- codonVariants = new String[][] { { "a", "t" }, { "G", "C" },
- { "t", "g" } };
- // agt agg act acg tgt tgg tct tcg code for S, R, T, T, C, W, S, S
- variants = AlignmentUtils.computePeptideVariants(codonVariants, "S");
- assertEquals("[C, R, T, W]", variants.toString());
+ SequenceFeature[] sfs = peptide.getSequenceFeatures();
+ assertEquals(5, sfs.length);
+ SequenceFeature sf = sfs[0];
+ assertEquals(1, sf.getBegin());
+ assertEquals(1, sf.getEnd());
+ assertEquals("K->E", sf.getDescription());
+ assertEquals("var1.125A>G", sf.getValue("ID"));
+ assertNull(sf.getValue("clinical_significance"));
+ assertEquals(1, sf.links.size());
+ // link to variation is urlencoded
+ assertEquals(
+ "K->E var1.125A>G|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var1.125A%3EG",
+ sf.links.get(0));
+ sf = sfs[1];
+ assertEquals(1, sf.getBegin());
+ assertEquals(1, sf.getEnd());
+ assertEquals("K->Q", sf.getDescription());
+ assertEquals("var2", sf.getValue("ID"));
+ assertEquals("Dodgy", sf.getValue("clinical_significance"));
+ assertEquals(1, sf.links.size());
+ assertEquals(
+ "K->Q var2|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var2",
+ sf.links.get(0));
+ sf = sfs[2];
+ assertEquals(1, sf.getBegin());
+ assertEquals(1, sf.getEnd());
+ assertEquals("K->N", sf.getDescription());
+ assertEquals("var4", sf.getValue("ID"));
+ assertEquals("Benign", sf.getValue("clinical_significance"));
+ assertEquals(1, sf.links.size());
+ assertEquals(
+ "K->N var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
+ sf.links.get(0));
+ sf = sfs[3];
+ assertEquals(3, sf.getBegin());
+ assertEquals(3, sf.getEnd());
+ assertEquals("P->H", sf.getDescription());
+ assertEquals("var6", sf.getValue("ID"));
+ assertEquals("Good", sf.getValue("clinical_significance"));
+ assertEquals(1, sf.links.size());
+ assertEquals(
+ "P->H var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
+ sf.links.get(0));
+ // var5 generates two distinct protein variant features
+ sf = sfs[4];
+ assertEquals(3, sf.getBegin());
+ assertEquals(3, sf.getEnd());
+ assertEquals("P->R", sf.getDescription());
+ assertEquals("var6", sf.getValue("ID"));
+ assertEquals("Good", sf.getValue("clinical_significance"));
+ assertEquals(1, sf.links.size());
+ assertEquals(
+ "P->R var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
+ sf.links.get(0));