source.jalview.org Git - jalview.git/commit

git://source.jalview.org / jalview.git / commit

author	gmungoc <g.m.carstairs@dundee.ac.uk>
	Wed, 8 Jul 2015 14:53:51 +0000 (15:53 +0100)
committer	gmungoc <g.m.carstairs@dundee.ac.uk>
	Wed, 8 Jul 2015 14:53:51 +0000 (15:53 +0100)
commit	fddf3084802b37e5cee17829e32692a4aac3e60d
tree	c30573f6b4bb42068d4836aa2ee26dec868731c9	tree \| snapshot
parent	7e5b8f22ed3a1b76f6389a4c7d6b7ebc7f9bf74d	commit \| diff

JAL-1759 merge from develop

179 files changed:

THIRDPARTYLIBS		diff \| blob \| history
build.xml		diff \| blob \| history
examples/biojson-doc/.gitignore	[new file with mode: 0755]	blob
examples/biojson-doc/LICENSE	[new file with mode: 0755]	blob
examples/biojson-doc/README.md	[new file with mode: 0755]	blob
examples/biojson-doc/biojsonschema.json	[new file with mode: 0644]	blob
examples/biojson-doc/bower.json	[new file with mode: 0755]	blob
examples/biojson-doc/css/docson.css	[new file with mode: 0755]	blob
examples/biojson-doc/docson-swagger.js	[new file with mode: 0755]	blob
examples/biojson-doc/docson.js	[new file with mode: 0755]	blob
examples/biojson-doc/index.html	[new file with mode: 0755]	blob
examples/biojson-doc/lib/handlebars.js	[new file with mode: 0755]	blob
examples/biojson-doc/lib/highlight.js	[new file with mode: 0755]	blob
examples/biojson-doc/lib/jquery.js	[new file with mode: 0755]	blob
examples/biojson-doc/lib/jsonpointer.js	[new file with mode: 0755]	blob
examples/biojson-doc/lib/marked.js	[new file with mode: 0755]	blob
examples/biojson-doc/lib/require.js	[new file with mode: 0755]	blob
examples/biojson-doc/lib/traverse.js	[new file with mode: 0755]	blob
examples/biojson-doc/templates/box.html	[new file with mode: 0755]	blob
examples/biojson-doc/templates/signature.html	[new file with mode: 0755]	blob
examples/biojson-doc/tests/additionalItems.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/additionalProperties.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/address.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/allOf.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/anyOf.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/basic.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/definitions.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/dependencies.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/enum.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/example2.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/fstab.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/geo.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/invoice.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/items.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/maxItems.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/maxLength.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/maxProperties.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/maximum.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/minItems.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/minLength.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/minProperties.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/minimum.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/multipleOf.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/not.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/oneOf.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/pattern.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/patternProperties.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/properties.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/ref.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/refRemote.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/required.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/schema.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/test.html	[new file with mode: 0755]	blob
examples/biojson-doc/tests/type.json	[new file with mode: 0755]	blob
examples/biojson-doc/tests/uniqueItems.json	[new file with mode: 0755]	blob
examples/biojson-doc/widget.js	[new file with mode: 0755]	blob
examples/biojsonschema.json	[new file with mode: 0644]	blob
src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java		diff \| blob \| history
src/jalview/analysis/AAFrequency.java		diff \| blob \| history
src/jalview/appletgui/AlignFrame.java		diff \| blob \| history
src/jalview/appletgui/AlignmentPanel.java		diff \| blob \| history
src/jalview/bin/Jalview.java		diff \| blob \| history
src/jalview/datamodel/Sequence.java		diff \| blob \| history
src/jalview/datamodel/xdb/embl/EmblEntry.java		diff \| blob \| history
src/jalview/ext/varna/RnaModel.java		diff \| blob \| history
src/jalview/gui/AlignExportSettings.java		diff \| blob \| history
src/jalview/gui/AlignFrame.java		diff \| blob \| history
src/jalview/gui/AnnotationPanel.java		diff \| blob \| history
src/jalview/gui/AppVarna.java		diff \| blob \| history
src/jalview/gui/AppVarnaBinding.java		diff \| blob \| history
src/jalview/gui/CutAndPasteTransfer.java		diff \| blob \| history
src/jalview/gui/Jalview2XML.java		diff \| blob \| history
src/jalview/gui/ProgressBar.java		diff \| blob \| history
src/jalview/io/BioJsHTMLOutput.java		diff \| blob \| history
src/jalview/io/FileLoader.java		diff \| blob \| history
src/jalview/io/IdentifyFile.java		diff \| blob \| history
src/jalview/jbgui/GAlignFrame.java		diff \| blob \| history
src/jalview/jbgui/PDBDocFieldPreferences.java		diff \| blob \| history
src/jalview/json/binding/v1/BioJSRepositoryPojo.java		diff \| blob \| history
src/jalview/renderer/AnnotationRenderer.java		diff \| blob \| history
src/jalview/util/ImageMaker.java		diff \| blob \| history
src/jalview/util/StringUtils.java		diff \| blob \| history
src/jalview/ws/dbsources/PDBRestClient.java		diff \| blob \| history
test/MCview/AtomTest.java		diff \| blob \| history
test/MCview/BondTest.java		diff \| blob \| history
test/MCview/PDBChainTest.java		diff \| blob \| history
test/MCview/PDBfileTest.java		diff \| blob \| history
test/MCview/ResidueTest.java		diff \| blob \| history
test/com/stevesoft/pat/RegexWriterTest.java		diff \| blob \| history
test/jalview/analysis/AAFrequencyTest.java		diff \| blob \| history
test/jalview/analysis/AlignSeqTest.java		diff \| blob \| history
test/jalview/analysis/AlignmentAnnotationUtilsTest.java		diff \| blob \| history
test/jalview/analysis/AlignmentUtilsTests.java		diff \| blob \| history
test/jalview/analysis/AnnotationSorterTest.java		diff \| blob \| history
test/jalview/analysis/CodingUtilsTest.java		diff \| blob \| history
test/jalview/analysis/CrossRefTest.java		diff \| blob \| history
test/jalview/analysis/DnaTest.java		diff \| blob \| history
test/jalview/analysis/GroupingTest.java		diff \| blob \| history
test/jalview/analysis/ParsePropertiesTest.java		diff \| blob \| history
test/jalview/analysis/RnaTest.java	[new file with mode: 0644]	blob
test/jalview/analysis/TestAlignSeq.java		diff \| blob \| history
test/jalview/analysis/scoremodels/FeatureScoreModelTest.java		diff \| blob \| history
test/jalview/bin/CommandLineOperations.java		diff \| blob \| history
test/jalview/commands/EditCommandTest.java		diff \| blob \| history
test/jalview/datamodel/AlignedCodonFrameTest.java		diff \| blob \| history
test/jalview/datamodel/AlignedCodonIteratorTest.java		diff \| blob \| history
test/jalview/datamodel/AlignedCodonTest.java		diff \| blob \| history
test/jalview/datamodel/AlignmentAnnotationTests.java		diff \| blob \| history
test/jalview/datamodel/AlignmentTest.java		diff \| blob \| history
test/jalview/datamodel/ColumnSelectionTest.java		diff \| blob \| history
test/jalview/datamodel/DBRefEntryTest.java		diff \| blob \| history
test/jalview/datamodel/MappingTest.java		diff \| blob \| history
test/jalview/datamodel/PDBEntryTest.java		diff \| blob \| history
test/jalview/datamodel/SearchResultsTest.java		diff \| blob \| history
test/jalview/datamodel/SeqCigarTest.java		diff \| blob \| history
test/jalview/datamodel/SequenceDummyTest.java		diff \| blob \| history
test/jalview/datamodel/SequenceTest.java		diff \| blob \| history
test/jalview/datamodel/xdb/embl/EmblFileTest.java		diff \| blob \| history
test/jalview/ext/jmol/PDBFileWithJmolTest.java		diff \| blob \| history
test/jalview/ext/paradise/TestAnnotate3D.java		diff \| blob \| history
test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java		diff \| blob \| history
test/jalview/ext/rbvi/chimera/ChimeraConnect.java		diff \| blob \| history
test/jalview/ext/rbvi/chimera/JalviewChimeraView.java		diff \| blob \| history
test/jalview/gui/AlignViewportTest.java		diff \| blob \| history
test/jalview/gui/AnnotationChooserTest.java		diff \| blob \| history
test/jalview/gui/AppVarnaTest.java	[new file with mode: 0644]	blob
test/jalview/gui/FontChooserTest.java		diff \| blob \| history
test/jalview/gui/HelpTest.java		diff \| blob \| history
test/jalview/gui/JAL1353bugdemo.java		diff \| blob \| history
test/jalview/gui/JvSwingUtilsTest.java		diff \| blob \| history
test/jalview/gui/PDBSearchPanelTest.java		diff \| blob \| history
test/jalview/gui/PaintRefresherTest.java		diff \| blob \| history
test/jalview/gui/PopupMenuTest.java		diff \| blob \| history
test/jalview/gui/ProgressBarTest.java		diff \| blob \| history
test/jalview/gui/SequenceRendererTest.java		diff \| blob \| history
test/jalview/gui/StructureChooserTest.java		diff \| blob \| history
test/jalview/io/AnnotatedPDBFileInputTest.java		diff \| blob \| history
test/jalview/io/AnnotationFileIOTest.java		diff \| blob \| history
test/jalview/io/BioJsHTMLOutputTest.java		diff \| blob \| history
test/jalview/io/FileIOTester.java		diff \| blob \| history
test/jalview/io/Gff3tests.java		diff \| blob \| history
test/jalview/io/HtmlFileTest.java		diff \| blob \| history
test/jalview/io/JSONFileTest.java		diff \| blob \| history
test/jalview/io/Jalview2xmlTests.java		diff \| blob \| history
test/jalview/io/NewickFileTests.java		diff \| blob \| history
test/jalview/io/PhylipFileTests.java		diff \| blob \| history
test/jalview/io/RNAMLfileTest.java		diff \| blob \| history
test/jalview/io/StockholmFileTest.java		diff \| blob \| history
test/jalview/io/TCoffeeScoreFileTest.java		diff \| blob \| history
test/jalview/schemes/DnaCodonTests.java		diff \| blob \| history
test/jalview/schemes/ResiduePropertiesTest.java		diff \| blob \| history
test/jalview/schemes/ScoreMatrixPrinter.java		diff \| blob \| history
test/jalview/structure/Mapping.java		diff \| blob \| history
test/jalview/structure/StructureSelectionManagerTest.java		diff \| blob \| history
test/jalview/structures/models/AAStructureBindingModelTest.java		diff \| blob \| history
test/jalview/util/ColorUtilsTest.java		diff \| blob \| history
test/jalview/util/ComparisonTest.java		diff \| blob \| history
test/jalview/util/DBRefUtilsTest.java		diff \| blob \| history
test/jalview/util/MapListTest.java		diff \| blob \| history
test/jalview/util/MappingUtilsTest.java		diff \| blob \| history
test/jalview/util/QuickSortTest.java		diff \| blob \| history
test/jalview/util/ShiftListTest.java		diff \| blob \| history
test/jalview/util/StringUtilsTest.java		diff \| blob \| history
test/jalview/viewmodel/styles/ViewStyleTest.java		diff \| blob \| history
test/jalview/ws/PDBSequenceFetcherTest.java		diff \| blob \| history
test/jalview/ws/dbsources/PDBRestClientTest.java		diff \| blob \| history
test/jalview/ws/dbsources/UniprotTest.java		diff \| blob \| history
test/jalview/ws/gui/Jws2ParamView.java		diff \| blob \| history
test/jalview/ws/jabaws/DisorderAnnotExportImport.java		diff \| blob \| history
test/jalview/ws/jabaws/JalviewJabawsTestUtils.java		diff \| blob \| history
test/jalview/ws/jabaws/JpredJabaStructExportImport.java		diff \| blob \| history
test/jalview/ws/jabaws/MinJabawsClientTests.java		diff \| blob \| history
test/jalview/ws/jabaws/RNAStructExportImport.java		diff \| blob \| history
test/jalview/ws/jws2/ParameterUtilsTest.java		diff \| blob \| history
test/jalview/ws/rest/RestClientTest.java		diff \| blob \| history
test/jalview/ws/rest/ShmmrRSBSService.java		diff \| blob \| history
test/jalview/ws/seqfetcher/DasSequenceFetcher.java		diff \| blob \| history
test/jalview/ws/seqfetcher/DbRefFetcherTest.java		diff \| blob \| history
utils/InstallAnywhere/Jalview.iap_xml		diff \| blob \| history

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