-
- @Override
- public void loadScores_actionPerformed(ActionEvent e)
- {
- // Pick the tree file
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Select a T-Coffee scores ascii file");
- chooser.setToolTipText("Load a score file");
-
- int value = chooser.showOpenDialog(null);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- String sFilePath = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", sFilePath);
-
-
- try
- {
- TCoffeeScoreFile result = new TCoffeeScoreFile(sFilePath, FormatAdapter.FILE);
- if (!result.isValid()) {
- JOptionPane.showMessageDialog(Desktop.desktop, result.getWarningMessage(),
- "Problem reading T-COFFEE score file", JOptionPane.WARNING_MESSAGE);
- return;
- }
-
- /*
- * check that the score matrix matches the alignment dimensions
- */
- AlignmentI aln;
- if( (aln=viewport.getAlignment()) != null && (aln.getHeight() != result.getHeight() || aln.getWidth() != result.getWidth()) ) {
- // TODO: raise a dialog box here rather than bomb out.
- JOptionPane.showMessageDialog(Desktop.desktop, "The scores matrix does not match the alignment dimensions",
- "Problem reading T-COFFEE score file", JOptionPane.WARNING_MESSAGE);
- }
- if (result.annotateAlignment(alignPanel.getAlignment(), true))
- {
- tcoffeeColour.setEnabled(true);
- tcoffeeColour.setSelected(true);
- // switch to this color
- changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
- } else {
- tcoffeeColour.setEnabled(false);
- tcoffeeColour.setSelected(false);
- }
- if (result.getWarningMessage()!=null)
- {
- JOptionPane.showMessageDialog(Desktop.desktop, result.getWarningMessage(),"Problem reading T-COFEEE score file", JOptionPane.WARNING_MESSAGE);
- }
- }
- catch (Exception ex) {
- JOptionPane.showMessageDialog(
- Desktop.desktop,
- ex.getMessage(),
- "unexpected problem reading T-COFFEE score file",
- JOptionPane.WARNING_MESSAGE);
-
- ex.printStackTrace();
- }
- }
-
- }
-
-
- @Override
- protected void tcoffeeColorScheme_actionPerformed(ActionEvent e) {
- changeColour( new TCoffeeColourScheme(alignPanel.getAlignment()) );
- }
-
-// /**
-// * Load the (T-Coffee) score file from the specified url
-// *
-// * @param url The absolute path from where download and read the score file
-// * @throws IOException
-// */
-// public void loadScoreFile(URL url ) throws IOException {
-//
-// TCoffeeScoreFile result = new TCoffeeScoreFile();
-// result.parse( new InputStreamReader( url.openStream() ) );
-// tcoffeeScoreFile = result;
-// }
-