JAL-1705 include stop codons in derived CDS; support ensemblgenomes
authorgmungoc <g.m.carstairs@dundee.ac.uk>
Thu, 3 Mar 2016 09:53:40 +0000 (09:53 +0000)
committergmungoc <g.m.carstairs@dundee.ac.uk>
Thu, 3 Mar 2016 09:53:40 +0000 (09:53 +0000)
commitb8058f3f849f44740a695c83e96bdca3a197af5c
tree8734b4f6e07a263ae6159f237f482041e376f6ea
parent3aa60eb1704441d7db522c13d6b45ab05cb43e2b
JAL-1705 include stop codons in derived CDS; support ensemblgenomes
18 files changed:
src/jalview/analysis/AlignmentUtils.java
src/jalview/ext/ensembl/EnsemblCdna.java
src/jalview/ext/ensembl/EnsemblCds.java
src/jalview/ext/ensembl/EnsemblFeatures.java
src/jalview/ext/ensembl/EnsemblGene.java
src/jalview/ext/ensembl/EnsemblGenome.java
src/jalview/ext/ensembl/EnsemblGenomes.java [new file with mode: 0644]
src/jalview/ext/ensembl/EnsemblLookup.java
src/jalview/ext/ensembl/EnsemblProtein.java
src/jalview/ext/ensembl/EnsemblRestClient.java
src/jalview/ext/ensembl/EnsemblSeqProxy.java
src/jalview/ext/ensembl/EnsemblSymbol.java
src/jalview/ext/ensembl/EnsemblXref.java
src/jalview/util/MappingUtils.java
src/jalview/ws/SequenceFetcher.java
test/jalview/ext/ensembl/EnsemblSeqProxyAdapter.java
test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
test/jalview/util/MappingUtilsTest.java