Changeset [9b6578c1669ae18bfd796fdcb42e0192080f693c] by Robert Buels
August 7th, 2013 @ 08:18 AM
Merge branch 'master' into multiview
Conflicts:
css/base/browser.css src/JBrowse/Browser.js
src/JBrowse/GenomeView.js src/JBrowse/Store/SeqFeature/NCList.js
src/JBrowse/Store/SeqFeature/REST.js
src/JBrowse/View/Dialog/SetHighlight.js
src/JBrowse/View/Track/BlockBased/Block.js
src/JBrowse/View/Track/ExportMixin.js
src/JBrowse/View/Track/HTMLFeatures.js
https://github.com/GMOD/jbrowse/commit/9b6578c1669ae18bfd796fdcb42e...
Committed by Robert Buels
- A bin/maker2jbrowse
- A combination_tracks.css
- A docs/tutorial/data_files/volvox_fromconfig.conf
- A export_dialog.css
- A maker.css
- A src/FileSaver
- A src/JBrowse/Model/BinaryTreeNode.js
- A src/JBrowse/Store/SeqFeature/BAMCombination.js
- A src/JBrowse/Store/SeqFeature/Combination.js
- A src/JBrowse/Store/SeqFeature/CombinationBase.js
- A src/JBrowse/Store/SeqFeature/FromConfig.js
- A src/JBrowse/Store/SeqFeature/Mask.js
- A src/JBrowse/Store/SeqFeature/QuantitativeCombination.js
- A src/JBrowse/View/FeatureGlyph/Gene.js
- A src/JBrowse/View/FeatureGlyph/ProcessedTranscript.js
- A src/JBrowse/View/FeatureGlyph/Segments.js
- A src/JBrowse/View/Track/Combination.js
- A src/JBrowse/View/Track/Combination/CombinationDialog.js
- A src/JBrowse/View/Track/_FeatureContextMenusMixin.js
- A src/JBrowse/View/Track/_TrackDetailsStatsMixin.js
- A src/JBrowse/View/_FeatureDescriptionMixin.js
- A src/perl5/Bio/JBrowse/FeatureStream/Genbank.pm
- A src/perl5/Bio/JBrowse/FeatureStream/Genbank/Parser.pm
- A tests/data/NG_009246.1.fa
- A tests/data/NT_077402.2.fa
- A tests/data/NT_077402.2.gb
- A tests/data/NT_077402.2.gene.gff3
- A tests/data/gstmu_full_record.gb
- A tests/data/gstmu_region_from_chromosome.gb
- A tests/data/maker_dmel_example/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500/contig-dpp-500-500.gff
- A tests/data/maker_dmel_example/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500/contig-dpp-500-500.maker.proteins.fasta
- A tests/data/maker_dmel_example/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500/contig-dpp-500-500.maker.transcripts.fasta
- A tests/data/maker_dmel_example/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500/run.log
- A tests/data/maker_dmel_example/dpp_contig.maker.output/dpp_contig_master_datastore_index.log
- A tests/data/volvox.sizes
- A tests/perl_tests/maker2jbrowse.t
- M .gitmodules
- M Makefile.PL
- M bin/flatfile-to-json.pl
- M bin/prepare-refseqs.pl
- M build/Makefile
- M build/init.js
- M compat_121.html
- M css/base/browser.css
- M css/base/faceted_track_selector.css
- M css/base/icons.css
- M css/base/main.css
- M css/base/track_styles.css
- M docs/featureglyphs.html
- M docs/tutorial/conf_files/volvox.json
- M docs/tutorial/data_files/volvox.gff3
- M docs/tutorial/index.html
- M img/commonIconsDisabled.png
- M img/commonIconsEnabled.png
- M index.html
- M release-notes.txt
- M sample_data/json/modencode/trackList.json
- M setup.sh
- M src/JBrowse/BehaviorManager.js
- M src/JBrowse/Browser.js
- M src/JBrowse/Component.js
- M src/JBrowse/GenomeView.js
- M src/JBrowse/JBrowse.profile.js
- M src/JBrowse/Model/ArrayRepr.js
- M src/JBrowse/Store/LRUCache.js
- M src/JBrowse/Store/NCList.js
- M src/JBrowse/Store/RemoteBinaryFile.js
- M src/JBrowse/Store/SeqFeature.js
- M src/JBrowse/Store/SeqFeature/BigWig/RequestWorker.js
- M src/JBrowse/Store/SeqFeature/NCList.js
- M src/JBrowse/Store/SeqFeature/REST.js
- M src/JBrowse/Store/SeqFeature/SNPCoverage.js
- M src/JBrowse/Store/TrackMetaData.js
- M src/JBrowse/Util.js
- M src/JBrowse/Util/GFF3.js
- M src/JBrowse/View/DetailsMixin.js
- M src/JBrowse/View/Dialog/SetHighlight.js
- M src/JBrowse/View/Export/GFF3.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/_FeatureLabelMixin.js
- M src/JBrowse/View/GranularRectLayout.js
- M src/JBrowse/View/Ruler.js
- M src/JBrowse/View/Track/BlockBased.js
- M src/JBrowse/View/Track/BlockBased/Block.js
- M src/JBrowse/View/Track/CanvasFeatures.js
- M src/JBrowse/View/Track/ExportMixin.js
- M src/JBrowse/View/Track/FeatureDetailMixin.js
- M src/JBrowse/View/Track/HTMLFeatures.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/Track/YScaleMixin.js
- M src/JBrowse/has.js
- M src/JBrowse/main.js
- M src/perl5/Bio/JBrowse/Cmd/FlatFileToJson.pm
- M src/perl5/Bio/JBrowse/Cmd/FormatSequences.pm
- M src/perl5/Bio/JBrowse/FeatureStream.pm
- M src/perl5/FastaDatabase.pm
- M src/perl5/FeatureTrack.pm
- M src/perl5/GenomeDB.pm
- M tests/data/hg19_formatted/trackList.json
- M tests/data/volvox_formatted_1_2_1/trackInfo.js
- M tests/data/volvox_formatted_refseqs/trackList.json
- M tests/js_tests/index.html
- M tests/js_tests/spec/GFF3.spec.js
- M tests/js_tests/spec/RESTStore.spec.js
- M tests/perl_tests/biodb-to-json.pl.t
- M tests/perl_tests/flatfile-to-json.pl.t
- M tests/perl_tests/prepare-refseqs.pl.t
- M tests/perl_tests/wig-to-json.pl.t
- M tests/selenium_tests/volvox_biodb_test.py
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