20500, 0f, null);
assertFalse(testee.retainFeature(sf, accId));
- sf.setType("aberrant_processed_transcript");
+ sf = new SequenceFeature("aberrant_processed_transcript", "", 20000,
+ 20500, 0f, null);
assertFalse(testee.retainFeature(sf, accId));
- sf.setType("NMD_transcript_variant");
+ sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
+ 0f, null);
assertFalse(testee.retainFeature(sf, accId));
// other feature with no parent is retained
- sf.setType("sequence_variant");
+ sf = new SequenceFeature("sequence_variant", "", 20000, 20500, 0f, null);
assertTrue(testee.retainFeature(sf, accId));
// other feature with desired parent is retained
assertTrue(testee.identifiesSequence(sf, accId));
// exon sub-type with right parent is valid
- sf.setType("coding_exon");
+ sf = new SequenceFeature("coding_exon", "", 1, 2, 0f, null);
+ sf.setValue("Parent", "transcript:" + accId);
assertTrue(testee.identifiesSequence(sf, accId));
// transcript not valid:
- sf.setType("transcript");
+ sf = new SequenceFeature("transcript", "", 1, 2, 0f, null);
+ sf.setValue("Parent", "transcript:" + accId);
assertFalse(testee.identifiesSequence(sf, accId));
// CDS not valid:
- sf.setType("CDS");
+ sf = new SequenceFeature("CDS", "", 1, 2, 0f, null);
+ sf.setValue("Parent", "transcript:" + accId);
assertFalse(testee.identifiesSequence(sf, accId));
}