{
AlignmentI al = new Alignment(seqs);
HiddenSequences hs = al.getHiddenSequences();
- for (int i = 0; i < SEQ_COUNT; i++)
+ int height = al.getHeight();
+ for (int i = 0; i < height; i++)
{
assertEquals(i, hs.findIndexWithoutHiddenSeqs(i));
}
/*
* alignment is now seq0/2/3/4/7/8/9
*/
- assertEquals(SEQ_COUNT - 3, al.getHeight());
+ assertEquals(height - 3, al.getHeight());
assertEquals(0, hs.findIndexWithoutHiddenSeqs(0));
assertEquals(0, hs.findIndexWithoutHiddenSeqs(1));
assertEquals(1, hs.findIndexWithoutHiddenSeqs(2));
assertEquals(4, hs.findIndexWithoutHiddenSeqs(7));
assertEquals(5, hs.findIndexWithoutHiddenSeqs(8));
assertEquals(6, hs.findIndexWithoutHiddenSeqs(9));
+
+ /*
+ * hide first two sequences
+ */
+ hs.showAll(null);
+ hs.hideSequence(seqs[0]);
+ hs.hideSequence(seqs[1]);
+ assertEquals(-1, hs.findIndexWithoutHiddenSeqs(0));
+ assertEquals(-1, hs.findIndexWithoutHiddenSeqs(1));
+ for (int i = 2; i < height; i++)
+ {
+ assertEquals(i - 2, hs.findIndexWithoutHiddenSeqs(i));
+ }
}
/**