--- /dev/null
+package fr.orsay.lri.varna.applications.templateEditor;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.ComponentOrientation;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.GridLayout;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTarget;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.net.URLConnection;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.BoxLayout;
+import javax.swing.ButtonGroup;
+import javax.swing.Icon;
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JDialog;
+import javax.swing.JFileChooser;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
+import javax.swing.JScrollPane;
+import javax.swing.JToggleButton;
+import javax.swing.JToolBar;
+import javax.swing.UIManager;
+import javax.swing.UIManager.LookAndFeelInfo;
+import javax.swing.filechooser.FileFilter;
+import javax.swing.undo.UndoManager;
+
+import fr.orsay.lri.varna.VARNAPanel;
+import fr.orsay.lri.varna.applications.FileNameExtensionFilter;
+import fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate;
+import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
+import fr.orsay.lri.varna.exceptions.ExceptionXMLGeneration;
+import fr.orsay.lri.varna.models.templates.Benchmark;
+import fr.orsay.lri.varna.models.templates.DrawRNATemplateCurveMethod;
+import fr.orsay.lri.varna.models.templates.DrawRNATemplateMethod;
+import fr.orsay.lri.varna.models.templates.RNATemplate;
+import fr.orsay.lri.varna.models.templates.RNATemplateDrawingAlgorithmException;
+import fr.orsay.lri.varna.models.templates.RNATemplateMapping;
+import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement;
+
+
+
+
+public class TemplateEditor extends JFrame implements KeyListener, ActionListener,DropTargetListener {
+
+ private TemplatePanel _sk;
+ private VARNAPanel _vp;
+ private File currentFilePath = null;
+ private JButton saveButton;
+ private JScrollPane jp;
+ private UndoManager manager;
+ private JButton flipButton;
+ private JComboBox ellipseMethodList;
+ private JComboBox applyMethodList;
+ /*private JRadioButton ellipseButtons[];
+ private JRadioButton methodButtons[];
+ */
+
+
+ public TemplateEditor()
+ {
+ init();
+ clearCurrentFilePath();
+ }
+
+ public JScrollPane getJp() {
+ return jp;
+ }
+
+ private void init()
+ {
+ try {
+ _vp = new VARNAPanel(" ",".");
+ } catch (ExceptionNonEqualLength e) {
+ e.printStackTrace();
+ }
+ _vp.setNumPeriod(0);
+ JPanel p = new JPanel();
+ p.setLayout(new GridLayout(1,2));
+
+ JToolBar systemBar = new JToolBar();
+ JToolBar optionsBar = new JToolBar();
+ JButton newButton = new JButton("New",UIManager.getIcon("FileView.fileIcon"));
+ newButton.setActionCommand("new");
+ newButton.addActionListener(this);
+ newButton.addKeyListener(this);
+ JButton loadButton = new JButton("Open...",UIManager.getIcon("FileView.directoryIcon"));
+ loadButton.setActionCommand("open");
+ loadButton.addActionListener(this);
+ loadButton.addKeyListener(this);
+ saveButton = new JButton("Save",UIManager.getIcon("FileView.floppyDriveIcon"));
+ saveButton.setActionCommand("save");
+ saveButton.addActionListener(this);
+ saveButton.addKeyListener(this);
+ saveButton.setEnabled(false);
+ JButton saveAsButton = new JButton("Save As...",UIManager.getIcon("FileView.floppyDriveIcon"));
+ saveAsButton.setActionCommand("save as");
+ saveAsButton.addActionListener(this);
+ saveAsButton.addKeyListener(this);
+ JButton undoButton = new JButton("Undo");
+ undoButton.setActionCommand("undo");
+ undoButton.addActionListener(this);
+ undoButton.addKeyListener(this);
+ JButton redoButton = new JButton("Redo");
+ redoButton.setActionCommand("redo");
+ redoButton.addActionListener(this);
+ redoButton.addKeyListener(this);
+
+ JButton benchmarkButton = new JButton("Benchmark");
+ benchmarkButton.setActionCommand("benchmark");
+ benchmarkButton.addActionListener(this);
+ benchmarkButton.addKeyListener(this);
+
+ DrawRNATemplateMethod applyMethods[] = DrawRNATemplateMethod.values();
+ applyMethodList = new JComboBox(applyMethods);
+ applyMethodList.setSelectedItem(DrawRNATemplateMethod.getDefault());
+
+ DrawRNATemplateCurveMethod ellipseMethods[] = DrawRNATemplateCurveMethod.values();
+ ellipseMethodList = new JComboBox(ellipseMethods);
+ ellipseMethodList.setSelectedItem(DrawRNATemplateCurveMethod.getDefault());
+
+ JButton applyButton = new JButton("Apply");
+ applyButton.setActionCommand("apply");
+ applyButton.addActionListener(this);
+ applyButton.addKeyListener(this);
+
+ JButton retrieveButton = new JButton("Retrieve Templates");
+ retrieveButton.setActionCommand("retrieve");
+ retrieveButton.addActionListener(this);
+
+
+ flipButton = new JButton("Flip helix");
+ flipButton.setActionCommand("flip");
+ flipButton.addActionListener(this);
+ flipButton.addKeyListener(this);
+ flipButton.setEnabled(false);
+
+
+ systemBar.add(newButton);
+ systemBar.add(loadButton);
+ systemBar.add(saveButton);
+ systemBar.add(saveAsButton);
+ systemBar.addSeparator();
+
+ systemBar.addSeparator();
+ systemBar.addSeparator();
+ systemBar.add(benchmarkButton);
+ systemBar.addKeyListener(this);
+
+ optionsBar.setLayout(new FlowLayout(FlowLayout.LEFT));
+ optionsBar.add(new JLabel("Single-Stranded "));
+ optionsBar.add(this.ellipseMethodList);
+ optionsBar.addSeparator();
+ optionsBar.add(new JLabel("Layout "));
+ optionsBar.add(this.applyMethodList);
+ optionsBar.addSeparator();
+ optionsBar.add(applyButton);
+ optionsBar.addSeparator();
+ optionsBar.add(retrieveButton);
+ optionsBar.doLayout();
+
+ /*optionsBar.add(new JLabel("Curves:"));
+ for (int i=0; i<ellipseButtons.length; i++)
+ optionsBar.add(ellipseButtons[i]);
+ optionsBar.addSeparator();
+ optionsBar.add(new JLabel("Helix positions:"));
+ for (int i=0; i<methodButtons.length; i++)
+ optionsBar.add(methodButtons[i]);
+ optionsBar.addKeyListener(this);
+ */
+
+ JToolBar toolBar = new JToolBar();
+ ButtonGroup bg = new ButtonGroup();
+ toolBar.setOrientation(JToolBar.VERTICAL);
+ //toolBar.setLayout(new BoxLayout(toolBar, BoxLayout.PAGE_AXIS));
+ JToggleButton selectButton = new JToggleButton("Select");
+ selectButton.setActionCommand("select");
+ selectButton.addActionListener(this);
+ selectButton.addKeyListener(this);
+ JToggleButton helixButton = new JToggleButton("Helix");
+ helixButton.setActionCommand("helix");
+ helixButton.addActionListener(this);
+ helixButton.addKeyListener(this);
+ helixButton.setSelected(true);
+ JToggleButton unpairedButton = new JToggleButton("Unpaired");
+ unpairedButton.setActionCommand("unpaired");
+ unpairedButton.addActionListener(this);
+ unpairedButton.addKeyListener(this);
+
+ bg.add(selectButton);
+ bg.add(helixButton);
+ bg.add(unpairedButton);
+
+ toolBar.add(undoButton);
+ toolBar.add(redoButton);
+ toolBar.addSeparator();
+ toolBar.add(new JLabel("Tools:"));
+ toolBar.add(selectButton);
+ toolBar.add(helixButton);
+ toolBar.add(unpairedButton);
+ toolBar.addSeparator();
+ toolBar.add(flipButton);
+ systemBar.addKeyListener(this);
+
+
+ this.setLayout(new BorderLayout());
+ _sk = new TemplatePanel(this);
+ _sk.setPreferredSize(new Dimension(800,600));
+ manager = new UndoManager();
+ manager.setLimit(2000);
+ _sk.addUndoableEditListener(manager);
+ _sk.addKeyListener(this);
+
+ jp = new JScrollPane(_sk,JScrollPane.VERTICAL_SCROLLBAR_ALWAYS,JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
+ p.add(jp);
+ p.add(_vp);
+ JPanel bars = new JPanel();
+ BoxLayout barsLayout = new BoxLayout(bars, BoxLayout.Y_AXIS);
+ bars.setLayout(barsLayout);
+ systemBar.setAlignmentX(0);
+ bars.add(systemBar);
+ optionsBar.setAlignmentX(0);
+ bars.add(optionsBar);
+ getContentPane().add(bars,BorderLayout.PAGE_START);
+ getContentPane().add(toolBar,BorderLayout.WEST);
+ getContentPane().add(p,BorderLayout.CENTER);
+ this.addKeyListener(this);
+
+ new DropTarget(_vp, this);
+ new DropTarget(_sk, this);
+ this.pack();
+
+ _sk.requestFocusInWindow();
+ }
+
+
+ private File getCurrentFilePath() {
+ return currentFilePath;
+ }
+
+ private void setCurrentFilePath(File currentFilePath) {
+ this.currentFilePath = currentFilePath;
+ saveButton.setEnabled(true);
+ setTitle("VARNA Template Editor: " + currentFilePath);
+ }
+
+ private void clearCurrentFilePath() {
+ currentFilePath = null;
+ saveButton.setEnabled(false);
+ setTitle("VARNA Template Editor: New file");
+ }
+
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = -5942729520783690050L;
+
+ public static void main(String[] argv)
+ {
+ try {
+ LookAndFeelInfo[] lfs = UIManager.getInstalledLookAndFeels();
+ int i = 1;
+ LookAndFeelInfo info = lfs[i % lfs.length];
+ UIManager.setLookAndFeel(info.getClassName());
+ } catch (Exception e) {
+ // If Nimbus is not available, you can set the GUI to another look and feel.
+ }
+ TemplateEditor frame = new TemplateEditor();
+ frame.pack();
+ frame.setVisible(true);
+ frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+ }
+
+ public void keyPressed(KeyEvent e) {
+ System.out.println(e);
+ switch (e.getKeyCode())
+ {
+ case (KeyEvent.VK_DELETE):
+ {
+ GraphicalTemplateElement h = _sk.getSelected();
+ _sk.Unselect();
+ _sk.getTemplateUI().removeElementUI(h);
+ _sk.repaint();
+ }
+ break;
+ case (KeyEvent.VK_Z):
+ {
+ if (e.isControlDown())
+ {
+ undo();
+ }
+ }
+ break;
+ case (KeyEvent.VK_Y):
+ {
+ if (e.isControlDown())
+ {
+ redo();
+ }
+ }
+ break;
+ }
+ }
+
+ public void undo()
+ {
+ if (manager.canUndo())
+ {
+ //System.out.println("Undo: "+manager.getUndoPresentationName());
+ manager.undo();
+ }
+ }
+
+ public void redo()
+ {
+ if (manager.canRedo())
+ {
+ //System.out.println("Redo: "+manager.getRedoPresentationName());
+ manager.redo();
+ }
+ }
+
+ public void clearTemplate() {
+ _sk.clearTemplate();
+ clearCurrentFilePath();
+
+ // Empty the cancel history
+ manager.discardAllEdits();
+ }
+
+ public void loadTemplate(File templatePath) {
+ _sk.loadFromXmlFile(templatePath);
+ setCurrentFilePath(templatePath);
+
+ // Empty the cancel history
+ manager.discardAllEdits();
+ }
+
+ public void keyReleased(KeyEvent e) {
+ System.out.println(e);
+ }
+
+ public void keyTyped(KeyEvent e) {
+ System.out.println(e);
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ if (e.getActionCommand().equals("undo"))
+ {
+ undo();
+ }
+ else if (e.getActionCommand().equals("redo"))
+ {
+ redo();
+ }
+ else if (e.getActionCommand().equals("flip"))
+ {
+ GraphicalTemplateElement gr = _sk.getSelected();
+ if (gr != null)
+ {
+ if (gr instanceof Helix)
+ {
+ _sk.getTemplateUI().flipHelixUI((Helix)gr);
+ }
+ }
+ }
+ else if (e.getActionCommand().equals("select")) {
+ _sk.getTemplateUI().setSelectedTool(TemplateEditorPanelUI.Tool.SELECT);
+ }
+ else if (e.getActionCommand().equals("helix")) {
+ _sk.getTemplateUI().setSelectedTool(TemplateEditorPanelUI.Tool.CREATE_HELIX);
+ }
+ else if (e.getActionCommand().equals("retrieve")) {
+ retrieveTemplates();
+ }
+ else if (e.getActionCommand().equals("unpaired")) {
+ _sk.getTemplateUI().setSelectedTool(TemplateEditorPanelUI.Tool.CREATE_UNPAIRED);
+ }
+ else if (e.getActionCommand().equals("apply"))
+ {
+ try {
+ DrawRNATemplateMethod method = (DrawRNATemplateMethod)applyMethodList.getSelectedItem();
+ DrawRNATemplateCurveMethod curveMethod = (DrawRNATemplateCurveMethod)ellipseMethodList.getSelectedItem();
+ RNATemplateMapping map = _vp.getRNA().drawRNATemplate(_sk.getTemplate(),_vp.getConfig(), method, curveMethod, getStraightBulges());
+ for(int i: map.getSourceElemsAsSet())
+ {
+ RNATemplateElement t = map.getPartner(i);
+ Color c = _sk.getElement(t).getDominantColor();
+ _vp.getRNA().getBaseAt(i).getStyleBase().setBaseInnerColor(c);
+ }
+ _vp.repaint();
+ } catch (RNATemplateDrawingAlgorithmException e1) {
+ e1.printStackTrace();
+ JOptionPane.showMessageDialog(this, e1.getMessage(), "Template-based RNA drawing error", JOptionPane.ERROR_MESSAGE);
+ }
+ }
+ else if (e.getActionCommand().equals("save"))
+ {
+ try {
+ _sk.getTemplate().toXMLFile(getCurrentFilePath());
+ System.out.println("Template saved in " + getCurrentFilePath().toString());
+ } catch (ExceptionXMLGeneration e1) {
+ e1.printStackTrace();
+ } catch (ExceptionInvalidRNATemplate e1) {
+ e1.printStackTrace();
+ }
+ }
+ else if (e.getActionCommand().equals("save as"))
+ {
+ JFileChooser chooser = new JFileChooser();
+ FileFilter filter = new FileNameExtensionFilter("VARNA RNA template (.xml)", "xml");
+ chooser.setFileFilter(filter);
+ if (chooser.showSaveDialog(_sk) == JFileChooser.APPROVE_OPTION) {
+ String path = chooser.getSelectedFile().getAbsolutePath();
+ if (!path.toLowerCase().endsWith(".xml")) {
+ path = path + ".xml";
+ }
+ try {
+ _sk.getTemplate().toXMLFile(new File(path));
+ System.out.println("Template saved in " + path);
+ setCurrentFilePath(new File(path));
+ } catch (ExceptionXMLGeneration e1) {
+ e1.printStackTrace();
+ } catch (ExceptionInvalidRNATemplate e1) {
+ e1.printStackTrace();
+ }
+ }
+ }
+ else if (e.getActionCommand().equals("new"))
+ {
+ clearTemplate();
+ }
+ else if (e.getActionCommand().equals("open"))
+ {
+ JFileChooser chooser = new JFileChooser();
+ FileFilter filter = new FileNameExtensionFilter("VARNA RNA template (.xml)", "xml");
+ chooser.setFileFilter(filter);
+ if (chooser.showOpenDialog(_sk) == JFileChooser.APPROVE_OPTION) {
+ File templatePath = chooser.getSelectedFile();
+ loadTemplate(templatePath);
+ }
+ }
+ else if (e.getActionCommand().equals("benchmark")) {
+ new Benchmark(_vp.getRNA()).printAll();
+ }
+
+ }
+
+
+ private boolean getStraightBulges() {
+ return false;
+ }
+
+ public void dragEnter(DropTargetDragEvent arg0) {
+ }
+
+ public void dragExit(DropTargetEvent arg0) {
+ }
+
+ public void dragOver(DropTargetDragEvent arg0) {
+ }
+
+ public void drop(DropTargetDropEvent dtde)
+ {
+ try
+ {
+ Transferable tr = dtde.getTransferable();
+ DataFlavor[] flavors = tr.getTransferDataFlavors();
+ for (int i = 0; i < flavors.length; i++)
+ {
+ if (flavors[i].isFlavorJavaFileListType())
+ {
+ dtde.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+ List list = (List) tr.getTransferData(flavors[i]);
+ for (int j = 0; j < list.size(); j++)
+ {
+ Object o = list.get(j);
+ if (dtde.getSource() instanceof DropTarget)
+ {
+ DropTarget dt = (DropTarget) dtde.getSource();
+ Component c = dt.getComponent();
+ if (c instanceof VARNAPanel)
+ {
+ VARNAPanel vp = (VARNAPanel) c;
+ //String path = o.toString();
+ vp.loadFile((File) o, true); // BH SwingJS
+ vp.repaint();
+ }
+ else if (c instanceof TemplatePanel)
+ {
+ TemplatePanel sk = (TemplatePanel) c;
+ //String path = o.toString();
+ sk.loadFromXmlFile((File) o); // BH SwingJS
+ sk.repaint();
+ }
+ }
+ }
+ dtde.dropComplete(true);
+ return;
+ }
+ }
+ dtde.rejectDrop();
+ }
+ catch (Exception e)
+ {
+ e.printStackTrace();
+ dtde.rejectDrop();
+ }
+ }
+
+ public void dropActionChanged(DropTargetDragEvent arg0) {
+ }
+
+ public VARNAPanel getVarnaPanel() {
+ return _vp;
+ }
+
+ public void flipButtonEnable() {
+ flipButton.setEnabled(true);
+ }
+
+ public void flipButtonDisable() {
+ flipButton.setEnabled(false);
+ }
+
+ public void retrieveTemplates()
+ {
+ URL u;
+
+ try {
+ u = new URL("http://127.0.0.1/VARNA/templateShare/actions.php?action=retrieve&nbHelices=3&nbMultiLoops=1&length=50");
+ URLConnection uc = u.openConnection();
+ InputStreamReader isr = new InputStreamReader(uc.getInputStream());
+ BufferedReader b = new BufferedReader(isr);
+ ArrayList<String> res = new ArrayList<String>();
+ String s = b.readLine();
+ while(s!=null)
+ {
+ res.add(s);
+ s = b.readLine();
+ }
+ } catch (MalformedURLException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff