/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.analysis.AlignSeq;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.RnaViewerModel;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
@Override
public void selection(SequenceGroup seqsel, ColumnSelection colsel,
- SelectionSource source)
+ HiddenColumns hidden, SelectionSource source)
{
if (source != ap.av)
{
ShiftList offset = new ShiftList();
int ofstart = -1;
int sleng = seq.getLength();
- char[] seqChars = seq.getSequence();
for (int i = 0; i < sleng; i++)
{
- if (Comparison.isGap(seqChars[i]))
+ if (Comparison.isGap(seq.getCharAt(i)))
{
if (ofstart == -1)
{