- assertEquals(4, sf.otherDetails.size());
- assertEquals("ECO;0000255,PROSITE=ProRule:PRU00465",
- sf.otherDetails.get("evidence"));
- assertEquals("Iron-sulfur (2Fe-2S),another note",
- sf.otherDetails.get("Note"));
+ assertEquals(5, sf.otherDetails.size());
+ assertEquals("ECO;0000255,PROSITE=ProRule:PRU00465", // url decoded
+ sf.getValue("evidence"));
+ assertEquals("Iron-sulfur (2Fe-2S),another note,and another",
+ sf.getValue("Note"));
+ assertEquals("21", sf.getValueAsString("CSQ", "AF"));
+ assertEquals("benign,possibly_damaging",
+ sf.getValueAsString("CSQ", "POLYPHEN"));
+ assertEquals("Benign=good", sf.getValueAsString("CSQ", "clin_sig")); // url
+ // decoded
+ // todo change STRAND and !Phase into fields of SequenceFeature instead