JAL-653 JAL-1968 FeaturesFile now handles Jalview or GFF2 or GFF3
authorgmungoc <g.m.carstairs@dundee.ac.uk>
Sat, 21 Nov 2015 19:24:24 +0000 (19:24 +0000)
committergmungoc <g.m.carstairs@dundee.ac.uk>
Sat, 21 Nov 2015 19:24:24 +0000 (19:24 +0000)
commit26ba864a6c290121fe6cf616794d2d0bea65fb7d
tree626662e11903a74ffb37b99bce7d339c35cc6e0e
parent2a76c758f4fa73532801c1aeadf4360a531c66b3
JAL-653 JAL-1968 FeaturesFile now handles Jalview or GFF2 or GFF3
(partially); feature links option removed
40 files changed:
examples/exampleFeatures.txt
examples/testdata/exonerateoutput.gff
examples/testdata/simpleGff3.gff [moved from examples/testdata/simplegff3.gff with 64% similarity]
help/html/features/featuresFormat.html
src/jalview/appletgui/AlignFrame.java
src/jalview/appletgui/CutAndPasteTransfer.java
src/jalview/appletgui/FeatureRenderer.java
src/jalview/bin/Jalview.java
src/jalview/bin/JalviewLite.java
src/jalview/bin/JalviewLiteURLRetrieve.java
src/jalview/controller/AlignViewController.java
src/jalview/datamodel/SequenceDummy.java
src/jalview/datamodel/SequenceFeature.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AnnotationExporter.java
src/jalview/gui/CutAndPasteTransfer.java
src/jalview/gui/Desktop.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/SequenceFetcher.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/FeaturesFile.java
src/jalview/io/FileLoader.java
src/jalview/io/FileParse.java
src/jalview/io/Gff3File.java [deleted file]
src/jalview/io/IdentifyFile.java
src/jalview/io/packed/JalviewDataset.java
src/jalview/io/packed/ParsePackedSet.java
src/jalview/io/vamsas/Sequencefeature.java
src/jalview/schemes/UserColourScheme.java
src/jalview/util/StringUtils.java
src/jalview/ws/jws1/JPredThread.java
src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
test/jalview/datamodel/SequenceFeatureTest.java [new file with mode: 0644]
test/jalview/io/AnnotationFileIOTest.java
test/jalview/io/FeaturesFileTest.java
test/jalview/io/FileIOTester.java
test/jalview/io/GffFileTest.java [moved from test/jalview/io/Gff3tests.java with 81% similarity]
test/jalview/io/IdentifyFileTest.java
test/jalview/io/StockholmFileTest.java
test/jalview/util/StringUtilsTest.java