Changeset [bb05077da0cc53ec617e1edb88e9593caec52b60] 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...
Committed by Robert Buels
- 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
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