seq0.setEnd(end);
AlignmentI alignment = new Alignment(new SequenceI[] { seq0 });
alignment.setDataset(null);
+
/*
* create a new alignment with shared dataset sequence
*/
assertEquals(func(5), sfs.size());
assertEquals(sfs, copySeq0.getSequenceFeatures());
String copySequenceFeatures = copySeq0.getSequenceFeatures().toString();
+
/*
* now perform all possible cuts of subranges of columns 1-5
* and validate the resulting remaining sequence features!
*/
SequenceI[] sqs = new SequenceI[] { seq0 };
- boolean checkDsSize = false;
+ boolean checkDsSize = true;
for (int from = 0; from < seq0.getLength(); from++)
{
EditCommand ec = new EditCommand("Cut", Action.CUT, sqs, from, (to
- from + 1), alignment);
final String msg = String.format("Cut %d-%d ", from + 1, to + 1);
+ boolean newDatasetSequence = copySeq0.getDatasetSequence() != seq0
+ .getDatasetSequence();
verifyCut(seq0, from, to, msg, start);
assertEquals("Original dataset sequence was modified",
copySequenceFeatures,
copySeq0.getSequenceFeatures().toString());
+
if (checkDsSize)
{
/*
* verify a new dataset sequence has appeared
*/
assertEquals("Wrong Dataset size after cut",
- copySeq0.getDatasetSequence() == seq0.getDatasetSequence()
- ? 1
- : 2,
- alignment.getDataset().getHeight());
+ newDatasetSequence ? 2 : 1, alignment.getDataset()
+ .getHeight());
}
/*
* undo and verify all restored
/*
* verify dataset sequence has shrunk
*/
- assertEquals("Wrong Dataset size after cut",
- copySeq0.getDatasetSequence() == seq0.getDatasetSequence()
- ? 1
- : 2,
+ assertEquals("Wrong Dataset size after cut", 1,
alignment.getDataset().getHeight());
}
/*
* verify a new dataset sequence has appeared again
*/
assertEquals("Wrong Dataset size after cut",
- copySeq0.getDatasetSequence() == seq0.getDatasetSequence()
- ? 1
- : 2,
- alignment.getDataset().getHeight());
+ newDatasetSequence ? 2 : 1, alignment.getDataset()
+ .getHeight());
}
/*
* undo ready for next cut
/*
* and that dataset sequence has shrunk
*/
- assertEquals("Wrong Dataset size after cut",
- copySeq0.getDatasetSequence() == seq0.getDatasetSequence()
- ? 1
- : 2,
+ assertEquals("Wrong Dataset size after cut", 1,
alignment.getDataset().getHeight());
}
}