Changeset [7dac8b9904496b0f50f7754309110896524f02f7] 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...
Committed by Robert Buels
- A .htaccess
- A file_dialog.css
- A img/black_20x2.png
- A img/glyphs_black.png
- A img/glyphs_white.png
- 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/img/loading.gif
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- A plugins/WebApollo/img/minus-transcript-head.png
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- A plugins/WebApollo/img/warning_exclamation.png
- A plugins/WebApollo/img/warning_exclamation_small.png
- 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
- A plugins/WebApollo/jslib/jqueryui/autocomplete.js
- A plugins/WebApollo/jslib/jqueryui/button.js
- A plugins/WebApollo/jslib/jqueryui/core.js
- A plugins/WebApollo/jslib/jqueryui/datepicker-af.js
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- A plugins/WebApollo/jslib/jqueryui/datepicker-az.js
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- A plugins/WebApollo/jslib/jqueryui/datepicker-fr.js
- A plugins/WebApollo/jslib/jqueryui/datepicker-gl.js
- A plugins/WebApollo/jslib/jqueryui/datepicker-he.js
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- A plugins/WebApollo/jslib/jqueryui/datepicker-lt.js
- A plugins/WebApollo/jslib/jqueryui/datepicker-lv.js
- A plugins/WebApollo/jslib/jqueryui/datepicker-mk.js
- A plugins/WebApollo/jslib/jqueryui/datepicker-ml.js
- A plugins/WebApollo/jslib/jqueryui/datepicker-ms.js
- A plugins/WebApollo/jslib/jqueryui/datepicker-nl-BE.js
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- A plugins/WebApollo/jslib/jqueryui/datepicker-no.js
- A plugins/WebApollo/jslib/jqueryui/datepicker-pl.js
- A plugins/WebApollo/jslib/jqueryui/datepicker-pt-BR.js
- A plugins/WebApollo/jslib/jqueryui/datepicker-pt.js
- A plugins/WebApollo/jslib/jqueryui/datepicker-rm.js
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- A plugins/WebApollo/jslib/jqueryui/datepicker-sv.js
- A plugins/WebApollo/jslib/jqueryui/datepicker-ta.js
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- A plugins/WebApollo/jslib/jqueryui/datepicker-uk.js
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- A plugins/WebApollo/jslib/jqueryui/datepicker-zh-TW.js
- A plugins/WebApollo/jslib/jqueryui/datepicker.js
- A plugins/WebApollo/jslib/jqueryui/dialog.js
- A plugins/WebApollo/jslib/jqueryui/draggable.js
- A plugins/WebApollo/jslib/jqueryui/droppable.js
- A plugins/WebApollo/jslib/jqueryui/effects/blind.js
- A plugins/WebApollo/jslib/jqueryui/effects/bounce.js
- A plugins/WebApollo/jslib/jqueryui/effects/clip.js
- A plugins/WebApollo/jslib/jqueryui/effects/core.js
- A plugins/WebApollo/jslib/jqueryui/effects/drop.js
- A plugins/WebApollo/jslib/jqueryui/effects/explode.js
- A plugins/WebApollo/jslib/jqueryui/effects/fade.js
- A plugins/WebApollo/jslib/jqueryui/effects/fold.js
- A plugins/WebApollo/jslib/jqueryui/effects/highlight.js
- 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
- A plugins/WebApollo/jslib/jqueryui/themes/base/images/ui-bg_flat_75_ffffff_40x100.png
- A plugins/WebApollo/jslib/jqueryui/themes/base/images/ui-bg_glass_55_fbf9ee_1x400.png
- A plugins/WebApollo/jslib/jqueryui/themes/base/images/ui-bg_glass_65_ffffff_1x400.png
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- A plugins/WebApollo/jslib/jqueryui/themes/base/images/ui-icons_222222_256x240.png
- A plugins/WebApollo/jslib/jqueryui/themes/base/images/ui-icons_2e83ff_256x240.png
- A plugins/WebApollo/jslib/jqueryui/themes/base/images/ui-icons_454545_256x240.png
- A plugins/WebApollo/jslib/jqueryui/themes/base/images/ui-icons_888888_256x240.png
- A plugins/WebApollo/jslib/jqueryui/themes/base/images/ui-icons_cd0a0a_256x240.png
- 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
- 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/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
- M src/JBrowse/Model/FileBlob.js
- M src/JBrowse/Store/LRUCache.js
- M src/JBrowse/Store/NCList.js
- M src/JBrowse/Store/RemoteBinaryFile.js
- M src/JBrowse/Store/SeqFeature/BAM.js
- M src/JBrowse/Store/SeqFeature/BAM/File.js
- M src/JBrowse/Store/SeqFeature/BAM/Util.js
- M src/JBrowse/Store/SeqFeature/BigWig.js
- M src/JBrowse/Store/SeqFeature/NCList.js
- M src/JBrowse/Store/SeqFeature/NCList_v0.js
- M src/JBrowse/Store/Sequence/StaticChunked.js
- M src/JBrowse/Store/TrackMetaData.js
- M src/JBrowse/Util.js
- M src/JBrowse/View/Export/GFF3.js
- M src/JBrowse/View/GranularRectLayout.js
- M src/JBrowse/View/Ruler.js
- M src/JBrowse/View/Track/Alignments.js
- M src/JBrowse/View/Track/BlockBased.js
- M src/JBrowse/View/Track/Canvas.js
- M src/JBrowse/View/Track/ExportMixin.js
- M src/JBrowse/View/Track/FeatureCoverage.js
- M src/JBrowse/View/Track/FixedImage.js
- M src/JBrowse/View/Track/FixedImage/Wiggle.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/Sequence.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/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
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