assertEquals(sf.getFeatureGroup(), "VCF");
assertEquals(sf.getBegin(), 1);
assertEquals(sf.getEnd(), 1);
- assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+ assertEquals(sf.getType(), SequenceOntologyI.NONSYNONYMOUS_VARIANT);
assertEquals(sf.getDescription(), "p.Ser1Thr");
}
assertEquals(sf.getFeatureGroup(), "VCF");
assertEquals(sf.getBegin(), 6);
assertEquals(sf.getEnd(), 6);
- assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+ assertEquals(sf.getType(), SequenceOntologyI.NONSYNONYMOUS_VARIANT);
assertEquals(sf.getDescription(), "p.Ala6Gly");
}
}
}
List<SequenceFeature> proteinFeatures = peptide.getSequenceFeatures();
- assertEquals(proteinFeatures.size(), 1);
+ SequenceFeatures.sortFeatures(proteinFeatures, true);
+ assertEquals(proteinFeatures.size(), 2);
sf = proteinFeatures.get(0);
assertEquals(sf.getFeatureGroup(), "VCF");
+ assertEquals(sf.getBegin(), 1);
+ assertEquals(sf.getEnd(), 1);
+ assertEquals(sf.getType(), SequenceOntologyI.SYNONYMOUS_VARIANT);
+ assertEquals(sf.getDescription(), "agC/agT");
+ sf = proteinFeatures.get(1);
+ assertEquals(sf.getFeatureGroup(), "VCF");
assertEquals(sf.getBegin(), 4);
assertEquals(sf.getEnd(), 4);
- assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+ assertEquals(sf.getType(), SequenceOntologyI.NONSYNONYMOUS_VARIANT);
assertEquals(sf.getDescription(), "p.Glu4Gly");
/*