Changeset [066b2c886b39bd04fdc320034a495820fa976f5e] by Robert Buels
March 18th, 2012 @ 06:46 PM
Merge branch 'master' into rubberband
Conflicts:
genome.css
js/GenomeView.js
https://github.com/GMOD/jbrowse/commit/066b2c886b39bd04fdc320034a49...
Committed by Robert Buels
- A Makefile.PL
- A Makefile.deploy
- A README.md
- A bin/cpanm
- A bin/jbdoc
- A compat_121.html
- A dist.ini
- A img/closedhand.cur
- A img/openhand.cur
- A js/ArrayRepr.js
- A js/ConfigAdaptor/JB_json_v0.js
- A js/ConfigAdaptor/JB_json_v1.js
- A js/GridTrack.js
- A js/NCList_v0.js
- A js/SeqFeatureStore.js
- A js/SeqFeatureStore/NCList.js
- A js/SeqFeatureStore/NCList_v0.js
- A js/SequenceStore/StaticChunked.js
- A js/StaticTrack.js
- A js/Store.js
- A js/TiledImageStore/Fixed.js
- A js/TiledImageStore/Fixed_v0.js
- A jslib/jsdoc_toolkit-2.4.0/README.txt
- A jslib/jsdoc_toolkit-2.4.0/app/frame.js
- A jslib/jsdoc_toolkit-2.4.0/app/frame/Chain.js
- A jslib/jsdoc_toolkit-2.4.0/app/frame/Dumper.js
- A jslib/jsdoc_toolkit-2.4.0/app/frame/Hash.js
- A jslib/jsdoc_toolkit-2.4.0/app/frame/Link.js
- A jslib/jsdoc_toolkit-2.4.0/app/frame/Namespace.js
- A jslib/jsdoc_toolkit-2.4.0/app/frame/Opt.js
- A jslib/jsdoc_toolkit-2.4.0/app/frame/Reflection.js
- A jslib/jsdoc_toolkit-2.4.0/app/frame/String.js
- A jslib/jsdoc_toolkit-2.4.0/app/frame/Testrun.js
- A jslib/jsdoc_toolkit-2.4.0/app/handlers/FOODOC.js
- A jslib/jsdoc_toolkit-2.4.0/app/handlers/XMLDOC.js
- A jslib/jsdoc_toolkit-2.4.0/app/handlers/XMLDOC/DomReader.js
- A jslib/jsdoc_toolkit-2.4.0/app/handlers/XMLDOC/XMLDoc.js
- A jslib/jsdoc_toolkit-2.4.0/app/handlers/XMLDOC/XMLParse.js
- A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC.js
- A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/DocComment.js
- A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/DocTag.js
- A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/JsDoc.js
- A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/JsPlate.js
- A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/Lang.js
- A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/Parser.js
- A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/PluginManager.js
- A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/Symbol.js
- A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/SymbolSet.js
- A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/TextStream.js
- A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/Token.js
- A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/TokenReader.js
- A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/TokenStream.js
- A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/Util.js
- A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/Walker.js
- A jslib/jsdoc_toolkit-2.4.0/app/main.js
- A jslib/jsdoc_toolkit-2.4.0/app/plugins/commentSrcJson.js
- A jslib/jsdoc_toolkit-2.4.0/app/plugins/frameworkPrototype.js
- A jslib/jsdoc_toolkit-2.4.0/app/plugins/functionCall.js
- A jslib/jsdoc_toolkit-2.4.0/app/plugins/publishSrcHilite.js
- A jslib/jsdoc_toolkit-2.4.0/app/plugins/symbolLink.js
- A jslib/jsdoc_toolkit-2.4.0/app/plugins/tagParamConfig.js
- A jslib/jsdoc_toolkit-2.4.0/app/plugins/tagSynonyms.js
- A jslib/jsdoc_toolkit-2.4.0/app/run.js
- A jslib/jsdoc_toolkit-2.4.0/app/t/TestDoc.js
- A jslib/jsdoc_toolkit-2.4.0/app/t/runner.js
- A jslib/jsdoc_toolkit-2.4.0/app/test.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/addon.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/anon_inner.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/augments.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/augments2.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/borrows.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/borrows2.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/config.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/constructs.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/encoding.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/encoding_other.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/event.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/exports.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/functions_anon.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/functions_nested.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/global.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/globals.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/ignore.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/inner.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/jsdoc_test.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/lend.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/memberof.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/memberof2.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/memberof3.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/memberof_constructor.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/module.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/multi_methods.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/name.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/namespace_nested.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/nocode.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/oblit_anon.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/overview.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/param_inline.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/params_optional.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/prototype.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/prototype_nested.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/prototype_oblit.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/prototype_oblit_constructor.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/public.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/scripts/code.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/scripts/notcode.txt
- A jslib/jsdoc_toolkit-2.4.0/app/test/shared.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/shared2.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/shortcuts.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/static_this.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/synonyms.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/tosource.js
- A jslib/jsdoc_toolkit-2.4.0/app/test/variable_redefine.js
- A jslib/jsdoc_toolkit-2.4.0/changes.txt
- A jslib/jsdoc_toolkit-2.4.0/conf/sample.conf
- A jslib/jsdoc_toolkit-2.4.0/java/build.xml
- A jslib/jsdoc_toolkit-2.4.0/java/build_1.4.xml
- A jslib/jsdoc_toolkit-2.4.0/java/classes/js.jar
- A jslib/jsdoc_toolkit-2.4.0/java/src/JsDebugRun.java
- A jslib/jsdoc_toolkit-2.4.0/java/src/JsRun.java
- A jslib/jsdoc_toolkit-2.4.0/jsdebug.jar
- A jslib/jsdoc_toolkit-2.4.0/jsrun.jar
- A jslib/jsdoc_toolkit-2.4.0/jsrun.sh
- A jslib/jsdoc_toolkit-2.4.0/templates/jsdoc/allclasses.tmpl
- A jslib/jsdoc_toolkit-2.4.0/templates/jsdoc/allfiles.tmpl
- A jslib/jsdoc_toolkit-2.4.0/templates/jsdoc/class.tmpl
- A jslib/jsdoc_toolkit-2.4.0/templates/jsdoc/index.tmpl
- A jslib/jsdoc_toolkit-2.4.0/templates/jsdoc/publish.js
- A jslib/jsdoc_toolkit-2.4.0/templates/jsdoc/static/default.css
- A jslib/jsdoc_toolkit-2.4.0/templates/jsdoc/static/header.html
- A jslib/jsdoc_toolkit-2.4.0/templates/jsdoc/static/index.html
- A jslib/jsdoc_toolkit-2.4.0/templates/jsdoc/symbol.tmpl
- A lib/ArrayRepr.pm
- A lib/FeatureTrack.pm
- A lib/GenomeDB.pm
- A lib/ImageTrack.pm
- A lib/IntervalStore.pm
- A lib/JsonFileStorage.pm
- A sample_data/json/.exists
- A sample_data/raw/Dmel.json
- A sample_data/raw/ideograms/human_cytobands.gff
- A sample_data/raw/ideograms/mouse_cytobands.gff
- A sample_data/raw/ideograms/rat_cytobands.gff
- A sample_data/raw/pop_demo/pop_demo.gff3
- A sample_data/raw/tomato.json
- A sample_data/raw/volvox
- A sample_data/raw/volvox.json
- A sample_data/raw/yeast.json
- A sample_data/raw/yeast_chr1+2/yeast_chr1+2.gff3
- A sample_data/raw/yeast_gbk/NC_001133.gbk
- A sample_data/raw/yeast_gbk/NC_001133.gbk.gff
- A sample_data/raw/yeast_genbank.json
- A sample_data/raw/yeast_scaffolds/chr1.fa.gz
- A sample_data/raw/yeast_scaffolds/chr2.fa.gzip
- A sample_data/raw/yeast_scaffolds/chromosomes.gff3
- A t
- A tests/data/AU9/seq/refSeqs.json
- A tests/data/AU9/single_au9_gene.gff3
- A tests/data/base_pairing/XdecoderStructure.gff
- A tests/data/base_pairing/mahoney.fa
- A tests/data/base_pairing/mahoney_formatted/seq/mahoney/0.txt
- A tests/data/base_pairing/mahoney_formatted/seq/refSeqs.json
- A tests/data/base_pairing/mahoney_formatted/trackList.json
- A tests/data/hg19/database/knownGene.sql
- A tests/data/hg19/database/knownGene.txt.gz
- A tests/data/hg19/database/trackDb.sql
- A tests/data/hg19/database/trackDb.txt.gz
- A tests/data/hg19_chromosomes.fkfa
- A tests/data/hg19_formatted/trackList.json
- A tests/data/hg19_formatted/tracks/knownGene/chr1/hist-100000-0.jsonz
- A tests/data/hg19_formatted/tracks/knownGene/chr1/hist-1000000-0.jsonz
- A tests/data/hg19_formatted/tracks/knownGene/chr1/hist-200000-0.jsonz
- A tests/data/hg19_formatted/tracks/knownGene/chr1/hist-2000000-0.jsonz
- A tests/data/hg19_formatted/tracks/knownGene/chr1/hist-500000-0.jsonz
- A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-1.jsonz
- A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-10.jsonz
- A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-11.jsonz
- A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-2.jsonz
- A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-3.jsonz
- A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-4.jsonz
- A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-5.jsonz
- A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-6.jsonz
- A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-7.jsonz
- A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-8.jsonz
- A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-9.jsonz
- A tests/data/hg19_formatted/tracks/knownGene/chr1/names.json
- A tests/data/hg19_formatted/tracks/knownGene/chr1/trackData.jsonz
- A tests/data/tomato_features.json
- A tests/data/tomato_features_nclist_with_chunksize_10000.json
- A tests/data/volvox_formatted_1_2_1/refSeqs.js
- A tests/data/volvox_formatted_1_2_1/seq/ctgA/0.txt
- A tests/data/volvox_formatted_1_2_1/seq/ctgA/1.txt
- A tests/data/volvox_formatted_1_2_1/seq/ctgA/2.txt
- A tests/data/volvox_formatted_1_2_1/trackInfo.js
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Alignments/hist-10000-0.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Alignments/names.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Alignments/trackData.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/CDS/hist-50000-0.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/CDS/names.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/CDS/trackData.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Clones/hist-200000-0.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Clones/names.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Clones/trackData.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/EST/hist-50000-0.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/EST/names.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/EST/trackData.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/ExampleFeatures/hist-10000-0.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/ExampleFeatures/names.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/ExampleFeatures/trackData.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Genes/hist-200000-0.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Genes/names.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Genes/trackData.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Motifs/hist-10000-0.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Motifs/names.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Motifs/trackData.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/NameTest/hist-50000-0.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/NameTest/names.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/NameTest/trackData.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/ReadingFrame/hist-50000-0.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/ReadingFrame/names.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/ReadingFrame/trackData.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Transcript/hist-200000-0.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Transcript/names.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Transcript/trackData.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-100-0.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-1000-0.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-20-0.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-200-0.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-40-0.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-400-0.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/lazyfeatures-0.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/lazyfeatures-1.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/lazyfeatures-2.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/lazyfeatures-3.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/trackData.json
- A tests/data/volvox_formatted_1_2_1/tracks/ctgA/volvox_microarray.wig.json
- A tests/data/volvox_formatted_refseqs/seq/ctgA/0.txt
- A tests/data/volvox_formatted_refseqs/seq/ctgA/1.txt
- A tests/data/volvox_formatted_refseqs/seq/ctgA/2.txt
- A tests/data/volvox_formatted_refseqs/seq/ctgB/0.txt
- A tests/data/volvox_formatted_refseqs/seq/refSeqs.json
- A tests/data/volvox_formatted_refseqs/trackList.json
- A tests/js_tests/LazyArray-test.js
- A tests/js_tests/lazyarray-0.json
- A tests/js_tests/lazyarray-1.json
- A tests/js_tests/lazyarray-2.json
- A tests/js_tests/runner.html
- A tests/perl_tests/00.compile.t
- A tests/perl_tests/FastaDatabase.t
- A tests/perl_tests/bam-to-json.pl.t
- A tests/perl_tests/bin/fasta_to_fkfa.pl
- A tests/perl_tests/bin/fkfa_to_fasta.pl
- A tests/perl_tests/biodb-to-json.pl.t
- A tests/perl_tests/draw-basepair-track.pl.t
- A tests/perl_tests/fakefasta.t
- A tests/perl_tests/flatfile-to-json.pl.t
- A tests/perl_tests/lazy_nclist.t
- A tests/perl_tests/lib/FakeFasta.pm
- A tests/perl_tests/lib/FileSlurping.pm
- A tests/perl_tests/nclist.t
- A tests/perl_tests/prepare-refseqs.pl.t
- A tests/perl_tests/ucsc-to-json.pl.t
- A tests/perl_tests/wig-to-json.pl.t
- A tests/selenium_tests/jbrowse_selenium.py
- A tests/selenium_tests/volvox_biodb_121_test.py
- A tests/selenium_tests/volvox_biodb_test.py
- A tests/selenium_tests/yeast_biodb_test.py
- A wig2png/Makefile.in
- A wig2png/configure
- A wig2png/src/config.h.in
- A wig2png/src/macros.h
- A wig2png/src/opts_list.cc
- A wig2png/src/opts_list.h
- A wig2png/src/wig2png.cc
- R Makefile
- R Makefile.in
- R closedhand.cur
- R openhand.cur
- R js/UITracks.js
- R lib/AutoHash.pm
- R src/config.h
- R tests/jasmine
- R tests/LazyArray-test.js
- R tests/lazyarray-0.json
- R tests/lazyarray-1.json
- R tests/lazyarray-2.json
- R tests/runner.html
- R touch.html
- R configure
- R src/config.h.in
- R src/macros.h
- R src/opts_list.cc
- R src/opts_list.h
- R src/wig2png.cc
- M .gitignore
- M .gitmodules
- M INSTALL
- M bin/bam-to-json.pl
- M bin/biodb-to-json.pl
- M bin/draw-basepair-track.pl
- M bin/flatfile-to-json.pl
- M bin/generate-names.pl
- M bin/prepare-refseqs.pl
- M bin/ucsc-to-json.pl
- M bin/wig-to-json.pl
- M docs/docs.css
- M docs/featureglyphs.html
- M docs/tutorial/conf_files/volvox.json
- M docs/tutorial/data_files/volvox.fa
- M docs/tutorial/data_files/volvox.gff3
- M docs/tutorial/index.html
- M genome.css
- M index.html
- M js/Browser.js
- M js/FeatureTrack.js
- M js/GenomeView.js
- M js/ImageTrack.js
- M js/Layout.js
- M js/LazyArray.js
- M js/LazyPatricia.js
- M js/NCList.js
- M js/SequenceTrack.js
- M js/Track.js
- M js/Util.js
- M js/touchJBrowse.js
- M lib/BioperlFlattener.pm
- M lib/ExternalSorter.pm
- M lib/FastaDatabase.pm
- M lib/ImageTrackRenderer.pm
- M lib/JsonGenerator.pm
- M lib/LazyNCList.pm
- M lib/LazyPatricia.pm
- M lib/NCLSorter.pm
- M lib/NCList.pm
- M lib/NameHandler.pm
- M lib/TiledImage.pm
- M release-notes.txt
- M twiki/JBrowsePlugin.pm
- M twiki/JBrowsePlugin/Makefile.jbrowse
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