sf.links.get(0));
assertEquals(ensembl, sf.getFeatureGroup());
- // AAA -> TAA -> stop codon
- sf = sfs.get(1);
- assertEquals(1, sf.getBegin());
- assertEquals(1, sf.getEnd());
- assertEquals("nonsynonymous_variant", sf.getType());
- assertEquals("p.Lys1null", sf.getDescription()); // stop codon badly handled
- 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(
- "p.Lys1null var3|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var3",
- sf.links.get(0));
- assertEquals(dbSnp, sf.getFeatureGroup());
-
// AAA -> CAA -> K/Q
- sf = sfs.get(2);
+ sf = sfs.get(1);
assertEquals(1, sf.getBegin());
assertEquals(1, sf.getEnd());
assertEquals("nonsynonymous_variant", sf.getType());
assertEquals(dbSnp, sf.getFeatureGroup());
// AAA -> GAA -> K/E
- sf = sfs.get(3);
+ sf = sfs.get(2);
assertEquals(1, sf.getBegin());
assertEquals(1, sf.getEnd());
assertEquals("nonsynonymous_variant", sf.getType());
sf.links.get(0));
assertEquals(ensembl, sf.getFeatureGroup());
+ // AAA -> TAA -> stop codon
+ sf = sfs.get(3);
+ 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());