import java.util.Deque;
import java.util.HashMap;
import java.util.Hashtable;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
if (alignment.getHiddenColumns() != null
&& alignment.getHiddenColumns().hasHiddenColumns())
{
- selection = alignment.getHiddenColumns()
- .getVisibleSequenceStrings(start, end, seqs);
+ for (i = 0; i < iSize; i++)
+ {
+ Iterator<int[]> blocks = alignment.getHiddenColumns()
+ .getVisContigsIterator(start, end + 1, false);
+ selection[i] = seqs[i].getSequenceStringFromIterator(blocks);
+ }
}
else
{
start = hidden.visibleToAbsoluteColumn(start);
}
- end = hidden.getHiddenBoundaryRight(start);
+ end = hidden.getNextHiddenBoundary(false, start);
if (start == end)
{
end = max;
if (hidden != null && hidden.hasHiddenColumns())
{
start = hidden.visibleToAbsoluteColumn(end);
- start = hidden.getHiddenBoundaryLeft(start) + 1;
+ start = hidden.getNextHiddenBoundary(true, start) + 1;
}
} while (end < max);
int lastSeq = alignment.getHeight() - 1;
List<AlignedCodonFrame> seqMappings = null;
for (int seqNo = ranges
- .getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
+ .getStartSeq(); seqNo <= lastSeq; seqNo++, seqOffset++)
{
sequence = getAlignment().getSequenceAt(seqNo);
if (hiddenSequences != null && hiddenSequences.isHidden(sequence))