Changeset [68ae3042102efac54e0fdff5eb3c3deba2023b43] by Colin

March 5th, 2016 @ 08:52 PM

Committed by Colin

  • A ".jshintrc"
  • A ".travis.yml"
  • A browser/main.js
  • A browser/menu.js
  • A css/combination_tracks.css
  • A css/export_dialog.css
  • A css/faceted_track_selector.css
  • A css/file_dialog.css
  • A css/genome.css
  • A css/hierarchical_track_selector.css
  • A css/icons.css
  • A css/main.css
  • A css/maker.css
  • A css/menubar.css
  • A css/protein.css
  • A css/sequence.css
  • A css/toolbar.css
  • A css/track_styles.css
  • A css/tristate.css
  • A docs/tutorial/data_files/bookmarks.conf
  • A docs/tutorial/data_files/volvox.fa.fai
  • A docs/tutorial/data_files/volvox.sort.gff3.gz.1
  • A docs/tutorial/data_files/volvox.sort.gff3.gz.conf
  • A docs/tutorial/data_files/volvox.sort.gff3.gz.tbi
  • A img/JBrowseLogo.png
  • A package.json
  • A plugins/CategoryUrl/README.md
  • A plugins/CategoryUrl/css/main.css
  • A plugins/CategoryUrl/js/CategoryUrl.profile.js
  • A plugins/CategoryUrl/js/main.js
  • A plugins/DebugEvents/css/main.css
  • A plugins/DebugEvents/js/DebugEvents.profile.js
  • A plugins/DebugEvents/js/main.js
  • A plugins/HideTrackLabels/css/main.css
  • A plugins/HideTrackLabels/img/eye_bl.png
  • A plugins/HideTrackLabels/img/eye_open.png
  • A plugins/HideTrackLabels/js/HideTrackLabels.profile.js
  • A plugins/HideTrackLabels/js/main.js
  • A plugins/NeatCanvasFeatures/README.md
  • A plugins/NeatCanvasFeatures/css/main.css
  • A plugins/NeatCanvasFeatures/js/NeatCanvasFeatures.profile.js
  • A plugins/NeatCanvasFeatures/js/main.js
  • A plugins/NeatHTMLFeatures/README.md
  • A plugins/NeatHTMLFeatures/css/main.css
  • A plugins/NeatHTMLFeatures/js/NeatHTMLFeatures.profile.js
  • A plugins/NeatHTMLFeatures/js/main.js
  • A plugins/SVGLollipopTrack/SVGFeatures.js
  • A plugins/SVGLollipopTrack/readme.md
  • A sample_data/json/modencode/tracks.conf
  • A src/JBrowse/Store/SeqFeature/GFF3Tabix.js
  • A src/JBrowse/Store/SeqFeature/GFF3Tabix/LazyFeature.js
  • A src/JBrowse/Store/SeqFeature/IndexedFasta.js
  • A src/JBrowse/Store/SeqFeature/IndexedFasta/File.js
  • A src/JBrowse/Store/SeqFeature/UnindexedFasta.js
  • A src/JBrowse/Store/SeqFeature/UnindexedFasta/File.js
  • A src/JBrowse/Store/Sequence/IndexedFasta.js
  • A src/JBrowse/View/Dialog/OpenDirectory.js
  • A src/JBrowse/View/Dialog/Preferences.js
  • A src/JBrowse/View/FastaFileDialog.js
  • A src/JBrowse/View/FileDialog/TrackList/FASTADriver.js
  • A src/JBrowse/View/FileDialog/TrackList/GFF3TabixDriver.js
  • A src/JBrowse/View/FileDialog/TrackList/IndexedFASTADriver.js
  • A src/JBrowse/View/Resource/Welcome.html
  • A src/JBrowse/View/Resource/Welcome_old.html
  • A tests/js_tests/run-jasmine.js
  • A tests/js_tests/spec/GFF3Tabix.spec.js
  • A tests/travis.conf
  • R combination_tracks.css
  • R export_dialog.css
  • R faceted_track_selector.css
  • R file_dialog.css
  • R genome.css
  • R hierarchical_track_selector.css
  • R icons.css
  • R main.css
  • R maker.css
  • R menubar.css
  • R sample_data/json/modencode/tracks/volvox_microarray.wig
  • R sequence.css
  • R src/JBrowse/Store/SeqFeature/GFF3/GFF3Parser.js
  • R tests/data/SL2.40_all_rna_seq.v1.bigwig
  • R track_styles.css
  • R tristate.css
  • M ".gitignore"
  • M Makefile.PL
  • M README.md
  • M bin/add-bw-track.pl
  • M bin/cpanm
  • M bin/maker2jbrowse
  • M bin/new-plugin.pl
  • M bin/prepare-refseqs.pl
  • M build/Makefile
  • M compat_121.html
  • M docs/tutorial/conf_files/volvox.json
  • M docs/tutorial/data_files/volvox_sine.bw.conf
  • M docs/tutorial/index.html
  • M index.html
  • M jbrowse.conf
  • M plugins/RegexSequenceSearch/js/Store/SeqFeature/RegexSearch.js
  • M plugins/RegexSequenceSearch/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/CodonTable.js
  • M src/JBrowse/ConfigAdaptor/JB_json_v1.js
  • M src/JBrowse/ConfigAdaptor/conf.js
  • M src/JBrowse/ConfigManager.js
  • M src/JBrowse/GenomeView.js
  • M src/JBrowse/Model/BinaryTreeNode.js
  • M src/JBrowse/Model/DataView.js
  • M src/JBrowse/Model/Range.js
  • M src/JBrowse/Model/modEncodeTrackMetadata.js
  • M src/JBrowse/Store/LRUCache.js
  • M src/JBrowse/Store/NCList.js
  • M src/JBrowse/Store/NCList_v0.js
  • M src/JBrowse/Store/Names/LazyTrieDojoData.js
  • M src/JBrowse/Store/RemoteBinaryFile.js
  • M src/JBrowse/Store/SeqFeature.js
  • M src/JBrowse/Store/SeqFeature/BAM.js
  • M src/JBrowse/Store/SeqFeature/BAM/LazyFeature.js
  • M src/JBrowse/Store/SeqFeature/BAMCombination.js
  • M src/JBrowse/Store/SeqFeature/BigWig.js
  • M src/JBrowse/Store/SeqFeature/BigWig/RequestWorker.js
  • M src/JBrowse/Store/SeqFeature/Combination.js
  • M src/JBrowse/Store/SeqFeature/CombinationBase.js
  • M src/JBrowse/Store/SeqFeature/GFF3.js
  • M src/JBrowse/Store/SeqFeature/GFF3/Parser.js
  • M src/JBrowse/Store/SeqFeature/GTF.js
  • M src/JBrowse/Store/SeqFeature/GlobalStatsEstimationMixin.js
  • M src/JBrowse/Store/SeqFeature/Mask.js
  • M src/JBrowse/Store/SeqFeature/NCList.js
  • M src/JBrowse/Store/SeqFeature/QuantitativeCombination.js
  • M src/JBrowse/Store/SeqFeature/SNPCoverage.js
  • M src/JBrowse/Store/SeqFeature/SPARQL.js
  • M src/JBrowse/Store/SeqFeature/SequenceChunks.js
  • M src/JBrowse/Store/SeqFeature/VCFTabix.js
  • M src/JBrowse/Store/SeqFeature/VCFTabix/Parser.js
  • M src/JBrowse/Store/TrackMetaData.js
  • M src/JBrowse/TouchScreenSupport.js
  • M src/JBrowse/Util.js
  • M src/JBrowse/Util/GFF3.js
  • M src/JBrowse/Util/GTF.js
  • M src/JBrowse/View/Animation.js
  • M src/JBrowse/View/DetailsMixin.js
  • M src/JBrowse/View/Export/GFF3.js
  • M src/JBrowse/View/FeatureGlyph.js
  • M src/JBrowse/View/FeatureGlyph/Alignment.js
  • M src/JBrowse/View/FeatureGlyph/Box.js
  • M src/JBrowse/View/FeatureGlyph/Diamond.js
  • M src/JBrowse/View/FeatureGlyph/ProcessedTranscript.js
  • M src/JBrowse/View/FeatureGlyph/Segments.js
  • M src/JBrowse/View/FeatureGlyph/_FeatureLabelMixin.js
  • M src/JBrowse/View/FileDialog.js
  • M src/JBrowse/View/FileDialog/ResourceList.js
  • M src/JBrowse/View/Track/Alignments2.js
  • M src/JBrowse/View/Track/BlockBased.js
  • M src/JBrowse/View/Track/CanvasFeatures.js
  • M src/JBrowse/View/Track/Combination.js
  • M src/JBrowse/View/Track/Combination/CombinationDialog.js
  • M src/JBrowse/View/Track/FixedImage.js
  • M src/JBrowse/View/Track/GridLines.js
  • M src/JBrowse/View/Track/HTMLFeatures.js
  • M src/JBrowse/View/Track/LocationScale.js
  • M src/JBrowse/View/Track/SNPCoverage.js
  • M src/JBrowse/View/Track/Sequence.js
  • M src/JBrowse/View/Track/Wiggle/XYPlot.js
  • M src/JBrowse/View/Track/Wiggle/_Scale.js
  • M src/JBrowse/View/Track/WiggleBase.js
  • M src/JBrowse/View/Track/_AlignmentsMixin.js
  • M src/JBrowse/View/Track/_ExportMixin.js
  • M src/JBrowse/View/Track/_VariantDetailMixin.js
  • M src/JBrowse/View/TrackList/Faceted.js
  • M src/JBrowse/View/TrackList/Hierarchical.js
  • M src/JBrowse/View/TrackList/_TextFilterMixin.js
  • M src/JBrowse/package.json
  • M src/perl5/Bio/JBrowse/Cmd/FormatSequences.pm
  • M src/perl5/Bio/JBrowse/Cmd/IndexNames.pm
  • M src/perl5/Bio/JBrowse/FeatureStream.pm
  • M src/perl5/Bio/JBrowse/HashStore.pm
  • M tests/data/volvox_formatted_refseqs/trackList.json
  • M tests/js_tests/index.html
  • M tests/js_tests/spec/BAM.spec.js
  • M tests/js_tests/spec/GBrowseParseTestBasic.conf
  • M tests/js_tests/spec/TabixIndexedFile.spec.js
  • M tests/perl_tests/biodb-to-json.pl.t
  • M tests/perl_tests/wig-to-json.pl.t
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