private void selectModel(SubstitutionModel m) {
manager.inputData.model = m;
for (JMenuItem mi : modelButtons) {
if (mi.getText().equals(m.getMenuName())) {
mi.setSelected(true);
break;
}
}
}
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);
}
}
}
}
/** The only constructor of the class. It launches the main window. */
@SuppressWarnings("unchecked")
public MainFrame() throws Exception {
super("StatAlign " + StatAlign.version);
try {
String syslook = UIManager.getSystemLookAndFeelClassName();
if (!UIManager.getLookAndFeel().getClass().getName().equals(syslook)) {
UIManager.setLookAndFeel(syslook);
SwingUtilities.updateComponentTreeUI(this);
}
} catch (Exception ex) {
JOptionPane.showMessageDialog(this, ex);
}
ArrayList<Class<?>> substModList = new ArrayList<Class<?>>();
for (String model :
Utils.classesInPackage(SubstitutionModel.class.getPackage().getName() + ".plugins")) {
try {
Class<?> cl = Class.forName(model);
/* Only include non-abstract substitution models that extend SubstitutionModel */
if (!Modifier.isAbstract(cl.getModifiers()) && SubstitutionModel.class.isAssignableFrom(cl))
substModList.add(cl);
} catch (Exception ex) {
}
}
substModels =
(Class<? extends SubstitutionModel>[])
substModList.toArray(new Class<?>[substModList.size()]);
manager = new MainManager(this);
mcmcSettingsDlg = new McmcSettingsDlg(this);
setMinimumSize(new Dimension(500, 250));
///
/// Creates the MenuBar and the ToolBar
///
toolBar = new JToolBar();
toolBar.setFloatable(false);
toolBar.setRollover(true);
JMenuBar menubar = new JMenuBar();
JMenu menu = new JMenu("File");
menu.setMnemonic(KeyEvent.VK_F);
JMenuItem item;
String openText = "Add sequence(s)...";
ImageIcon icon = new ImageIcon(ClassLoader.getSystemResource("icons/open.png"));
openItem = createMenuItem(openText, true);
openItem.setAccelerator(KeyStroke.getKeyStroke("control O"));
openItem.setMnemonic(KeyEvent.VK_A);
openItem.setIcon(icon);
menu.add(openItem);
openButton = createButton(icon, "Add sequence(s)...");
toolBar.add(openButton);
toolBar.addSeparator();
JMenuItem ioPreferencesItem = createMenuItem("Preferences...", true);
ioPreferencesItem.setAccelerator(KeyStroke.getKeyStroke("control 1"));
ioPreferencesItem.setMnemonic(KeyEvent.VK_P);
menu.add(ioPreferencesItem);
menu.addSeparator();
item = createMenuItem("Exit", true);
item.setAccelerator(KeyStroke.getKeyStroke("alt F4"));
item.setMnemonic(KeyEvent.VK_X);
menu.add(item);
menubar.add(menu);
// menu = new JMenu("Edit");
// menu.setMnemonic(KeyEvent.VK_E);
// item = new JMenuItem("Cut");
// item.addActionListener(this);
// item.setAccelerator(KeyStroke.getKeyStroke("control X"));
// menu.add(item);
// item = new JMenuItem("Copy");
// item.addActionListener(this);
// item.setAccelerator(KeyStroke.getKeyStroke("control C"));
// menu.add(item);
// item = new JMenuItem("Paste");
// item.addActionListener(this);
// item.setAccelerator(KeyStroke.getKeyStroke("control V"));
// menu.add(item);
// menubar.add(menu);
menu = new JMenu("Analysis");
menu.setMnemonic(KeyEvent.VK_M);
// item = createMenuItem("Settings", true);
// item.setAccelerator(KeyStroke.getKeyStroke("control M"));
// item.setMnemonic(KeyEvent.VK_S);
// menu.add(item);
String runText = "Set up and run";
icon = new ImageIcon(ClassLoader.getSystemResource("icons/play.png"));
runItem = createMenuItem(runText, false);
runItem.setAccelerator(KeyStroke.getKeyStroke("control ENTER"));
runItem.setIcon(icon);
menu.add(runItem);
menu.addSeparator();
runButton = createButton(icon, runText);
runButton.setEnabled(false);
toolBar.add(runButton);
String pauseText = "Pause";
icon = new ImageIcon(ClassLoader.getSystemResource("icons/pause.png"));
pauseItem = createMenuItem("Pause", false);
pauseItem.setIcon(icon);
menu.add(pauseItem);
pauseButton = createButton(icon, pauseText);
pauseButton.setEnabled(false);
toolBar.add(pauseButton);
String resumeText = "Resume";
icon = new ImageIcon(ClassLoader.getSystemResource("icons/resume.png"));
resumeItem = createMenuItem(resumeText, false);
resumeItem.setIcon(icon);
menu.add(resumeItem);
resumeButton = createButton(icon, resumeText);
resumeButton.setEnabled(false);
toolBar.add(resumeButton);
String stopText = "Stop";
icon = new ImageIcon(ClassLoader.getSystemResource("icons/stop.png"));
stopItem = createMenuItem("Stop", false);
stopItem.setIcon(icon);
menu.add(stopItem);
menubar.add(menu);
stopButton = createButton(icon, stopText);
stopButton.setEnabled(false);
toolBar.add(stopButton);
String rnaText = "RNA mode";
rnaButton =
createToggleButton(new ImageIcon(ClassLoader.getSystemResource("icons/rna1.png")), rnaText);
rnaButton.setEnabled(false);
rnaButton.setSelected(false);
toolBar.add(rnaButton);
// String settingsText = "Settings";
// JButton settingsButton = createButton(new ImageIcon(ClassLoader.
// getSystemResource("icons/settings.png")), settingsText);
// toolBar.add(settingsButton);
menu = new JMenu("Model");
menu.setMnemonic(KeyEvent.VK_L);
modelButtons = new JMenuItem[substModels.length];
ButtonGroup modelGroup = new ButtonGroup();
HashMap<String, ArrayList<Class<? extends SubstitutionModel>>> substModTypes =
new HashMap<String, ArrayList<Class<? extends SubstitutionModel>>>();
for (Class<? extends SubstitutionModel> cl : substModels) {
String type = SubstitutionModel.getType(cl);
ArrayList<Class<? extends SubstitutionModel>> arr = substModTypes.get(type);
if (arr == null)
substModTypes.put(type, arr = new ArrayList<Class<? extends SubstitutionModel>>());
arr.add(cl);
}
String[] typeArr = new String[substModTypes.keySet().size()];
int s = 0;
if (typeArr.length >= 2) {
typeArr[0] = "protein"; // amino acid subst models first
typeArr[1] = "nucleotide"; // then nucleotide models, then the rest
s = 2;
}
for (String type : substModTypes.keySet()) {
if (!type.equals("protein") && !type.equals("nucleotide")) typeArr[s++] = type;
}
s = 0;
for (String type : typeArr) {
if (s > 0) menu.addSeparator();
for (Class<? extends SubstitutionModel> cl : substModTypes.get(type)) {
String name = SubstitutionModel.getMenuName(cl);
item = new JRadioButtonMenuItem(name);
item.addActionListener(this);
modelButtons[s++] = item;
modelGroup.add(item);
menu.add(item);
}
}
modelGroup.clearSelection();
menubar.add(menu);
/*menu = new JMenu("View");
menu.setMnemonic(KeyEvent.VK_V);
JMenuItem zoomInItem = new JMenuItem("Zoom in");
zoomInItem.setEnabled(false);
zoomInItem.addActionListener(this);
menu.add(zoomInItem);
JMenuItem zoomOutItem = new JMenuItem("Zoom out");
zoomOutItem.setEnabled(false);
zoomOutItem.addActionListener(this);
menu.add(zoomOutItem);
JMenuItem autofitItem = new JMenuItem("Fit to frame");
autofitItem.setEnabled(false);
autofitItem.addActionListener(this);
menu.add(autofitItem);
menubar.add(menu);*/
menu = new JMenu("Help");
menu.setMnemonic(KeyEvent.VK_H);
item = new JMenuItem("About...");
item.addActionListener(this);
menu.add(item);
menu.addSeparator();
item = new JMenuItem("Help for users");
item.addActionListener(this);
menu.add(item);
menu.addSeparator();
item = new JMenuItem("Html doc for developers");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Description of plugins");
item.addActionListener(this);
menu.add(item);
menubar.add(menu);
setJMenuBar(menubar);
add(toolBar, BorderLayout.PAGE_START);
///
/// Creates the main panel
///
Container cp = getContentPane();
JPanel mainPanel = new JPanel(new BorderLayout());
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
mainPanel.setMinimumSize(new Dimension(screenSize.width / 3, screenSize.height / 3));
mainPanel.setMaximumSize(new Dimension(screenSize.width, screenSize.height));
mainPanel.setPreferredSize(new Dimension(screenSize.width / 2, screenSize.height / 2));
tab = new JTabbedPane();
input = new Input(manager);
tab.addTab(input.getTabName(), input.getIcon(), input.getJPanel(), input.getTip());
manager.inputgui = input.inputgui;
// Sorts the tab according to their getTabOrder()
pluginTabs = manager.postProcMan.plugins.clone();
Arrays.sort(
pluginTabs,
new Comparator<Postprocess>() {
@Override
public int compare(Postprocess firstTab, Postprocess secondTab) {
return Double.compare(firstTab.getTabOrder(), secondTab.getTabOrder());
}
});
tabPluginMap = new HashMap<Integer, Postprocess>();
for (int i = 0; i < pluginTabs.length; i++) {
Postprocess plugin = pluginTabs[i];
if (plugin.selected && !plugin.rnaAssociated) {
tabPluginMap.put(i + 1, plugin); // TODO: Jesus Java, horrible.
tab.addTab(plugin.getTabName(), plugin.getIcon(), plugin.getJPanel(), plugin.getTip());
}
}
tab.addChangeListener(
new ChangeListener() {
@Override
public void stateChanged(ChangeEvent changeEvent) {
JTabbedPane pane = (JTabbedPane) changeEvent.getSource();
Integer i = pane.getSelectedIndex();
// Remove the last tabs toolbar items.
if (lastSelectedTabIndex != -1) {
Postprocess lastPlugin = tabPluginMap.get(lastSelectedTabIndex);
if (lastPlugin != null && lastPlugin.hasToolBar) {
for (JComponent item : lastPlugin.getToolBarItems()) {
toolBar.remove(item);
}
toolBar.revalidate(); // TODO: optimize.
toolBar.repaint();
}
}
// Add the currents tab toolbar items.
Postprocess plugin = tabPluginMap.get(i);
if (plugin != null && plugin.hasToolBar) {
for (JComponent item : plugin.getToolBarItems()) {
toolBar.add(item);
}
toolBar.revalidate();
toolBar.repaint();
}
lastSelectedTabIndex = i;
}
});
mainPanel.add(tab, BorderLayout.CENTER);
cp.add(mainPanel, BorderLayout.CENTER);
JPanel statusBar = new JPanel(new BorderLayout());
statusText = new JLabel(IDLE_STATUS_MESSAGE);
statusBar.add(statusText, BorderLayout.CENTER);
cp.add(statusBar, BorderLayout.SOUTH);
// setSize(300, 200);
// setLocationByPlatform(true);
// setLocation(screenSize.width/4,screenSize.height/4);
pack();
setBounds(
screenSize.width / 5 - 15,
screenSize.height / 5 - 15,
screenSize.width * 3 / 5 + 30,
screenSize.height * 3 / 5 + 30);
setVisible(true);
setDefaultCloseOperation(EXIT_ON_CLOSE);
}