protected void outputText_actionPerformed(ActionEvent e)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
- JInternalFrame frame = new JInternalFrame();
- frame.setContentPane(cap);
- Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
+ Desktop.addInternalFrame(cap, "Alignment output - "+e.getActionCommand(), 600, 500);
cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));
}
viewport.alignment.deleteSequence(i);
}
}
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
updateEditMenuBar();
viewport.updateConsensus();
viewport.updateConservation();
alignPanel.repaint();
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
}
public void moveSelectedSequences(boolean up)
protected void delete_actionPerformed(ActionEvent e)
{
boolean seqsdeleted=false;
- addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));
if (viewport.getSelectionGroup() == null)
return;
+ addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));
+
SequenceGroup sg = viewport.getSelectionGroup();
for (int i=0;i < sg.sequences.size(); i++)
{
public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
- RedundancyPanel sp = new RedundancyPanel(alignPanel);
+ RedundancyPanel sp = new RedundancyPanel(alignPanel,this);
JInternalFrame frame = new JInternalFrame();
frame.setContentPane(sp);
Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);
public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
{
- if(viewport.getSelectionGroup().getSize()<2)
+ if((viewport.getSelectionGroup()==null) ||
+ viewport.getSelectionGroup().getSize()<2)
JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
else
{
}
if (msa!=null) {
+ jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", title, msa, false, true);
+ }
+ }
+ public void ClustalRealign_actionPerformed(ActionEvent e)
+ {
+ // TODO:resolve which menu item was actually selected
+ // Now, check we have enough sequences
+ SequenceI[] msa=null;
+ if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
+ {
+ // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+ SequenceGroup seqs = viewport.getSelectionGroup();
+ int sz;
+ msa = new SequenceI[sz=seqs.getSize()];
+ for (int i = 0; i < sz; i++)
+ {
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);
+ }
+
+ }
+ else
+ {
+ Vector seqs = viewport.getAlignment().getSequences();
+
+ if (seqs.size() > 1) {
+ msa = new SequenceI[seqs.size()];
+ for (int i = 0; i < seqs.size(); i++)
+ {
+ msa[i] = (SequenceI) seqs.elementAt(i);
+ }
+
+ }
+
+ }
+ if (msa!=null) {
jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", title, msa, true, true);
}
}
+
protected void jpred_actionPerformed(ActionEvent e)
{
SequenceI seq=null;
}
if (msa!=null) {
- MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS",title, msa, true, true);
+ MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS",title, msa, false, true);
}
}
protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {