String transcriptId = "ABC123";
// transcript at (start+10000) length 501
- SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
- 20500, 0f, null);
+ SequenceFeature sf = new SequenceFeature("transcript", "", 20000, 20500,
+ 0f, null);
sf.setValue("id", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// Ensembl treats NMD_transcript_variant as if transcript
// although strictly it is a sequence_variant in SO
- sf = new SequenceFeature("NMD_transcript_variant", "", 11000, 12000,
- 0f, null);
+ sf = new SequenceFeature("NMD_transcript_variant", "", 11000, 12000, 0f,
+ null);
sf.setValue("id", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
String accId = "ABC123";
EnsemblGenome testee = new EnsemblGenome();
- SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
- 20500, 0f, null);
+ SequenceFeature sf = new SequenceFeature("transcript", "", 20000, 20500,
+ 0f, null);
assertFalse(testee.retainFeature(sf, accId));
sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f,
null);
assertFalse(testee.retainFeature(sf, accId));
- sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
- 0f, null);
+ sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500, 0f,
+ null);
assertFalse(testee.retainFeature(sf, accId));
// other feature with no parent is kept