+++ /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