JAL-2106 removed setSourceDBRef, refactor getSourceDBRef to getPrimaryDBRefs
authorJim Procter <jprocter@issues.jalview.org>
Wed, 24 Aug 2016 16:28:30 +0000 (17:28 +0100)
committerJim Procter <jprocter@issues.jalview.org>
Wed, 24 Aug 2016 16:28:30 +0000 (17:28 +0100)
commitaf2dbf10bbcc54d9b9e4d398e9283b3c4a758e06
treea8362638c22b4df4d4ab3ad386e0730a2abe8244
parent9a0e53e18ba1280658e1424c5e08b90e7beeebde
JAL-2106 removed setSourceDBRef, refactor getSourceDBRef to getPrimaryDBRefs
 * minimal test for PDB cornercase
 * minimal revision of AlignmentUtils/Tests, CrossRef
 * basic patch to SIFTSClient - need to revisit

TODO
 * jalview.io.StructureFile re ‘PDB’ primary dbrefs generated from filenames.
 * verify primary refs added correctly for Uniprot, EMBL,  Ensembl and EnsemblGenomes in their unit tests.
12 files changed:
src/jalview/analysis/AlignmentUtils.java
src/jalview/analysis/CrossRef.java
src/jalview/datamodel/Sequence.java
src/jalview/datamodel/SequenceI.java
src/jalview/datamodel/xdb/embl/EmblEntry.java
src/jalview/ext/ensembl/EnsemblSeqProxy.java
src/jalview/gui/StructureChooser.java
src/jalview/io/StructureFile.java
src/jalview/ws/dbsources/Uniprot.java
src/jalview/ws/sifts/SiftsClient.java
test/jalview/analysis/AlignmentUtilsTests.java
test/jalview/datamodel/SequenceTest.java