Changeset [734da4b877e87d1a8cd937c786819355e7fd13b2] by Robert Buels
September 5th, 2013 @ 07:16 AM
Merge branch 'master' into regex_search
https://github.com/GMOD/jbrowse/commit/734da4b877e87d1a8cd937c78681...
Committed by Robert Buels
- A bin/add-bam-track.pl
- A bin/add-bw-track.pl
- A sequence.css
- A src/JBrowse/Model/DataView.js
- A src/JBrowse/Track.js
- A src/perl5/Bio/JBrowse/FeatureStream/Genbank/LocationParser.pm
- A tests/perl_tests/genbank.t
- R bin/add_bam_track.pl
- R bin/add_bw_track.pl
- R plugins/WebApollo/bin/flatfile-to-json.pl
- R plugins/WebApollo/css/add_sequence_alteration.css
- R plugins/WebApollo/css/edit_comments.css
- R plugins/WebApollo/css/edit_dbxrefs.css
- R plugins/WebApollo/css/export.css
- R plugins/WebApollo/css/genome.css
- R plugins/WebApollo/css/get_history.css
- R plugins/WebApollo/css/get_sequence.css
- R plugins/WebApollo/css/main.css
- R plugins/WebApollo/css/search_sequence.css
- R plugins/WebApollo/css/webapollo_track_styles.css
- R plugins/WebApollo/img/ApolloLogo_100x36.png
- R plugins/WebApollo/img/exclamation_circle_orange.png
- R plugins/WebApollo/img/loading.gif
- R plugins/WebApollo/img/marker_rounded_red.png
- R plugins/WebApollo/img/marker_squared_red.png
- R plugins/WebApollo/img/minus-transcript-head.png
- R plugins/WebApollo/img/plus-transcript-head.png
- R plugins/WebApollo/img/warning_exclamation.png
- R plugins/WebApollo/img/warning_exclamation_small.png
- R plugins/WebApollo/js/BioFeatureUtils.js
- R plugins/WebApollo/js/FeatureEdgeMatchManager.js
- R plugins/WebApollo/js/FeatureSelectionManager.js
- R plugins/WebApollo/js/FileLoader.js
- R plugins/WebApollo/js/GFF3toJbrowseJson.js
- R plugins/WebApollo/js/JSONUtils.js
- R plugins/WebApollo/js/Permission.js
- R plugins/WebApollo/js/SequenceOntologyUtils.js
- R plugins/WebApollo/js/SequenceSearch.js
- R plugins/WebApollo/js/Store/SeqFeature/PseudoNCList.js
- R plugins/WebApollo/js/Store/SeqFeature/ScratchPad.js
- R plugins/WebApollo/js/View/Track/AnnotSequenceTrack.js
- R plugins/WebApollo/js/View/Track/AnnotTrack.js
- R plugins/WebApollo/js/View/Track/DraggableAlignments.js
- R plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js
- R plugins/WebApollo/js/View/Track/SequenceTrack.js
- R plugins/WebApollo/js/main.js
- R plugins/WebApollo/jslib/jquery/jquery.js
- R plugins/WebApollo/jslib/jqueryui/accordion.js
- R plugins/WebApollo/jslib/jqueryui/autocomplete.js
- R plugins/WebApollo/jslib/jqueryui/button.js
- R plugins/WebApollo/jslib/jqueryui/core.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-af.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-ar-DZ.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-ar.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-az.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-bg.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-bs.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-ca.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-cs.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-cy-GB.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-da.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-de.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-el.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-en-AU.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-en-GB.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-en-NZ.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-eo.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-es.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-et.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-eu.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-fa.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-fi.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-fo.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-fr-CH.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-fr.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-gl.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-he.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-hi.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-hr.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-hu.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-hy.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-id.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-is.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-it.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-ja.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-kk.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-km.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-ko.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-lb.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-lt.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-lv.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-mk.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-ml.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-ms.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-nl-BE.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-nl.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-no.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-pl.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-pt-BR.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-pt.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-rm.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-ro.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-ru.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-sk.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-sl.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-sq.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-sr-SR.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-sr.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-sv.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-ta.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-th.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-tj.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-tr.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-uk.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-vi.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-zh-CN.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-zh-HK.js
- R plugins/WebApollo/jslib/jqueryui/datepicker-zh-TW.js
- R plugins/WebApollo/jslib/jqueryui/datepicker.js
- R plugins/WebApollo/jslib/jqueryui/dialog.js
- R plugins/WebApollo/jslib/jqueryui/draggable.js
- R plugins/WebApollo/jslib/jqueryui/droppable.js
- R plugins/WebApollo/jslib/jqueryui/effects/blind.js
- R plugins/WebApollo/jslib/jqueryui/effects/bounce.js
- R plugins/WebApollo/jslib/jqueryui/effects/clip.js
- R plugins/WebApollo/jslib/jqueryui/effects/core.js
- R plugins/WebApollo/jslib/jqueryui/effects/drop.js
- R plugins/WebApollo/jslib/jqueryui/effects/explode.js
- R plugins/WebApollo/jslib/jqueryui/effects/fade.js
- R plugins/WebApollo/jslib/jqueryui/effects/fold.js
- R plugins/WebApollo/jslib/jqueryui/effects/highlight.js
- R plugins/WebApollo/jslib/jqueryui/effects/pulsate.js
- R plugins/WebApollo/jslib/jqueryui/effects/scale.js
- R plugins/WebApollo/jslib/jqueryui/effects/shake.js
- R plugins/WebApollo/jslib/jqueryui/effects/slide.js
- R plugins/WebApollo/jslib/jqueryui/effects/transfer.js
- R plugins/WebApollo/jslib/jqueryui/mouse.js
- R plugins/WebApollo/jslib/jqueryui/position.js
- R plugins/WebApollo/jslib/jqueryui/progressbar.js
- R plugins/WebApollo/jslib/jqueryui/resizable.js
- R plugins/WebApollo/jslib/jqueryui/selectable.js
- R plugins/WebApollo/jslib/jqueryui/slider.js
- R plugins/WebApollo/jslib/jqueryui/sortable.js
- R plugins/WebApollo/jslib/jqueryui/tabs.js
- R plugins/WebApollo/jslib/jqueryui/themes/base/images/ui-bg_flat_0_aaaaaa_40x100.png
- R plugins/WebApollo/jslib/jqueryui/themes/base/images/ui-bg_flat_75_ffffff_40x100.png
- R plugins/WebApollo/jslib/jqueryui/themes/base/images/ui-bg_glass_55_fbf9ee_1x400.png
- R plugins/WebApollo/jslib/jqueryui/themes/base/images/ui-bg_glass_65_ffffff_1x400.png
- R plugins/WebApollo/jslib/jqueryui/themes/base/images/ui-bg_glass_75_dadada_1x400.png
- R plugins/WebApollo/jslib/jqueryui/themes/base/images/ui-bg_glass_75_e6e6e6_1x400.png
- R plugins/WebApollo/jslib/jqueryui/themes/base/images/ui-bg_glass_95_fef1ec_1x400.png
- R plugins/WebApollo/jslib/jqueryui/themes/base/images/ui-bg_highlight-soft_75_cccccc_1x100.png
- R plugins/WebApollo/jslib/jqueryui/themes/base/images/ui-icons_222222_256x240.png
- R plugins/WebApollo/jslib/jqueryui/themes/base/images/ui-icons_2e83ff_256x240.png
- R plugins/WebApollo/jslib/jqueryui/themes/base/images/ui-icons_454545_256x240.png
- R plugins/WebApollo/jslib/jqueryui/themes/base/images/ui-icons_888888_256x240.png
- R plugins/WebApollo/jslib/jqueryui/themes/base/images/ui-icons_cd0a0a_256x240.png
- R plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.accordion.css
- R plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.all.css
- R plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.autocomplete.css
- R plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.base.css
- R plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.button.css
- R plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.core.css
- R plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.datepicker.css
- R plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.dialog.css
- R plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.progressbar.css
- R plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.resizable.css
- R plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.selectable.css
- R plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.slider.css
- R plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.tabs.css
- R plugins/WebApollo/jslib/jqueryui/themes/base/jquery.ui.theme.css
- R plugins/WebApollo/jslib/jqueryui/widget.js
- R plugins/WebApollo/perl5/Bio/WebApollo/Cmd/FlatFileToJson.pm
- R plugins/WebApollo/tests/data/MAKER/Group1.33_Amel_4.5.maker.gff
- R plugins/WebApollo/tests/data/MAKER/Group1.33_Amel_4.5.maker.jbrowse.expected.json
- R plugins/WebApollo/tests/data/MAKER/Group1.33_Amel_4.5.maker.jbrowse.expected_PRETTIFIED.json
- R plugins/WebApollo/tests/data/MAKER/Group1.33_Amel_4.5.maker.webapollo.expected.json
- R plugins/WebApollo/tests/js_tests/index.html
- R plugins/WebApollo/tests/js_tests/lib/jasmine-1.2.0/MIT.LICENSE
- R plugins/WebApollo/tests/js_tests/lib/jasmine-1.2.0/jasmine-html.js
- R plugins/WebApollo/tests/js_tests/lib/jasmine-1.2.0/jasmine.css
- R plugins/WebApollo/tests/js_tests/lib/jasmine-1.2.0/jasmine.js
- R plugins/WebApollo/tests/js_tests/spec/GFF3toJbrowseJsonSpec.js
- R plugins/WebApollo/tests/js_tests/spec/JSONUtilsSpec.js
- R plugins/WebApollo/tests/perl_tests/flatfile-to-json.pl.t
- R plugins/WebApollo/tests/selenium_tests/lib/WebApolloTest.py
- R plugins/WebApollo/tests/selenium_tests/lib/__init__.py
- R plugins/WebApollo/tests/selenium_tests/pythium_test.py
- M bin/flatfile-to-json.pl
- M bin/generate-names.pl
- M docs/tutorial/data_files/volvox.vcf.conf
- M docs/tutorial/index.html
- M genome.css
- M index.html
- M main.css
- M release-notes.txt
- M src/JBrowse/Browser.js
- M src/JBrowse/ConfigManager.js
- M src/JBrowse/FeatureFiltererMixin.js
- M src/JBrowse/GenomeView.js
- M src/JBrowse/Store/RemoteBinaryFile.js
- M src/JBrowse/Store/SeqFeature/BAM/LazyFeature.js
- M src/JBrowse/Store/SeqFeature/BigWig.js
- M src/JBrowse/Store/SeqFeature/BigWig/RequestWorker.js
- M src/JBrowse/Store/SeqFeature/BigWig/Window.js
- M src/JBrowse/Store/SeqFeature/SNPCoverage.js
- M src/JBrowse/Store/SeqFeature/SPARQL.js
- M src/JBrowse/Store/SeqFeature/_MismatchesMixin.js
- M src/JBrowse/Store/TiledImage/Fixed.js
- M src/JBrowse/Util.js
- M src/JBrowse/Util/RejectableFastPromise.js
- M src/JBrowse/View/DetailsMixin.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/Gene.js
- M src/JBrowse/View/FeatureGlyph/_FeatureLabelMixin.js
- M src/JBrowse/View/FileDialog/TrackList.js
- M src/JBrowse/View/Track/Alignments.js
- M src/JBrowse/View/Track/Alignments2.js
- M src/JBrowse/View/Track/BlockBased/Block.js
- M src/JBrowse/View/Track/CanvasFeatures.js
- M src/JBrowse/View/Track/FixedImage.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/WiggleBase.js
- M src/JBrowse/View/Track/_AlignmentsMixin.js
- M src/JBrowse/has.js
- M src/perl5/Bio/JBrowse/FeatureStream/Genbank.pm
- M src/perl5/Bio/JBrowse/FeatureStream/Genbank/Parser.pm
- M tests/js_tests/spec/SPARQLStore.spec.js
- M tests/js_tests/spec/Util.spec.js
- M tests/perl_tests/flatfile-to-json.pl.t
- M track_styles.css
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