if (ignoreHidden)
{
seqString = getVisibleSequence(seq);
+ this.searchedSequenceStartPosition = 1;
}
else
{
*/
private String getVisibleSequence(SequenceI seq)
{
- int seqStartCol = seq.findIndex(seq.getStart());
- int seqEndCol = seq.findIndex(seq.getStart() + seq.getLength() - 1);
+ /*
+ * get start / end columns of sequence and convert to base 0
+ * (so as to match the visible column ranges)
+ */
+ int seqStartCol = seq.findIndex(seq.getStart()) - 1;
+ int seqEndCol = seq.findIndex(seq.getStart() + seq.getLength() - 1) - 1;
Iterator<int[]> visibleColumns = viewport.getViewAsVisibleContigs(true);
StringBuilder visibleSeq = new StringBuilder(seqEndCol - seqStartCol);
List<int[]> fromRanges = new ArrayList<>();
* so add the range to the mapping being constructed
*/
int seqResFrom = seq.findPosition(range[0]);
- int seqResTo = seq.findPosition(range[1]);
+ int seqResTo = seqResFrom + ungapped.length() - 1;
fromRanges.add(new int[] { seqResFrom, seqResTo });
}
}