Lighthouse has a new layout. Prefer the old one? Return to the old layout, and switch back any time from the link at the top of each page.

All changesets

Changeset [066b2c886b39bd04fdc320034a495820fa976f5e] by Robert Buels

Revision 066b2c886b39bd04fdc320034a495820fa976f5e, committed by Robert Buels · March 18th, 2012 @ 06:46 PM

Merge branch 'master' into rubberband

Conflicts:

genome.css
js/GenomeView.js

https://github.com/GMOD/jbrowse/commit/066b2c886b39bd04fdc320034a49...

339 changed files

  • A Makefile.PL
  • A Makefile.deploy
  • A README.md
  • A bin/cpanm
  • A bin/jbdoc
  • A compat_121.html
  • A dist.ini
  • A img/closedhand.cur
  • A img/openhand.cur
  • A js/ArrayRepr.js
  • A js/ConfigAdaptor/JB_json_v0.js
  • A js/ConfigAdaptor/JB_json_v1.js
  • A js/GridTrack.js
  • A js/NCList_v0.js
  • A js/SeqFeatureStore.js
  • A js/SeqFeatureStore/NCList.js
  • A js/SeqFeatureStore/NCList_v0.js
  • A js/SequenceStore/StaticChunked.js
  • A js/StaticTrack.js
  • A js/Store.js
  • A js/TiledImageStore/Fixed.js
  • A js/TiledImageStore/Fixed_v0.js
  • A jslib/jsdoc_toolkit-2.4.0/README.txt
  • A jslib/jsdoc_toolkit-2.4.0/app/frame.js
  • A jslib/jsdoc_toolkit-2.4.0/app/frame/Chain.js
  • A jslib/jsdoc_toolkit-2.4.0/app/frame/Dumper.js
  • A jslib/jsdoc_toolkit-2.4.0/app/frame/Hash.js
  • A jslib/jsdoc_toolkit-2.4.0/app/frame/Link.js
  • A jslib/jsdoc_toolkit-2.4.0/app/frame/Namespace.js
  • A jslib/jsdoc_toolkit-2.4.0/app/frame/Opt.js
  • A jslib/jsdoc_toolkit-2.4.0/app/frame/Reflection.js
  • A jslib/jsdoc_toolkit-2.4.0/app/frame/String.js
  • A jslib/jsdoc_toolkit-2.4.0/app/frame/Testrun.js
  • A jslib/jsdoc_toolkit-2.4.0/app/handlers/FOODOC.js
  • A jslib/jsdoc_toolkit-2.4.0/app/handlers/XMLDOC.js
  • A jslib/jsdoc_toolkit-2.4.0/app/handlers/XMLDOC/DomReader.js
  • A jslib/jsdoc_toolkit-2.4.0/app/handlers/XMLDOC/XMLDoc.js
  • A jslib/jsdoc_toolkit-2.4.0/app/handlers/XMLDOC/XMLParse.js
  • A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC.js
  • A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/DocComment.js
  • A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/DocTag.js
  • A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/JsDoc.js
  • A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/JsPlate.js
  • A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/Lang.js
  • A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/Parser.js
  • A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/PluginManager.js
  • A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/Symbol.js
  • A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/SymbolSet.js
  • A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/TextStream.js
  • A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/Token.js
  • A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/TokenReader.js
  • A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/TokenStream.js
  • A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/Util.js
  • A jslib/jsdoc_toolkit-2.4.0/app/lib/JSDOC/Walker.js
  • A jslib/jsdoc_toolkit-2.4.0/app/main.js
  • A jslib/jsdoc_toolkit-2.4.0/app/plugins/commentSrcJson.js
  • A jslib/jsdoc_toolkit-2.4.0/app/plugins/frameworkPrototype.js
  • A jslib/jsdoc_toolkit-2.4.0/app/plugins/functionCall.js
  • A jslib/jsdoc_toolkit-2.4.0/app/plugins/publishSrcHilite.js
  • A jslib/jsdoc_toolkit-2.4.0/app/plugins/symbolLink.js
  • A jslib/jsdoc_toolkit-2.4.0/app/plugins/tagParamConfig.js
  • A jslib/jsdoc_toolkit-2.4.0/app/plugins/tagSynonyms.js
  • A jslib/jsdoc_toolkit-2.4.0/app/run.js
  • A jslib/jsdoc_toolkit-2.4.0/app/t/TestDoc.js
  • A jslib/jsdoc_toolkit-2.4.0/app/t/runner.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/addon.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/anon_inner.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/augments.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/augments2.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/borrows.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/borrows2.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/config.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/constructs.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/encoding.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/encoding_other.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/event.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/exports.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/functions_anon.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/functions_nested.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/global.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/globals.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/ignore.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/inner.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/jsdoc_test.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/lend.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/memberof.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/memberof2.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/memberof3.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/memberof_constructor.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/module.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/multi_methods.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/name.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/namespace_nested.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/nocode.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/oblit_anon.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/overview.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/param_inline.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/params_optional.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/prototype.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/prototype_nested.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/prototype_oblit.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/prototype_oblit_constructor.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/public.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/scripts/code.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/scripts/notcode.txt
  • A jslib/jsdoc_toolkit-2.4.0/app/test/shared.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/shared2.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/shortcuts.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/static_this.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/synonyms.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/tosource.js
  • A jslib/jsdoc_toolkit-2.4.0/app/test/variable_redefine.js
  • A jslib/jsdoc_toolkit-2.4.0/changes.txt
  • A jslib/jsdoc_toolkit-2.4.0/conf/sample.conf
  • A jslib/jsdoc_toolkit-2.4.0/java/build.xml
  • A jslib/jsdoc_toolkit-2.4.0/java/build_1.4.xml
  • A jslib/jsdoc_toolkit-2.4.0/java/classes/js.jar
  • A jslib/jsdoc_toolkit-2.4.0/java/src/JsDebugRun.java
  • A jslib/jsdoc_toolkit-2.4.0/java/src/JsRun.java
  • A jslib/jsdoc_toolkit-2.4.0/jsdebug.jar
  • A jslib/jsdoc_toolkit-2.4.0/jsrun.jar
  • A jslib/jsdoc_toolkit-2.4.0/jsrun.sh
  • A jslib/jsdoc_toolkit-2.4.0/templates/jsdoc/allclasses.tmpl
  • A jslib/jsdoc_toolkit-2.4.0/templates/jsdoc/allfiles.tmpl
  • A jslib/jsdoc_toolkit-2.4.0/templates/jsdoc/class.tmpl
  • A jslib/jsdoc_toolkit-2.4.0/templates/jsdoc/index.tmpl
  • A jslib/jsdoc_toolkit-2.4.0/templates/jsdoc/publish.js
  • A jslib/jsdoc_toolkit-2.4.0/templates/jsdoc/static/default.css
  • A jslib/jsdoc_toolkit-2.4.0/templates/jsdoc/static/header.html
  • A jslib/jsdoc_toolkit-2.4.0/templates/jsdoc/static/index.html
  • A jslib/jsdoc_toolkit-2.4.0/templates/jsdoc/symbol.tmpl
  • A lib/ArrayRepr.pm
  • A lib/FeatureTrack.pm
  • A lib/GenomeDB.pm
  • A lib/ImageTrack.pm
  • A lib/IntervalStore.pm
  • A lib/JsonFileStorage.pm
  • A sample_data/json/.exists
  • A sample_data/raw/Dmel.json
  • A sample_data/raw/ideograms/human_cytobands.gff
  • A sample_data/raw/ideograms/mouse_cytobands.gff
  • A sample_data/raw/ideograms/rat_cytobands.gff
  • A sample_data/raw/pop_demo/pop_demo.gff3
  • A sample_data/raw/tomato.json
  • A sample_data/raw/volvox
  • A sample_data/raw/volvox.json
  • A sample_data/raw/yeast.json
  • A sample_data/raw/yeast_chr1+2/yeast_chr1+2.gff3
  • A sample_data/raw/yeast_gbk/NC_001133.gbk
  • A sample_data/raw/yeast_gbk/NC_001133.gbk.gff
  • A sample_data/raw/yeast_genbank.json
  • A sample_data/raw/yeast_scaffolds/chr1.fa.gz
  • A sample_data/raw/yeast_scaffolds/chr2.fa.gzip
  • A sample_data/raw/yeast_scaffolds/chromosomes.gff3
  • A t
  • A tests/data/AU9/seq/refSeqs.json
  • A tests/data/AU9/single_au9_gene.gff3
  • A tests/data/base_pairing/XdecoderStructure.gff
  • A tests/data/base_pairing/mahoney.fa
  • A tests/data/base_pairing/mahoney_formatted/seq/mahoney/0.txt
  • A tests/data/base_pairing/mahoney_formatted/seq/refSeqs.json
  • A tests/data/base_pairing/mahoney_formatted/trackList.json
  • A tests/data/hg19/database/knownGene.sql
  • A tests/data/hg19/database/knownGene.txt.gz
  • A tests/data/hg19/database/trackDb.sql
  • A tests/data/hg19/database/trackDb.txt.gz
  • A tests/data/hg19_chromosomes.fkfa
  • A tests/data/hg19_formatted/trackList.json
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/hist-100000-0.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/hist-1000000-0.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/hist-200000-0.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/hist-2000000-0.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/hist-500000-0.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-1.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-10.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-11.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-2.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-3.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-4.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-5.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-6.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-7.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-8.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/lf-9.jsonz
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/names.json
  • A tests/data/hg19_formatted/tracks/knownGene/chr1/trackData.jsonz
  • A tests/data/tomato_features.json
  • A tests/data/tomato_features_nclist_with_chunksize_10000.json
  • A tests/data/volvox_formatted_1_2_1/refSeqs.js
  • A tests/data/volvox_formatted_1_2_1/seq/ctgA/0.txt
  • A tests/data/volvox_formatted_1_2_1/seq/ctgA/1.txt
  • A tests/data/volvox_formatted_1_2_1/seq/ctgA/2.txt
  • A tests/data/volvox_formatted_1_2_1/trackInfo.js
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Alignments/hist-10000-0.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Alignments/names.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Alignments/trackData.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/CDS/hist-50000-0.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/CDS/names.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/CDS/trackData.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Clones/hist-200000-0.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Clones/names.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Clones/trackData.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/EST/hist-50000-0.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/EST/names.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/EST/trackData.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/ExampleFeatures/hist-10000-0.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/ExampleFeatures/names.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/ExampleFeatures/trackData.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Genes/hist-200000-0.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Genes/names.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Genes/trackData.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Motifs/hist-10000-0.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Motifs/names.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Motifs/trackData.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/NameTest/hist-50000-0.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/NameTest/names.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/NameTest/trackData.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/ReadingFrame/hist-50000-0.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/ReadingFrame/names.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/ReadingFrame/trackData.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Transcript/hist-200000-0.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Transcript/names.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/Transcript/trackData.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-100-0.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-1000-0.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-20-0.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-200-0.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-40-0.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/hist-400-0.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/lazyfeatures-0.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/lazyfeatures-1.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/lazyfeatures-2.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/lazyfeatures-3.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/bam_simulated/trackData.json
  • A tests/data/volvox_formatted_1_2_1/tracks/ctgA/volvox_microarray.wig.json
  • A tests/data/volvox_formatted_refseqs/seq/ctgA/0.txt
  • A tests/data/volvox_formatted_refseqs/seq/ctgA/1.txt
  • A tests/data/volvox_formatted_refseqs/seq/ctgA/2.txt
  • A tests/data/volvox_formatted_refseqs/seq/ctgB/0.txt
  • A tests/data/volvox_formatted_refseqs/seq/refSeqs.json
  • A tests/data/volvox_formatted_refseqs/trackList.json
  • A tests/js_tests/LazyArray-test.js
  • A tests/js_tests/lazyarray-0.json
  • A tests/js_tests/lazyarray-1.json
  • A tests/js_tests/lazyarray-2.json
  • A tests/js_tests/runner.html
  • A tests/perl_tests/00.compile.t
  • A tests/perl_tests/FastaDatabase.t
  • A tests/perl_tests/bam-to-json.pl.t
  • A tests/perl_tests/bin/fasta_to_fkfa.pl
  • A tests/perl_tests/bin/fkfa_to_fasta.pl
  • A tests/perl_tests/biodb-to-json.pl.t
  • A tests/perl_tests/draw-basepair-track.pl.t
  • A tests/perl_tests/fakefasta.t
  • A tests/perl_tests/flatfile-to-json.pl.t
  • A tests/perl_tests/lazy_nclist.t
  • A tests/perl_tests/lib/FakeFasta.pm
  • A tests/perl_tests/lib/FileSlurping.pm
  • A tests/perl_tests/nclist.t
  • A tests/perl_tests/prepare-refseqs.pl.t
  • A tests/perl_tests/ucsc-to-json.pl.t
  • A tests/perl_tests/wig-to-json.pl.t
  • A tests/selenium_tests/jbrowse_selenium.py
  • A tests/selenium_tests/volvox_biodb_121_test.py
  • A tests/selenium_tests/volvox_biodb_test.py
  • A tests/selenium_tests/yeast_biodb_test.py
  • A wig2png/Makefile.in
  • A wig2png/configure
  • A wig2png/src/config.h.in
  • A wig2png/src/macros.h
  • A wig2png/src/opts_list.cc
  • A wig2png/src/opts_list.h
  • A wig2png/src/wig2png.cc
  • R Makefile
  • R Makefile.in
  • R closedhand.cur
  • R openhand.cur
  • R js/UITracks.js
  • R lib/AutoHash.pm
  • R src/config.h
  • R tests/jasmine
  • R tests/LazyArray-test.js
  • R tests/lazyarray-0.json
  • R tests/lazyarray-1.json
  • R tests/lazyarray-2.json
  • R tests/runner.html
  • R touch.html
  • R configure
  • R src/config.h.in
  • R src/macros.h
  • R src/opts_list.cc
  • R src/opts_list.h
  • R src/wig2png.cc
  • M .gitignore
  • M .gitmodules
  • M INSTALL
  • M bin/bam-to-json.pl
  • M bin/biodb-to-json.pl
  • M bin/draw-basepair-track.pl
  • M bin/flatfile-to-json.pl
  • M bin/generate-names.pl
  • M bin/prepare-refseqs.pl
  • M bin/ucsc-to-json.pl
  • M bin/wig-to-json.pl
  • M docs/docs.css
  • M docs/featureglyphs.html
  • M docs/tutorial/conf_files/volvox.json
  • M docs/tutorial/data_files/volvox.fa
  • M docs/tutorial/data_files/volvox.gff3
  • M docs/tutorial/index.html
  • M genome.css
  • M index.html
  • M js/Browser.js
  • M js/FeatureTrack.js
  • M js/GenomeView.js
  • M js/ImageTrack.js
  • M js/Layout.js
  • M js/LazyArray.js
  • M js/LazyPatricia.js
  • M js/NCList.js
  • M js/SequenceTrack.js
  • M js/Track.js
  • M js/Util.js
  • M js/touchJBrowse.js
  • M lib/BioperlFlattener.pm
  • M lib/ExternalSorter.pm
  • M lib/FastaDatabase.pm
  • M lib/ImageTrackRenderer.pm
  • M lib/JsonGenerator.pm
  • M lib/LazyNCList.pm
  • M lib/LazyPatricia.pm
  • M lib/NCLSorter.pm
  • M lib/NCList.pm
  • M lib/NameHandler.pm
  • M lib/TiledImage.pm
  • M release-notes.txt
  • M twiki/JBrowsePlugin.pm
  • M twiki/JBrowsePlugin/Makefile.jbrowse