- EnsemblSeqProxy testee = new EnsemblGene();
- assertFalse(testee.isGeneIdentifier(null));
- assertFalse(testee.isGeneIdentifier(""));
- assertFalse(testee.isGeneIdentifier("ENST00000012345"));
- assertTrue(testee.isGeneIdentifier("ENSG00000012345"));
- assertTrue(testee.isGeneIdentifier("ENSMUSG00000012345"));
- assertFalse(testee.isGeneIdentifier("ensg00000012345"));
- assertFalse(testee.isGeneIdentifier("ENSG000000123456"));
- assertFalse(testee.isGeneIdentifier("ENSG0000001234"));
+ String alleles = "C,G,-TAC,HGMD_MUTATION,gac";
+ SequenceFeature sf = new SequenceFeature("sequence_variant", alleles,
+ 1, 2, 0f, null);
+ sf.setValue("alleles", alleles);
+ sf.setAttributes("x=y,z;alleles=" + alleles + ";a=b,c");
+
+ EnsemblSeqProxy.reverseComplementAlleles(sf);
+ String revcomp = "G,C,GTA-,HGMD_MUTATION,gtc";
+ // verify description is updated with reverse complement
+ assertEquals(revcomp, sf.getDescription());
+ // verify alleles attribute is updated with reverse complement
+ assertEquals(revcomp, sf.getValue("alleles"));
+ // verify attributes string is updated with reverse complement
+ assertEquals("x=y,z;alleles=" + revcomp + ";a=b,c", sf.getAttributes());