+ assertEquals(1, sf.getBegin());
+ assertEquals(1, sf.getEnd());
+ assertEquals("stop_gained", sf.getType());
+ assertEquals("TAA", sf.getDescription());
+ assertEquals("var3", sf.getValue("ID"));
+ assertEquals("Bad", sf.getValue("clinical_significance"));
+ assertEquals("ID=var3;clinical_significance=Bad", sf.getAttributes());
+ assertEquals(1, sf.links.size());
+ assertEquals(
+ "TAA var3|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var3",
+ sf.links.get(0));
+ assertEquals(dbSnp, sf.getFeatureGroup());
+
+ // AAA -> AAG synonymous
+ sf = sfs.get(4);
+ assertEquals(1, sf.getBegin());
+ assertEquals(1, sf.getEnd());
+ assertEquals("synonymous_variant", sf.getType());
+ assertEquals("AAG", sf.getDescription());
+ assertEquals("var4", sf.getValue("ID"));
+ assertEquals("None", sf.getValue("clinical_significance"));
+ assertEquals("ID=var4;clinical_significance=None", sf.getAttributes());
+ assertEquals(1, sf.links.size());
+ assertEquals(
+ "AAG var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
+ sf.links.get(0));
+ assertEquals(cosmic, sf.getFeatureGroup());
+
+ // TTT -> TTC synonymous
+ sf = sfs.get(5);
+ assertEquals(2, sf.getBegin());
+ assertEquals(2, sf.getEnd());
+ assertEquals("synonymous_variant", sf.getType());
+ assertEquals("TTC", sf.getDescription());
+ assertEquals("var6", sf.getValue("ID"));
+ assertNull(sf.getValue("clinical_significance"));
+ assertEquals("ID=var6", sf.getAttributes());
+ assertEquals(1, sf.links.size());
+ assertEquals(
+ "TTC var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
+ sf.links.get(0));
+ assertEquals(dbSnp, sf.getFeatureGroup());
+
+ // var7 generates two distinct protein variant features (two alleles)
+ // CCC -> CGC -> P/R
+ sf = sfs.get(6);