Changeset [68ae3042102efac54e0fdff5eb3c3deba2023b43] by Colin

Revision 68ae3042102efac54e0fdff5eb3c3deba2023b43, committed by Colin · March 5th, 2016 @ 08:52 PM

Merge master
https://github.com/GMOD/jbrowse/commit/68ae3042102efac54e0fdff5eb3c...

187 changed files

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