private String tryModels() {
String message = "";
try {
SubstitutionModel[] defaultSubstList = {new Kimura3(), new Dayhoff()};
for (SubstitutionModel model : defaultSubstList) {
try {
model.acceptable(manager.inputData.seqs);
selectModel(model);
break;
} catch (RecognitionError e) {
}
}
if (manager.inputData.model == null) {
double max = 0.0;
int wrong = 0;
for (Class<? extends SubstitutionModel> cl : substModels) {
SubstitutionModel m;
try {
m = cl.newInstance();
if (m.acceptable(manager.inputData.seqs) > max) {
manager.inputData.model = m;
max = m.acceptable(manager.inputData.seqs);
selectModel(m);
}
} catch (RecognitionError e) {
wrong++;
message += e.message;
}
}
}
} catch (Exception e) {
JOptionPane.showMessageDialog(
this,
e.getLocalizedMessage(),
"Error accessing substitution models",
JOptionPane.ERROR_MESSAGE);
}
return message;
}
/**
* An ActioListener is implemented, so we have to implement this function. It handles actions on
* the menu bar.
*/
@Override
public void actionPerformed(ActionEvent ev) {
if (ev.getActionCommand() == "Add sequence(s)...") {
addSequences();
} else if (ev.getActionCommand() == "Exit") {
System.exit(0);
} else if (ev.getActionCommand() == "Preferences...") {
// System.out.println("here!!!");
op = new OutputPreferences(this);
} else if (ev.getActionCommand() == "Settings") {
mcmcSettingsDlg.display(this);
} else if (ev.getActionCommand() == "Set up and run") {
if (manager.inputData.seqs.sequences.size() < 2) {
JOptionPane.showMessageDialog(
this,
"At least two sequences are needed!!!",
"Not enough sequences",
JOptionPane.ERROR_MESSAGE);
// manager.finished();
return;
}
// disableAllButtons();
mcmcSettingsDlg.display(this);
// start();
} else if (ev.getActionCommand() == "Pause") {
pauseItem.setEnabled(false);
pauseButton.setEnabled(false);
resumeItem.setEnabled(true);
resumeButton.setEnabled(true);
setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
final String savTit = getTitle();
setTitle("Pausing...");
manager.thread.suspendSoft();
setTitle(savTit);
setCursor(Cursor.getDefaultCursor());
} else if (ev.getActionCommand() == "Resume") {
manager.thread.resumeSoft();
pauseItem.setEnabled(true);
pauseButton.setEnabled(true);
resumeItem.setEnabled(false);
resumeButton.setEnabled(false);
} else if (ev.getActionCommand() == "Stop") {
setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
final String savTit = getTitle();
setTitle("Stopping...");
manager.thread.stopSoft();
finished();
setTitle(savTit);
setCursor(Cursor.getDefaultCursor());
} else if (ev.getActionCommand() == "RNA mode") {
if (rnaButton.isSelected()) {
dlg = new RNASettingsDlg(this);
dlg.display(this);
// manager.inputgui = input.inputgui;
// manager.inputgui.updateSequences();
// tab.addTab(input.getTabName(), input.getIcon(), input.getJPanel(), input.getTip());
manager.inputgui = input.inputgui;
manager.inputgui.updateSequences();
// System.out.println("SELECTED!!!");
manager.postProcMan.rnaMode = true;
// manager.postProcMan.reload();
int count = tab.getTabCount();
for (Postprocess plugin : pluginTabs) {
// System.out.println(plugin.getTabName() + ": " + plugin.screenable);
if (plugin.rnaAssociated) {
tabPluginMap.put(count, plugin);
tab.addTab(plugin.getTabName(), plugin.getIcon(), plugin.getJPanel(), plugin.getTip());
count++;
}
// manager.postProcMan.init();
}
} else {
manager.postProcMan.rnaMode = false;
// System.out.println("NOT SELECTED!!!");
manager.inputgui = input.inputgui;
manager.inputgui.updateSequences();
int count = 0;
for (Postprocess plugin : pluginTabs) {
if (plugin.rnaAssociated) {
tabPluginMap.remove(plugin);
String removePlugin = tab.getTitleAt(count + 1);
tab.remove(count + 1);
count--;
}
count++;
}
}
} else if (ev.getActionCommand() == "About...") {
new HelpWindow(
this, "About", getClass().getClassLoader().getResource("doc/about/index.html"), false);
} else if (ev.getActionCommand() == "Html doc for developers") {
new HelpWindow(
this, "Html doc for Developers", ClassLoader.getSystemResource("doc/index.html"), true);
} else if (ev.getActionCommand() == "Description of plugins") {
new HelpWindow(
this,
"Description of plugins",
ClassLoader.getSystemResource("doc/plugin_description/index.html"),
true);
} else if (ev.getActionCommand() == "Help for users") {
helpUsers();
} else { // new substitution model selected
for (Class<? extends SubstitutionModel> cl : substModels) {
try {
if (ev.getActionCommand().equals(SubstitutionModel.getMenuName(cl))) {
try {
SubstitutionModel model = cl.newInstance();
model.acceptable(manager.inputData.seqs);
manager.inputData.model = model;
break;
} catch (RecognitionError e) {
selectModel(manager.inputData.model);
JOptionPane.showMessageDialog(
this, e.message, "Cannot apply this model...", JOptionPane.ERROR_MESSAGE);
break;
}
}
} catch (Exception e) {
ErrorMessage.showPane(this, e, true);
}
}
}
}