else
{
// Now add any sequences between min and max
- sg.getSequences(null).removeAllElements();
+ sg.clear();
for (int i = min; i < max; i++)
{
sg.addSequence(av.getAlignment().getSequenceAt(i), false);
if (groupEditing)
{
- Vector vseqs = sg.getSequences(av.getHiddenRepSequences());
- int g, groupSize = vseqs.size();
- SequenceI[] groupSeqs = new SequenceI[groupSize];
- for (g = 0; g < groupSeqs.length; g++)
- {
- groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
- }
+ SequenceI[] groupSeqs = sg.getSequences(av.getHiddenRepSequences()).toArray(new SequenceI[0]);
// drag to right
if (insertGap)
{
blank = true;
- for (g = 0; g < groupSize; g++)
+ for (SequenceI gs:groupSeqs)
{
for (int j = 0; j < startres - lastres; j++)
{
- if (!jalview.util.Comparison.isGap(groupSeqs[g]
+ if (!jalview.util.Comparison.isGap(gs
.getCharAt(fixedRight - j)))
{
blank = false;
// / Are we able to delete?
// ie are all columns blank?
- for (g = 0; g < groupSize; g++)
+ for (SequenceI gs:groupSeqs)
{
for (int j = startres; j < lastres; j++)
{
- if (groupSeqs[g].getLength() <= j)
+ if (gs.getLength() <= j)
{
continue;
}
- if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j)))
+ if (!jalview.util.Comparison.isGap(gs.getCharAt(j)))
{
// Not a gap, block edit not valid
endEditing();
{
if (stretchGroup.cs instanceof ClustalxColourScheme)
{
- ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(
- stretchGroup.getSequences(av.getHiddenRepSequences()),
- stretchGroup.getWidth());
+ ((ClustalxColourScheme) stretchGroup.cs).alignmentChanged(
+stretchGroup,av.getHiddenRepSequences());
}
if (stretchGroup.cs instanceof Blosum62ColourScheme