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Changeset [bb05077da0cc53ec617e1edb88e9593caec52b60] by Robert Buels

Revision bb05077da0cc53ec617e1edb88e9593caec52b60, committed by Robert Buels · January 28th, 2013 @ 12:57 PM

Merge branch 'master' into canvas_features

Conflicts:
src/JBrowse/Store/SeqFeature/BAM/File.js src/JBrowse/View/Track/BlockBased.js https://github.com/GMOD/jbrowse/commit/bb05077da0cc53ec617e1edb88e9...

136 changed files

  • A img/dark_20x2.png
  • A plugins/WebApollo/img/ApolloLogo_100x36.png
  • A src/JBrowse/ConfigAdaptor/AdaptorUtil.js
  • A src/JBrowse/ConfigAdaptor/conf.js
  • A src/JBrowse/Model/Location.js
  • A src/JBrowse/Model/NestedFrequencyTable.js
  • A src/JBrowse/Store/Hash.js
  • A src/JBrowse/Store/Names/Hash.js
  • A src/JBrowse/Store/Names/LazyTrieDojoData.js
  • A src/JBrowse/View/Export/SequinTable.js
  • A src/JBrowse/View/LocationChoiceDialog.js
  • A src/JBrowse/View/LocationList.js
  • A src/JBrowse/View/Track/SNPCoverage.js
  • A src/dbind
  • A src/dgrid
  • A src/json-schema
  • A src/perl5/Bio/JBrowse/ExternalSorter.pm
  • A src/perl5/Bio/JBrowse/HashStore.pm
  • A src/put-selector
  • A src/xstyle
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/names.txt
  • A tests/data/volvox_formatted_names/names/0.json
  • A tests/data/volvox_formatted_names/names/1.json
  • A tests/data/volvox_formatted_names/names/2.json
  • A tests/data/volvox_formatted_names/names/3.json
  • A tests/data/volvox_formatted_names/names/4.json
  • A tests/data/volvox_formatted_names/names/5.json
  • A tests/data/volvox_formatted_names/names/6.json
  • A tests/data/volvox_formatted_names/names/7.json
  • A tests/data/volvox_formatted_names/names/8.json
  • A tests/data/volvox_formatted_names/names/9.json
  • A tests/data/volvox_formatted_names/names/a.json
  • A tests/data/volvox_formatted_names/names/b.json
  • A tests/data/volvox_formatted_names/names/c.json
  • A tests/data/volvox_formatted_names/names/d.json
  • A tests/data/volvox_formatted_names/names/e.json
  • A tests/data/volvox_formatted_names/names/f.json
  • A tests/data/volvox_formatted_names/names/meta.json
  • A tests/data/volvox_formatted_names/tracks/Alignments/ctgA/names.txt
  • A tests/data/volvox_formatted_names/tracks/CDS/ctgA/names.txt
  • A tests/data/volvox_formatted_names/tracks/Clones/ctgA/names.txt
  • A tests/data/volvox_formatted_names/tracks/EST/ctgA/names.txt
  • A tests/data/volvox_formatted_names/tracks/ExampleFeatures/ctgA/names.txt
  • A tests/data/volvox_formatted_names/tracks/ExampleFeatures/ctgB/names.txt
  • A tests/data/volvox_formatted_names/tracks/Genes/ctgA/names.txt
  • A tests/data/volvox_formatted_names/tracks/Motifs/ctgA/names.txt
  • A tests/data/volvox_formatted_names/tracks/NameTest/ctgA/names.txt
  • A tests/data/volvox_formatted_names/tracks/ReadingFrame/ctgA/names.txt
  • A tests/data/volvox_formatted_names/tracks/Transcript/ctgA/names.txt
  • A tests/data/volvox_formatted_names/tracks/snps/ctgA/names.txt
  • A tests/js_tests/spec/GBrowseParseTestBasic.conf
  • A tests/js_tests/spec/GBrowseParser.spec.js
  • A tests/js_tests/spec/NestedFrequencyTable.spec.js
  • R img/black_20x2.png
  • R src/JBrowse/Store/Autocomplete.js
  • R src/perl5/ExternalSorter.pm
  • R tests/data/hg19_formatted/tracks/knownGene/chr1/names.json
  • R tests/data/volvox_formatted_names/names/root.json
  • R tests/data/volvox_formatted_names/tracks/Alignments/ctgA/names.json
  • R tests/data/volvox_formatted_names/tracks/CDS/ctgA/names.json
  • R tests/data/volvox_formatted_names/tracks/Clones/ctgA/names.json
  • R tests/data/volvox_formatted_names/tracks/EST/ctgA/names.json
  • R tests/data/volvox_formatted_names/tracks/ExampleFeatures/ctgA/names.json
  • R tests/data/volvox_formatted_names/tracks/ExampleFeatures/ctgB/names.json
  • R tests/data/volvox_formatted_names/tracks/Genes/ctgA/names.json
  • R tests/data/volvox_formatted_names/tracks/Motifs/ctgA/names.json
  • R tests/data/volvox_formatted_names/tracks/NameTest/ctgA/names.json
  • R tests/data/volvox_formatted_names/tracks/ReadingFrame/ctgA/names.json
  • R tests/data/volvox_formatted_names/tracks/Transcript/ctgA/names.json
  • R tests/data/volvox_formatted_names/tracks/snps/ctgA/names.json
  • M .gitignore
  • M .gitmodules
  • M Makefile.PL
  • M README.md
  • M bin/generate-names.pl
  • M bin/ucsc-to-json.pl
  • M build/init.js
  • M docs/docs.css
  • M docs/screencasts/demo_script.txt
  • M docs/tutorial/conf_files/volvox.json
  • M docs/tutorial/data_files/volvox-sorted.bam.coverage.conf
  • M docs/tutorial/data_files/volvox.gff3
  • M docs/tutorial/index.html
  • M index.html
  • M jbrowse_conf.json
  • M main.css
  • M plugins/WebApollo/css/genome.css
  • M plugins/WebApollo/css/webapollo_track_styles.css
  • M plugins/WebApollo/js/JSONUtils.js
  • M plugins/WebApollo/js/SequenceOntologyUtils.js
  • M plugins/WebApollo/js/View/Track/AnnotTrack.js
  • M plugins/WebApollo/js/View/Track/DraggableAlignments.js
  • M plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js
  • M plugins/WebApollo/js/View/Track/SequenceTrack.js
  • M plugins/WebApollo/js/main.js
  • M release-notes.txt
  • M sample_data/json/modencode/trackList.json
  • M setup.sh
  • M src/JBrowse/Browser.js
  • M src/JBrowse/ConfigAdaptor/JB_json_v1.js
  • M src/JBrowse/GenomeView.js
  • M src/JBrowse/JBrowse.profile.js
  • M src/JBrowse/Store/SeqFeature.js
  • M src/JBrowse/Store/SeqFeature/BAM.js
  • M src/JBrowse/Store/SeqFeature/BAM/File.js
  • M src/JBrowse/Store/SeqFeature/GFF3.js
  • M src/JBrowse/Store/TiledImage/Fixed.js
  • M src/JBrowse/Util.js
  • M src/JBrowse/View/Ruler.js
  • M src/JBrowse/View/Track/ExportMixin.js
  • M src/JBrowse/View/Track/FixedImage.js
  • M src/JBrowse/View/Track/HTMLFeatures.js
  • M src/JBrowse/View/Track/WiggleBase.js
  • M src/JBrowse/View/Track/YScaleMixin.js
  • M src/dijit
  • M src/dojo
  • M src/dojox
  • M src/perl5/Bio/JBrowse/Cmd/FormatSequences.pm
  • M src/perl5/Bio/JBrowse/Cmd/NCFormatter.pm
  • M src/perl5/Bio/JBrowse/FeatureStream.pm
  • M src/perl5/GenomeDB.pm
  • M src/perl5/NameHandler.pm
  • M src/util
  • M tests/data/volvox_formatted_1_2_1/trackInfo.js
  • M tests/data/volvox_formatted_names/seq/refSeqs.json
  • M tests/data/volvox_formatted_names/trackList.json
  • M tests/data/volvox_formatted_refseqs/seq/refSeqs.json
  • M tests/js_tests/index.html
  • M tests/js_tests/spec/GFF3toJbrowseJsonSpec.js
  • M tests/js_tests/spec/Util.spec.js
  • M tests/perl_tests/biodb-to-json.pl.t
  • M tests/perl_tests/flatfile-to-json.pl.t
  • M tests/perl_tests/generate-names.pl.t
  • M tests/selenium_tests/jbrowse_selenium/JBrowseTest.py
  • M tests/selenium_tests/volvox_biodb_test.py
  • M track_styles.css