public void actionPerformed(ActionEvent e)
{
addHistoryItem("sort");
+ // TODO: JBPNote - have to map order entries to curent SequenceI pointers
AlignmentSorter.sortBy(viewport.getAlignment(), order);
alignPanel.repaint();
}
jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", title, msa, true, true);
}
}
-/* Old cLustalW
- WebserviceInfo info = new WebserviceInfo("Clustal web service",
- "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"+
- " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
- +" Nucleic Acids Research, submitted, June 1994.",
- 450, 150);
-
- ClustalThread thread = new ClustalThread(info);
- thread.start();
- }
-
- class ClustalThread extends Thread
- {
- WebserviceInfo info;
- public ClustalThread(WebserviceInfo info)
- {this.info = info; }
-
- public void run()
- {
- info.setStatus(WebserviceInfo.STATE_RUNNING);
- jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
- Vector sv = viewport.getAlignment().getSequences();
- SequenceI[] seqs = new SequenceI[sv.size()];
-
- int i = 0;
- do
- {
- seqs[i] = (SequenceI) sv.elementAt(i);
- }
- while (++i < sv.size());
-
- SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
- if (alignment != null)
- {
- AlignFrame af = new AlignFrame(new Alignment(alignment));
- Desktop.addInternalFrame(af, title.concat(" - ClustalW Alignment"),
- NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
- af.clustalColour_actionPerformed(null);
- af.clustalColour.setSelected(true);
- info.setStatus(WebserviceInfo.STATE_STOPPED_OK);
- }
- else
- {
- info.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
- info.appendProgressText("Problem obtaining clustal alignment");
- }
- }
- }
-*/
protected void jpred_actionPerformed(ActionEvent e)
{