2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 import java.awt.BorderLayout;
21 import java.awt.Color;
22 import java.awt.Component;
23 import java.awt.Dimension;
25 import java.awt.GridLayout;
26 import java.awt.datatransfer.DataFlavor;
27 import java.awt.datatransfer.Transferable;
28 import java.awt.dnd.DnDConstants;
29 import java.awt.dnd.DropTarget;
30 import java.awt.dnd.DropTargetDragEvent;
31 import java.awt.dnd.DropTargetDropEvent;
32 import java.awt.dnd.DropTargetEvent;
33 import java.awt.dnd.DropTargetListener;
34 import java.awt.event.ActionEvent;
35 import java.awt.event.ActionListener;
36 import java.awt.event.ComponentEvent;
37 import java.awt.event.MouseEvent;
38 import java.awt.event.MouseListener;
40 import java.text.DateFormat;
41 import java.util.ArrayList;
42 import java.util.Date;
43 import java.util.List;
45 import javax.swing.DefaultListModel;
46 import javax.swing.DefaultListSelectionModel;
47 import javax.swing.Icon;
48 import javax.swing.JButton;
49 import javax.swing.JFrame;
50 import javax.swing.JLabel;
51 import javax.swing.JList;
52 import javax.swing.JOptionPane;
53 import javax.swing.JPanel;
54 import javax.swing.JScrollPane;
55 import javax.swing.JSplitPane;
56 import javax.swing.JTextField;
57 import javax.swing.ListModel;
58 import javax.swing.ListSelectionModel;
59 import javax.swing.UIManager;
60 import javax.swing.UnsupportedLookAndFeelException;
61 import javax.swing.event.ListSelectionEvent;
62 import javax.swing.event.ListSelectionListener;
64 import fr.orsay.lri.varna.VARNAPanel;
65 import fr.orsay.lri.varna.components.ReorderableJList;
66 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
67 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
68 import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
69 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
70 import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
71 import fr.orsay.lri.varna.models.FullBackup;
72 import fr.orsay.lri.varna.models.VARNAConfig;
73 import fr.orsay.lri.varna.models.rna.Mapping;
74 import fr.orsay.lri.varna.models.rna.RNA;
76 public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding implements DropTargetListener, InterfaceVARNAListener, MouseListener {
81 //private static final long serialVersionUID = -790155708306987257L;
83 private String DEFAULT_SEQUENCE = "CAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIA";
84 private String DEFAULT_STRUCTURE1 = "..(((((...(((((...(((((...(((((.....)))))...))))).....(((((...(((((.....)))))...))))).....)))))...)))))..";
85 private String DEFAULT_STRUCTURE2 = "..(((((...(((((...(((((........(((((...(((((.....)))))...)))))..................))))).....)))))...)))))..";
88 protected JPanel _tools = new JPanel();
89 private JPanel _input = new JPanel();
91 private JPanel _seqPanel = new JPanel();
92 private JPanel _strPanel = new JPanel();
93 private JLabel _info = new JLabel();
94 private JTextField _str = new JTextField();
95 private JTextField _seq = new JTextField();
96 private JLabel _strLabel = new JLabel(" Str:");
97 private JLabel _seqLabel = new JLabel(" Seq:");
98 private JButton _createButton = new JButton("Create");
99 private JButton _updateButton = new JButton("Update");
100 private JButton _deleteButton = new JButton("Delete");
101 private JButton _duplicateButton = new JButton("Snapshot");
103 protected JPanel _listPanel = new JPanel();
104 private ReorderableJList _sideList = null;
107 private static String errorOpt = "error";
108 @SuppressWarnings("unused")
109 private boolean _error;
111 private Color _backgroundColor = Color.white;
113 private static int _nextID = 1;
114 @SuppressWarnings("unused")
115 private int _algoCode;
117 private BackupHolder _rnaList;
120 /*public AppVarnaBinding() {
121 //super("VARNA in Jalview");
122 //this.set_seq("ATGC");
123 //this.set_str(".().");
124 //RNAPanelDemoInit();
126 //initVarna("ATGCATGATATATATATAT","....((((...))))....");
127 initVarna(this.DEFAULT_SEQUENCE,this.DEFAULT_STRUCTURE1);
130 public AppVarnaBinding(String seq,String struc){
131 //super("VARNA in Jalview");
132 initVarna(seq,struc);
135 public AppVarnaBinding(ArrayList<RNA> rnaList){
136 //super("VARNA in Jalview");
137 initVarnaEdit(rnaList);
142 private void initVarna(String seq, String str){
143 DefaultListModel dlm = new DefaultListModel();
145 DefaultListSelectionModel m = new DefaultListSelectionModel();
146 m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
147 m.setLeadAnchorNotificationEnabled(false);
149 _sideList = new ReorderableJList();
150 _sideList.setModel(dlm);
151 _sideList.addMouseListener(this);
152 _sideList.setSelectionModel(m);
153 _sideList.setPreferredSize(new Dimension(100, 0));
154 _sideList.addListSelectionListener( new ListSelectionListener(){
155 public void valueChanged(ListSelectionEvent arg0) {
156 if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
158 FullBackup sel = (FullBackup) _sideList.getSelectedValue();
159 Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA().getSize(), sel.rna.getSize());
160 vp.showRNAInterpolated(sel.rna,sel.config,map);
161 _seq.setText(sel.rna.getSeq());
162 _str.setText(sel.rna.getStructDBN());
167 _rnaList = new BackupHolder(dlm,_sideList);
168 RNA _RNA1 = new RNA("User defined 1");
171 vp = new VARNAPanel("0",".");
172 _RNA1.setRNA(seq, str);
173 _RNA1.drawRNARadiate(vp.getConfig());
174 } catch (ExceptionNonEqualLength e) {
176 } catch (ExceptionUnmatchedClosingParentheses e2) {
177 e2.printStackTrace();
178 } catch (ExceptionFileFormatOrSyntax e3) {
179 e3.printStackTrace();
181 vp.setPreferredSize(new Dimension(400, 400));
182 _rnaList.add(vp.getConfig().clone(),_RNA1,generateDefaultName(),true);
184 //TODO setBackground(_backgroundColor);
185 vp.setBackground(_backgroundColor);
187 //TODO getContentPane().setLayout(new BorderLayout());
188 //TODO getContentPane().add(vp, BorderLayout.CENTER);
191 vp.addVARNAListener(this);
194 private void initVarnaEdit(ArrayList<RNA> rnaInList)
196 DefaultListModel dlm = new DefaultListModel();
199 int marginTools = 40;
201 DefaultListSelectionModel m = new DefaultListSelectionModel();
202 m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
203 m.setLeadAnchorNotificationEnabled(false);
206 _sideList = new ReorderableJList();
207 _sideList.setModel(dlm);
208 _sideList.addMouseListener(this);
209 _sideList.setSelectionModel(m);
210 _sideList.setPreferredSize(new Dimension(100, 0));
211 _sideList.addListSelectionListener( new ListSelectionListener(){
212 public void valueChanged(ListSelectionEvent arg0) {
213 //System.out.println(arg0);
214 if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
216 FullBackup sel = (FullBackup) _sideList.getSelectedValue();
217 Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA().getSize(), sel.rna.getSize());
218 vp.showRNAInterpolated(sel.rna,sel.config,map);
219 //_seq.setText(sel.rna.getSeq());
220 _str.setText(sel.rna.getStructDBN());
225 _rnaList = new BackupHolder(dlm,_sideList);
228 vp = new VARNAPanel("0",".");
229 for(int i=0;i<rnaInList.size();i++){
230 rnaInList.get(i).drawRNARadiate(vp.getConfig());
232 } catch (ExceptionNonEqualLength e) {
235 vp.setPreferredSize(new Dimension(400, 400));
236 for(int i=0;i<rnaInList.size();i++){
237 if(i<rnaInList.size()-1){
238 _rnaList.add(vp.getConfig().clone(),rnaInList.get(i),rnaInList.get(i).getName());
240 _rnaList.add(vp.getConfig().clone(),rnaInList.get(i),rnaInList.get(i).getName(),true);
244 /*_rnaList.add(vp.getConfig().clone(),_RNA2,generateDefaultName());
245 _rnaList.add(vp.getConfig().clone(),_RNA1,generateDefaultName(),true);*/
247 JScrollPane listScroller = new JScrollPane(_sideList);
248 listScroller.setPreferredSize(new Dimension(150, 0));
250 vp.setBackground(_backgroundColor);
253 Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
255 //_seqLabel.setHorizontalTextPosition(JLabel.LEFT);
256 //_seqLabel.setPreferredSize(new Dimension(marginTools, 15));
257 _seq.setFont(textFieldsFont);
258 _seq.setText(rnaInList.get(0).getSeq());
260 _updateButton.addActionListener(new ActionListener() {
261 public void actionPerformed(ActionEvent e) {
262 FullBackup sel = (FullBackup) _sideList.getSelectedValue();
263 sel.rna.setSequence("A");
265 RNA nRNA = new RNA(generateDefaultName());
266 nRNA.setRNA(_seq.getText(), _str.getText());
267 nRNA.drawRNARadiate(vp.getConfig());
268 _rnaList.add(new VARNAConfig(),nRNA,true);
269 } catch (ExceptionUnmatchedClosingParentheses e1) {
270 JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
271 } catch (ExceptionFileFormatOrSyntax e1) {
272 JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
277 //_seqPanel.setLayout(new BorderLayout());
278 //_seqPanel.add(_seqLabel, BorderLayout.WEST);
279 //_seqPanel.add(_seq, BorderLayout.CENTER);
281 _strLabel.setPreferredSize(new Dimension(marginTools, 15));
282 _strLabel.setHorizontalTextPosition(JLabel.LEFT);
283 _str.setFont(textFieldsFont);
284 _strPanel.setLayout(new BorderLayout());
285 _strPanel.add(_strLabel, BorderLayout.WEST);
286 _strPanel.add(_str, BorderLayout.CENTER);
288 _input.setLayout(new GridLayout(1, 0));
289 //_input.add(_seqPanel);
290 _input.add(_strPanel);
292 JPanel goPanel = new JPanel();
293 goPanel.setLayout(new BorderLayout());
295 _tools.setLayout(new BorderLayout());
296 _tools.add(_input, BorderLayout.CENTER);
297 //_tools.add(_info, BorderLayout.SOUTH);
298 _tools.add(goPanel, BorderLayout.EAST);
300 /*_deleteButton.addActionListener(new ActionListener() {
301 public void actionPerformed(ActionEvent e) {
302 _rnaList.removeSelected();
305 _duplicateButton.addActionListener(new ActionListener() {
306 public void actionPerformed(ActionEvent e) {
307 _rnaList.add((VARNAConfig)vp.getConfig().clone(),vp.getRNA().clone(),vp.getRNA().getName()+"-"+DateFormat.getTimeInstance(DateFormat.LONG).format(new Date()),true);
310 goPanel.add(_updateButton, BorderLayout.CENTER);
313 JPanel ops = new JPanel();
314 ops.setLayout(new GridLayout(1,2));
315 ops.add(_deleteButton);
316 ops.add(_duplicateButton);
318 JLabel j = new JLabel("Structures Manager",JLabel.CENTER);
319 _listPanel.setLayout(new BorderLayout());
321 _listPanel.add(ops,BorderLayout.SOUTH);
322 _listPanel.add(j,BorderLayout.NORTH);
323 _listPanel.add(listScroller,BorderLayout.CENTER);
327 //JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,vp);
329 getContentPane().setLayout(new BorderLayout());
330 getContentPane().add(split, BorderLayout.CENTER);
331 getContentPane().add(_tools, BorderLayout.NORTH);
334 //TODO setVisible(true);
335 DropTarget dt = new DropTarget(vp, this);
337 vp.addVARNAListener(this);
340 public JPanel getTools(){
344 public JPanel getListPanel(){
349 private void RNAPanelDemoInit()
351 DefaultListModel dlm = new DefaultListModel();
354 int marginTools = 40;
356 DefaultListSelectionModel m = new DefaultListSelectionModel();
357 m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
358 m.setLeadAnchorNotificationEnabled(false);
361 _sideList = new ReorderableJList();
362 _sideList.setModel(dlm);
363 _sideList.addMouseListener(this);
364 _sideList.setSelectionModel(m);
365 _sideList.setPreferredSize(new Dimension(100, 0));
366 _sideList.addListSelectionListener( new ListSelectionListener(){
367 public void valueChanged(ListSelectionEvent arg0) {
368 //System.out.println(arg0);
369 if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
371 FullBackup sel = (FullBackup) _sideList.getSelectedValue();
372 Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA().getSize(), sel.rna.getSize());
373 vp.showRNAInterpolated(sel.rna,sel.config,map);
374 _seq.setText(sel.rna.getSeq());
375 _str.setText(sel.rna.getStructDBN());
380 _rnaList = new BackupHolder(dlm,_sideList);
381 RNA _RNA1 = new RNA("User defined 1");
382 RNA _RNA2 = new RNA("User defined 2");
384 vp = new VARNAPanel("0",".");
385 _RNA1.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE1);
386 _RNA1.drawRNARadiate(vp.getConfig());
387 _RNA2.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE2);
388 _RNA2.drawRNARadiate(vp.getConfig());
389 } catch (ExceptionNonEqualLength e) {
391 } catch (ExceptionUnmatchedClosingParentheses e2) {
392 e2.printStackTrace();
393 } catch (ExceptionFileFormatOrSyntax e3) {
394 e3.printStackTrace();
396 vp.setPreferredSize(new Dimension(400, 400));
397 _rnaList.add(vp.getConfig().clone(),_RNA2,generateDefaultName());
398 _rnaList.add(vp.getConfig().clone(),_RNA1,generateDefaultName(),true);
400 JScrollPane listScroller = new JScrollPane(_sideList);
401 listScroller.setPreferredSize(new Dimension(150, 0));
403 setBackground(_backgroundColor);
404 vp.setBackground(_backgroundColor);
407 Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
409 _seqLabel.setHorizontalTextPosition(JLabel.LEFT);
410 _seqLabel.setPreferredSize(new Dimension(marginTools, 15));
411 _seq.setFont(textFieldsFont);
412 _seq.setText(DEFAULT_SEQUENCE);
414 _createButton.addActionListener(new ActionListener() {
415 public void actionPerformed(ActionEvent e) {
417 RNA nRNA = new RNA(generateDefaultName());
418 nRNA.setRNA(_seq.getText(), _str.getText());
419 nRNA.drawRNARadiate(vp.getConfig());
420 _rnaList.add(new VARNAConfig(),nRNA,true);
421 } catch (ExceptionUnmatchedClosingParentheses e1) {
422 JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
423 } catch (ExceptionFileFormatOrSyntax e1) {
424 JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
430 _seqPanel.setLayout(new BorderLayout());
431 _seqPanel.add(_seqLabel, BorderLayout.WEST);
432 _seqPanel.add(_seq, BorderLayout.CENTER);
434 _strLabel.setPreferredSize(new Dimension(marginTools, 15));
435 _strLabel.setHorizontalTextPosition(JLabel.LEFT);
436 _str.setFont(textFieldsFont);
437 _strPanel.setLayout(new BorderLayout());
438 _strPanel.add(_strLabel, BorderLayout.WEST);
439 _strPanel.add(_str, BorderLayout.CENTER);
441 _input.setLayout(new GridLayout(2, 0));
442 _input.add(_seqPanel);
443 _input.add(_strPanel);
445 JPanel goPanel = new JPanel();
446 goPanel.setLayout(new BorderLayout());
448 _tools.setLayout(new BorderLayout());
449 _tools.add(_input, BorderLayout.CENTER);
450 _tools.add(_info, BorderLayout.SOUTH);
451 _tools.add(goPanel, BorderLayout.EAST);
453 _deleteButton.addActionListener(new ActionListener() {
454 public void actionPerformed(ActionEvent e) {
455 _rnaList.removeSelected();
458 _duplicateButton.addActionListener(new ActionListener() {
459 public void actionPerformed(ActionEvent e) {
460 _rnaList.add((VARNAConfig)vp.getConfig().clone(),vp.getRNA().clone(),vp.getRNA().getName()+"-"+DateFormat.getTimeInstance(DateFormat.LONG).format(new Date()),true);
463 JPanel ops = new JPanel();
464 ops.setLayout(new GridLayout(1,2));
465 ops.add(_deleteButton);
466 ops.add(_duplicateButton);
468 JLabel j = new JLabel("Structures Manager",JLabel.CENTER);
469 _listPanel.setLayout(new BorderLayout());
471 _listPanel.add(ops,BorderLayout.SOUTH);
472 _listPanel.add(j,BorderLayout.NORTH);
473 _listPanel.add(listScroller,BorderLayout.CENTER);
475 goPanel.add(_createButton, BorderLayout.CENTER);
477 JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,vp);
478 getContentPane().setLayout(new BorderLayout());
479 getContentPane().add(split, BorderLayout.CENTER);
480 getContentPane().add(_tools, BorderLayout.NORTH);
483 DropTarget dt = new DropTarget(vp, this);
485 vp.addVARNAListener(this);
488 public static String generateDefaultName()
490 return "User file #"+_nextID++;
493 public RNA getRNA() {
494 return (RNA)_sideList.getSelectedValue();
499 public String[][] getParameterInfo() {
501 // Parameter Name Kind of Value Description,
502 { "sequenceDBN", "String", "A raw RNA sequence" },
503 { "structureDBN", "String",
504 "An RNA structure in dot bracket notation (DBN)" },
505 { errorOpt, "boolean", "To show errors" }, };
510 vp.setBackground(_backgroundColor);
514 @SuppressWarnings("unused")
515 private Color getSafeColor(String col, Color def) {
518 result = Color.decode(col);
519 } catch (Exception e) {
521 result = Color.getColor(col, def);
522 } catch (Exception e2) {
529 public VARNAPanel get_varnaPanel() {
533 public void set_varnaPanel(VARNAPanel surface) {
538 public String get_seq() {
539 return _seq.getText();
542 public void set_seq(String _seq) {
543 this._seq.setText(_seq);
546 public String get_str(){
547 return _str.getText();
550 public void set_str(String _str){
551 this._str.setText(_str);
554 public JLabel get_info() {
558 public void set_info(JLabel _info) {
562 /*public static void main(String[] args) {
563 AppVarnaBinding d = new AppVarnaBinding();
564 d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
570 public void dragEnter(DropTargetDragEvent arg0) {
571 // TODO Auto-generated method stub
575 public void dragExit(DropTargetEvent arg0) {
576 // TODO Auto-generated method stub
580 public void dragOver(DropTargetDragEvent arg0) {
581 // TODO Auto-generated method stub
585 public void drop(DropTargetDropEvent dtde) {
587 Transferable tr = dtde.getTransferable();
588 DataFlavor[] flavors = tr.getTransferDataFlavors();
589 for (int i = 0; i < flavors.length; i++) {
590 if (flavors[i].isFlavorJavaFileListType()) {
591 dtde.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
592 Object ob = tr.getTransferData(flavors[i]);
593 if (ob instanceof List)
595 List list = (List) ob;
596 for (int j = 0; j < list.size(); j++) {
597 Object o = list.get(j);
599 if (dtde.getSource() instanceof DropTarget)
601 DropTarget dt = (DropTarget) dtde.getSource();
602 Component c = dt.getComponent();
603 if (c instanceof VARNAPanel)
605 String path = o.toString();
606 VARNAPanel vp = (VARNAPanel) c;
608 FullBackup bck = VARNAPanel.importSession(path);
609 _rnaList.add(bck.config, bck.rna,bck.name,true);
611 catch (ExceptionLoadingFailed e3)
615 r.drawRNA(vp.getConfig());
616 String name =r.getName();
619 name = path.substring(path.lastIndexOf(File.separatorChar)+1);
621 _rnaList.add(vp.getConfig().clone(),r,name,true);
627 // If we made it this far, everything worked.
628 dtde.dropComplete(true);
632 // Hmm, the user must not have dropped a file list
634 } catch (Exception e) {
641 public void dropActionChanged(DropTargetDragEvent arg0) {
644 private class BackupHolder{
645 private DefaultListModel _rnaList;
646 private ArrayList<RNA> _rnas = new ArrayList<RNA>();
649 public BackupHolder(DefaultListModel rnaList, JList l)
655 public void add(VARNAConfig c, RNA r)
657 add(c, r, r.getName(),false);
660 public void add(VARNAConfig c, RNA r,boolean select)
662 add(c, r, r.getName(),select);
665 public void add(VARNAConfig c, RNA r, String name)
667 add(c, r, name,false);
669 public void add(VARNAConfig c, RNA r, String name, boolean select)
672 _l.removeSelectionInterval(0, _rnaList.size());
676 name = generateDefaultName();
678 FullBackup bck = new FullBackup(c,r,name);
682 _l.setSelectedIndex(0);
686 public void remove(int i)
692 public DefaultListModel getModel()
696 public boolean contains(RNA r)
698 return _rnas.contains(r);
700 /*public int getSize()
702 return _rnaList.getSize();
704 public FullBackup getElementAt(int i)
706 return (FullBackup) _rnaList.getElementAt(i);
709 public void removeSelected()
711 int i = _l.getSelectedIndex();
714 if (_rnaList.getSize()==1)
719 } catch (ExceptionUnmatchedClosingParentheses e1) {
720 } catch (ExceptionFileFormatOrSyntax e1) {
728 if (newi==_rnaList.getSize())
730 newi = _rnaList.getSize()-2;
732 FullBackup bck = (FullBackup) _rnaList.getElementAt(newi);
733 _l.setSelectedValue(bck,true);
741 public void onLayoutChanged() {
742 // TODO Auto-generated method stub
746 public void onUINewStructure(VARNAConfig v, RNA r) {
747 _rnaList.add(v, r,"",true);
750 public void onWarningEmitted(String s) {
751 // TODO Auto-generated method stub
755 public void mouseClicked(MouseEvent e) {
756 if(e.getClickCount() == 2){
757 int index = _sideList.locationToIndex(e.getPoint());
758 ListModel dlm = _sideList.getModel();
759 FullBackup item = (FullBackup) dlm.getElementAt(index);;
760 _sideList.ensureIndexIsVisible(index);
761 /*TODO Object newName = JOptionPane.showInputDialog(
763 "Specify a new name for this RNA",
765 JOptionPane.QUESTION_MESSAGE,
771 item.name = newName.toString();
772 this._sideList.repaint();
777 public void mouseEntered(MouseEvent arg0) {
778 // TODO Auto-generated method stub
782 public void mouseExited(MouseEvent arg0) {
783 // TODO Auto-generated method stub
787 public void mousePressed(MouseEvent arg0) {
788 // TODO Auto-generated method stub
792 public void mouseReleased(MouseEvent arg0) {
793 // TODO Auto-generated method stub
798 public Color getColour(int atomIndex, int pdbResNum, String chain,
800 // TODO Auto-generated method stub
805 public String[] getPdbFile() {
806 // TODO Auto-generated method stub
811 public void highlightAtom(int atomIndex, int pdbResNum, String chain,
813 // TODO Auto-generated method stub
818 public void mouseOverStructure(int atomIndex, String strInfo) {
819 // TODO Auto-generated method stub
824 public void releaseReferences(Object svl) {
825 // TODO Auto-generated method stub
830 public void updateColours(Object source) {
831 // TODO Auto-generated method stub
836 public void componentHidden(ComponentEvent e) {
837 // TODO Auto-generated method stub
842 public void componentMoved(ComponentEvent e) {
843 // TODO Auto-generated method stub
848 public void componentResized(ComponentEvent e) {
849 // TODO Auto-generated method stub
854 public void componentShown(ComponentEvent e) {
855 // TODO Auto-generated method stub
862 public static void main(String[] args)
864 JTextField str = new JTextField("ATGC");
866 AppVarnaBinding vab = new AppVarnaBinding();
867 vab.varnagui.set_seq(str);
868 vab.varnagui.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
870 vab.varnagui.setVisible(true);