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Changeset [7dac8b9904496b0f50f7754309110896524f02f7] by Robert Buels

Revision 7dac8b9904496b0f50f7754309110896524f02f7, committed by Robert Buels · January 22nd, 2013 @ 01:17 PM

Merge branch 'master' into jsmithro_snpcoverage

Conflicts:

main.css
src/JBrowse/View/Track/Alignments.js

https://github.com/GMOD/jbrowse/commit/7dac8b9904496b0f50f775430911...

349 changed files

  • A .htaccess
  • A file_dialog.css
  • A img/black_20x2.png
  • A img/glyphs_black.png
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  • A img/red_crosshatch_bg.png
  • A menubar.css
  • A plugins/WebApollo/bin/flatfile-to-json.pl
  • A plugins/WebApollo/css/add_sequence_alteration.css
  • A plugins/WebApollo/css/edit_comments.css
  • A plugins/WebApollo/css/edit_dbxrefs.css
  • A plugins/WebApollo/css/export.css
  • A plugins/WebApollo/css/genome.css
  • A plugins/WebApollo/css/get_history.css
  • A plugins/WebApollo/css/get_sequence.css
  • A plugins/WebApollo/css/main.css
  • A plugins/WebApollo/css/search_sequence.css
  • A plugins/WebApollo/css/webapollo_track_styles.css
  • A plugins/WebApollo/img/ApolloLogo_100x36.png
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  • A plugins/WebApollo/js/BioFeatureUtils.js
  • A plugins/WebApollo/js/FeatureEdgeMatchManager.js
  • A plugins/WebApollo/js/FeatureSelectionManager.js
  • A plugins/WebApollo/js/FileLoader.js
  • A plugins/WebApollo/js/GFF3toJbrowseJson.js
  • A plugins/WebApollo/js/JSONUtils.js
  • A plugins/WebApollo/js/Permission.js
  • A plugins/WebApollo/js/SequenceOntologyUtils.js
  • A plugins/WebApollo/js/SequenceSearch.js
  • A plugins/WebApollo/js/Store/SeqFeature/PseudoNCList.js
  • A plugins/WebApollo/js/Store/SeqFeature/ScratchPad.js
  • A plugins/WebApollo/js/View/Track/AnnotSequenceTrack.js
  • A plugins/WebApollo/js/View/Track/AnnotTrack.js
  • A plugins/WebApollo/js/View/Track/DraggableAlignments.js
  • A plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js
  • A plugins/WebApollo/js/View/Track/SequenceTrack.js
  • A plugins/WebApollo/js/main.js
  • A plugins/WebApollo/jslib/jquery/jquery.js
  • A plugins/WebApollo/jslib/jqueryui/accordion.js
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  • A plugins/WebApollo/jslib/jqueryui/draggable.js
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  • A plugins/WebApollo/jslib/jqueryui/effects/blind.js
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  • A plugins/WebApollo/jslib/jqueryui/effects/drop.js
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  • A plugins/WebApollo/jslib/jqueryui/effects/pulsate.js
  • A plugins/WebApollo/jslib/jqueryui/effects/scale.js
  • A plugins/WebApollo/jslib/jqueryui/effects/shake.js
  • A plugins/WebApollo/jslib/jqueryui/effects/slide.js
  • A plugins/WebApollo/jslib/jqueryui/effects/transfer.js
  • A plugins/WebApollo/jslib/jqueryui/mouse.js
  • A plugins/WebApollo/jslib/jqueryui/position.js
  • A plugins/WebApollo/jslib/jqueryui/progressbar.js
  • A plugins/WebApollo/jslib/jqueryui/resizable.js
  • A plugins/WebApollo/jslib/jqueryui/selectable.js
  • A plugins/WebApollo/jslib/jqueryui/slider.js
  • A plugins/WebApollo/jslib/jqueryui/sortable.js
  • A plugins/WebApollo/jslib/jqueryui/tabs.js
  • A plugins/WebApollo/jslib/jqueryui/themes/base/images/ui-bg_flat_0_aaaaaa_40x100.png
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  • A plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.accordion.css
  • A plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.all.css
  • A plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.autocomplete.css
  • A plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.base.css
  • A plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.button.css
  • A plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.core.css
  • A plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.datepicker.css
  • A plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.dialog.css
  • A plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.progressbar.css
  • A plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.resizable.css
  • A plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.selectable.css
  • A plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.slider.css
  • A plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.tabs.css
  • A plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.theme.css
  • A plugins/WebApollo/jslib/jqueryui/widget.js
  • A plugins/WebApollo/perl5/Bio/WebApollo/Cmd/FlatFileToJson.pm
  • A plugins/WebApollo/tests/data/MAKER/Group1.33_Amel_4.5.maker.gff
  • A plugins/WebApollo/tests/data/MAKER/Group1.33_Amel_4.5.maker.jbrowse.expected.json
  • A plugins/WebApollo/tests/data/MAKER/Group1.33_Amel_4.5.maker.jbrowse.expected_PRETTIFIED.json
  • A plugins/WebApollo/tests/data/MAKER/Group1.33_Amel_4.5.maker.webapollo.expected.json
  • A plugins/WebApollo/tests/js_tests/index.html
  • A plugins/WebApollo/tests/js_tests/lib/jasmine-1.2.0/MIT.LICENSE
  • A plugins/WebApollo/tests/js_tests/lib/jasmine-1.2.0/jasmine-html.js
  • A plugins/WebApollo/tests/js_tests/lib/jasmine-1.2.0/jasmine.css
  • A plugins/WebApollo/tests/js_tests/lib/jasmine-1.2.0/jasmine.js
  • A plugins/WebApollo/tests/js_tests/spec/GFF3toJbrowseJsonSpec.js
  • A plugins/WebApollo/tests/js_tests/spec/JSONUtilsSpec.js
  • A plugins/WebApollo/tests/perl_tests/flatfile-to-json.pl.t
  • A plugins/WebApollo/tests/selenium_tests/lib/WebApolloTest.py
  • A plugins/WebApollo/tests/selenium_tests/lib/__init__.py
  • A plugins/WebApollo/tests/selenium_tests/pythium_test.py
  • A src/JBrowse/CodonTable.js
  • A src/JBrowse/ConfigAdaptor/AdaptorUtil.js
  • A src/JBrowse/ConfigAdaptor/conf.js
  • A src/JBrowse/Model/Location.js
  • A src/JBrowse/Model/SimpleFeature.js
  • A src/JBrowse/Store/Hash.js
  • A src/JBrowse/Store/Names/Hash.js
  • A src/JBrowse/Store/Names/LazyTrieDojoData.js
  • A src/JBrowse/Store/SeqFeature/BAM/LazyFeature.js
  • A src/JBrowse/Store/SeqFeature/GFF3.js
  • A src/JBrowse/Store/SeqFeature/GFF3/GFF3Parser.js
  • A src/JBrowse/View/ConfirmDialog.js
  • A src/JBrowse/View/Export/SequinTable.js
  • A src/JBrowse/View/FileDialog.js
  • A src/JBrowse/View/FileDialog/ResourceList.js
  • A src/JBrowse/View/FileDialog/TrackList.js
  • A src/JBrowse/View/FileDialog/TrackList/BAMDriver.js
  • A src/JBrowse/View/FileDialog/TrackList/BigWigDriver.js
  • A src/JBrowse/View/FileDialog/TrackList/GFF3Driver.js
  • A src/JBrowse/View/LocationChoiceDialog.js
  • A src/JBrowse/View/LocationList.js
  • A src/JBrowse/View/Track/CanvasFeatures.js
  • A src/JBrowse/View/TrackConfigEditor.js
  • A src/dgrid
  • A src/lazyload
  • A src/perl5/Bio/JBrowse/ExternalSorter.pm
  • A src/perl5/Bio/JBrowse/HashStore.pm
  • A src/put-selector
  • A src/xstyle
  • A tests/data/foo.bed
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/names.txt
  • A tests/data/redundant.gff3
  • 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
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  • 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/install_selenium.sh
  • A tests/js_tests/spec/AddFiles.spec.js
  • A tests/js_tests/spec/GBrowseParseTestBasic.conf
  • A tests/js_tests/spec/GBrowseParser.spec.js
  • A tests/js_tests/spec/GFF3ParserCheckDeeperFeatures.js
  • A tests/js_tests/spec/GFF3ParserSpec.js
  • A tests/js_tests/spec/GFF3toJbrowseJsonSpec.js
  • A tests/js_tests/spec/Util.spec.js
  • A tests/perl_tests/featurestream.t
  • R src/JBrowse/Store/Autocomplete.js
  • R src/JBrowse/Store/SeqFeature/BAM/Feature.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/Makefile
  • M docs/screencasts/demo_script.txt
  • M docs/tutorial/conf_files/volvox.json
  • M faceted_track_selector.css
  • M genome.css
  • M icons.css
  • M img/commonIconsEnabled.png
  • M img/minus-arrowhead.png
  • M img/plus-arrowhead.png
  • M index.html
  • M jbrowse_conf.json
  • M main.css
  • M release-notes.txt
  • M setup.sh
  • M src/JBrowse/Browser.js
  • M src/JBrowse/ConfigAdaptor/JB_json_v1.js
  • M src/JBrowse/ConfigManager.js
  • M src/JBrowse/Finisher.js
  • M src/JBrowse/GenomeView.js
  • M src/JBrowse/Model/ArrayRepr.js
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  • M src/JBrowse/Store/SeqFeature/BAM.js
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  • M src/JBrowse/Store/SeqFeature/BigWig.js
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  • M src/JBrowse/Store/Sequence/StaticChunked.js
  • M src/JBrowse/Store/TrackMetaData.js
  • M src/JBrowse/Util.js
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  • M src/JBrowse/View/TrackList/Faceted.js
  • M src/JBrowse/View/TrackList/Simple.js
  • M src/jszlib
  • M src/perl5/Bio/JBrowse/Cmd/FlatFileToJson.pm
  • 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/Bio/JBrowse/FeatureStream/BioPerl.pm
  • M src/perl5/Bio/JBrowse/FeatureStream/GFF3_LowLevel.pm
  • M src/perl5/GenomeDB.pm
  • M src/perl5/JBlibs.pm
  • M src/perl5/NameHandler.pm
  • 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/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