.length;ab<ae;ab++){var ac=Y.display_modes[ab];W[ac]=function(ai){return function(){Z(ai)}}(ac)}make_popupmenu(Y.mode_div,W)}else{Y.mode_div.hide()}}this.make_name_popup_menu()};extend(H.prototype,k.prototype,{make_name_popup_menu:function(){var X=this;var W={};W["Edit configuration"]=function(){var ad=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ab=function(){X.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(ae){if((ae.keyCode||ae.which)===27){ad()}else{if((ae.keyCode||ae.which)===13){ab()}}};$(window).bind("keypress.check_enter_esc",ac);show_modal("Configure Track",X.track_config.build_form(),{Cancel:ad,OK:ab})};if(X.filters_available>0){var aa=(X.filters_div.is(":visible")?"Hide filters":"Show filters");W[aa]=function(){X.filters_visible=(X.filters_div.is(":visible"));X.filters_div.toggle();X.make_name_popup_menu()}}if(X.tool){var aa=(X.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");W[aa]=function(){if(!X.dynamic_tool_div.is(":visible")){X.update_name(X.name+X.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";X.revert_name()}X.dynamic_tool_div.toggle();X.make_name_popup_menu()}}if(X.valid_chroms){W["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+X.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var Y=view;var Z=function(){$("#no-tracks").show()};if(this.parent_track){Y=this.parent_track;Z=function(){}}W.Remove=function(){Y.remove_track(X);if(Y.num_tracks===0){Z()}};make_popupmenu(X.name_div,W)},draw:function(W,Z){var an=this.view.low,ac=this.view.high,ae=ac-an,ag=this.view.container.width(),ab=ag/ae,ah=this.view.resolution,aa=$("<div style='position: relative;'></div>");if(!Z){this.content_div.children().remove()}this.content_div.append(aa);this.max_height=0;var aj=Math.floor(an/ah/J);var Y={};while((aj*J*ah)<ac){var am=ag+"_"+ab+"_"+aj;var ad=this.tile_cache.get(am);var ak=aj*J*this.view.resolution;var X=ak+J*this.view.resolution;if(!W&&ad){this.show_tile(ad,aa,ak,ab)}else{this.delayed_draw(W,am,ak,X,aj,ah,aa,ab,Y)}aj+=1}var af=this;var al=setInterval(function(){if(obj_length(Y)===0){clearInterval(al);if(Z){var aq=af.content_div.children();var ap=false;for(var ar=aq.length-1,ao=0;ar>=ao;ar--){var av=$(aq[ar]);if(ap){av.remove()}else{if(av.children().length!==0){ap=true}}}}for(var au=0;au<af.filters.length;au++){af.filters[au].update_ui_elt()}var at=false;if(af.example_feature){for(var au=0;au<af.filters.length;au++){if(af.filters[au].applies_to(af.example_feature)){at=true;break}}}if(af.filters_available!==at){af.filters_available=at;if(!af.filters_available){af.filters_div.hide()}af.make_name_popup_menu()}}},50);for(var ai=0;ai<this.child_tracks.length;ai++){this.child_tracks[ai].draw(W,Z)}},delayed_draw:function(X,ae,ac,ag,Y,aa,af,ah,ab){var Z=this;var ad=function(ap,ai,ak,aj,an,ao,al){returned_tile=Z.draw_tile(ai,ak,aj,an,ao,al);var am=$("<div class='track-tile'>").prepend(returned_tile);tile_element=am;Z.tile_cache.set(ae,tile_element);Z.show_tile(tile_element,an,ac,ao);delete ab[ap]};var W=setTimeout(function(){if(ac<=Z.view.high&&ag>=Z.view.low){var ai=(X?undefined:Z.tile_cache.get(ae));if(ai){Z.show_tile(ai,af,ac,ah);delete ab[W]}else{$.when(Z.data_cache.get_data(view.chrom,ac,ag,Z.mode,aa,Z.data_url_extra_params)).then(function(aj){if(view.reference_track&&ah>view.canvas_manager.char_width_px){$.when(view.reference_track.data_cache.get_data(view.chrom,ac,ag,Z.mode,aa,view.reference_track.data_url_extra_params)).then(function(ak){ad(W,aj,aa,Y,af,ah,ak)})}else{ad(W,aj,aa,Y,af,ah)}})}}},50);ab[W]=true},show_tile:function(W,ab,Z,ac){var X=this;var Y=this.view.high-this.view.low,aa=(Z-this.view.low)*ac;if(this.left_offset){aa-=this.left_offset}W.css({position:"absolute",top:0,left:aa,height:""});ab.append(W);X.max_height=Math.max(X.max_height,W.height());X.content_div.css("height",X.max_height+"px");ab.children().css("height",X.max_height+"px")},set_overview:function(){var W=this.view;if(this.initial_canvas&&this.is_overview){W.overview_close.show();W.overview_viewport.append(this.initial_canvas);W.overview_highlight.show().height(this.initial_canvas.height());W.overview_viewport.height(this.initial_canvas.height()+W.overview_box.height())}$(window).trigger("resize")},tool_region_and_parameters_str:function(Y,W,Z){var X=this,aa=(Y!==undefined&&W!==undefined&&Z!==undefined?Y+":"+W+"-"+Z:"all");return" - region=["+aa+"], parameters=["+X.tool.get_param_values().join(", ")+"]"},add_track:function(W){W.track_id=this.track_id+"_"+this.child_tracks.length;W.container_div.attr("id","track_"+W.track_id);this.child_tracks_container.append(W.container_div);B(W.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(W);this.view.has_changes=true},remove_track:function(W){W.container_div.fadeOut("slow",function(){$(this).remove()})}});var T=function(W,X){this.track_type="LabelTrack";this.hidden=true;k.call(this,null,W,X);this.container_div.addClass("label-track")};extend(T.prototype,k.prototype,{draw:function(){var Y=this.view,Z=Y.high-Y.low,ac=Math.floor(Math.pow(10,Math.floor(Math.log(Z)/Math.log(10)))),W=Math.floor(Y.low/ac)*ac,aa=this.view.container.width(),X=$("<div style='position: relative; height: 1.3em;'></div>");while(W<Y.high){var ab=(W-Y.low)/Z*aa;X.append($("<div class='label'>"+commatize(W)+"</div>").css({position:"absolute",left:ab-1}));W+=ac}this.content_div.children(":first").remove();this.content_div.append(X)}});var x=function(W){this.track_type="ReferenceTrack";this.hidden=true;k.call(this,null,W,W.top_labeltrack);H.call(this);W.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:W.dbkey};this.data_cache=new K(y,this,false);this.tile_cache=new c(q)};extend(x.prototype,H.prototype,{draw_tile:function(ag,ab,X,ad,ah){var aa=this,Y=J*ab;if(ah>this.view.canvas_manager.char_width_px){if(ag===null){aa.content_div.css("height","0px");return}var Z=this.view.canvas_manager.new_canvas();var af=Z.getContext("2d");Z.width=Math.ceil(Y*ah+aa.left_offset);Z.height=aa.height_px;af.font=af.canvas.manager.default_font;af.textAlign="center";for(var ac=0,ae=ag.length;ac<ae;ac++){var W=Math.round(ac*ah);af.fillText(ag[ac],W+aa.left_offset,10)}return Z}this.content_div.css("height","0px")}});var l=function(aa,Y,ab,W,Z){var X=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";k.call(this,aa,Y,Y.viewport_container);H.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=ab;this.dataset_id=W;this.original_dataset_id=W;this.data_cache=new K(y,this);this.tile_cache=new c(q);this.track_config=new S({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{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:Z,onchange:function(){X.vertical_range=X.prefs.max_value-X.prefs.min_value;$("#linetrack_"+X.track_id+"_minval").text(X.prefs.min_value);$("#linetrack_"+X.track_id+"_maxval").text(X.prefs.max_value);X.tile_cache.clear();X.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};extend(l.prototype,H.prototype,{add_resize_handle:function(){var W=this;var Z=false;var Y=false;var X=$("<div class='track-resize'>");$(W.container_div).hover(function(){Z=true;X.show()},function(){Z=false;if(!Y){X.hide()}});X.hide().bind("dragstart",function(aa,ab){Y=true;ab.original_height=$(W.content_div).height()}).bind("drag",function(ab,ac){var aa=Math.min(Math.max(ac.original_height+ac.deltaY,W.min_height_px),W.max_height_px);$(W.content_div).css("height",aa);W.height_px=aa;W.draw(true)}).bind("dragend",function(aa,ab){W.tile_cache.clear();Y=false;if(!Z){X.hide()}W.track_config.values.height=W.height_px}).appendTo(W.container_div)},predraw_init:function(){var W=this,X=W.view.tracks.indexOf(W);W.vertical_range=undefined;return $.getJSON(W.data_url,{stats:true,chrom:W.view.chrom,low:null,high:null,hda_ldda:W.hda_ldda,dataset_id:W.dataset_id},function(Y){W.container_div.addClass("line-track");var aa=Y.data;if(isNaN(parseFloat(W.prefs.min_value))||isNaN(parseFloat(W.prefs.max_value))){W.prefs.min_value=aa.min;W.prefs.max_value=aa.max;$("#track_"+X+"_minval").val(W.prefs.min_value);$("#track_"+X+"_maxval").val(W.prefs.max_value)}W.vertical_range=W.prefs.max_value-W.prefs.min_value;W.total_frequency=aa.total_frequency;W.container_div.find(".yaxislabel").remove();var ab=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+X+"_minval").text(t(W.prefs.min_value));var Z=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+X+"_maxval").text(t(W.prefs.max_value));Z.css({position:"absolute",top:"24px",left:"10px"});Z.prependTo(W.container_div);ab.css({position:"absolute",bottom:"2px",left:"10px"});ab.prependTo(W.container_div)})},draw_tile:function(ah,aa,X,ae,ag){if(this.vertical_range===undefined){return}var ab=X*J*aa,Z=J*aa,W=Math.ceil(Z*ag),ad=this.height_px;var Y=this.view.canvas_manager.new_canvas();Y.width=W,Y.height=ad;var af=Y.getContext("2d");var ac=new G.LinePainter(ah.data,ab,ab+Z,this.prefs.min_value,this.prefs.max_value,this.prefs.color,this.mode);ac.draw(af,W,ad);return Y}});var e=function(W,ab,aa,ae,ad,Y,Z,ac){var X=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];this.track_config=new S({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{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:ad,onchange:function(){X.tile_cache.clear();X.draw()}});this.prefs=this.track_config.values;k.call(this,W,ab,ab.viewport_container);H.call(this,Y,Z,ac);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=aa;this.dataset_id=ae;this.original_dataset_id=ae;this.zo_slots={};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_cache=new K(20,this);this.left_offset=200;this.painter=G.LinkedFeaturePainter};extend(e.prototype,H.prototype,{update_auto_mode:function(W){if(this.mode=="Auto"){if(W=="no_detail"){W="reduced to feature spans"}else{if(W=="summary_tree"){W="reduced to coverage histogram"}}this.mode_div.text("Auto ("+W+")")}},incremental_slots:function(aa,X,Z){var Y=this.view.canvas_manager.dummy_context,W=this.inc_slots[aa];if(!W||(W.mode!==Z)){W=new (o.FeatureSlotter)(aa,Z==="Pack",w,function(ab){return Y.measureText(ab)});W.mode=Z;this.inc_slots[aa]=W}return W.slot_features(X)},draw_tile:function(ai,aq,av,ae,ag,Z){var an=this,ax=av*J*aq,X=(av+1)*J*aq,ak=X-ax,ao=Math.ceil(ak*ag),am=this.mode,aB=25,aa=this.left_offset,aj,ab;if(am==="Auto"){if(ai.dataset_type==="summary_tree"){am=ai.dataset_type}else{if(ai.extra_info==="no_detail"){am="no_detail"}else{var aA=ai.data;if((aA.length&&aA.length<4)||(this.view.high-this.view.low>D)){am="Squish"}else{am="Pack"}}}this.update_auto_mode(am)}if(am==="summary_tree"){ab=this.summary_draw_height;ae.parent().css("height",Math.max(this.height_px,ab)+"px");this.container_div.find(".yaxislabel").remove();var W=$("<div />").addClass("yaxislabel");W.text(ai.max);W.css({position:"absolute",top:"22px",left:"10px"});W.prependTo(this.container_div);var Y=this.view.canvas_manager.new_canvas();Y.width=ao+aa;Y.height=ab+L;var ay=new G.SummaryTreePainter(ai.data,ai.delta,ai.max,ax,X,this.prefs.show_counts);var ap=Y.getContext("2d");ap.translate(aa,L);ay.draw(ap,ao,ab);return Y}var aj,ad=1;if(am==="no_detail"||am==="Squish"||am==="Pack"){ad=this.incremental_slots(ag,ai.data,am);aj=this.inc_slots[ag].slots}var af=[];if(ai.data){for(var ar=0,au=ai.data.length;ar<au;ar++){var ac=ai.data[ar];var at=false;var ah;for(var aw=0,az=this.filters.length;aw<az;aw++){ah=this.filters[aw];ah.update_attrs(ac);if(!ah.keep(ac)){at=true;break}}if(!at){af.push(ac)}}}var ay=new (this.painter)(af,ax,X,this.prefs,am,Z);var ab=ay.get_required_height(ad)+z;var Y=this.view.canvas_manager.new_canvas();Y.width=ao+aa;Y.height=ab;ae.parent().css("height",Math.max(this.height_px,ab)+"px");var ap=Y.getContext("2d");ap.fillStyle=this.prefs.block_color;ap.font=ap.canvas.manager.default_font;ap.textAlign="right";this.container_div.find(".yaxislabel").remove();if(ai.message){$(Y).css({"border-top":"1px solid red"});ap.fillStyle="red";ap.textAlign="left";var al=ap.textBaseline;ap.textBaseline="top";ap.fillText(ai.message,aa,0);ap.textBaseline=al;if(!ai.data){return Y}}this.example_feature=(ai.data.length?ai.data[0]:undefined);ap.translate(aa,z);ay.draw(ap,ao,ab,aj);return Y}});var M=function(Z,X,ab,W,Y,aa){e.call(this,Z,X,ab,W,Y,aa);this.track_type="VcfTrack";this.painter=G.VariantPainter};extend(M.prototype,H.prototype,e.prototype);var P=function(Z,X,ab,W,Y,aa){e.call(this,Z,X,ab,W,Y,aa);this.track_config=new S({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:Y,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.track_type="ReadTrack";this.painter=G.ReadPainter;this.make_name_popup_menu()};extend(P.prototype,H.prototype,e.prototype);var N=function(aa,Y,ac,W,Z,ab,X){e.call(this,aa,Y,ac,W,Z,ab,{},X);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};extend(N.prototype,H.prototype,e.prototype,{predraw_init:function(){var X=this;var W=function(){if(X.data_cache.size()===0){setTimeout(W,300)}else{X.data_url=default_data_url;X.data_query_wait=F;X.dataset_state_url=converted_datasets_state_url;$.getJSON(X.dataset_state_url,{dataset_id:X.dataset_id,hda_ldda:X.hda_ldda},function(Y){})}};W()}});Q.View=U;Q.LineTrack=l;Q.FeatureTrack=e;Q.ReadTrack=P};var slotting_module=function(c,b){var d=2,a=5;b.FeatureSlotter=function(h,g,e,f){this.slots={};this.start_end_dct={};this.w_scale=h;this.include_label=g;this.max_rows=e;this.measureText=f};extend(b.FeatureSlotter.prototype,{slot_features:function(l){var o=this.w_scale,r=this.slots,g=this.start_end_dct,x=[],z=[],m=0,y=this.max_rows;for(var v=0,w=l.length;v<w;v++){var k=l[v],n=k[0];if(r[n]!==undefined){m=Math.max(m,r[n]);z.push(r[n])}else{x.push(v)}}var p=function(F,G){for(var E=0;E<=y;E++){var C=false,H=g[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var A=H[B];if(G>A[0]&&F<A[1]){C=true;break}}}if(!C){return E}}return -1};for(var v=0,w=x.length;v<w;v++){var k=l[x[v]],n=k[0],t=k[1],e=k[2],q=k[3],f=Math.floor(t*o),j=Math.ceil(e*o),u=this.measureText(q).width,h;if(q!==undefined&&this.include_label){u+=(d+a);if(f-u>=0){f-=u;h="left"}else{j+=u;h="right"}}var s=p(f,j);if(s>=0){if(g[s]===undefined){g[s]=[]}g[s].push([f,j]);r[n]=s;m=Math.max(m,s)}else{}}return m+1}})};var painters_module=function(k,A){var q=function(L,D,J,C,I,G){if(G===undefined){G=4}var F=C-D;var E=I-J;var H=Math.floor(Math.sqrt(F*F+E*E)/G);var M=F/H;var K=E/H;var B;for(B=0;B<H;B++,D+=M,J+=K){if(B%2!==0){continue}L.fillRect(D,J,G,1)}};var r=function(D,C,B,G){var F=C-G/2,E=C+G/2,H=B-Math.sqrt(G*3/2);D.beginPath();D.moveTo(F,H);D.lineTo(E,H);D.lineTo(C,B);D.lineTo(F,H);D.strokeStyle=this.fillStyle;D.fill();D.stroke();D.closePath()};var v=function(E,G,C,F,B,D){this.data=E;this.delta=G;this.max=C;this.view_start=F;this.view_end=B;this.show_counts=D};v.prototype.draw=function(O,B,N){var G=this.view_start,Q=this.view_end-this.view_start,P=B/Q;var L=this.data,K=this.delta,I=this.max,D=N;delta_x_px=Math.ceil(K*P);O.save();for(var E=0,F=L.length;E<F;E++){var J=Math.floor((L[E][0]-G)*P);var H=L[E][1];if(!H){continue}var M=H/I*N;O.fillStyle="black";O.fillRect(J,D-M,delta_x_px,M);var C=4;if(this.show_counts&&(O.measureText(H).width+C)<delta_x_px){O.fillStyle="#666";O.textAlign="center";O.fillText(H,J+(delta_x_px/2),10)}}O.restore()};var c=function(E,H,B,C,G,D,F){this.data=E;this.view_start=H;this.view_end=B;this.min_value=C;this.max_value=G;this.color=D;this.mode=F;this.overflow_color="#F66"};c.prototype.draw=function(Q,P,N){var I=false,J=this.min_value,G=this.max_value,M=G-J,C=N,D=this.view_start,O=this.view_end-this.view_start,E=P/O,K=this.mode,U=this.data;Q.save();var V=Math.round(N+J/M*N);if(K!=="Intensity"){Q.fillStyle="#aaa";Q.fillRect(0,V,P,1)}Q.beginPath();Q.fillStyle=this.color;var T,H,F;if(U.length>1){F=Math.ceil((U[1][0]-U[0][0])*E)}else{F=10}for(var R=0,S=U.length;R<S;R++){T=Math.round((U[R][0]-D)*E);H=U[R][1];if(H===null){if(I&&K==="Filled"){Q.lineTo(T,C)}I=false;continue}if(H<J){H=J}else{if(H>G){H=G}}if(K==="Histogram"){H=Math.round(H/M*C);Q.fillRect(T,V,F,-H)}else{if(K==="Intensity"){H=255-Math.floor((H-J)/M*255);Q.fillStyle="rgb("+H+","+H+","+H+")";Q.fillRect(T,0,F,C)}else{H=Math.round(C-(H-J)/M*C);if(I){Q.lineTo(T,H)}else{I=true;if(K==="Filled"){Q.moveTo(T,C);Q.lineTo(T,H)}else{Q.moveTo(T,H)}}}}}if(K==="Filled"){if(I){Q.lineTo(T,V);Q.lineTo(0,V)}Q.fill()}else{Q.stroke()}var B=-1,L=-1;Q.fillStyle=this.overflow_color;for(var R=0,S=U.length;R<S;R++){H=U[R][1];T=Math.round((U[R][0]-D)*E);x_minus_scaled=Math.round((U[R][0]-1-D)*E);if(L>=0&&(H===null||H<G)){Q.fillRect(L,0,x_minus_scaled-L+1,2);L=-1}else{if(B>=0&&(H===null||H>J)){Q.fillRect(B,N-2,x_minus_scaled-B+1,2);B=-1}}if(H!==null&&H>G&&L<0){L=T}else{if(H!==null&&H<J&&B<0){B=T}}}Q.restore()};var p=function(D,F,B,C,E){this.data=D;this.view_start=F;this.view_end=B;this.prefs=C;this.mode=E};extend(p.prototype,{get_required_height:function(C){var B=y_scale=this.get_row_height(),D=this.mode;if(D==="no_detail"||D==="Squish"||D==="Pack"){B=C*y_scale}return B+Math.max(Math.round(y_scale/2),5)},draw:function(N,E,M,J){var H=this.data,K=this.view_start,O=this.view_end;N.save();N.fillStyle=this.prefs.block_color;N.textAlign="right";var R=this.view_end-this.view_start,Q=E/R,D=this.get_row_height();for(var G=0,I=H.length;G<I;G++){var P=H[G],F=P[0],B=P[1],C=P[2],L=(J&&J[F]!==undefined?J[F]:null);if((B<O&&C>K)&&(this.mode=="Dense"||L!==null)){this.draw_element(N,this.mode,P,L,K,O,Q,D,E)}}N.restore()}});var d=10,j=3,n=5,z=10,g=1,t=3,f=3,a=9,o=2,h="#ccc";var s=function(D,F,B,C,E){p.call(this,D,F,B,C,E)};extend(s.prototype,p.prototype,{get_row_height:function(){var C=this.mode,B;if(C==="Dense"){B=d}else{if(C==="no_detail"){B=j}else{if(C==="Squish"){B=n}else{B=z}}}return B},draw_element:function(N,G,V,I,P,af,aj,ak,B){var S=V[0],ah=V[1],Z=V[2]-1,Q=V[3],aa=Math.floor(Math.max(0,(ah-P)*aj)),O=Math.ceil(Math.min(B,Math.max(0,(Z-P)*aj))),Y=(G==="Dense"?0:(0+I))*ak,M,ad,R=null,al=null,E=this.prefs.block_color,ac=this.prefs.label_color;if(G=="Dense"){I=1}if(G==="no_detail"){N.fillStyle=E;N.fillRect(aa,Y+5,O-aa,g)}else{var L=V[4],X=V[5],ab=V[6],F=V[7];if(X&&ab){R=Math.floor(Math.max(0,(X-P)*aj));al=Math.ceil(Math.min(B,Math.max(0,(ab-P)*aj)))}var ai,T;if(G==="Squish"||G==="Dense"){ai=1;T=f}else{ai=5;T=a}if(!F){if(V.strand){if(V.strand==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(V.strand==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}}else{N.fillStyle=E}N.fillRect(aa,Y,O-aa,T)}else{var K,U;if(G==="Squish"||G==="Dense"){N.fillStyle=h;K=Y+Math.floor(f/2)+1;U=1}else{if(L){var K=Y;var U=T;if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand")}}}else{N.fillStyle=h;K+=(f/2)+1;U=1}}N.fillRect(aa,K,O-aa,U);for(var ag=0,D=F.length;ag<D;ag++){var H=F[ag],C=Math.floor(Math.max(0,(H[0]-P)*aj)),W=Math.ceil(Math.min(B,Math.max((H[1]-1-P)*aj)));if(C>W){continue}N.fillStyle=E;N.fillRect(C,Y+(T-ai)/2+1,W-C,ai);if(R!==undefined&&ab>X&&!(C>al||W<R)){var ae=Math.max(C,R),J=Math.min(W,al);N.fillRect(ae,Y+1,J-ae,T);if(F.length==1&&G=="Pack"){if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}if(ae+14<J){ae+=2;J-=2}N.fillRect(ae,Y+1,J-ae,T)}}}}if(G==="Pack"&&ah>P){N.fillStyle=ac;if(P===0&&aa-N.measureText(Q).width<0){N.textAlign="left";N.fillText(Q,O+o,Y+8)}else{N.textAlign="right";N.fillText(Q,aa-o,Y+8)}N.fillStyle=E}}}});var b=function(D,F,B,C,E){p.call(this,D,F,B,C,E)};extend(b.prototype,p.prototype,{draw_element:function(U,P,J,F,X,D,M,V,S){var J=data[i],L=J[0],T=J[1],E=J[2]-1,O=J[3],H=Math.floor(Math.max(0,(T-X)*M)),K=Math.ceil(Math.min(S,Math.max(0,(E-X)*M))),G=(P==="Dense"?0:(0+F))*V,B,Y,C=null,N=null;if(no_label){U.fillStyle=block_color;U.fillRect(H+left_offset,G+5,K-H,1)}else{var W=J[4],R=J[5],I=J[6];B=9;Y=1;U.fillRect(H+left_offset,G,K-H,B);if(P!=="Dense"&&O!==undefined&&T>X){U.fillStyle=label_color;if(X===0&&H-U.measureText(O).width<0){U.textAlign="left";U.fillText(O,K+2+left_offset,G+8)}else{U.textAlign="right";U.fillText(O,H-2+left_offset,G+8)}U.fillStyle=block_color}var Q=W+" / "+R;if(T>X&&U.measureText(Q).width<(K-H)){U.fillStyle="white";U.textAlign="center";U.fillText(Q,left_offset+H+(K-H)/2,G+8);U.fillStyle=block_color}}}});var y=1001,m=1002,e=1003,x=1004,l=1005;var w=function(F,C){var H=F[0],G=F[1],E=C[0],D=C[1],B;if(H<E){if(G<E){B=y}else{if(G<=D){B=e}else{B=m}}}else{if(H>D){B=y}else{if(G<=D){B=l}else{B=x}}}return B};var u=function(E,G,B,D,F,C){p.call(this,E,G,B,D,F);this.ref_seq=C};extend(u.prototype,p.prototype,{get_row_height:function(){var B,C=this.mode;if(C==="Dense"){B=d}else{if(C==="Squish"){B=n}else{B=z;if(this.prefs.show_insertions){B*=2}}}return B},draw_read:function(Y,T,O,ad,D,X,L,I,H){Y.textAlign="center";var W=this,C=[ad,D],R=0,Z=0,V=0;ref_seq=this.ref_seq,char_width_px=Y.canvas.manager.char_width_px;var ai=[];if((T==="Pack"||this.mode==="Auto")&&I!==undefined&&O>char_width_px){V=Math.round(O/2)}if(!L){L=[[0,I.length]]}for(var P=0,ab=L.length;P<ab;P++){var M=L[P],E="MIDNSHP=X"[M[0]],Q=M[1];if(E==="H"||E==="S"){R-=Q}var J=X+R,ah=Math.floor(Math.max(0,(J-ad)*O)),K=Math.floor(Math.max(0,(J+Q-ad)*O));switch(E){case"H":break;case"S":case"M":case"=":var S=w([J,J+Q],C);if(S!==y){var U=I.slice(Z,Z+Q);if(V>0){Y.fillStyle=this.prefs.block_color;Y.fillRect(ah-V,H+1,K-ah,9);Y.fillStyle=h;for(var af=0,B=U.length;af<B;af++){if(this.prefs.show_differences&&ref_seq){var N=ref_seq[J-ad+af];if(!N||N.toLowerCase()===U[af].toLowerCase()){continue}}if(J+af>=ad&&J+af<=D){var ag=Math.floor(Math.max(0,(J+af-ad)*O));Y.fillText(U[af],ag,H+9)}}}else{Y.fillStyle=this.prefs.block_color;Y.fillRect(ah,H+4,K-ah,f)}}Z+=Q;R+=Q;break;case"N":Y.fillStyle=h;Y.fillRect(ah-V,H+5,K-ah,1);R+=Q;break;case"D":Y.fillStyle="red";Y.fillRect(ah-V,H+4,K-ah,3);R+=Q;break;case"P":break;case"I":var S=w([J,J+Q],C),ac=ah-V;if(S!==y){var U=I.slice(Z,Z+Q);if(this.prefs.show_insertions){var G=ah-(K-ah)/2;if((T==="Pack"||this.mode==="Auto")&&I!==undefined&&O>char_width_px){Y.fillStyle="yellow";Y.fillRect(G-V,H-9,K-ah,9);ai[ai.length]={type:"triangle",data:[ac,H+4,5]};Y.fillStyle=h;switch(S){case (e):U=U.slice(ad-J);break;case (x):U=U.slice(0,J-D);break;case (l):break;case (m):U=U.slice(ad-J,J-D);break}for(var af=0,B=U.length;af<B;af++){var ag=Math.floor(Math.max(0,(J+af-ad)*O));Y.fillText(U[af],ag-(K-ah)/2,H)}}else{Y.fillStyle="yellow";Y.fillRect(G,H+(this.mode!=="Dense"?2:5),K-ah,(T!=="Dense"?f:t))}}else{if((T==="Pack"||this.mode==="Auto")&&I!==undefined&&O>char_width_px){ai[ai.length]={type:"text",data:[U.length,ac,H+9]}}else{}}}Z+=Q;break;case"X":Z+=Q;break}}Y.fillStyle="yellow";var ae,F,aj;for(var aa=0;aa<ai.length;aa++){ae=ai[aa];F=ae.type;aj=ae.data;if(F==="text"){Y.save();Y.font="bold "+Y.font;Y.fillText(aj[0],aj[1],aj[2]);Y.restore()}else{if(F=="triangle"){r(Y,aj[0],aj[1],aj[2])}}}},draw_element:function(U,P,H,E,X,C,L,V,S){var K=H[0],T=H[1],D=H[2],M=H[3],G=Math.floor(Math.max(0,(T-X)*L)),I=Math.ceil(Math.min(S,Math.max(0,(D-X)*L))),F=(P==="Dense"?0:(0+E))*V,Y=this.prefs.block_color,J=this.prefs.label_color,R=0;if((P==="Pack"||this.mode==="Auto")&&L>U.canvas.manager.char_width_px){var R=Math.round(L/2)}U.fillStyle=Y;if(H[5] instanceof Array){var Q=Math.floor(Math.max(0,(H[4][0]-X)*L)),O=Math.ceil(Math.min(S,Math.max(0,(H[4][1]-X)*L))),N=Math.floor(Math.max(0,(H[5][0]-X)*L)),B=Math.ceil(Math.min(S,Math.max(0,(H[5][1]-X)*L)));if(H[4][1]>=X&&H[4][0]<=C&&H[4][2]){this.draw_read(U,P,L,X,C,H[4][0],H[4][2],H[4][3],F)}if(H[5][1]>=X&&H[5][0]<=C&&H[5][2]){this.draw_read(U,P,L,X,C,H[5][0],H[5][2],H[5][3],F)}if(N>O){U.fillStyle=h;q(U,O-R,F+5,N-R,F+5)}}else{U.fillStyle=Y;this.draw_read(U,P,L,X,C,T,H[4],H[5],F)}if(P==="Pack"&&T>X){U.fillStyle=this.prefs.label_color;var W=1;if(W===0&&G-U.measureText(M).width<0){U.textAlign="left";U.fillText(M,I+o-R,F+8)}else{U.textAlign="right";U.fillText(M,G-o-R,F+8)}U.fillStyle=Y}}});A.SummaryTreePainter=v;A.LinePainter=c;A.LinkedFeaturePainter=s;A.ReadPainter=u;A.VariantPainter=b};(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("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 --- a/static/scripts/trackster.js Sun Mar 27 19:50:50 2011 -0400 +++ b/static/scripts/trackster.js Tue Apr 05 13:57:14 2011 -0400 @@ -2,56 +2,79 @@ 2010-2011: James Taylor, Kanwei Li, Jeremy Goecks */ -/** - * Draw a dashed line on a canvas using filled rectangles. This function is based on: - * http://vetruvet.blogspot.com/2010/10/drawing-dashed-lines-on-html5-canvas.h… - * However, that approach uses lines, which don't seem to render as well, so use - * rectangles instead. - */ -CanvasRenderingContext2D.prototype.dashedLine = function(x1, y1, x2, y2, dashLen) { - if (dashLen === undefined) { dashLen = 4; } - var dX = x2 - x1; - var dY = y2 - y1; - var dashes = Math.floor(Math.sqrt(dX * dX + dY * dY) / dashLen); - var dashX = dX / dashes; - var dashY = dY / dashes; - var q; - - for (q = 0; q < dashes; q++, x1 += dashX, y1 += dashY) { - if (q % 2 !== 0) { - continue; +/** Simple extend function for inheritence */ +var extend = function() { + var target = arguments[0]; + for ( var i = 1; i < arguments.length; i++ ) { + var other = arguments[i]; + for ( key in other ) { + target[key] = other[key]; } - this.fillRect(x1, y1, dashLen, 1); } }; +// Encapsulate -- anything to be availabe outside this block is added to exports +var trackster_module = function(require, exports){ + +var slotting = require('slotting'), + painters = require('painters'); + +// ---- Canvas management and extensions ---- + /** - * Draw an isosceles triangle that points down. + * Canvas manager is used to create canvases, for browsers, this deals with + * backward comparibility using excanvas, as well as providing a pattern cache */ -CanvasRenderingContext2D.prototype.drawDownwardEquilateralTriangle = function(down_vertex_x, down_vertex_y, side_len) { - // Compute other two points of triangle. - var - x1 = down_vertex_x - side_len/2, - x2 = down_vertex_x + side_len/2, - y = down_vertex_y - Math.sqrt( side_len*3/2 ); - - // Draw and fill. - this.beginPath(); - this.moveTo(x1, y); - this.lineTo(x2, y); - this.lineTo(down_vertex_x, down_vertex_y); - this.lineTo(x1, y); +var CanvasManager = function( document, default_font ) { + this.document = document; + this.default_font = default_font !== undefined ? default_font : "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.strokeStyle = this.fillStyle; - this.fill(); - this.stroke(); - this.closePath(); -}; + // FIXME: move somewhere to make this more general + 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" ); +} + +extend( CanvasManager.prototype, { + load_pattern: function( key, path ) { + var patterns = this.patterns, + dummy_context = this.dummy_context, + image = new Image(); + // FIXME: where does image_path come from? not in browser.mako... + image.src = image_path + path; + image.onload = function() { + patterns[key] = dummy_context.createPattern( image, "repeat" ); + } + }, + get_pattern: function( key ) { + return this.patterns[key]; + }, + new_canvas: function() { + var canvas = this.document.createElement("canvas"); + // If using excanvas in IE, we need to explicately attach the canvas + // methods to the DOM element + if (window.G_vmlCanvasManager) { G_vmlCanvasManager.initElement(canvas); } + // Keep a reference back to the manager + canvas.manager = this; + return canvas; + } +}); + +// ---- Web UI specific utilities ---- /** * Make `element` sortable in parent by dragging `handle` (a selector) */ -function sortable( element, handle ) { +var sortable = function( element, handle ) { element.bind( "drag", { handle: handle, relative: true }, function ( e, d ) { var parent = $(this).parent(); var children = parent.children(); @@ -77,47 +100,11 @@ } /** - * Compute the type of overlap between two regions. They are assumed to be on the same chrom/contig. - * The overlap is computed relative to the second region; hence, OVERLAP_START indicates that the first - * region overlaps the start (but not the end) of the second region. + * Calculates step for slider with a given min, max. */ -var NO_OVERLAP = 1001, CONTAINS = 1002, OVERLAP_START = 1003, OVERLAP_END = 1004, CONTAINED_BY = 1005; -function compute_overlap(first_region, second_region) { - var - first_start = first_region[0], first_end = first_region[1], - second_start = second_region[0], second_end = second_region[1], - overlap; - if (first_start < second_start) { - if (first_end < second_start) { - overlap = NO_OVERLAP; - } - else if (first_end <= second_end) { - overlap = OVERLAP_START; - } - else { // first_end > second_end - overlap = CONTAINS; - } - } - else { // first_start >= second_start - if (first_start > second_end) { - overlap = NO_OVERLAP; - } - else if (first_end <= second_end) { - overlap = CONTAINED_BY; - } - else { - overlap = OVERLAP_END; - } - } - - return overlap; -} - -/** - * Returns true if there is any overlap between regions. - */ -function is_overlap(first_region, second_region) { - return (compute_overlap(first_region, second_region) !== NO_OVERLAP); +var get_slider_step = function(min, max) { + var range = max - min; + return (range <= 2 ? 0.01 : (range <= 100 ? 1 : (range <= 1000 ? 5 : 10))); } /** @@ -126,30 +113,21 @@ var // Drawing constants; track height is (constant) height of track, and feature height is the // height of individual features within tracks. Feature height, then, should always be less - // than track height. - DENSE_TRACK_HEIGHT = 10, - NO_DETAIL_TRACK_HEIGHT = 3, - SQUISH_TRACK_HEIGHT = 5, - PACK_TRACK_HEIGHT = 10, - NO_DETAIL_FEATURE_HEIGHT = 1, - DENSE_FEATURE_HEIGHT = 1, - SQUISH_FEATURE_HEIGHT = 3, - PACK_FEATURE_HEIGHT = 9, + // than track height. + CHAR_HEIGHT_PX = 9, // FIXME: font size may not be static ERROR_PADDING = 10, // Padding at the top of tracks for error messages - LABEL_SPACING = 2, - PACK_SPACING = 5, + SUMMARY_TREE_TOP_PADDING = CHAR_HEIGHT_PX + 2, + // Maximum number of rows un a slotted track + MAX_FEATURE_DEPTH = 100, // Minimum width for window for squish to be used. MIN_SQUISH_VIEW_WIDTH = 12000, // Other constants. - DEFAULT_FONT = "9px Monaco, Lucida Console, monospace", DENSITY = 200, FEATURE_LEVELS = 10, - MAX_FEATURE_DEPTH = 100, DEFAULT_DATA_QUERY_WAIT = 5000, // Maximum number of chromosomes that are selectable at any one time. MAX_CHROMS_SELECTABLE = 100, - CONNECTOR_COLOR = "#ccc", DATA_ERROR = "There was an error in indexing this dataset. ", DATA_NOCONVERTER = "A converter for this dataset is not installed. Please check your datatypes_conf.xml file.", DATA_NONE = "No data for this chrom/contig.", @@ -159,41 +137,7 @@ DATA_OK = "Ready for display", CACHED_TILES_FEATURE = 10, CACHED_TILES_LINE = 5, - CACHED_DATA = 5, - DUMMY_CANVAS = document.createElement("canvas"), - RIGHT_STRAND, LEFT_STRAND; - -// Get information for rendering canvas elements. -if (window.G_vmlCanvasManager) { - G_vmlCanvasManager.initElement(DUMMY_CANVAS); -} -var - CONTEXT = DUMMY_CANVAS.getContext("2d"); -CONTEXT.font = DEFAULT_FONT; // To ensure consistent measureText width -var - CHAR_WIDTH_PX = CONTEXT.measureText("A").width, - CHAR_HEIGHT_PX = 9; // Taken from DEFAULT_FONT. - -var right_img = new Image(); -right_img.src = image_path + "/visualization/strand_right.png"; -right_img.onload = function() { - RIGHT_STRAND = CONTEXT.createPattern(right_img, "repeat"); -}; -var left_img = new Image(); -left_img.src = image_path + "/visualization/strand_left.png"; -left_img.onload = function() { - LEFT_STRAND = CONTEXT.createPattern(left_img, "repeat"); -}; -var right_img_inv = new Image(); -right_img_inv.src = image_path + "/visualization/strand_right_inv.png"; -right_img_inv.onload = function() { - RIGHT_STRAND_INV = CONTEXT.createPattern(right_img_inv, "repeat"); -}; -var left_img_inv = new Image(); -left_img_inv.src = image_path + "/visualization/strand_left_inv.png"; -left_img_inv.onload = function() { - LEFT_STRAND_INV = CONTEXT.createPattern(left_img_inv, "repeat"); -}; + CACHED_DATA = 5; function round_1000(num) { return Math.round(num * 1000) / 1000; @@ -206,7 +150,7 @@ this.num_elements = num_elements; this.clear(); }; -$.extend(Cache.prototype, { +extend(Cache.prototype, { get: function(key) { var index = this.key_ary.indexOf(key); if (index !== -1) { @@ -250,15 +194,25 @@ this.track = track; this.subset = (subset !== undefined ? subset : true); }; -$.extend(DataManager.prototype, Cache.prototype, { +extend(DataManager.prototype, Cache.prototype, { /** * Load data from server; returns AJAX object so that use of Deferred is possible. */ load_data: function(chrom, low, high, mode, resolution, extra_params) { + // Setup data request params. var params = {"chrom": chrom, "low": low, "high": high, "mode": mode, "resolution": resolution, "dataset_id" : this.track.dataset_id, "hda_ldda": this.track.hda_ldda}; $.extend(params, extra_params); + + // Add track filters to params. + var filter_names = []; + for (var i = 0; i < this.track.filters.length; i++) { + filter_names[filter_names.length] = this.track.filters[i].name; + } + params.filter_cols = JSON.stringify(filter_names); + + // Do request. var manager = this; return $.getJSON(this.track.data_url, params, function (result) { manager.set_data(low, high, mode, result); @@ -291,6 +245,8 @@ // the data was "index" or "data." Also could slice the data so that // only data points in request are returned. // + + /* Disabling for now, more detailed data is never loaded for line tracks if (this.subset) { var key, split_key, entry_low, entry_high, mode, entry; for (var i = 0; i < this.key_ary.length; i++) { @@ -310,11 +266,13 @@ } } } + */ - // - // Load data from server. - // - return this.load_data(chrom, low, high, mode, resolution, extra_params); + // Load data from server. The deferred is immediately saved until the + // data is ready, it then replaces itself with the actual data + entry = this.load_data(chrom, low, high, mode, resolution, extra_params); + this.set_data( low, high, mode, entry ); + return entry }, set_data: function(low, high, mode, result) { //console.log("set_data", low, high, mode, result); @@ -354,9 +312,10 @@ this.min_separation = 30; this.has_changes = false; this.init( callback ); + this.canvas_manager = new CanvasManager( container.get(0).ownerDocument ); this.reset(); }; -$.extend( View.prototype, { +extend( View.prototype, { init: function( callback ) { // Create DOM elements var parent_element = this.container, @@ -797,63 +756,175 @@ }); /** - * Encapsulation of tools that users can apply to tracks/datasets. + * Encapsulation of a tool that users can apply to tracks/datasets. */ -var Tool = function(name, params) { - this.name = name; - this.params = params; +var Tool = function(track, tool_dict) { + // + // Unpack tool information from dictionary. + // + this.track = track; + this.name = tool_dict.name; + this.params = []; + var params_dict = tool_dict.params; + for (var i = 0; i < params_dict.length; i++) { + var param_dict = params_dict[i], + name = param_dict.name, + label = param_dict.label, + html = unescape(param_dict.html), + type = param_dict.type; + if (type === "number") { + this.params[this.params.length] = + new NumberParameter(name, label, html, param_dict.min, param_dict.max); + } + else if (type == "select") { + this.params[this.params.length] = new ToolParameter(name, label, html); + } + else { + console.log("WARNING: unrecognized tool parameter type:", name, type); + } + } + + // + // Create div elt for tool UI. + // + this.parent_div = $("<div/>").addClass("dynamic-tool").hide(); + // Disable dragging, clicking, double clicking on div so that actions on slider do not impact viz. + this.parent_div.bind("drag", function(e) { + e.stopPropagation(); + }).bind("click", function(e) { + e.stopPropagation(); + }).bind("dblclick", function(e) { + e.stopPropagation(); + }); + var name_div = $("<div class='tool-name'>").appendTo(this.parent_div).text(this.name); + var tool_params = this.params; + var tool = this; + $.each(this.params, function(index, param) { + var param_div = $("<div>").addClass("param-row").appendTo(tool.parent_div); + // Param label. + var label_div = $("<div>").addClass("param-label").text(param.label).appendTo(param_div); + // Param HTML. + // TODO: either generalize .slider CSS attributes or create new rule for tool input div. + var html_div = $("<div/>").addClass("slider").html(param.html).appendTo(param_div); + + // Add to clear floating layout. + $("<div style='clear: both;'/>").appendTo(param_div); + }); + + // Highlight value for inputs for easy replacement. + this.parent_div.find("input").click(function() { $(this).select() }); + + // Add 'Go' button. + var run_tool_row = $("<div>").addClass("slider-row").appendTo(this.parent_div); + var run_tool_button = $("<input type='submit'>").attr("value", "Run").appendTo(run_tool_row); + var tool = this; + run_tool_button.click( function() { + tool.run(); + }); }; -$.extend(Tool.prototype, { - // Returns a dictionary of parameter values; key is parameter name, value - // is parameter value. +extend(Tool.prototype, { + /** + * Returns dictionary of parameter name-values. + */ get_param_values_dict: function() { var param_dict = {}; - for (var i = 0; i < this.params.length; i++) { - var param = this.params[i]; - param_dict[param.name] = param.value; - } + this.parent_div.find(":input").each(function() { + var name = $(this).attr("name"), value = $(this).val(); + param_dict[name] = JSON.stringify(value); + }); return param_dict; }, - // Returns an array of parameter values. + /** + * Returns array of parameter values. + */ get_param_values: function() { var param_values = []; - for (var i = 0; i < this.params.length; i++) { - param_values[i] = this.params[i].value; + var param_dict = {}; + this.parent_div.find(":input").each(function() { + // Only include inputs with names; this excludes Run button. + var name = $(this).attr("name"), value = $(this).val(); + if (name) { + param_values[param_values.length] = value; + } + }); + return param_values; + }, + /** + * Run tool. This creates a new child track, runs tool, and places tool's output in the new track. + */ + run: function() { + // Put together params for running tool. + var url_params = { + 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 + }; + $.extend(url_params, this.get_param_values_dict()); + + // + // Create track for tool's output immediately to provide user feedback. + // + var + current_track = this.track, + // Set name of track to include tool name, parameters, and region used. + track_name = url_params.tool_id + + current_track.tool_region_and_parameters_str(url_params.chrom, url_params.low, url_params.high), + new_track; + + // TODO: add support for other kinds of tool data tracks. + if (current_track.track_type === 'FeatureTrack') { + new_track = new ToolDataFeatureTrack(track_name, view, current_track.hda_ldda, undefined, {}, {}, current_track); } - return param_values; + + this.track.add_track(new_track); + new_track.content_div.text("Starting job."); + + // Run tool. + var json_run_tool = function() { + $.getJSON(run_tool_url, url_params, function(track_data) { + if (track_data === "no converter") { + // No converter available for input datasets, so cannot run tool. + new_track.container_div.addClass("error"); + new_track.content_div.text(DATA_NOCONVERTER); + } + else if (track_data.error) { + // General error. + new_track.container_div.addClass("error"); + new_track.content_div.text(DATA_CANNOT_RUN_TOOL + track_data.message); + } + else if (track_data === "pending") { + // Converting/indexing input datasets; show message and try again. + new_track.container_div.addClass("pending"); + new_track.content_div.text("Converting input data so that it can be easily reused."); + setTimeout(json_run_tool, 2000); + } + else { + // Job submitted and running. + new_track.dataset_id = track_data.dataset_id; + new_track.content_div.text("Running job."); + new_track.init(); + } + }); + }; + json_run_tool(); } }); -var NumberToolParameter = function(name, label, min, max, init_value) { +/** + * Tool parameters. + */ +var ToolParameter = function(name, label, html) { this.name = name; this.label = label; + this.html = html; +}; + +var NumberParameter = function(name, label, html, min, max) { + ToolParameter.call(this, name, label, html) this.min = min; this.max = max; - this.value = init_value; -} - -// Uses a dictionary to construct a tool object. -var get_tool_from_dict = function(tool_dict) { - if (obj_length(tool_dict) === 0) { - return undefined; - } - - // Get tool. - var tool_name = tool_dict.name; - var params_dict = tool_dict.params; - var params = Array(); - for (var i = 0; i < params_dict.length; i++) { - var param_dict = params_dict[i]; - var - name = param_dict.name, - label = param_dict.label, - type = param_dict.type, - min = param_dict.min, - max = param_dict.max, - value = param_dict.value; - params[params.length] = new NumberToolParameter(name, label, min, max, value); - } - return new Tool(tool_name, params); }; /** @@ -864,6 +935,9 @@ this.index = index; this.value = value; }; +/** + * Number filters have a min, max as well as a low, high; low and high are used + */ var NumberFilter = function(name, index) { this.name = name; // Index into payload to filter. @@ -872,21 +946,25 @@ this.low = -Number.MAX_VALUE; this.high = Number.MAX_VALUE; // Slide min/max. These values are used to set/update slider. - this.slider_min = Number.MAX_VALUE; - this.slider_max = -Number.MAX_VALUE; + this.min = Number.MAX_VALUE; + this.max = -Number.MAX_VALUE; // UI Slider element and label that is associated with filter. this.slider = null; this.slider_label = null; }; -$.extend(NumberFilter.prototype, { - // Returns true if filter can be applied to element. +extend(NumberFilter.prototype, { + /** + * Returns true if filter can be applied to element. + */ applies_to: function(element) { if (element.length > this.index) { return true; } return false; }, - // Returns true iff element is in [low, high]; range is inclusive. + /** + * Returns true iff element is in [low, high]; range is inclusive. + */ keep: function(element) { if ( !this.applies_to( element ) ) { // No element to filter on. @@ -894,7 +972,9 @@ } return (element[this.index] >= this.low && element[this.index] <= this.high); }, - // Update filter's min and max values based on element's values. + /** + * Update filter's min and max values based on element's values. + */ update_attrs: function(element) { var updated = false; if (!this.applies_to(element) ) { @@ -902,29 +982,32 @@ } // Update filter's min, max based on element values. - if (element[this.index] < this.slider_min) { - this.slider_min = element[this.index]; + if (element[this.index] < this.min) { + this.min = Math.floor(element[this.index]); updated = true; } - if (element[this.index] > this.slider_max) { - this.slider_max = element[this.index]; - updated = false; + if (element[this.index] > this.max) { + this.max = Math.ceil(element[this.index]); + updated = true; } return updated; }, - // Update filter's slider. + /** + * Update filter's slider. + */ update_ui_elt: function () { var slider_min = this.slider.slider("option", "min"), slider_max = this.slider.slider("option", "max"); - if (this.slider_min < slider_min || this.slider_max > slider_max) { - // Need to update slider. - this.slider.slider("option", "min", this.slider_min); - this.slider.slider("option", "max", this.slider_max); + if (this.min < slider_min || this.max > slider_max) { + // Update slider min, max, step. + this.slider.slider("option", "min", this.min); + this.slider.slider("option", "max", this.max); + this.slider.slider("option", "step", get_slider_step(this.min, this.max)); // Refresh slider: // TODO: do we want to keep current values or reset to min/max? // Currently we reset values: - this.slider.slider("option", "values", [this.slider_min, this.slider_max]); + this.slider.slider("option", "values", [this.min, this.max]); // To use the current values. //var values = this.slider.slider( "option", "values" ); //this.slider.slider( "option", "values", values ); @@ -932,7 +1015,9 @@ } }); -// Parse filters dict and return filters. +/** + * Parse filters dict and return filters. + */ var get_filters_from_dict = function(filters_dict) { var filters = []; for (var i = 0; i < filters_dict.length; i++) { @@ -947,6 +1032,9 @@ return filters; }; +/** + * Container for track configuration data. + */ var TrackConfig = function( options ) { this.track = options.track; this.params = options.params; @@ -956,7 +1044,7 @@ } this.onchange = options.onchange } -$.extend( TrackConfig.prototype, { +extend( TrackConfig.prototype, { restore_values: function( values ) { var track_config = this; $.each( this.params, function( index, param ) { @@ -1036,6 +1124,15 @@ }); /** + * Tiles for TiledTracks. + */ +var Tile = function(track, canvas, histo_max) { + this.track = track; + this.canvas = canvas; + this.histo_max = histo_max; +}; + +/** * Tracks are objects can be added to the View. * * Track object hierarchy: @@ -1078,7 +1175,7 @@ this.content_div = $("<div class='track-content'>").appendTo(this.container_div); this.parent_element.append(this.container_div); }; -$.extend( Track.prototype, { +extend(Track.prototype, { /** * Initialize and draw the track. */ @@ -1159,7 +1256,7 @@ } }); -var TiledTrack = function(filters, tool, parent_track) { +var TiledTrack = function(filters, tool_dict, parent_track) { var track = this, view = track.view; @@ -1168,7 +1265,7 @@ // filters_available is determined by data, filters_visible is set by user. this.filters_available = false; this.filters_visible = false; - this.tool = (tool !== undefined ? get_tool_from_dict( tool ) : undefined); + this.tool = (tool_dict !== undefined && obj_length(tool_dict) > 0 ? new Tool(this, tool_dict) : undefined); // // TODO: Right now there is only the notion of a parent track and multiple child tracks. However, @@ -1185,6 +1282,66 @@ // Init HTML elements for tool, filters. // + // Function that supports inline text editing of slider values for tools, filters. + // Enable users to edit parameter's value via a text box. + var edit_slider_values = function(container, span, slider) { + container.click(function() { + var cur_value = span.text(); + max = parseFloat(slider.slider("option", "max")), + input_size = (max <= 1 ? 4 : max <= 1000000 ? max.toString().length : 6), + multi_value = false; + // Increase input size if there are two values. + if (slider.slider("option", "values")) { + input_size = 2*input_size + 1; + multi_value = true; + } + span.text(""); + // Temporary input for changing value. + $("<input type='text'/>").attr("size", input_size).attr("maxlength", input_size) + .attr("value", cur_value).appendTo(span).focus().select() + .click(function(e) { + // Don't want click to propogate up to values_span and restart everything. + e.stopPropagation(); + }).blur(function() { + $(this).remove(); + span.text(cur_value); + }).keyup(function(e) { + if (e.keyCode === 27) { + // Escape key. + $(this).trigger("blur"); + } else if (e.keyCode === 13) { + // + // Enter/return key initiates callback. If new value(s) are in slider range, + // change value (which calls slider's change() function). + // + var slider_min = slider.slider("option", "min"), + slider_max = slider.slider("option", "max"), + invalid = function(a_val) { + return (isNaN(a_val) || a_val > slider_max || a_val < slider_min); + }, + new_value = $(this).val(); + if (!multi_value) { + new_value = parseFloat(new_value); + if (invalid(new_value)) { + alert("Parameter value must be in the range [" + slider_min + "-" + slider_max + "]"); + return $(this); + } + } + else { // Multi value. + new_value = new_value.split("-"); + new_value = [parseFloat(new_value[0]), parseFloat(new_value[1])]; + if (invalid(new_value[0]) || invalid(new_value[1])) { + alert("Parameter value must be in the range [" + slider_min + "-" + slider_max + "]"); + return $(this); + } + } + slider.slider((multi_value ? "values" : "value"), new_value); + } + }); + }); + }; + + // If track has parent: // -replace drag handle with child-track icon button; (TODO: eventually, we'll want to be able // to make a set of child tracks dragable.) @@ -1201,6 +1358,8 @@ // Disable dragging, double clicking on div so that actions on slider do not impact viz. this.filters_div.bind("drag", function(e) { e.stopPropagation(); + }).bind("click", function(e) { + e.stopPropagation(); }).bind("dblclick", function(e) { e.stopPropagation(); }); @@ -1209,36 +1368,49 @@ // Set up filter label (name, values). var filter_label = $("<div/>").addClass("slider-label").appendTo(filter_div) - var name_span = $("<span/>").addClass("name").appendTo(filter_label); - name_span.text(filter.name + " "); // Extra spacing to separate name and values - var values_span = $("<span/>").addClass("values").appendTo(filter_label); + var name_span = $("<span/>").addClass("slider-name").text(filter.name + " ").appendTo(filter_label); + var values_span = $("<span/>"); + var values_span_container = $("<span/>").addClass("slider-value").appendTo(filter_label).append("[").append(values_span).append("]"); // Set up slider for filter. - // TODO: generate custom interaction elements based on filter type. var slider_div = $("<div/>").addClass("slider").appendTo(filter_div); filter.control_element = $("<div/>").attr("id", filter.name + "-filter-control").appendTo(slider_div); + var prev_values = [0,0]; filter.control_element.slider({ range: true, min: Number.MAX_VALUE, max: -Number.MIN_VALUE, values: [0, 0], slide: function(event, ui) { - var values = ui.values; - // Set new values in UI. - values_span.text("[" + values[0] + "-" + values[1] + "]"); - // Set new values in filter. - filter.low = values[0]; - filter.high = values[1]; - // Redraw track. - track.draw(true, true); + // + // Always update UI values, but set timeout for doing more--especially drawing-- + // so that viz is more responsive. + // + prev_values = ui.values; + values_span.text(ui.values[0] + "-" + ui.values[1]); + setTimeout(function() { + if (ui.values[0] == prev_values[0] && ui.values[1] == prev_values[1]) { + var values = ui.values; + // Set new values in UI. + values_span.text(values[0] + "-" + values[1]); + // Set new values in filter. + filter.low = values[0]; + filter.high = values[1]; + // Redraw track. + track.draw(true, true); + } + }, 50); }, - change: function( event, ui ) { - filter.control_element.slider("option", "slide").call( filter.control_element, event, ui ); + change: function(event, ui) { + filter.control_element.slider("option", "slide").call(filter.control_element, event, ui); } }); filter.slider = filter.control_element; filter.slider_label = values_span; + // Enable users to edit slider values via text box. + edit_slider_values(values_span_container, values_span, filter.control_element); + // Add to clear floating layout. $("<div style='clear: both;'/>").appendTo(filter_div); }); @@ -1247,102 +1419,8 @@ // Create dynamic tool div. // if (this.tool) { - // Create div elt for tool UI. - this.dynamic_tool_div = $("<div/>").addClass("dynamic-tool").hide(); + this.dynamic_tool_div = this.tool.parent_div; this.header_div.after(this.dynamic_tool_div); - // Disable dragging, clicking, double clicking on div so that actions on slider do not impact viz. - this.dynamic_tool_div.bind( "drag", function(e) { - e.stopPropagation(); - }).bind("click", function( e ) { - e.stopPropagation(); - }).bind("dblclick", function( e ) { - e.stopPropagation(); - }); - var name_div = $("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name); - var tool_params = this.tool.params; - var track = this; - $.each(this.tool.params, function(index, param) { - var param_div = $("<div>").addClass("slider-row").appendTo(track.dynamic_tool_div); - - // Slider label. - var label_div = $("<div>").addClass("slider-label").appendTo(param_div); - var name_span = $("<span class='param-name'>").text(param.label + " ").appendTo(label_div); - var values_span = $("<span/>").text(param.value); - var values_span_container = $("<span class='param-value'>").appendTo(label_div).append("[").append(values_span).append("]"); - - // Slider. - var slider_div = $("<div/>").addClass("slider").appendTo(param_div); - var slider = $("<div id='" + param.name + "-param-control'>").appendTo(slider_div); - // Make step reasonable. - var step = (param.max <= 1 ? 0.01 : (param.max <= 1000 ? 1 : 5)); - slider.slider({ - min: param.min, - max: param.max, - step: step, - value: param.value, - slide: function(event, ui) { - var value = ui.value; - param.value = value; - // Set new value in UI. - if (0 < value && value < 1) { - value = parseFloat(value).toFixed(2); - } - values_span.text(value); - }, - change: function(event, ui) { - param.value = ui.value; - } - }); - - // Enable users to edit parameter's value via a text box. - values_span_container.click(function() { - var span = values_span, - cur_value = span.text(), - // TODO: is there a better way to handle input size when param max is <= 1? - input_size = (param.max <= 1 ? 4 : param.max.length); - span.text(""); - // Temporary input for changing value. - $("<input type='text'/>").attr("size", input_size).attr("maxlength", input_size) - .attr("value", cur_value).appendTo(span).focus().select() - .click(function(e) { - // Don't want click to propogate up to values_span and restart everything. - e.stopPropagation(); - }).blur(function() { - $(this).remove(); - span.text(cur_value); - }).keyup(function(e) { - if ( e.keyCode === 27 ) { - // Escape key. - $(this).trigger("blur"); - } else if ( e.keyCode === 13 ) { - // Enter/return key sets new value. - var input = $(this), - new_value = parseFloat(input.val()); - if (isNaN(new_value) || new_value > param.max || new_value < param.min) { - // TODO: display popup menu instead of alert? - alert("Parameter value must be in the range [" + param.min + "-" + param.max + "]"); - return $(this); - } - // Update value in three places; update param value last b/c slider updates param value - // as well and slider may round values depending on its settings. - span.text(new_value); - slider.slider('value', new_value); - param.value = new_value; - } - }); - }); - - // Add to clear floating layout. - $("<div style='clear: both;'/>").appendTo(param_div); - }); - - // Add 'Go' button. - var run_tool_row = $("<div>").addClass("slider-row").appendTo(this.dynamic_tool_div); - var run_tool_button = $("<input type='submit'>").attr("value", "Run").appendTo(run_tool_row); - var track = this; - run_tool_button.click( function() { - track.run_tool(); - }); } // @@ -1403,7 +1481,7 @@ } */ }; -$.extend( TiledTrack.prototype, Track.prototype, { +extend(TiledTrack.prototype, Track.prototype, { /** * Make popup menu for track name. */ @@ -1467,7 +1545,7 @@ // if (track.tool) { // Show/hide dynamic tool menu item. - var text = (track.dynamic_tool_div.is(":visible") ? "Hide Tool" : "Show Tool"); + var text = (track.dynamic_tool_div.is(":visible") ? "Hide tool" : "Show tool"); track_dropdown[text] = function() { // Set track name, toggle tool div, and remake menu. if (!track.dynamic_tool_div.is(":visible")) { @@ -1521,10 +1599,10 @@ high = this.view.high, range = high - low, width = this.view.container.width(), - resolution = this.view.resolution; - - var parent_element = $("<div style='position: relative;'></div>"), - w_scale = width / range; + // w_scale units are pixels per base. + w_scale = width / range, + resolution = this.view.resolution, + parent_element = $("<div style='position: relative;'></div>"); if (!clear_after) { this.content_div.children().remove(); } this.content_div.append( parent_element ); @@ -1551,15 +1629,17 @@ } // - // Actions to take after tiles have been drawn: - // (1) remove old tile(s); - // (2) update filtering UI elements. + // Post-draw actions: // - if (clear_after) { - var track = this; - var intervalId = setInterval(function() { - if (obj_length(draw_tile_dict) === 0) { - // All tiles have been drawn; clear out track content in order to show the most recent content. + var track = this; + var intervalId = setInterval(function() { + if (obj_length(draw_tile_dict) === 0) { + // All tiles have been drawn. + clearInterval(intervalId); + + // Clear tiles? + if (clear_after) { + // Clear out track content in order to show the most recent content. // Most recent content is the div with children (tiles) most recently appended to track. // However, do not delete recently-appended empty content as calls to draw() may still be active // and using these divs. @@ -1575,12 +1655,38 @@ remove = true; } } + } + + // + // Update filter attributes, UI. + // - // Method complete; do not call it again. - clearInterval(intervalId); + // Update filtering UI. + for (var f = 0; f < track.filters.length; f++) { + track.filters[f].update_ui_elt(); } - }, 50); - } + + // Determine if filters are available; this is based on the example feature. + var filters_available = false; + if (track.example_feature) { + for (var f = 0; f < track.filters.length; f++) { + if (track.filters[f].applies_to(track.example_feature)) { + filters_available = true; + break; + } + } + } + + // If filter availability changed, hide filter div if necessary and update menu. + if (track.filters_available !== filters_available) { + track.filters_available = filters_available; + if (!track.filters_available) { + track.filters_div.hide(); + } + track.make_name_popup_menu(); + } + } + }, 50); // // Draw child tracks. @@ -1593,6 +1699,8 @@ var track = this; // Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data var draw_and_show_tile = function(id, result, resolution, tile_index, parent_element, w_scale, seq_data) { + // DEBUG: this is still called too many times when moving slowly, + // console.log( "draw_and_show_tile", resolution, tile_index, w_scale ); returned_tile = track.draw_tile(result, resolution, tile_index, parent_element, w_scale, seq_data) // Wrap element in div for background @@ -1631,23 +1739,17 @@ // Really draw tile: get data, seq data if available, and draw tile. // $.when(track.data_cache.get_data(view.chrom, tile_low, tile_high, track.mode, - resolution, track.data_url_extra_params)).then(function() { - // Data available for track. - var result = track.data_cache.get_data(view.chrom, tile_low, tile_high, track.mode, - resolution, track.data_url_extra_params); + resolution, track.data_url_extra_params)).then(function(tile_data) { // If sequence data needed, get that and draw. Otherwise draw. - if (view.reference_track && w_scale > CHAR_WIDTH_PX) { + if (view.reference_track && w_scale > view.canvas_manager.char_width_px) { $.when(view.reference_track.data_cache.get_data(view.chrom, tile_low, tile_high, track.mode, resolution, - view.reference_track.data_url_extra_params)).then(function() { - var seq_data = view.reference_track.data_cache.get_data(view.chrom, tile_low, tile_high, - track.mode, resolution, - view.reference_track.data_url_extra_params); - draw_and_show_tile(id, result, resolution, tile_index, parent_element, w_scale, seq_data); + view.reference_track.data_url_extra_params)).then(function(seq_data) { + draw_and_show_tile(id, tile_data, resolution, tile_index, parent_element, w_scale, seq_data); }); } else { - draw_and_show_tile(id, result, resolution, tile_index, parent_element, w_scale); + draw_and_show_tile(id, tile_data, resolution, tile_index, parent_element, w_scale); } }); } @@ -1678,40 +1780,7 @@ parent_element.append(tile_element); track.max_height = Math.max(track.max_height, tile_element.height()); track.content_div.css("height", track.max_height + "px"); - parent_element.children().css("height", track.max_height + "px"); - - if (track.hidden) { return; } - - // - // Update filter attributes, UI. - // TODO: this could be done after all tiles are drawn, but there's no reliable way to detect - // that right now. - // - - // Update filtering UI. - for (var f = 0; f < track.filters.length; f++) { - track.filters[f].update_ui_elt(); - } - - // Determine if filters are available; this is based on the example feature. - var filters_available = false; - if (track.example_feature) { - for (var f = 0; f < track.filters.length; f++) { - if (track.filters[f].applies_to(track.example_feature)) { - filters_available = true; - break; - } - } - } - - // If filter availability changed, hide filter div if necessary and update menu. - if (track.filters_available !== filters_available) { - track.filters_available = filters_available; - if (!track.filters_available) { - track.filters_div.hide(); - } - track.make_name_popup_menu(); - } + parent_element.children().css("height", track.max_height + "px"); }, // Set track as the overview track in the visualization. set_overview: function() { @@ -1725,66 +1794,6 @@ } $(window).trigger("resize"); }, - // Run track's tool. - run_tool: function() { - // Put together params for running tool. - var url_params = { - dataset_id: this.original_dataset_id, - chrom: this.view.chrom, - low: this.view.low, - high: this.view.high, - tool_id: this.tool.name - }; - $.extend(url_params, this.tool.get_param_values_dict()); - - // - // Create track for tool's output immediately to provide user feedback. - // - var - current_track = this, - // Set name of track to include tool name, parameters, and region used. - track_name = url_params.tool_id + - current_track.tool_region_and_parameters_str(url_params.chrom, url_params.low, url_params.high), - new_track; - - // TODO: add support for other kinds of tool data tracks. - if (current_track.track_type === 'FeatureTrack') { - new_track = new ToolDataFeatureTrack(track_name, view, current_track.hda_ldda, undefined, {}, {}, current_track); - } - - this.add_track(new_track); - new_track.content_div.text("Starting job."); - view.has_changes = true; - - // Run tool. - var json_run_tool = function() { - $.getJSON(run_tool_url, url_params, function(track_data) { - if (track_data === "no converter") { - // No converter available for input datasets, so cannot run tool. - new_track.container_div.addClass("error"); - new_track.content_div.text(DATA_NOCONVERTER); - } - else if (track_data.error) { - // General error. - new_track.container_div.addClass("error"); - new_track.content_div.text(DATA_CANNOT_RUN_TOOL + track_data.message); - } - else if (track_data === "pending") { - // Converting/indexing input datasets; show message and try again. - new_track.container_div.addClass("pending"); - new_track.content_div.text("Converting input data so that it can be easily reused."); - setTimeout(json_run_tool, 2000); - } - else { - // Job submitted and running. - new_track.dataset_id = track_data.dataset_id; - new_track.content_div.text("Running job."); - new_track.init(); - } - }); - }; - json_run_tool(); - }, /** * Utility function that creates a label string describing the region and parameters of a track's tool. */ @@ -1808,6 +1817,7 @@ this.child_tracks_container.show(); } this.child_tracks.push(child_track); + this.view.has_changes = true; }, /** * Remove a child track from this track. @@ -1823,7 +1833,7 @@ Track.call( this, null, view, parent_element ); this.container_div.addClass( "label-track" ); }; -$.extend( LabelTrack.prototype, Track.prototype, { +extend( LabelTrack.prototype, Track.prototype, { draw: function() { var view = this.view, range = view.high - view.low, @@ -1854,7 +1864,6 @@ view.reference_track = this; this.left_offset = 200; this.height_px = 12; - this.font = DEFAULT_FONT; this.container_div.addClass( "reference-track" ); this.content_div.css("background", "none"); this.content_div.css("min-height", "0px"); @@ -1864,7 +1873,7 @@ this.data_cache = new DataManager(CACHED_DATA, this, false); this.tile_cache = new Cache(CACHED_TILES_LINE); }; -$.extend(ReferenceTrack.prototype, TiledTrack.prototype, { +extend(ReferenceTrack.prototype, TiledTrack.prototype, { /** * Draw ReferenceTrack tile. */ @@ -1872,19 +1881,16 @@ var track = this, tile_length = DENSITY * resolution; - if (w_scale > CHAR_WIDTH_PX) { + if (w_scale > this.view.canvas_manager.char_width_px) { if (seq === null) { track.content_div.css("height", "0px"); return; } - var canvas = document.createElement("canvas"); - if (window.G_vmlCanvasManager) { G_vmlCanvasManager.initElement(canvas); } // EXCANVAS HACK - canvas = $(canvas); - - var ctx = canvas.get(0).getContext("2d"); - canvas.get(0).width = Math.ceil( tile_length * w_scale + track.left_offset); - canvas.get(0).height = track.height_px; - ctx.font = DEFAULT_FONT; + var canvas = this.view.canvas_manager.new_canvas(); + var ctx = canvas.getContext("2d"); + canvas.width = Math.ceil( tile_length * w_scale + track.left_offset); + canvas.height = track.height_px; + ctx.font = ctx.canvas.manager.default_font; ctx.textAlign = "center"; for (var c = 0, str_len = seq.length; c < str_len; c++) { var c_start = Math.round(c * w_scale); @@ -1938,10 +1944,14 @@ this.height_px = this.track_config.values.height; this.vertical_range = this.track_config.values.max_value - this.track_config.values.min_value; - // Add control for resizing - // Trickery here to deal with the hovering drag handle, can probably be - // pulled out and reused. - (function( track ){ + this.add_resize_handle(); +}; +extend(LineTrack.prototype, TiledTrack.prototype, { + add_resize_handle: function () { + // Add control for resizing + // Trickery here to deal with the hovering drag handle, can probably be + // pulled out and reused. + var track = this; var in_handle = false; var in_drag = false; var drag_control = $( "<div class='track-resize'>" ) @@ -1969,9 +1979,7 @@ if ( ! in_handle ) { drag_control.hide(); } track.track_config.values.height = track.height_px; }).appendTo( track.container_div ); - })(this); -}; -$.extend(LineTrack.prototype, TiledTrack.prototype, { + }, predraw_init: function() { var track = this, track_id = track.view.tracks.indexOf(track); @@ -2012,98 +2020,22 @@ return; } - var track = this, - tile_low = tile_index * DENSITY * resolution, + var tile_low = tile_index * DENSITY * resolution, tile_length = DENSITY * resolution, - key = resolution + "_" + tile_index, - params = { hda_ldda: this.hda_ldda, dataset_id: this.dataset_id, resolution: this.view.resolution }; + width = Math.ceil( tile_length * w_scale ), + height = this.height_px; + // Create canvas + var canvas = this.view.canvas_manager.new_canvas(); + canvas.width = width, + canvas.height = height; - var canvas = document.createElement("canvas"), - data = result.data; - if (window.G_vmlCanvasManager) { G_vmlCanvasManager.initElement(canvas); } // EXCANVAS HACK - canvas = $(canvas); - - canvas.get(0).width = Math.ceil( tile_length * w_scale ); - canvas.get(0).height = track.height_px; - var ctx = canvas.get(0).getContext("2d"), - in_path = false, - min_value = track.prefs.min_value, - max_value = track.prefs.max_value, - vertical_range = track.vertical_range, - total_frequency = track.total_frequency, - height_px = track.height_px, - mode = track.mode; - - // Pixel position of 0 on the y axis - var y_zero = Math.round( height_px + min_value / vertical_range * height_px ); - - // Line at 0.0 - ctx.beginPath(); - ctx.moveTo( 0, y_zero ); - ctx.lineTo( tile_length * w_scale, y_zero ); - // ctx.lineWidth = 0.5; - ctx.fillStyle = "#aaa"; - ctx.stroke(); + // Paint line onto full canvas + var ctx = canvas.getContext("2d"); + var painter = new painters.LinePainter( result.data, tile_low, tile_low + tile_length, + this.prefs.min_value, this.prefs.max_value, this.prefs.color, this.mode ); + painter.draw( ctx, width, height ); - ctx.beginPath(); - ctx.fillStyle = track.prefs.color; - var x_scaled, y, delta_x_px; - if (data.length > 1) { - delta_x_px = Math.ceil((data[1][0] - data[0][0]) * w_scale); - } else { - delta_x_px = 10; - } - for (var i = 0, len = data.length; i < len; i++) { - x_scaled = Math.round((data[i][0] - tile_low) * w_scale); - y = data[i][1]; - if (y === null) { - if (in_path && mode === "Filled") { - ctx.lineTo(x_scaled, height_px); - } - in_path = false; - continue; - } - if (y < min_value) { - y = min_value; - } else if (y > max_value) { - y = max_value; - } - - if (mode === "Histogram") { - // y becomes the bar height in pixels, which is the negated for canvas coords - y = Math.round( y / vertical_range * height_px ); - ctx.fillRect(x_scaled, y_zero, delta_x_px, - y ); - } else if (mode === "Intensity" ) { - y = 255 - Math.floor( (y - min_value) / vertical_range * 255 ); - ctx.fillStyle = "rgb(" +y+ "," +y+ "," +y+ ")"; - ctx.fillRect(x_scaled, 0, delta_x_px, height_px); - } else { - // console.log(y, track.min_value, track.vertical_range, (y - track.min_value) / track.vertical_range * track.height_px); - y = Math.round( height_px - (y - min_value) / vertical_range * height_px ); - // console.log(canvas.get(0).height, canvas.get(0).width); - if (in_path) { - ctx.lineTo(x_scaled, y); - } else { - in_path = true; - if (mode === "Filled") { - ctx.moveTo(x_scaled, height_px); - ctx.lineTo(x_scaled, y); - } else { - ctx.moveTo(x_scaled, y); - } - } - } - } - if (mode === "Filled") { - if (in_path) { - ctx.lineTo( x_scaled, y_zero ); - ctx.lineTo( 0, y_zero ); - } - ctx.fill(); - } else { - ctx.stroke(); - } return canvas; } }); @@ -2148,14 +2080,25 @@ this.show_labels_scale = 0.001; this.showing_details = false; this.summary_draw_height = 30; - this.default_font = DEFAULT_FONT; this.inc_slots = {}; this.start_end_dct = {}; this.tile_cache = new Cache(CACHED_TILES_FEATURE); this.data_cache = new DataManager(20, this); this.left_offset = 200; + + this.painter = painters.LinkedFeaturePainter; }; -$.extend(FeatureTrack.prototype, TiledTrack.prototype, { +extend(FeatureTrack.prototype, TiledTrack.prototype, { + update_auto_mode: function( mode ) { + if ( this.mode == "Auto" ) { + if ( mode == "no_detail" ) { + mode = "reduced to feature spans"; + } else if ( mode == "summary_tree" ) { + mode = "reduced to coverage histogram"; + } + this.mode_div.text( "Auto (" + mode + ")" ); + } + }, /** * Place features in slots for drawing (i.e. pack features). * this.inc_slots[level] is created in this method. this.inc_slots[level] @@ -2164,27 +2107,292 @@ * Returns the number of slots used to pack features. */ incremental_slots: function(level, features, mode) { - // + // Get/create incremental slots for level. If display mode changed, // need to create new slots. - // - var inc_slots = this.inc_slots[level]; + + var dummy_context = this.view.canvas_manager.dummy_context, + inc_slots = this.inc_slots[level]; if (!inc_slots || (inc_slots.mode !== mode)) { - inc_slots = {}; - inc_slots.w_scale = level; + inc_slots = new (slotting.FeatureSlotter)( level, mode === "Pack", MAX_FEATURE_DEPTH, function ( x ) { return dummy_context.measureText( x ) } ); inc_slots.mode = mode; this.inc_slots[level] = inc_slots; - this.start_end_dct[level] = {}; + } + + return inc_slots.slot_features( features ); + }, + /** + * Draw FeatureTrack tile. + */ + draw_tile: function(result, resolution, tile_index, parent_element, w_scale, ref_seq) { + var track = this, + tile_low = tile_index * DENSITY * resolution, + tile_high = ( tile_index + 1 ) * DENSITY * resolution, + tile_span = tile_high - tile_low, + width = Math.ceil( tile_span * w_scale ), + mode = this.mode, + min_height = 25, + left_offset = this.left_offset, + slots, + required_height; + + // Set display mode if Auto. + if (mode === "Auto") { + if (result.dataset_type === "summary_tree") { + mode = result.dataset_type; + } else if (result.extra_info === "no_detail") { + mode = "no_detail"; + } else { + // Choose b/t Squish and Pack. + // Proxy measures for using Squish: + // (a) error message re: limiting number of features shown; + // (b) X number of features shown; + // (c) size of view shown. + // TODO: cannot use (a) and (b) because it requires coordinating mode across tiles; + // fix this so that tiles are redrawn as necessary to use the same mode. + //if ( (result.message && result.message.match(/^Only the first [\d]+/)) || + // (result.data && result.data.length > 2000) || + var data = result.data; + if ( (data.length && data.length < 4) || + (this.view.high - this.view.low > MIN_SQUISH_VIEW_WIDTH) ) { + mode = "Squish"; + } else { + mode = "Pack"; + } + } + this.update_auto_mode( mode ); } - // + // Drawing the summary tree (feature coverage histogram) + if ( mode === "summary_tree" ) { + // Set height of parent_element + required_height = this.summary_draw_height; + parent_element.parent().css("height", Math.max(this.height_px, required_height) + "px"); + // Add label to container div showing maximum count + // TODO: this shouldn't be done at the tile level + this.container_div.find(".yaxislabel").remove(); + var max_label = $("<div />").addClass('yaxislabel'); + max_label.text( result.max ); + max_label.css({ position: "absolute", top: "22px", left: "10px" }); + max_label.prependTo(this.container_div); + // Create canvas + var canvas = this.view.canvas_manager.new_canvas(); + canvas.width = width + left_offset; + // Extra padding at top of summary tree + canvas.height = required_height + SUMMARY_TREE_TOP_PADDING; + // Paint summary tree into canvas + var painter = new painters.SummaryTreePainter( result.data, result.delta, result.max, tile_low, tile_high, this.prefs.show_counts ); + var ctx = canvas.getContext("2d"); + // Deal with left_offset by translating + ctx.translate( left_offset, SUMMARY_TREE_TOP_PADDING ); + painter.draw( ctx, width, required_height ); + // Canvas element is returned + return canvas; + } + + // Start dealing with row-by-row tracks + + // If working with a mode where slotting is neccesary, update the incremental slotting + var slots, slots_required = 1; + if ( mode === "no_detail" || mode === "Squish" || mode === "Pack" ) { + slots_required = this.incremental_slots(w_scale, result.data, mode); + slots = this.inc_slots[w_scale].slots; + } + + // Filter features + var filtered = []; + if ( result.data ) { + for (var i = 0, len = result.data.length; i < len; i++) { + var feature = result.data[i]; + var hide_feature = false; + var filter; + for (var f = 0, flen = this.filters.length; f < flen; f++) { + filter = this.filters[f]; + filter.update_attrs(feature); + if (!filter.keep(feature)) { + hide_feature = true; + break; + } + } + if (!hide_feature) { + filtered.push( feature ); + } + } + } + + // Create painter, and canvas of sufficient size to contain all features + // HACK: ref_seq will only be defined for ReadTracks, and only the ReadPainter accepts that argument + var painter = new (this.painter)( filtered, tile_low, tile_high, this.prefs, mode, ref_seq ); + // FIXME: ERROR_PADDING is an ugly gap most of the time + var required_height = painter.get_required_height( slots_required ) + ERROR_PADDING; + var canvas = this.view.canvas_manager.new_canvas(); + + canvas.width = width + left_offset; + canvas.height = required_height; + + parent_element.parent().css("height", Math.max(this.height_px, required_height) + "px"); + // console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale); + var ctx = canvas.getContext("2d"); + ctx.fillStyle = this.prefs.block_color; + ctx.font = ctx.canvas.manager.default_font; + ctx.textAlign = "right"; + this.container_div.find(".yaxislabel").remove(); + + // If there is a message, draw it on canvas so that it moves around with canvas, and make the border red + // to indicate region where message is applicable + if (result.message) { + $(canvas).css({ + "border-top": "1px solid red" + }); + + ctx.fillStyle = "red"; + ctx.textAlign = "left"; + var old_base = ctx.textBaseline; + ctx.textBaseline = "top"; + ctx.fillText(result.message, left_offset, 0); + ctx.textBaseline = old_base; + + // If there's no data, return. + if (!result.data) { + return canvas; + } + } + + // Set example feature. This is needed so that track can update its UI based on feature attributes. + this.example_feature = (result.data.length ? result.data[0] : undefined); + + // Draw features + ctx.translate( left_offset, ERROR_PADDING ); + painter.draw( ctx, width, required_height, slots ); + + return canvas; + } +}); + +var VcfTrack = function(name, view, hda_ldda, dataset_id, prefs, filters) { + FeatureTrack.call(this, name, view, hda_ldda, dataset_id, prefs, filters); + this.track_type = "VcfTrack"; + this.painter = painters.VariantPainter; +}; + +extend(VcfTrack.prototype, TiledTrack.prototype, FeatureTrack.prototype); + + +var ReadTrack = function (name, view, hda_ldda, dataset_id, prefs, filters) { + FeatureTrack.call(this, name, view, hda_ldda, dataset_id, prefs, filters); + + this.track_config = new TrackConfig( { + track: this, + params: [ + { key: 'block_color', label: 'Block color', type: 'color', default_value: '#444' }, + { 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: prefs, + onchange: function() { + this.track.tile_cache.clear(); + this.track.draw(); + } + }); + this.prefs = this.track_config.values; + + this.track_type = "ReadTrack"; + this.painter = painters.ReadPainter; + this.make_name_popup_menu(); +}; +extend(ReadTrack.prototype, TiledTrack.prototype, FeatureTrack.prototype); + +/** + * Feature track that displays data generated from tool. + */ +var ToolDataFeatureTrack = function(name, view, hda_ldda, dataset_id, prefs, filters, parent_track) { + FeatureTrack.call(this, name, view, hda_ldda, dataset_id, prefs, filters, {}, parent_track); + this.track_type = "ToolDataFeatureTrack"; + + // Set up track to fetch initial data from raw data URL when the dataset--not the converted datasets-- + // is ready. + this.data_url = raw_data_url; + this.data_query_wait = 1000; + this.dataset_check_url = dataset_state_url; +}; + +extend(ToolDataFeatureTrack.prototype, TiledTrack.prototype, FeatureTrack.prototype, { + /** + * For this track type, the predraw init sets up postdraw init. + */ + predraw_init: function() { + // Postdraw init: once data has been fetched, reset data url, wait time and start indexing. + var track = this; + var post_init = function() { + if (track.data_cache.size() === 0) { + // Track still drawing initial data, so do nothing. + setTimeout(post_init, 300); + } + else { + // Track drawing done: reset dataset check, data URL, wait time and get dataset state to start + // indexing. + track.data_url = default_data_url; + track.data_query_wait = DEFAULT_DATA_QUERY_WAIT; + track.dataset_state_url = converted_datasets_state_url; + $.getJSON(track.dataset_state_url, {dataset_id : track.dataset_id, hda_ldda: track.hda_ldda}, function(track_data) {}); + } + }; + post_init(); + } +}); + +// Exports + +exports.View = View; +exports.LineTrack = LineTrack; +exports.FeatureTrack = FeatureTrack; +exports.ReadTrack = ReadTrack; + +// End trackster_module encapsulation +}; + +// ---- To be extracted ------------------------------------------------------ + +// ---- Feature Packing ---- + +// Encapsulation +var slotting_module = function(require, exports) { + +// HACK: LABEL_SPACING is currently duplicated between here and painters +var LABEL_SPACING = 2, + PACK_SPACING = 5; + +/** + * FeatureSlotter determines slots in which to draw features for vertical + * packing. + * + * This implementation is incremental, any feature assigned a slot will be + * retained for slotting future features. + */ +exports.FeatureSlotter = function ( w_scale, include_label, max_rows, measureText ) { + this.slots = {}; + this.start_end_dct = {}; + this.w_scale = w_scale; + this.include_label = include_label; + this.max_rows = max_rows; + this.measureText = measureText; +} + +/** + * Slot a set of features, `this.slots` will be updated with slots by id, and + * the largest slot required for the passed set of features is returned + */ +extend( exports.FeatureSlotter.prototype, { + slot_features: function( features ) { + var w_scale = this.w_scale, inc_slots = this.slots, start_end_dct = this.start_end_dct, + undone = [], slotted = [], highest_slot = 0, max_rows = this.max_rows; + // If feature already exists in slots (from previously seen tiles), use the same slot, // otherwise if not seen, add to "undone" list for slot calculation. - // - var w_scale = inc_slots.w_scale, - undone = [], slotted = [], - highest_slot = 0, // To measure how big to draw canvas - max_low = this.view.max_low; + // TODO: Should calculate zoom tile index, which will improve performance // by only having to look at a smaller subset // if (this.start_end_dct[0] === undefined) { this.start_end_dct[0] = []; } @@ -2198,16 +2406,14 @@ undone.push(i); } } - - // + // Slot unslotted features. - // - var start_end_dct = this.start_end_dct[level]; // Find the first slot such that current feature doesn't overlap any other features in that slot. // Returns -1 if no slot was found. var find_slot = function(f_start, f_end) { - for (var slot_num = 0; slot_num <= MAX_FEATURE_DEPTH; slot_num++) { + // TODO: Fix constants + for (var slot_num = 0; slot_num <= max_rows; slot_num++) { var has_overlap = false, slot = start_end_dct[slot_num]; if (slot !== undefined) { @@ -2236,15 +2442,16 @@ feature_end = feature[2], feature_name = feature[3], // Where to start, end drawing on screen. - f_start = Math.floor( (feature_start - max_low) * w_scale ), - f_end = Math.ceil( (feature_end - max_low) * w_scale ), - text_len = CONTEXT.measureText(feature_name).width, + f_start = Math.floor( feature_start * w_scale ), + f_end = Math.ceil( feature_end * w_scale ), + text_len = this.measureText(feature_name).width, text_align; // Update start, end drawing locations to include feature name. // Try to put the name on the left, if not, put on right. - if (feature_name !== undefined && mode === "Pack") { + if (feature_name !== undefined && this.include_label ) { // Add gap for label spacing and extra pack space padding + // TODO: Fix constants text_len += (LABEL_SPACING + PACK_SPACING); if (f_start - text_len >= 0) { f_start -= text_len; @@ -2257,6 +2464,7 @@ // Find slot. var slot_num = find_slot(f_start, f_end); + /* if (slot_num < 0) { @@ -2275,7 +2483,7 @@ if (slot_num >= 0) { console.log(feature_uid, "found slot with text on the right"); } - + } */ // Do slotting. @@ -2308,188 +2516,325 @@ } */ return highest_slot + 1; - }, - /** - * Draw summary tree on canvas. - */ - draw_summary_tree: function(canvas, points, delta, max, w_scale, required_height, tile_low, left_offset) { - var - // Set base Y so that max label and data do not overlap. Base Y is where rectangle bases - // start. However, height of each rectangle is relative to required_height; hence, the - // max rectangle is required_height. - base_y = required_height + LABEL_SPACING + CHAR_HEIGHT_PX; - delta_x_px = Math.ceil(delta * w_scale); + } +}); + +// End slotting_module encapsulation +}; + +// ---- Painters ---- + +var painters_module = function(require, exports){ + +/** + * Draw a dashed line on a canvas using filled rectangles. This function is based on: + * http://vetruvet.blogspot.com/2010/10/drawing-dashed-lines-on-html5-canvas.h… + * However, that approach uses lines, which don't seem to render as well, so use + * rectangles instead. + */ +var dashedLine = function(ctx, x1, y1, x2, y2, dashLen) { + if (dashLen === undefined) { dashLen = 4; } + var dX = x2 - x1; + var dY = y2 - y1; + var dashes = Math.floor(Math.sqrt(dX * dX + dY * dY) / dashLen); + var dashX = dX / dashes; + var dashY = dY / dashes; + var q; + + for (q = 0; q < dashes; q++, x1 += dashX, y1 += dashY) { + if (q % 2 !== 0) { + continue; + } + ctx.fillRect(x1, y1, dashLen, 1); + } +}; + +/** + * Draw an isosceles triangle that points down. + */ +var drawDownwardEquilateralTriangle = function(ctx, down_vertex_x, down_vertex_y, side_len) { + // Compute other two points of triangle. + var + x1 = down_vertex_x - side_len/2, + x2 = down_vertex_x + side_len/2, + y = down_vertex_y - Math.sqrt( side_len*3/2 ); - var max_label = $("<div />").addClass('yaxislabel'); - max_label.text(max); + // Draw and fill. + ctx.beginPath(); + ctx.moveTo(x1, y); + ctx.lineTo(x2, y); + ctx.lineTo(down_vertex_x, down_vertex_y); + ctx.lineTo(x1, y); + + ctx.strokeStyle = this.fillStyle; + ctx.fill(); + ctx.stroke(); + ctx.closePath(); +}; + +/** + * SummaryTreePainter, a histogram showing number of intervals in a region + */ +var SummaryTreePainter = function( data, delta, max, view_start, view_end, show_counts ) { + // Data and data properties + this.data = data; + this.delta = delta; + this.max = max; + // View + this.view_start = view_start; + this.view_end = view_end; + // Drawing prefs + this.show_counts = show_counts; +} + +SummaryTreePainter.prototype.draw = function( ctx, width, height ) { + + var view_start = this.view_start, + view_range = this.view_end - this.view_start, + w_scale = width / view_range; + + var points = this.data, delta = this.delta, max = this.max, + // Set base Y so that max label and data do not overlap. Base Y is where rectangle bases + // start. However, height of each rectangle is relative to required_height; hence, the + // max rectangle is required_height. + base_y = height; + delta_x_px = Math.ceil(delta * w_scale); + + ctx.save(); + + for (var i = 0, len = points.length; i < len; i++) { - max_label.css({ position: "absolute", top: "22px", left: "10px" }); - max_label.prependTo(this.container_div); - - var ctx = canvas.get(0).getContext("2d"); - for (var i = 0, len = points.length; i < len; i++) { - var x = Math.floor( (points[i][0] - tile_low) * w_scale ); - var y = points[i][1]; - - if (!y) { continue; } - var y_px = y / max * required_height; - - ctx.fillStyle = "black"; - ctx.fillRect(x + left_offset, base_y - y_px, delta_x_px, y_px); - - // Draw number count if it can fit the number with some padding, otherwise things clump up - var text_padding_req_x = 4; - if (this.prefs.show_counts && (ctx.measureText(y).width + text_padding_req_x) < delta_x_px) { - ctx.fillStyle = "#666"; - ctx.textAlign = "center"; - ctx.fillText(y, x + left_offset + (delta_x_px/2), 10); + var x = Math.floor( (points[i][0] - view_start) * w_scale ); + var y = points[i][1]; + + if (!y) { continue; } + var y_px = y / max * height; + + ctx.fillStyle = "black"; + ctx.fillRect( x, base_y - y_px, delta_x_px, y_px ); + + // Draw number count if it can fit the number with some padding, otherwise things clump up + var text_padding_req_x = 4; + if (this.show_counts && (ctx.measureText(y).width + text_padding_req_x) < delta_x_px) { + ctx.fillStyle = "#666"; + ctx.textAlign = "center"; + ctx.fillText(y, x + (delta_x_px/2), 10); + } + } + + ctx.restore(); +} + +var LinePainter = function( data, view_start, view_end, min_value, max_value, color, mode ) { + // Data and data properties + this.data = data; + // View + this.view_start = view_start; + this.view_end = view_end; + // Drawing prefs + this.min_value = min_value; + this.max_value = max_value; + this.color = color; + this.mode = mode; + this.overflow_color = "#F66"; +} + +LinePainter.prototype.draw = function( ctx, width, height ) { + var + in_path = false, + min_value = this.min_value, + max_value = this.max_value, + vertical_range = max_value - min_value, + height_px = height, + view_start = this.view_start, + view_range = this.view_end - this.view_start, + w_scale = width / view_range, + mode = this.mode, + data = this.data; + + ctx.save(); + + // Pixel position of 0 on the y axis + var y_zero = Math.round( height + min_value / vertical_range * height ); + + // Line at 0.0 + if ( mode !== "Intensity" ) { + ctx.fillStyle = "#aaa"; + ctx.fillRect( 0, y_zero, width, 1 ); + } + + ctx.beginPath(); + ctx.fillStyle = this.color; + var x_scaled, y, delta_x_px; + if (data.length > 1) { + delta_x_px = Math.ceil((data[1][0] - data[0][0]) * w_scale); + } else { + delta_x_px = 10; + } + for (var i = 0, len = data.length; i < len; i++) { + x_scaled = Math.round((data[i][0] - view_start) * w_scale); + y = data[i][1]; + if (y === null) { + if (in_path && mode === "Filled") { + ctx.lineTo(x_scaled, height_px); + } + in_path = false; + continue; + } + if (y < min_value) { + y = min_value; + } else if (y > max_value) { + y = max_value; + } + + if (mode === "Histogram") { + // y becomes the bar height in pixels, which is the negated for canvas coords + y = Math.round( y / vertical_range * height_px ); + ctx.fillRect(x_scaled, y_zero, delta_x_px, - y ); + } else if (mode === "Intensity" ) { + y = 255 - Math.floor( (y - min_value) / vertical_range * 255 ); + ctx.fillStyle = "rgb(" +y+ "," +y+ "," +y+ ")"; + ctx.fillRect(x_scaled, 0, delta_x_px, height_px); + } else { + // console.log(y, track.min_value, track.vertical_range, (y - track.min_value) / track.vertical_range * track.height_px); + y = Math.round( height_px - (y - min_value) / vertical_range * height_px ); + // console.log(canvas.get(0).height, canvas.get(0).width); + if (in_path) { + ctx.lineTo(x_scaled, y); + } else { + in_path = true; + if (mode === "Filled") { + ctx.moveTo(x_scaled, height_px); + ctx.lineTo(x_scaled, y); + } else { + ctx.moveTo(x_scaled, y); + } } } + } + if (mode === "Filled") { + if (in_path) { + ctx.lineTo( x_scaled, y_zero ); + ctx.lineTo( 0, y_zero ); + } + ctx.fill(); + } else { + ctx.stroke(); + } + + // Draw lines at bounderies if overflowing min or max + var overflow_min_start = -1, + overflow_max_start = -1; + ctx.fillStyle = this.overflow_color; + for (var i = 0, len = data.length; i < len; i++) { + y = data[i][1]; + x_scaled = Math.round((data[i][0] - view_start) * w_scale); + x_minus_scaled = Math.round((data[i][0] - 1 - view_start) * w_scale); + + // If we are in a min/max run, check if it should be ended + if ( overflow_max_start >= 0 && ( y === null || y < max_value ) ) { + // Value does not exist or is in valid range, any overflow ends + ctx.fillRect( overflow_max_start, 0, x_minus_scaled - overflow_max_start + 1, 2 ); + overflow_max_start = -1; + } else if ( overflow_min_start >= 0 && ( y === null || y > min_value ) ) { + // Draw bottom overflow bar + ctx.fillRect( overflow_min_start, height - 2, x_minus_scaled - overflow_min_start + 1, 2 ); + overflow_min_start = -1; + } + + // Now check if we should start a new one (this may happen on the same + // base as above if switching between min/max) + if ( y !== null && y > max_value && overflow_max_start < 0 ) { + // Top overflows and we are not already in a run of overflow + overflow_max_start = x_scaled; + } else if ( y !== null && y < min_value && overflow_min_start < 0 ) { + // Bottom overflows and we are not already in a run + overflow_min_start = x_scaled; + } + } + + ctx.restore(); +} + +var FeaturePainter = function( data, view_start, view_end, prefs, mode ) { + this.data = data; + this.view_start = view_start; + this.view_end = view_end; + this.prefs = prefs; + this.mode = mode; +} + +extend( FeaturePainter.prototype, { + + get_required_height: function( rows_required ) { + // y_scale is the height per row + var required_height = y_scale = this.get_row_height(), mode = this.mode; + // If using a packing mode, need to multiply by the number of slots used + if (mode === "no_detail" || mode === "Squish" || mode === "Pack") { + required_height = rows_required * y_scale; + } + // Pad bottom by half a row, at least 5 px + return required_height + Math.max( Math.round( y_scale / 2 ), 5 ); }, - /** - * Draw feature. - */ - draw_element: function(ctx, tile_index, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width, left_offset) { - var - feature_uid = feature[0], - feature_start = feature[1], - // -1 b/c intervals are half-open. - feature_end = feature[2] - 1, - feature_name = feature[3], - f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ), - f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ), - y_center = ERROR_PADDING + (mode === "Dense" ? 0 : (0 + slot)) * y_scale, - thickness, y_start, thick_start = null, thick_end = null, - block_color = this.prefs.block_color, - label_color = this.prefs.label_color; - - // Dense mode displays the same for all data. - if (mode === "Dense") { - ctx.fillStyle = block_color; - ctx.fillRect(f_start + left_offset, y_center, f_end - f_start, DENSE_FEATURE_HEIGHT); - } - else if (mode === "no_detail") { - // No details for feature, so only one way to display. - ctx.fillStyle = block_color; - // TODO: what should width be here? - ctx.fillRect(f_start + left_offset, y_center + 5, f_end - f_start, DENSE_FEATURE_HEIGHT); - } - else { // Mode is either Squish or Pack: - // Feature details. - var feature_strand = feature[5], - feature_ts = feature[6], - feature_te = feature[7], - feature_blocks = feature[8]; - - if (feature_ts && feature_te) { - thick_start = Math.floor( Math.max(0, (feature_ts - tile_low) * w_scale) ); - thick_end = Math.ceil( Math.min(width, Math.max(0, (feature_te - tile_low) * w_scale)) ); - } - - // Set vars that depend on mode. - var thin_height, thick_height; - if (mode === "Squish") { - thin_height = 1; - thick_height = SQUISH_FEATURE_HEIGHT; - } else { // mode === "Pack" - thin_height = 5; - thick_height = PACK_FEATURE_HEIGHT; - } - - // Draw feature/feature blocks + connectors. - if (!feature_blocks) { - // If there are no blocks, treat the feature as one big exon. - if ( feature.strand ) { - if (feature.strand === "+") { - ctx.fillStyle = RIGHT_STRAND_INV; - } else if (feature.strand === "-") { - ctx.fillStyle = LEFT_STRAND_INV; - } - } - else { // No strand. - ctx.fillStyle = block_color; - } - ctx.fillRect(f_start + left_offset, y_center, f_end - f_start, thick_height); - } else { - // There are feature blocks and mode is either Squish or Pack. - // - // Approach: (a) draw whole feature as connector/intron and (b) draw blocks as - // needed. This ensures that whole feature, regardless of whether it starts with - // a block, is visible. - // + + draw: function( ctx, width, height, slots ) { + + var data = this.data, view_start = this.view_start, view_end = this.view_end; + + ctx.save(); + + ctx.fillStyle = this.prefs.block_color; + ctx.textAlign = "right"; + + var view_range = this.view_end - this.view_start, + w_scale = width / view_range, + y_scale = this.get_row_height(); + + for (var i = 0, len = data.length; i < len; i++) { + var feature = data[i], + feature_uid = feature[0], + feature_start = feature[1], + feature_end = feature[2], + // Slot valid only if features are slotted and this feature is slotted; + // feature may not be due to lack of space. + slot = (slots && slots[feature_uid] !== undefined ? slots[feature_uid] : null); - // Draw whole feature as connector/intron. - var cur_y_center, cur_height; - if (mode === "Squish") { - ctx.fillStyle = CONNECTOR_COLOR; - cur_y_center = y_center + Math.floor(SQUISH_FEATURE_HEIGHT/2) + 1; - cur_height = 1; - } - else { // mode === "Pack" - if (feature_strand) { - var cur_y_center = y_center; - var cur_height = thick_height; - if (feature_strand === "+") { - ctx.fillStyle = RIGHT_STRAND; - } else if (feature_strand === "-") { - ctx.fillStyle = LEFT_STRAND; - } - } - else { - ctx.fillStyle = CONNECTOR_COLOR; - cur_y_center += (SQUISH_FEATURE_HEIGHT/2) + 1; - cur_height = 1; - } - } - ctx.fillRect(f_start + left_offset, cur_y_center, f_end - f_start, cur_height); - - for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) { - var block = feature_blocks[k], - block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ), - // -1 b/c intervals are half-open. - block_end = Math.ceil( Math.min(width, Math.max((block[1] - 1 - tile_low) * w_scale)) ); - - // Skip drawing if block not on tile. - if (block_start > block_end) { continue; } - - // Draw thin block. - ctx.fillStyle = block_color; - ctx.fillRect(block_start + left_offset, y_center + (thick_height-thin_height)/2 + 1, - block_end - block_start, thin_height); - - // If block intersects with thick region, draw block as thick. - if (thick_start !== undefined && !(block_start > thick_end || block_end < thick_start) ) { - var block_thick_start = Math.max(block_start, thick_start), - block_thick_end = Math.min(block_end, thick_end); - ctx.fillRect(block_thick_start + left_offset, y_center + 1, - block_thick_end - block_thick_start, thick_height); - } - } - } - - // Draw label for Pack mode. - if (mode === "Pack" && feature_start > tile_low) { - ctx.fillStyle = label_color; - if (tile_index === 0 && f_start - ctx.measureText(feature_name).width < 0) { - ctx.textAlign = "left"; - ctx.fillText(feature_name, f_end + left_offset + LABEL_SPACING, y_center + 8); - } else { - ctx.textAlign = "right"; - ctx.fillText(feature_name, f_start + left_offset - LABEL_SPACING, y_center + 8); - } - ctx.fillStyle = block_color; + // Draw feature if there's overlap and mode is dense or feature is slotted (as it must be for all non-dense modes). + if ( ( feature_start < view_end && feature_end > view_start ) && (this.mode == "Dense" || slot !== null)) { + this.draw_element(ctx, this.mode, feature, slot, view_start, view_end, w_scale, y_scale, + width ); } } - }, + + ctx.restore(); + } +}); + +// Contstants specific to feature tracks moved here (HACKING, these should +// basically all be configuration options) +var DENSE_TRACK_HEIGHT = 10, + NO_DETAIL_TRACK_HEIGHT = 3, + SQUISH_TRACK_HEIGHT = 5, + PACK_TRACK_HEIGHT = 10, + NO_DETAIL_FEATURE_HEIGHT = 1, + DENSE_FEATURE_HEIGHT = 3, + SQUISH_FEATURE_HEIGHT = 3, + PACK_FEATURE_HEIGHT = 9, + LABEL_SPACING = 2, + CONNECTOR_COLOR = "#ccc"; + +var LinkedFeaturePainter = function( data, view_start, view_end, prefs, mode ) { + FeaturePainter.call( this, data, view_start, view_end, prefs, mode ); +} + +extend( LinkedFeaturePainter.prototype, FeaturePainter.prototype, { + /** - * Returns y_scale based on mode. + * Height of a single row, depends on mode */ - get_y_scale: function(mode) { - var y_scale; - if (mode === "summary_tree") { - // No scale needed. - } - if (mode === "Dense") { + get_row_height: function() { + var mode = this.mode, y_scale; + if (mode === "Dense") { y_scale = DENSE_TRACK_HEIGHT; } else if (mode === "no_detail") { @@ -2503,174 +2848,172 @@ } return y_scale; }, - /** - * Draw FeatureTrack tile. - */ - draw_tile: function(result, resolution, tile_index, parent_element, w_scale, ref_seq) { - var track = this; - var tile_low = tile_index * DENSITY * resolution, - tile_high = ( tile_index + 1 ) * DENSITY * resolution, - tile_span = tile_high - tile_low, - params = { hda_ldda: track.hda_ldda, dataset_id: track.dataset_id, - resolution: this.view.resolution, mode: this.mode }; - - // - // Create/set/compute some useful vars. - // - var width = Math.ceil( tile_span * w_scale ), - mode = this.mode, - min_height = 25, - left_offset = this.left_offset, - slots, required_height; + + draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width ) { + var + feature_uid = feature[0], + feature_start = feature[1], + // -1 b/c intervals are half-open. + feature_end = feature[2] - 1, + feature_name = feature[3], + f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ), + f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ), + y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale, + thickness, y_start, thick_start = null, thick_end = null, + block_color = this.prefs.block_color, + label_color = this.prefs.label_color; + + // Dense mode displays the same for all data. + /* + if (mode === "Dense") { + ctx.fillStyle = block_color; + ctx.fillRect(f_start, y_center, f_end - f_start, DENSE_FEATURE_HEIGHT); + } + */ - var canvas = document.createElement("canvas"); - if (window.G_vmlCanvasManager) { G_vmlCanvasManager.initElement(canvas); } // EXCANVAS HACK - canvas = $(canvas); - - // - // Set mode if Auto. - // - if (mode === "Auto") { - if (result.dataset_type === "summary_tree") { - mode = result.dataset_type; - } else if (result.extra_info === "no_detail") { - mode = "no_detail"; - } else { - // Choose b/t Squish and Pack. - // Proxy measures for using Squish: - // (a) error message re: limiting number of features shown; - // (b) X number of features shown; - // (c) size of view shown. - // TODO: cannot use (a) and (b) because it requires coordinating mode across tiles; - // fix this so that tiles are redrawn as necessary to use the same mode. - //if ( (result.message && result.message.match(/^Only the first [\d]+/)) || - // (result.data && result.data.length > 2000) || - var data = result.data; - if ( (data.length && data.length < 4) || - (this.view.high - this.view.low > MIN_SQUISH_VIEW_WIDTH) ) { - mode = "Squish"; - } else { - mode = "Pack"; - } - } - } - - var y_scale = this.get_y_scale(mode); - - // - // Pack reads, set required height. - // - if (mode === "summary_tree") { - required_height = this.summary_draw_height; - } - if (mode === "Dense") { - required_height = min_height; - } - else if (mode === "no_detail" || mode === "Squish" || mode === "Pack") { - // Calculate new slots incrementally for this new chunk of data and update height if necessary. - required_height = this.incremental_slots(w_scale, result.data, mode) * y_scale + min_height; - slots = this.inc_slots[w_scale]; + if ( mode == "Dense" ) { + slot = 1; } - // - // Set up for drawing. - // - canvas.get(0).width = width + left_offset; - canvas.get(0).height = required_height; - if (result.dataset_type === "summary_tree") { - // Increase canvas height in order to display max label. - canvas.get(0).height += LABEL_SPACING + CHAR_HEIGHT_PX; - } - parent_element.parent().css("height", Math.max(this.height_px, required_height) + "px"); - // console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale); - var ctx = canvas.get(0).getContext("2d"); - ctx.fillStyle = this.prefs.block_color; - ctx.font = this.default_font; - ctx.textAlign = "right"; - this.container_div.find(".yaxislabel").remove(); - - // - // Draw summary tree. If tree is drawn, canvas is returned. - // - if (mode === "summary_tree") { - this.draw_summary_tree(canvas, result.data, result.delta, result.max, w_scale, required_height, - tile_low, left_offset); - return canvas; - } - - // - // If there is a message, draw it on canvas so that it moves around with canvas, and make the border red - // to indicate region where message is applicable - if (result.message) { - canvas.css({ - "border-top": "1px solid red" - }); + if (mode === "no_detail") { + // No details for feature, so only one way to display. + ctx.fillStyle = block_color; + // TODO: what should width be here? + ctx.fillRect(f_start, y_center + 5, f_end - f_start, NO_DETAIL_FEATURE_HEIGHT); + } + else { // Mode is either Squish or Pack: + // Feature details. + var feature_strand = feature[4], + feature_ts = feature[5], + feature_te = feature[6], + feature_blocks = feature[7]; + + if (feature_ts && feature_te) { + thick_start = Math.floor( Math.max(0, (feature_ts - tile_low) * w_scale) ); + thick_end = Math.ceil( Math.min(width, Math.max(0, (feature_te - tile_low) * w_scale)) ); + } + + // Set vars that depend on mode. + var thin_height, thick_height; + if (mode === "Squish" || mode === "Dense" ) { + thin_height = 1; + thick_height = SQUISH_FEATURE_HEIGHT; + } else { // mode === "Pack" + thin_height = 5; + thick_height = PACK_FEATURE_HEIGHT; + } + + // Draw feature/feature blocks + connectors. + if (!feature_blocks) { + // If there are no blocks, treat the feature as one big exon. + if ( feature.strand ) { + if (feature.strand === "+") { + ctx.fillStyle = ctx.canvas.manager.get_pattern( 'right_strand_inv' ); + } else if (feature.strand === "-") { + ctx.fillStyle = ctx.canvas.manager.get_pattern( 'left_strand_inv' ); + } + } + else { // No strand. + ctx.fillStyle = block_color; + } + ctx.fillRect(f_start, y_center, f_end - f_start, thick_height); + } else { + // There are feature blocks and mode is either Squish or Pack. + // + // Approach: (a) draw whole feature as connector/intron and (b) draw blocks as + // needed. This ensures that whole feature, regardless of whether it starts with + // a block, is visible. + // + + // Draw whole feature as connector/intron. + var cur_y_center, cur_height; + if (mode === "Squish" || mode === "Dense") { + ctx.fillStyle = CONNECTOR_COLOR; + cur_y_center = y_center + Math.floor(SQUISH_FEATURE_HEIGHT/2) + 1; + cur_height = 1; + } + else { // mode === "Pack" + if (feature_strand) { + var cur_y_center = y_center; + var cur_height = thick_height; + if (feature_strand === "+") { + ctx.fillStyle = ctx.canvas.manager.get_pattern( 'right_strand' ); + } else if (feature_strand === "-") { + ctx.fillStyle = ctx.canvas.manager.get_pattern( 'left_strand' ); + } + } + else { + ctx.fillStyle = CONNECTOR_COLOR; + cur_y_center += (SQUISH_FEATURE_HEIGHT/2) + 1; + cur_height = 1; + } + } + ctx.fillRect(f_start, cur_y_center, f_end - f_start, cur_height); + + for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) { + var block = feature_blocks[k], + block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ), + // -1 b/c intervals are half-open. + block_end = Math.ceil( Math.min(width, Math.max((block[1] - 1 - tile_low) * w_scale)) ); - ctx.fillStyle = "red"; - ctx.textAlign = "left"; - var old_base = ctx.textBaseline; - ctx.textBaseline = "top"; - ctx.fillText(result.message, left_offset, 0); - ctx.textBaseline = old_base; + // Skip drawing if block not on tile. + if (block_start > block_end) { continue; } - // If there's no data, return. - if (!result.data) { - return canvas; + // Draw thin block. + ctx.fillStyle = block_color; + ctx.fillRect(block_start, y_center + (thick_height-thin_height)/2 + 1, + block_end - block_start, thin_height); + + // If block intersects with thick region, draw block as thick. + // - No thick is sometimes encoded as thick_start == thick_end, so don't draw in that case + if (thick_start !== undefined && feature_te > feature_ts && !(block_start > thick_end || block_end < thick_start) ) { + var block_thick_start = Math.max(block_start, thick_start), + block_thick_end = Math.min(block_end, thick_end); + ctx.fillRect(block_thick_start, y_center + 1, + block_thick_end - block_thick_start, thick_height); + if ( feature_blocks.length == 1 && mode == "Pack") { + // Exactly one block means we have no introns, but do have a distinct "thick" region, + // draw arrows over it if in pack mode + if (feature_strand === "+") { + ctx.fillStyle = ctx.canvas.manager.get_pattern( 'right_strand_inv' ); + } else if (feature_strand === "-") { + ctx.fillStyle = ctx.canvas.manager.get_pattern( 'left_strand_inv' ); + } + // If region is wide enough in pixels, pad a bit + if ( block_thick_start + 14 < block_thick_end ) { + block_thick_start += 2; + block_thick_end -= 2; + } + ctx.fillRect( block_thick_start, y_center + 1, + block_thick_end - block_thick_start, thick_height ); + } + } + } + } + + // Draw label for Pack mode. + if (mode === "Pack" && feature_start > tile_low) { + ctx.fillStyle = label_color; + // FIXME: assumption here that the entire view starts at 0 + if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) { + ctx.textAlign = "left"; + ctx.fillText(feature_name, f_end + LABEL_SPACING, y_center + 8); + } else { + ctx.textAlign = "right"; + ctx.fillText(feature_name, f_start - LABEL_SPACING, y_center + 8); + } + ctx.fillStyle = block_color; } } - - // - // Set example feature. This is needed so that track can update its UI based on feature attributes. - // - this.example_feature = (result.data.length ? result.data[0] : undefined); - - // - // Draw elements. - // - var data = result.data; - for (var i = 0, len = data.length; i < len; i++) { - var feature = data[i], - feature_uid = feature[0], - feature_start = feature[1], - feature_end = feature[2], - // Slot valid only if features are slotted and this feature is slotted; - // feature may not be due to lack of space. - slot = (slots && slots[feature_uid] !== undefined ? slots[feature_uid] : null); - - // Apply filters to feature. - var hide_feature = false; - var filter; - for (var f = 0; f < this.filters.length; f++) { - filter = this.filters[f]; - filter.update_attrs( feature ); - if ( !filter.keep( feature ) ) { - hide_feature = true; - break; - } - } - if (hide_feature) { - continue; - } - - // Draw feature if there's overlap and mode is dense or feature is slotted (as it must be for all non-dense modes). - if (is_overlap([feature_start, feature_end], [tile_low, tile_high]) && (mode == "Dense" || slot !== null)) { - this.draw_element(ctx, tile_index, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, - width, left_offset, ref_seq); - } - } - return canvas; } }); -var VcfTrack = function(name, view, hda_ldda, dataset_id, prefs, filters) { - FeatureTrack.call(this, name, view, hda_ldda, dataset_id, prefs, filters); - this.track_type = "VcfTrack"; -}; -$.extend(VcfTrack.prototype, TiledTrack.prototype, FeatureTrack.prototype, { - /** - * Draw a VCF entry. - */ +var VariantPainter = function( data, view_start, view_end, prefs, mode ) { + FeaturePainter.call( this, data, view_start, view_end, prefs, mode ); +} + +extend( VariantPainter.prototype, FeaturePainter.prototype, { draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width) { var feature = data[i], feature_uid = feature[0], @@ -2681,7 +3024,7 @@ // All features need a start, end, and vertical center. f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ), - y_center = ERROR_PADDING + (mode === "Dense" ? 0 : (0 + slot)) * y_scale, + y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale, thickness, y_start, thick_start = null, thick_end = null; if (no_label) { @@ -2700,7 +3043,7 @@ if (mode !== "Dense" && feature_name !== undefined && feature_start > tile_low) { // Draw label ctx.fillStyle = label_color; - if (tile_index === 0 && f_start - ctx.measureText(feature_name).width < 0) { + if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) { ctx.textAlign = "left"; ctx.fillText(feature_name, f_end + 2 + left_offset, y_center + 8); } else { @@ -2722,39 +3065,54 @@ } }); -var ReadTrack = function (name, view, hda_ldda, dataset_id, prefs, filters) { - FeatureTrack.call(this, name, view, hda_ldda, dataset_id, prefs, filters); +/** + * Compute the type of overlap between two regions. They are assumed to be on the same chrom/contig. + * The overlap is computed relative to the second region; hence, OVERLAP_START indicates that the first + * region overlaps the start (but not the end) of the second region. + */ +var NO_OVERLAP = 1001, CONTAINS = 1002, OVERLAP_START = 1003, OVERLAP_END = 1004, CONTAINED_BY = 1005; +var compute_overlap = function(first_region, second_region) { + var + first_start = first_region[0], first_end = first_region[1], + second_start = second_region[0], second_end = second_region[1], + overlap; + if (first_start < second_start) { + if (first_end < second_start) { + overlap = NO_OVERLAP; + } + else if (first_end <= second_end) { + overlap = OVERLAP_START; + } + else { // first_end > second_end + overlap = CONTAINS; + } + } + else { // first_start >= second_start + if (first_start > second_end) { + overlap = NO_OVERLAP; + } + else if (first_end <= second_end) { + overlap = CONTAINED_BY; + } + else { + overlap = OVERLAP_END; + } + } - this.track_config = new TrackConfig( { - track: this, - params: [ - { key: 'block_color', label: 'Block color', type: 'color', default_value: '#444' }, - { 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: prefs, - onchange: function() { - this.track.tile_cache.clear(); - this.track.draw(); - } - }); - this.prefs = this.track_config.values; - - this.track_type = "ReadTrack"; - this.make_name_popup_menu(); -}; -$.extend(ReadTrack.prototype, TiledTrack.prototype, FeatureTrack.prototype, { + return overlap; +} + +var ReadPainter = function( data, view_start, view_end, prefs, mode, ref_seq ) { + FeaturePainter.call( this, data, view_start, view_end, prefs, mode ); + this.ref_seq = ref_seq; +} + +extend( ReadPainter.prototype, FeaturePainter.prototype, { /** * Returns y_scale based on mode. */ - get_y_scale: function(mode) { - var y_scale; - if (mode === "summary_tree") { - // No scale needed. - } + get_row_height: function() { + var y_scale, mode = this.mode; if (mode === "Dense") { y_scale = DENSE_TRACK_HEIGHT; } @@ -2763,7 +3121,7 @@ } else { // mode === "Pack" y_scale = PACK_TRACK_HEIGHT; - if (this.track_config.values.show_insertions) { + if (this.prefs.show_insertions) { y_scale *= 2; } } @@ -2772,20 +3130,22 @@ /** * Draw a single read. */ - draw_read: function(ctx, mode, w_scale, tile_low, tile_high, feature_start, cigar, orig_seq, y_center, ref_seq) { + draw_read: function(ctx, mode, w_scale, tile_low, tile_high, feature_start, cigar, orig_seq, y_center) { ctx.textAlign = "center"; var track = this, tile_region = [tile_low, tile_high], base_offset = 0, seq_offset = 0, - gap = 0; + gap = 0 + ref_seq = this.ref_seq, + char_width_px = ctx.canvas.manager.char_width_px; // Keep list of items that need to be drawn on top of initial drawing layer. var draw_last = []; // Gap is needed so that read is offset and hence first base can be drawn on read. // TODO-FIX: using this gap offsets reads so that their start is not visually in sync with other tracks. - if ((mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > CHAR_WIDTH_PX) { + if ((mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > char_width_px) { gap = Math.round(w_scale/2); } if (!cigar) { @@ -2819,12 +3179,12 @@ var seq = orig_seq.slice(seq_offset, seq_offset + cig_len); if (gap > 0) { ctx.fillStyle = this.prefs.block_color; - ctx.fillRect(s_start + this.left_offset - gap, y_center + 1, s_end - s_start, 9); + ctx.fillRect(s_start - gap, y_center + 1, s_end - s_start, 9); ctx.fillStyle = CONNECTOR_COLOR; // TODO: this can be made much more efficient by computing the complete sequence // to draw and then drawing it. for (var c = 0, str_len = seq.length; c < str_len; c++) { - if (this.track_config.values.show_differences && ref_seq) { + if (this.prefs.show_differences && ref_seq) { var ref_char = ref_seq[seq_start - tile_low + c]; if (!ref_char || ref_char.toLowerCase() === seq[c].toLowerCase()) { continue; @@ -2832,16 +3192,13 @@ } if (seq_start + c >= tile_low && seq_start + c <= tile_high) { var c_start = Math.floor( Math.max(0, (seq_start + c - tile_low) * w_scale) ); - ctx.fillText(seq[c], c_start + this.left_offset, y_center + 9); + ctx.fillText(seq[c], c_start, y_center + 9); } } } else { ctx.fillStyle = this.prefs.block_color; // TODO: This is a pretty hack-ish way to fill rectangle based on mode. - ctx.fillRect(s_start + this.left_offset, - y_center + (this.mode !== "Dense" ? 4 : 5), - s_end - s_start, - (mode !== "Dense" ? SQUISH_FEATURE_HEIGHT : DENSE_FEATURE_HEIGHT) ); + ctx.fillRect(s_start, y_center + 4, s_end - s_start, SQUISH_FEATURE_HEIGHT); } } seq_offset += cig_len; @@ -2849,14 +3206,14 @@ break; case "N": // Skipped bases. ctx.fillStyle = CONNECTOR_COLOR; - ctx.fillRect(s_start + this.left_offset - gap, y_center + 5, s_end - s_start, 1); + ctx.fillRect(s_start - gap, y_center + 5, s_end - s_start, 1); //ctx.dashedLine(s_start + this.left_offset, y_center + 5, this.left_offset + s_end, y_center + 5); // No change in seq_offset because sequence not used when skipping. base_offset += cig_len; break; case "D": // Deletion. ctx.fillStyle = "red"; - ctx.fillRect(s_start + this.left_offset - gap, y_center + 4, s_end - s_start, 3); + ctx.fillRect(s_start - gap, y_center + 4, s_end - s_start, 3); // TODO: is this true? No change in seq_offset because sequence not used when skipping. base_offset += cig_len; break; @@ -2868,21 +3225,21 @@ // the sequence region and the tile region. var seq_tile_overlap = compute_overlap([seq_start, seq_start + cig_len], tile_region), - insert_x_coord = this.left_offset + s_start - gap; + insert_x_coord = s_start - gap; if (seq_tile_overlap !== NO_OVERLAP) { var seq = orig_seq.slice(seq_offset, seq_offset + cig_len); // Insertion point is between the sequence start and the previous base: (-gap) moves // back from sequence start to insertion point. - if (this.track_config.values.show_insertions) { + if (this.prefs.show_insertions) { // // Show inserted sequence above, centered on insertion point. // // Draw sequence. // X center is offset + start - <half_sequence_length> - var x_center = this.left_offset + s_start - (s_end - s_start)/2; - if ( (mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > CHAR_WIDTH_PX) { + var x_center = s_start - (s_end - s_start)/2; + if ( (mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > char_width_px) { // Draw sequence container. ctx.fillStyle = "yellow"; ctx.fillRect(x_center - gap, y_center - 9, s_end - s_start, 9); @@ -2906,7 +3263,7 @@ // Draw sequence. for (var c = 0, str_len = seq.length; c < str_len; c++) { var c_start = Math.floor( Math.max(0, (seq_start + c - tile_low) * w_scale) ); - ctx.fillText(seq[c], c_start + this.left_offset - (s_end - s_start)/2, y_center); + ctx.fillText(seq[c], c_start - (s_end - s_start)/2, y_center); } } else { @@ -2918,7 +3275,7 @@ } } else { - if ( (mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > CHAR_WIDTH_PX) { + if ( (mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > char_width_px) { // Show insertions with a single number at the insertion point. draw_last[draw_last.length] = {type: "text", data: [seq.length, insert_x_coord, y_center + 9]}; } @@ -2947,31 +3304,37 @@ type = item["type"]; data = item["data"]; if (type === "text") { - ctx.font = "bold " + DEFAULT_FONT; + ctx.save(); + ctx.font = "bold " + ctx.font; ctx.fillText(data[0], data[1], data[2]); - ctx.font = DEFAULT_FONT; + ctx.restore(); } else if (type == "triangle") { - ctx.drawDownwardEquilateralTriangle(data[0], data[1], data[2]); + drawDownwardEquilateralTriangle(ctx, data[0], data[1], data[2]); } } }, /** - * Draw a complete read. + * Draw a complete read pair */ - draw_element: function(ctx, tile_index, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width, left_offset, ref_seq) { + draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width ) { // All features need a start, end, and vertical center. - var - feature_uid = feature[0], + var feature_uid = feature[0], feature_start = feature[1], feature_end = feature[2], feature_name = feature[3], f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ), - y_center = (mode === "Dense" ? 1 : (1 + slot)) * y_scale, + y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale, block_color = this.prefs.block_color, - label_color = this.prefs.label_color; - gap = 0; // Left-gap for label text since we align chrom text to the position tick + label_color = this.prefs.label_color, + // Left-gap for label text since we align chrom text to the position tick. + gap = 0; + + // TODO: fix gap usage; also see note on gap in draw_read. + if ((mode === "Pack" || this.mode === "Auto") && w_scale > ctx.canvas.manager.char_width_px) { + var gap = Math.round(w_scale/2); + } // Draw read. ctx.fillStyle = block_color; @@ -2984,78 +3347,71 @@ // Draw left/forward read. if (feature[4][1] >= tile_low && feature[4][0] <= tile_high && feature[4][2]) { - this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature[4][0], feature[4][2], feature[4][3], y_center, ref_seq); + this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature[4][0], feature[4][2], feature[4][3], y_center); } // Draw right/reverse read. if (feature[5][1] >= tile_low && feature[5][0] <= tile_high && feature[5][2]) { - this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature[5][0], feature[5][2], feature[5][3], y_center, ref_seq); + this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature[5][0], feature[5][2], feature[5][3], y_center); } // Draw connector. if (b2_start > b1_end) { ctx.fillStyle = CONNECTOR_COLOR; - //ctx.fillRect(b1_end + left_offset, y_center + 5, b2_start - b1_end, 1); - ctx.dashedLine(b1_end + left_offset, y_center + 5, left_offset + b2_start, y_center + 5); + dashedLine(ctx, b1_end - gap, y_center + 5, b2_start - gap, y_center + 5); } } else { // Read is single. ctx.fillStyle = block_color; - this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature_start, feature[4], feature[5], y_center, ref_seq); + this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature_start, feature[4], feature[5], y_center); } if (mode === "Pack" && feature_start > tile_low) { // Draw label. ctx.fillStyle = this.prefs.label_color; - if ( (mode === "Pack" || this.mode === "Auto") && w_scale > CHAR_WIDTH_PX) { - var gap = Math.round(w_scale/2); - } + // FIXME: eliminate tile_index + var tile_index = 1; if (tile_index === 0 && f_start - ctx.measureText(feature_name).width < 0) { ctx.textAlign = "left"; - ctx.fillText(feature_name, f_end + left_offset + LABEL_SPACING - gap, y_center + 8); + ctx.fillText(feature_name, f_end + LABEL_SPACING - gap, y_center + 8); } else { ctx.textAlign = "right"; - ctx.fillText(feature_name, f_start + left_offset - LABEL_SPACING - gap, y_center + 8); + ctx.fillText(feature_name, f_start - LABEL_SPACING - gap, y_center + 8); } ctx.fillStyle = block_color; } } }); -/** - * Feature track that displays data generated from tool. - */ -var ToolDataFeatureTrack = function(name, view, hda_ldda, dataset_id, prefs, filters, parent_track) { - FeatureTrack.call(this, name, view, hda_ldda, dataset_id, prefs, filters, {}, parent_track); - this.track_type = "ToolDataFeatureTrack"; - - // Set up track to fetch initial data from raw data URL when the dataset--not the converted datasets-- - // is ready. - this.data_url = raw_data_url; - this.data_query_wait = 1000; - this.dataset_check_url = dataset_state_url; +exports.SummaryTreePainter = SummaryTreePainter; +exports.LinePainter = LinePainter; +exports.LinkedFeaturePainter = LinkedFeaturePainter; +exports.ReadPainter = ReadPainter; +exports.VariantPainter = VariantPainter; + +// End painters_module encapsulation }; -$.extend(ToolDataFeatureTrack.prototype, TiledTrack.prototype, FeatureTrack.prototype, { - /** - * For this track type, the predraw init sets up postdraw init. - */ - predraw_init: function() { - // Postdraw init: once data has been fetched, reset data url, wait time and start indexing. - var track = this; - var post_init = function() { - if (track.data_cache.size() === 0) { - // Track still drawing initial data, so do nothing. - setTimeout(post_init, 300); - } - else { - // Track drawing done: reset dataset check, data URL, wait time and get dataset state to start - // indexing. - track.data_url = default_data_url; - track.data_query_wait = DEFAULT_DATA_QUERY_WAIT; - track.dataset_state_url = converted_datasets_state_url; - $.getJSON(track.dataset_state_url, { dataset_id : track.dataset_id, hda_ldda: track.hda_ldda }, function(track_data) {}); - } - }; - post_init(); +// Finally, compose and export trackster module exports into globals +// These will be replaced with require statements in CommonJS +(function(target){ + // Faking up a CommonJS like loader here, each module gets a require and + // and exports. We avoid resolution problems by just ordering carefully. + var modules = {}; + // Provide a require function + var require = function( name ) { + return modules[name]; + }; + // Run module will run the module_function provided and store in the + // require dict using key + var run_module = function( key, module_function ) { + var exports = {}; + module_function( require, exports ); + modules[key] = exports; + }; + // Run all modules + run_module( 'slotting', slotting_module ); + run_module( 'painters', painters_module ); + run_module( 'trackster', trackster_module ); + // Export trackster stuff + for ( key in modules.trackster ) { + target[key] = modules.trackster[key]; } -}); - - +})(window); \ No newline at end of file --- a/templates/tracks/browser.mako Sun Mar 27 19:50:50 2011 -0400 +++ b/templates/tracks/browser.mako Tue Apr 05 13:57:14 2011 -0400 @@ -69,6 +69,7 @@ chrom_url = "${h.url_for( action='chroms' )}", dataset_state_url = "${h.url_for( action='dataset_state' )}", converted_datasets_state_url = "${h.url_for( action='converted_datasets_state' )}", + filters_url = "${h.url_for( action='filters' )}", addable_track_types = { "LineTrack": LineTrack, "FeatureTrack": FeatureTrack, "ReadTrack": ReadTrack }, view; --- a/test-data/blastp_rhodopsin_vs_four_human.tabular Sun Mar 27 19:50:50 2011 -0400 +++ b/test-data/blastp_rhodopsin_vs_four_human.tabular Tue Apr 05 13:57:14 2011 -0400 @@ -1,6 +1,6 @@ -gi|57163783|ref|NP_001009242.1| Subject_4 96.55 348 12 0 1 348 1 348 0.0 679 -gi|3024260|sp|P56514.1|OPSD_BUFBU Subject_4 83.33 354 53 2 1 354 1 348 6e-178 605 -gi|283855846|gb|ADB45242.1| Subject_4 94.82 328 17 0 1 328 11 338 0.0 630 -gi|283855823|gb|ADB45229.1| Subject_4 94.82 328 17 0 1 328 11 338 0.0 630 -gi|223523|prf||0811197A Subject_4 93.10 348 23 1 1 347 1 348 0.0 651 -gi|12583665|dbj|BAB21486.1| Subject_4 81.09 349 65 1 1 349 1 348 2e-172 587 +gi|57163783|ref|NP_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 348 1 348 0.0 679 +gi|3024260|sp|P56514.1|OPSD_BUFBU sp|P08100|OPSD_HUMAN 83.33 354 53 2 1 354 1 348 6e-178 605 +gi|283855846|gb|ADB45242.1| sp|P08100|OPSD_HUMAN 94.82 328 17 0 1 328 11 338 0.0 630 +gi|283855823|gb|ADB45229.1| sp|P08100|OPSD_HUMAN 94.82 328 17 0 1 328 11 338 0.0 630 +gi|223523|prf||0811197A sp|P08100|OPSD_HUMAN 93.10 348 23 1 1 347 1 348 0.0 651 +gi|12583665|dbj|BAB21486.1| sp|P08100|OPSD_HUMAN 81.09 349 65 1 1 349 1 348 2e-172 587 --- a/test-data/tblastn_four_human_vs_rhodopsin.tabular Sun Mar 27 19:50:50 2011 -0400 +++ b/test-data/tblastn_four_human_vs_rhodopsin.tabular Tue Apr 05 13:57:14 2011 -0400 @@ -1,10 +1,10 @@ -sp|P08100|OPSD_HUMAN Subject_1 96.55 348 12 0 1 348 1 1044 0.0 732 -sp|P08100|OPSD_HUMAN Subject_2 84.80 342 51 1 1 341 42 1067 0.0 646 -sp|P08100|OPSD_HUMAN Subject_3 93.24 74 5 0 239 312 3147 3368 1e-72 151 -sp|P08100|OPSD_HUMAN Subject_3 91.53 59 5 0 177 235 2855 3031 1e-72 126 -sp|P08100|OPSD_HUMAN Subject_3 96.40 111 4 0 11 121 1 333 1e-64 229 -sp|P08100|OPSD_HUMAN Subject_3 93.22 59 4 0 119 177 1404 1580 1e-32 122 -sp|P08100|OPSD_HUMAN Subject_3 88.46 26 3 0 312 337 4222 4299 6e-13 57.7 -sp|P08100|OPSD_HUMAN Subject_4 95.09 326 16 0 11 336 1 978 0.0 658 -sp|P08100|OPSD_HUMAN Subject_5 93.39 348 23 0 1 348 1 1044 0.0 711 -sp|P08100|OPSD_HUMAN Subject_6 82.16 342 60 1 1 341 23 1048 0.0 626 +sp|P08100|OPSD_HUMAN gi|57163782|ref|NM_001009242.1| 96.55 348 12 0 1 348 1 1044 0.0 732 +sp|P08100|OPSD_HUMAN gi|2734705|gb|U59921.1|BBU59921 84.80 342 51 1 1 341 42 1067 0.0 646 +sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.24 74 5 0 239 312 3147 3368 1e-72 151 +sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 91.53 59 5 0 177 235 2855 3031 1e-72 126 +sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 96.40 111 4 0 11 121 1 333 1e-64 229 +sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.22 59 4 0 119 177 1404 1580 1e-32 122 +sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 88.46 26 3 0 312 337 4222 4299 6e-13 57.7 +sp|P08100|OPSD_HUMAN gi|283855822|gb|GQ290312.1| 95.09 326 16 0 11 336 1 978 0.0 658 +sp|P08100|OPSD_HUMAN gi|18148870|dbj|AB062417.1| 93.39 348 23 0 1 348 1 1044 0.0 711 +sp|P08100|OPSD_HUMAN gi|12583664|dbj|AB043817.1| 82.16 342 60 1 1 341 23 1048 0.0 626 --- a/tool-data/shared/ucsc/manual_builds.txt Sun Mar 27 19:50:50 2011 -0400 +++ b/tool-data/shared/ucsc/manual_builds.txt Tue Apr 05 13:57:14 2011 -0400 @@ -698,3 +698,5 @@ Hydra_JCVI Hydra magnipapillata str. 105 Araly1 Arabidopsis lyrata Zea_mays_B73_RefGen_v2 Maize (Zea mays) chr1=301354135,chr2=237068928,chr3=232140222,chr4=241473566,chr5=217872898,chr6=169174371,chr7=176764813,chr8=175793772,chr9=156750718,chr10=150189513,chr11=7140224 +Homo_sapiens_AK1 Korean Man chrM=16571,chr1=247249719,chr2=242951149,chr3=199501827,chr4=191273063,chr5=180857866,chr6=170899992,chr7=158821424,chr8=146274826,chr9=140273252,chr10=135374737,chr11=134452384,chr12=132349534,chr13=114142980,chr14=106368585,chr15=100338915,chr16=88827254,chr17=78774742,chr18=76117153,chr19=63811651,chr20=62435964,chr21=46944323,chr22=49691432,chrX=154913754,chrY=57772954 +Tcas_3.0 Red Flour Beetle (Tribolium castaneum) --- a/tool_conf.xml.main Sun Mar 27 19:50:50 2011 -0400 +++ b/tool_conf.xml.main Tue Apr 05 13:57:14 2011 -0400 @@ -169,6 +169,12 @@ <tool file="evolution/mutate_snp_codon.xml" /></section> + <section name="Motif Tools" id="motifs"> + <tool file="rgenetics/rgWebLogo3.xml" /> + </section> + <section name="Multiple Alignments" id="clustal"> + <tool file="rgenetics/rgClustalw.xml" /> + </section><section name="Metagenomic analyses" id="tax_manipulation"><tool file="taxonomy/gi2taxonomy.xml" /><tool file="taxonomy/t2t_report.xml" /> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Sun Mar 27 19:50:50 2011 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Tue Apr 05 13:57:14 2011 -0400 @@ -133,6 +133,8 @@ <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /><param name="database" value="" /><param name="evalue_cutoff" value="1e-8" /> + <param name="blast_type" value="blastp" /> + <param name="out_format" value="6" /><param name="adv_opts_selector" value="advanced" /><param name="filter_query" value="True" /><param name="matrix" value="BLOSUM62" /> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Sun Mar 27 19:50:50 2011 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Tue Apr 05 13:57:14 2011 -0400 @@ -138,7 +138,7 @@ <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" /></test><test> -  + <param name="query" value="four_human_proteins.fasta" ftype="fasta" /><param name="db_opts_selector" value="file" /><param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> @@ -151,7 +151,7 @@ <param name="max_hits" value="0" /><param name="word_size" value="0" /><param name="parse_deflines" value="true" /> - <output name="output1" file="tblastn_four_human_vs_rhodopsin_parse_deflines.tabular" ftype="tabular" /> + <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" /></test></tests><help> --- a/tools/new_operations/intersect.xml Sun Mar 27 19:50:50 2011 -0400 +++ b/tools/new_operations/intersect.xml Tue Apr 05 13:57:14 2011 -0400 @@ -28,7 +28,7 @@ <param format="interval,gff" name="input2" type="data" help="Second dataset"><label>that intersect</label></param> - <param name="min" size="4" type="integer" value="1" help="(bp)"> + <param name="min" size="4" type="integer" value="1" min="1" help="(bp)"><label>for at least</label></param></inputs> --- a/tools/new_operations/subtract.xml Sun Mar 27 19:50:50 2011 -0400 +++ b/tools/new_operations/subtract.xml Tue Apr 05 13:57:14 2011 -0400 @@ -31,7 +31,7 @@ <option value="-p">Non-overlapping pieces of intervals</option></param> - <param name="min" size="4" type="integer" value="1" help="(bp)"> + <param name="min" size="4" type="integer" value="1" min="1" help="(bp)"><label>where minimal overlap is</label></param></inputs> --- a/tools/ngs_rna/cufflinks_wrapper.xml Sun Mar 27 19:50:50 2011 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Tue Apr 05 13:57:14 2011 -0400 @@ -42,7 +42,7 @@ </command><inputs><param format="sam,bam" name="input" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/> - <param name="max_intron_len" type="integer" value="300000" min="0" max="600000" label="Max Intron Length" help=""/> + <param name="max_intron_len" type="integer" value="300000" min="1" max="600000" label="Max Intron Length" help=""/><param name="min_isoform_fraction" type="float" value="0.05" min="0" max="1" label="Min Isoform Fraction" help=""/><param name="pre_mrna_fraction" type="float" value="0.05" min="0" max="1" label="Pre MRNA Fraction" help=""/><param name="min_map_quality" type="integer" value="0" min="0" max="255" label="Min SAM Map Quality" help=""/> --- a/tools/ngs_rna/tophat_wrapper.py Sun Mar 27 19:50:50 2011 -0400 +++ b/tools/ngs_rna/tophat_wrapper.py Tue Apr 05 13:57:14 2011 -0400 @@ -208,6 +208,10 @@ tmp_stderr.close() if returncode != 0: raise Exception, stderr + + # Copy output files from tmp directory to specified files. + shutil.copyfile( os.path.join( "tophat_out", "junctions.bed" ), options.junctions_output_file ) + shutil.copyfile( os.path.join( "tophat_out", "accepted_hits.bam" ), options.accepted_hits_output_file ) # TODO: look for errors in program output. except Exception, e: --- a/tools/ngs_rna/tophat_wrapper.xml Sun Mar 27 19:50:50 2011 -0400 +++ b/tools/ngs_rna/tophat_wrapper.xml Tue Apr 05 13:57:14 2011 -0400 @@ -397,8 +397,8 @@ ) </filter></data> - <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions" from_work_dir="tophat_out/junctions.bed"/> - <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits" from_work_dir="tophat_out/accepted_hits.bam"/> + <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions"/> + <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"/></outputs><tests> http://bitbucket.org/galaxy/galaxy-central/changeset/b643d662fe14/ changeset: r5344:b643d662fe14 user: fubar date: 2011-04-05 20:07:10 summary: change to weblogo test jpg comparison and code cleanups to rgCaCo affected #: 2 files (723 bytes) --- a/tool_conf.xml.main Tue Apr 05 13:57:14 2011 -0400 +++ b/tool_conf.xml.main Tue Apr 05 14:07:10 2011 -0400 @@ -169,12 +169,6 @@ <tool file="evolution/mutate_snp_codon.xml" /></section> - <section name="Motif Tools" id="motifs"> - <tool file="rgenetics/rgWebLogo3.xml" /> - </section> - <section name="Multiple Alignments" id="clustal"> - <tool file="rgenetics/rgClustalw.xml" /> - </section><section name="Metagenomic analyses" id="tax_manipulation"><tool file="taxonomy/gi2taxonomy.xml" /><tool file="taxonomy/t2t_report.xml" /> --- a/tools/rgenetics/rgWebLogo3.xml Tue Apr 05 13:57:14 2011 -0400 +++ b/tools/rgenetics/rgWebLogo3.xml Tue Apr 05 14:07:10 2011 -0400 @@ -5,7 +5,7 @@ #if $range.mode == 'part' -l "$range.seqstart" -u "$range.seqend" #end if - </command> + </command><inputs><page><param format="fasta" name="input" type="data" label="Fasta File" /> @@ -71,7 +71,7 @@ <param name = "mode" value="complete" /><param name = "size" value="medium" /><param name = "colours" value="auto" /> - <output name="output" file="rgWebLogo3_test.jpg" ftype="jpg" /> + <output name="output" file="rgWebLogo3_test.jpg" ftype="jpg" compare="sim_size" delta="10000" /></test></tests> @@ -90,6 +90,15 @@ ---- +**Warning about input Fasta format files** + +The Weblogo3 program used by this tool will fail if your fasta sequences are not all EXACTLY the same length. + +Fasta alignments from the companion ClustalW Galaxy tool will work but many other fasta files may cause this tool to fail - please do not file +a Galaxy bug report - this is a feature of the tool and a problem with your source data - not a tool error - please make certain all your fasta +sequences are the same length! + +---- **Attribution** Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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