{
if (ofstart > -1)
{
- offset.addShift(ofstart, ofstart - i);
+ offset.addShift(offset.shift(ofstart), ofstart - i);
ofstart = -1;
}
}
// final gap
if (ofstart > -1)
{
- offset.addShift(ofstart, ofstart - sleng);
+ offset.addShift(offset.shift(ofstart), ofstart - sleng);
ofstart = -1;
}
String newSeq = rnaTrim.getSeq().replace("-", "");
public void mouseOverSequence(SequenceI sequence, int index)
{
RNA rna = vab.getSelectedRNA();
- if (rnas.get(sequence) == rna)
+ if (seqs.get(rna) == sequence)
{
ShiftList shift = offsets.get(rna);
if (shift != null)
{
- index = shift.shift(index);
+ // System.err.print("Orig pos:"+index);
+ index = shift.shift(index);
+ // System.err.println("\nFinal pos:"+index);
}
mouseOverHighlighter.highlightRegion(rna, index, index);
vab.updateSelectedRNA(rna);
{
if (shift != null)
{
- int i=shift.shift(arg1.getIndex());
- ssm.mouseOverVamsasSequence(seq,
- i, this);
+ int i = shift.shift(arg1.getIndex());
+ // System.err.println("shifted "+(arg1.getIndex())+" to "+i);
+ ssm.mouseOverVamsasSequence(seq, i, this);
}
else
{