All changesets

Changeset [a1dc26f7df64dfeaabc834f964c880e4ec86bbd0] by jsmirob

Revision a1dc26f7df64dfeaabc834f964c880e4ec86bbd0, committed by jsmirob · April 23rd, 2013 @ 07:32 AM

147 changed files

• A bin/add-json.pl
• A bin/new-plugin.pl
• A docs/tutorial/data_files/volvox.filtered.vcf.
• A docs/tutorial/data_files/volvox.filtered.vcf.
• A docs/tutorial/data_files/volvox.raw.bcf
• A docs/tutorial/data_files/volvox.test.vcf.gz
• A docs/tutorial/data_files/volvox.test.vcf.gz.t
• A docs/tutorial/data_files/volvox.vcf.conf
• A img/JBrowseLogo_small.png
• A img/commonIconsDisabled.png
• A img/spriteArrows.png
• A src/JBrowse/Component.js
• A src/JBrowse/Model/BGZip/BGZBlob.js
• A src/JBrowse/Model/BGZip/VirtualOffset.js
• A src/JBrowse/Model/CoverageFeature.js
• A src/JBrowse/Model/TabixIndex.js
• A src/JBrowse/Store/SeqFeature/Coverage.js
• A src/JBrowse/Store/SeqFeature/GlobalStatsEstim
• A src/JBrowse/Store/SeqFeature/REST.js
• A src/JBrowse/Store/SeqFeature/SNPCoverage.js
• A src/JBrowse/Store/SeqFeature/VCFTabix.js
• A src/JBrowse/Store/SeqFeature/VCFTabix/Parser.
• A src/JBrowse/Store/SeqFeature/_MismatchesMixin
• A src/JBrowse/Store/TabixIndexedFile.js
• A src/JBrowse/Util/FastPromise.js
• A src/JBrowse/View/DetailsMixin.js
• A src/JBrowse/View/Dialog/SetHighlight.js
• A src/JBrowse/View/Dialog/WithActionBar.js
• A src/JBrowse/View/FeatureGlyph.js
• A src/JBrowse/View/FeatureGlyph/Alignment.js
• A src/JBrowse/View/FeatureGlyph/Box.js
• A src/JBrowse/View/FeatureGlyph/_FeatureLabelMi
• A src/JBrowse/View/FileDialog/TrackList/VCFTabi
• A src/JBrowse/View/FileDialog/TrackList/_Indexe
• A src/JBrowse/View/Track/BlockBased/Block.js
• A src/JBrowse/View/Track/HTMLVariants.js
• A src/JBrowse/View/Track/VariantDetailMixin.js
• A src/JBrowse/View/Track/Wiggle/_Scale.js
• A src/JBrowse/View/Track/_AlignmentsMixin.js
• A src/jDataView
• A src/perl5/Bio/JBrowse/JSON.pm
• A tests/data/rest_store_test/features/ctgA
• A tests/data/rest_store_test/stats/global
• A tests/js_tests/spec/RESTStore.spec.js
• A tests/js_tests/spec/TabixIndex.spec.js
• A tests/js_tests/spec/TabixIndexedFile.spec.js
• A tests/perl_tests/add-json.pl.t
• A tests/perl_tests/json.t
• R src/JBrowse/View/Track/Canvas.js
• R src/JBrowse/View/Track/MismatchesMixin.js
• M .gitmodules
• M Makefile.PL
• M README.md
• M bin/add-track-json.pl
• M bin/bam-to-json.pl
• M bin/prepare-refseqs.pl
• M bin/ucsc-to-json.pl
• M bin/wig-to-json.pl
• M build/Makefile
• M build/init.js
• M docs/tutorial/conf_files/volvox.json
• M docs/tutorial/data_files/volvox-sorted.bam.co
• M docs/tutorial/data_files/volvox-sorted.bam.co
• M docs/tutorial/data_files/volvox_microarray.bw
• M icons.css
• M index.html
• M jbrowse_conf.json
• M main.css
• M menubar.css
• 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/Model/Location.js
• M src/JBrowse/Model/NestedFrequencyTable.js
• M src/JBrowse/Model/SimpleFeature.js
• M src/JBrowse/Plugin.js
• M src/JBrowse/Store.js
• M src/JBrowse/Store/DeferredFeaturesMixin.js
• M src/JBrowse/Store/DeferredStatsMixin.js
• M src/JBrowse/Store/LRUCache.js
• M src/JBrowse/Store/Names/Hash.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/File.js
• M src/JBrowse/Store/SeqFeature/BAM/LazyFeature.
• M src/JBrowse/Store/SeqFeature/BigWig.js
• M src/JBrowse/Store/SeqFeature/BigWig/RequestWo
• M src/JBrowse/Store/SeqFeature/BigWig/Window.js
• M src/JBrowse/Store/TrackMetaData.js
• M src/JBrowse/Util.js
• M src/JBrowse/View/ConfirmDialog.js
• M src/JBrowse/View/Export/GFF3.js
• M src/JBrowse/View/FileDialog/ResourceList.js
• M src/JBrowse/View/FileDialog/TrackList.js
• M src/JBrowse/View/FileDialog/TrackList/BAMDriv
• M src/JBrowse/View/FileDialog/TrackList/BigWigD
• M src/JBrowse/View/FileDialog/TrackList/GFF3Dri
• M src/JBrowse/View/GranularRectLayout.js
• M src/JBrowse/View/InfoDialog.js
• M src/JBrowse/View/LocationChoiceDialog.js
• M src/JBrowse/View/LocationList.js
• M src/JBrowse/View/Track/Alignments.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/ExportMixin.js
• M src/JBrowse/View/Track/FeatureCoverage.js
• M src/JBrowse/View/Track/FeatureDetailMixin.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/Density.js
• M src/JBrowse/View/Track/Wiggle/XYPlot.js
• M src/JBrowse/View/Track/WiggleBase.js
• M src/JBrowse/View/TrackList/Faceted.js
• M src/JBrowse/View/TrackList/Simple.js
• M src/jszlib
• M src/perl5/Bio/JBrowse/Cmd/BioDBToJson.pm
• M src/perl5/Bio/JBrowse/Cmd/FlatFileToJson.pm
• M src/perl5/Bio/JBrowse/Cmd/FormatSequences.pm
• M src/perl5/Bio/JBrowse/Cmd/RemoveTrack.pm
• M src/perl5/Bio/JBrowse/HashStore.pm
• M src/perl5/ImageTrackRenderer.pm
• M tests/data/volvox_formatted_1_2_1/trackInfo.j
• M tests/data/volvox_formatted_refseqs/trackList
• M tests/js_tests/index.html
• M tests/js_tests/spec/AddFiles.spec.js
• M tests/js_tests/spec/BAM.spec.js
• M tests/js_tests/spec/BigWig.spec.js
• M tests/js_tests/spec/FeatureLayout.spec.js
• 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/wig-to-json.pl.t
• M tests/selenium_tests/jbrowse_selenium/JBrowse
• M tests/selenium_tests/jbrowse_selenium/track_s
• M tests/selenium_tests/modencode_faceted_tracks
• M tests/selenium_tests/volvox_biodb_test.py
• M tests/selenium_tests/yeast_biodb_test.py