}
else
{
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
viewport.setEndSeq(viewport.alignment.getHeight());
viewport.alignment.getWidth();
viewport.updateConservation();
//are the sequences aligned?
if(!viewport.alignment.isAligned())
{
- JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
+ JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.\n"
+ +"Try using the Pad function in the edit menu.",
"Sequences not aligned", JOptionPane.WARNING_MESSAGE);
return;
}
protected void jpred_actionPerformed(ActionEvent e)
{
+ SequenceI seq=null;
+ SequenceI[] msa=null;
if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
{
SequenceGroup seqs = viewport.getSelectionGroup();
if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
{
- JPredClient ct = new JPredClient( (SequenceI)seqs.getSequenceAt(0));
+ seq = (SequenceI)seqs.getSequenceAt(0);
}
else
{
int sz;
- SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
+ msa = new SequenceI[sz=seqs.getSize()];
for (int i = 0; i < sz; i++)
{
msa[i] = (SequenceI) seqs.getSequenceAt(i);
}
-
- JPredClient ct = new JPredClient(title, msa);
}
-
}
else
{
if (seqs.size() == 1 || !viewport.alignment.isAligned())
{
- JPredClient ct = new JPredClient( (SequenceI)
- seqs.elementAt(0));
+ seq = (SequenceI) seqs.elementAt(0);
}
else
{
- SequenceI[] msa = new SequenceI[seqs.size()];
+ msa = new SequenceI[seqs.size()];
for (int i = 0; i < seqs.size(); i++)
{
msa[i] = (SequenceI) seqs.elementAt(i);
}
-
- JPredClient ct = new JPredClient(title, msa);
}
-
+ }
+ if (msa!=null) {
+ JPredClient ct = new JPredClient(title, msa);
+ } else
+ if (seq!=null) {
+ JPredClient ct = new JPredClient(title, seq);
+ } else {
+ System.out.print("JALVIEW ERROR! - Unexpected JPred selection state!\n");
}
}
protected void msaAlignMenuItem_actionPerformed(ActionEvent e)