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 private 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 _deleteButton = new JButton("Delete");
100 private JButton _duplicateButton = new JButton("Snapshot");
102 private JPanel _listPanel = new JPanel();
103 private ReorderableJList _sideList = null;
106 private static String errorOpt = "error";
107 @SuppressWarnings("unused")
108 private boolean _error;
110 private Color _backgroundColor = Color.white;
112 private static int _nextID = 1;
113 @SuppressWarnings("unused")
114 private int _algoCode;
116 private BackupHolder _rnaList;
119 /*public AppVarnaBinding() {
120 //super("VARNA in Jalview");
121 //this.set_seq("ATGC");
122 //this.set_str(".().");
123 //RNAPanelDemoInit();
125 //initVarna("ATGCATGATATATATATAT","....((((...))))....");
126 initVarna(this.DEFAULT_SEQUENCE,this.DEFAULT_STRUCTURE1);
129 public AppVarnaBinding(String seq,String struc){
130 //super("VARNA in Jalview");
131 initVarna(seq,struc);
134 public AppVarnaBinding(ArrayList<RNA> rnalist){
135 //super("VARNA in Jalview");
136 initVarnaEdit(rnalist);
141 private void initVarna(String seq, String str){
142 DefaultListModel dlm = new DefaultListModel();
144 DefaultListSelectionModel m = new DefaultListSelectionModel();
145 m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
146 m.setLeadAnchorNotificationEnabled(false);
148 _sideList = new ReorderableJList();
149 _sideList.setModel(dlm);
150 _sideList.addMouseListener(this);
151 _sideList.setSelectionModel(m);
152 _sideList.setPreferredSize(new Dimension(100, 0));
153 _sideList.addListSelectionListener( new ListSelectionListener(){
154 public void valueChanged(ListSelectionEvent arg0) {
155 if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
157 FullBackup sel = (FullBackup) _sideList.getSelectedValue();
158 Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA().getSize(), sel.rna.getSize());
159 vp.showRNAInterpolated(sel.rna,sel.config,map);
160 _seq.setText(sel.rna.getSeq());
161 _str.setText(sel.rna.getStructDBN());
166 _rnaList = new BackupHolder(dlm,_sideList);
167 RNA _RNA1 = new RNA("User defined 1");
170 vp = new VARNAPanel("0",".");
171 _RNA1.setRNA(seq, str);
172 _RNA1.drawRNARadiate(vp.getConfig());
173 } catch (ExceptionNonEqualLength e) {
175 } catch (ExceptionUnmatchedClosingParentheses e2) {
176 e2.printStackTrace();
177 } catch (ExceptionFileFormatOrSyntax e3) {
178 e3.printStackTrace();
180 vp.setPreferredSize(new Dimension(400, 400));
181 _rnaList.add(vp.getConfig().clone(),_RNA1,generateDefaultName(),true);
183 //TODO setBackground(_backgroundColor);
184 vp.setBackground(_backgroundColor);
186 //TODO getContentPane().setLayout(new BorderLayout());
187 //TODO getContentPane().add(vp, BorderLayout.CENTER);
190 vp.addVARNAListener(this);
193 private void initVarnaEdit(ArrayList<RNA> rnaInList)
195 DefaultListModel dlm = new DefaultListModel();
198 int marginTools = 40;
200 DefaultListSelectionModel m = new DefaultListSelectionModel();
201 m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
202 m.setLeadAnchorNotificationEnabled(false);
205 _sideList = new ReorderableJList();
206 _sideList.setModel(dlm);
207 _sideList.addMouseListener(this);
208 _sideList.setSelectionModel(m);
209 _sideList.setPreferredSize(new Dimension(100, 0));
210 _sideList.addListSelectionListener( new ListSelectionListener(){
211 public void valueChanged(ListSelectionEvent arg0) {
212 //System.out.println(arg0);
213 if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
215 FullBackup sel = (FullBackup) _sideList.getSelectedValue();
216 Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA().getSize(), sel.rna.getSize());
217 vp.showRNAInterpolated(sel.rna,sel.config,map);
218 _seq.setText(sel.rna.getSeq());
219 _str.setText(sel.rna.getStructDBN());
224 _rnaList = new BackupHolder(dlm,_sideList);
226 vp = new VARNAPanel("0",".");
227 for(int i=0;i<rnaInList.size();i++){
228 rnaInList.get(i).drawRNARadiate(vp.getConfig());
230 } catch (ExceptionNonEqualLength e) {
233 vp.setPreferredSize(new Dimension(400, 400));
234 for(int i=0;i<rnaInList.size();i++){
235 _rnaList.add(vp.getConfig().clone(),rnaInList.get(i),generateDefaultName(),true);
237 /*_rnaList.add(vp.getConfig().clone(),_RNA2,generateDefaultName());
238 _rnaList.add(vp.getConfig().clone(),_RNA1,generateDefaultName(),true);*/
240 JScrollPane listScroller = new JScrollPane(_sideList);
241 listScroller.setPreferredSize(new Dimension(150, 0));
243 //TODO setBackground(_backgroundColor);
244 vp.setBackground(_backgroundColor);
247 Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
249 _seqLabel.setHorizontalTextPosition(JLabel.LEFT);
250 _seqLabel.setPreferredSize(new Dimension(marginTools, 15));
251 _seq.setFont(textFieldsFont);
252 _seq.setText(rnaInList.get(0).getSeq());
254 _createButton.addActionListener(new ActionListener() {
255 public void actionPerformed(ActionEvent e) {
257 RNA nRNA = new RNA(generateDefaultName());
258 nRNA.setRNA(_seq.getText(), _str.getText());
259 nRNA.drawRNARadiate(vp.getConfig());
260 _rnaList.add(new VARNAConfig(),nRNA,true);
261 } catch (ExceptionUnmatchedClosingParentheses e1) {
262 JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
263 } catch (ExceptionFileFormatOrSyntax e1) {
264 JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
270 _seqPanel.setLayout(new BorderLayout());
271 _seqPanel.add(_seqLabel, BorderLayout.WEST);
272 _seqPanel.add(_seq, BorderLayout.CENTER);
274 _strLabel.setPreferredSize(new Dimension(marginTools, 15));
275 _strLabel.setHorizontalTextPosition(JLabel.LEFT);
276 _str.setFont(textFieldsFont);
277 _strPanel.setLayout(new BorderLayout());
278 _strPanel.add(_strLabel, BorderLayout.WEST);
279 _strPanel.add(_str, BorderLayout.CENTER);
281 _input.setLayout(new GridLayout(2, 0));
282 _input.add(_seqPanel);
283 _input.add(_strPanel);
285 JPanel goPanel = new JPanel();
286 goPanel.setLayout(new BorderLayout());
288 _tools.setLayout(new BorderLayout());
289 _tools.add(_input, BorderLayout.CENTER);
290 _tools.add(_info, BorderLayout.SOUTH);
291 _tools.add(goPanel, BorderLayout.EAST);
293 _deleteButton.addActionListener(new ActionListener() {
294 public void actionPerformed(ActionEvent e) {
295 _rnaList.removeSelected();
298 _duplicateButton.addActionListener(new ActionListener() {
299 public void actionPerformed(ActionEvent e) {
300 _rnaList.add((VARNAConfig)vp.getConfig().clone(),vp.getRNA().clone(),vp.getRNA().getName()+"-"+DateFormat.getTimeInstance(DateFormat.LONG).format(new Date()),true);
303 JPanel ops = new JPanel();
304 ops.setLayout(new GridLayout(1,2));
305 ops.add(_deleteButton);
306 ops.add(_duplicateButton);
308 JLabel j = new JLabel("Structures Manager",JLabel.CENTER);
309 _listPanel.setLayout(new BorderLayout());
311 _listPanel.add(ops,BorderLayout.SOUTH);
312 _listPanel.add(j,BorderLayout.NORTH);
313 _listPanel.add(listScroller,BorderLayout.CENTER);
315 goPanel.add(_createButton, BorderLayout.CENTER);
317 JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,vp);
319 getContentPane().setLayout(new BorderLayout());
320 getContentPane().add(split, BorderLayout.CENTER);
321 getContentPane().add(_tools, BorderLayout.NORTH);
324 //TODO setVisible(true);
325 DropTarget dt = new DropTarget(vp, this);
327 vp.addVARNAListener(this);
331 /*private void RNAPanelDemoInit()
333 DefaultListModel dlm = new DefaultListModel();
336 int marginTools = 40;
338 DefaultListSelectionModel m = new DefaultListSelectionModel();
339 m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
340 m.setLeadAnchorNotificationEnabled(false);
343 _sideList = new ReorderableJList();
344 _sideList.setModel(dlm);
345 _sideList.addMouseListener(this);
346 _sideList.setSelectionModel(m);
347 _sideList.setPreferredSize(new Dimension(100, 0));
348 _sideList.addListSelectionListener( new ListSelectionListener(){
349 public void valueChanged(ListSelectionEvent arg0) {
350 //System.out.println(arg0);
351 if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
353 FullBackup sel = (FullBackup) _sideList.getSelectedValue();
354 Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA().getSize(), sel.rna.getSize());
355 vp.showRNAInterpolated(sel.rna,sel.config,map);
356 _seq.setText(sel.rna.getSeq());
357 _str.setText(sel.rna.getStructDBN());
362 _rnaList = new BackupHolder(dlm,_sideList);
363 RNA _RNA1 = new RNA("User defined 1");
364 RNA _RNA2 = new RNA("User defined 2");
366 vp = new VARNAPanel("0",".");
367 _RNA1.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE1);
368 _RNA1.drawRNARadiate(vp.getConfig());
369 _RNA2.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE2);
370 _RNA2.drawRNARadiate(vp.getConfig());
371 } catch (ExceptionNonEqualLength e) {
373 } catch (ExceptionUnmatchedClosingParentheses e2) {
374 e2.printStackTrace();
375 } catch (ExceptionFileFormatOrSyntax e3) {
376 e3.printStackTrace();
378 vp.setPreferredSize(new Dimension(400, 400));
379 _rnaList.add(vp.getConfig().clone(),_RNA2,generateDefaultName());
380 _rnaList.add(vp.getConfig().clone(),_RNA1,generateDefaultName(),true);
382 JScrollPane listScroller = new JScrollPane(_sideList);
383 listScroller.setPreferredSize(new Dimension(150, 0));
385 setBackground(_backgroundColor);
386 vp.setBackground(_backgroundColor);
389 Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
391 _seqLabel.setHorizontalTextPosition(JLabel.LEFT);
392 _seqLabel.setPreferredSize(new Dimension(marginTools, 15));
393 _seq.setFont(textFieldsFont);
394 _seq.setText(DEFAULT_SEQUENCE);
396 _createButton.addActionListener(new ActionListener() {
397 public void actionPerformed(ActionEvent e) {
399 RNA nRNA = new RNA(generateDefaultName());
400 nRNA.setRNA(_seq.getText(), _str.getText());
401 nRNA.drawRNARadiate(vp.getConfig());
402 _rnaList.add(new VARNAConfig(),nRNA,true);
403 } catch (ExceptionUnmatchedClosingParentheses e1) {
404 JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
405 } catch (ExceptionFileFormatOrSyntax e1) {
406 JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
412 _seqPanel.setLayout(new BorderLayout());
413 _seqPanel.add(_seqLabel, BorderLayout.WEST);
414 _seqPanel.add(_seq, BorderLayout.CENTER);
416 _strLabel.setPreferredSize(new Dimension(marginTools, 15));
417 _strLabel.setHorizontalTextPosition(JLabel.LEFT);
418 _str.setFont(textFieldsFont);
419 _strPanel.setLayout(new BorderLayout());
420 _strPanel.add(_strLabel, BorderLayout.WEST);
421 _strPanel.add(_str, BorderLayout.CENTER);
423 _input.setLayout(new GridLayout(2, 0));
424 _input.add(_seqPanel);
425 _input.add(_strPanel);
427 JPanel goPanel = new JPanel();
428 goPanel.setLayout(new BorderLayout());
430 _tools.setLayout(new BorderLayout());
431 _tools.add(_input, BorderLayout.CENTER);
432 _tools.add(_info, BorderLayout.SOUTH);
433 _tools.add(goPanel, BorderLayout.EAST);
435 _deleteButton.addActionListener(new ActionListener() {
436 public void actionPerformed(ActionEvent e) {
437 _rnaList.removeSelected();
440 _duplicateButton.addActionListener(new ActionListener() {
441 public void actionPerformed(ActionEvent e) {
442 _rnaList.add((VARNAConfig)vp.getConfig().clone(),vp.getRNA().clone(),vp.getRNA().getName()+"-"+DateFormat.getTimeInstance(DateFormat.LONG).format(new Date()),true);
445 JPanel ops = new JPanel();
446 ops.setLayout(new GridLayout(1,2));
447 ops.add(_deleteButton);
448 ops.add(_duplicateButton);
450 JLabel j = new JLabel("Structures Manager",JLabel.CENTER);
451 _listPanel.setLayout(new BorderLayout());
453 _listPanel.add(ops,BorderLayout.SOUTH);
454 _listPanel.add(j,BorderLayout.NORTH);
455 _listPanel.add(listScroller,BorderLayout.CENTER);
457 goPanel.add(_createButton, BorderLayout.CENTER);
459 JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,vp);
460 getContentPane().setLayout(new BorderLayout());
461 getContentPane().add(split, BorderLayout.CENTER);
462 getContentPane().add(_tools, BorderLayout.NORTH);
465 DropTarget dt = new DropTarget(vp, this);
467 vp.addVARNAListener(this);
470 public static String generateDefaultName()
472 return "User file #"+_nextID++;
475 public RNA getRNA() {
476 return (RNA)_sideList.getSelectedValue();
481 public String[][] getParameterInfo() {
483 // Parameter Name Kind of Value Description,
484 { "sequenceDBN", "String", "A raw RNA sequence" },
485 { "structureDBN", "String",
486 "An RNA structure in dot bracket notation (DBN)" },
487 { errorOpt, "boolean", "To show errors" }, };
492 vp.setBackground(_backgroundColor);
496 @SuppressWarnings("unused")
497 private Color getSafeColor(String col, Color def) {
500 result = Color.decode(col);
501 } catch (Exception e) {
503 result = Color.getColor(col, def);
504 } catch (Exception e2) {
511 public VARNAPanel get_varnaPanel() {
515 public void set_varnaPanel(VARNAPanel surface) {
520 public String get_seq() {
521 return _seq.getText();
524 public void set_seq(String _seq) {
525 this._seq.setText(_seq);
528 public String get_str(){
529 return _str.getText();
532 public void set_str(String _str){
533 this._str.setText(_str);
536 public JLabel get_info() {
540 public void set_info(JLabel _info) {
544 /*public static void main(String[] args) {
545 AppVarnaBinding d = new AppVarnaBinding();
546 d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
552 public void dragEnter(DropTargetDragEvent arg0) {
553 // TODO Auto-generated method stub
557 public void dragExit(DropTargetEvent arg0) {
558 // TODO Auto-generated method stub
562 public void dragOver(DropTargetDragEvent arg0) {
563 // TODO Auto-generated method stub
567 public void drop(DropTargetDropEvent dtde) {
569 Transferable tr = dtde.getTransferable();
570 DataFlavor[] flavors = tr.getTransferDataFlavors();
571 for (int i = 0; i < flavors.length; i++) {
572 if (flavors[i].isFlavorJavaFileListType()) {
573 dtde.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
574 Object ob = tr.getTransferData(flavors[i]);
575 if (ob instanceof List)
577 List list = (List) ob;
578 for (int j = 0; j < list.size(); j++) {
579 Object o = list.get(j);
581 if (dtde.getSource() instanceof DropTarget)
583 DropTarget dt = (DropTarget) dtde.getSource();
584 Component c = dt.getComponent();
585 if (c instanceof VARNAPanel)
587 String path = o.toString();
588 VARNAPanel vp = (VARNAPanel) c;
590 FullBackup bck = VARNAPanel.importSession(path);
591 _rnaList.add(bck.config, bck.rna,bck.name,true);
593 catch (ExceptionLoadingFailed e3)
597 r.drawRNA(vp.getConfig());
598 String name =r.getName();
601 name = path.substring(path.lastIndexOf(File.separatorChar)+1);
603 _rnaList.add(vp.getConfig().clone(),r,name,true);
609 // If we made it this far, everything worked.
610 dtde.dropComplete(true);
614 // Hmm, the user must not have dropped a file list
616 } catch (Exception e) {
623 public void dropActionChanged(DropTargetDragEvent arg0) {
626 private class BackupHolder{
627 private DefaultListModel _rnaList;
628 private ArrayList<RNA> _rnas = new ArrayList<RNA>();
631 public BackupHolder(DefaultListModel rnaList, JList l)
637 public void add(VARNAConfig c, RNA r)
639 add(c, r, r.getName(),false);
642 public void add(VARNAConfig c, RNA r,boolean select)
644 add(c, r, r.getName(),select);
647 public void add(VARNAConfig c, RNA r, String name)
649 add(c, r, name,false);
651 public void add(VARNAConfig c, RNA r, String name, boolean select)
654 _l.removeSelectionInterval(0, _rnaList.size());
658 name = generateDefaultName();
660 FullBackup bck = new FullBackup(c,r,name);
664 _l.setSelectedIndex(0);
668 public void remove(int i)
674 public DefaultListModel getModel()
678 public boolean contains(RNA r)
680 return _rnas.contains(r);
682 /*public int getSize()
684 return _rnaList.getSize();
686 public FullBackup getElementAt(int i)
688 return (FullBackup) _rnaList.getElementAt(i);
691 public void removeSelected()
693 int i = _l.getSelectedIndex();
696 if (_rnaList.getSize()==1)
701 } catch (ExceptionUnmatchedClosingParentheses e1) {
702 } catch (ExceptionFileFormatOrSyntax e1) {
710 if (newi==_rnaList.getSize())
712 newi = _rnaList.getSize()-2;
714 FullBackup bck = (FullBackup) _rnaList.getElementAt(newi);
715 _l.setSelectedValue(bck,true);
723 public void onLayoutChanged() {
724 // TODO Auto-generated method stub
728 public void onUINewStructure(VARNAConfig v, RNA r) {
729 _rnaList.add(v, r,"",true);
732 public void onWarningEmitted(String s) {
733 // TODO Auto-generated method stub
737 public void mouseClicked(MouseEvent e) {
738 if(e.getClickCount() == 2){
739 int index = _sideList.locationToIndex(e.getPoint());
740 ListModel dlm = _sideList.getModel();
741 FullBackup item = (FullBackup) dlm.getElementAt(index);;
742 _sideList.ensureIndexIsVisible(index);
743 /*TODO Object newName = JOptionPane.showInputDialog(
745 "Specify a new name for this RNA",
747 JOptionPane.QUESTION_MESSAGE,
753 item.name = newName.toString();
754 this._sideList.repaint();
759 public void mouseEntered(MouseEvent arg0) {
760 // TODO Auto-generated method stub
764 public void mouseExited(MouseEvent arg0) {
765 // TODO Auto-generated method stub
769 public void mousePressed(MouseEvent arg0) {
770 // TODO Auto-generated method stub
774 public void mouseReleased(MouseEvent arg0) {
775 // TODO Auto-generated method stub
780 public Color getColour(int atomIndex, int pdbResNum, String chain,
782 // TODO Auto-generated method stub
787 public String[] getPdbFile() {
788 // TODO Auto-generated method stub
793 public void highlightAtom(int atomIndex, int pdbResNum, String chain,
795 // TODO Auto-generated method stub
800 public void mouseOverStructure(int atomIndex, String strInfo) {
801 // TODO Auto-generated method stub
806 public void releaseReferences(Object svl) {
807 // TODO Auto-generated method stub
812 public void updateColours(Object source) {
813 // TODO Auto-generated method stub
818 public void componentHidden(ComponentEvent e) {
819 // TODO Auto-generated method stub
824 public void componentMoved(ComponentEvent e) {
825 // TODO Auto-generated method stub
830 public void componentResized(ComponentEvent e) {
831 // TODO Auto-generated method stub
836 public void componentShown(ComponentEvent e) {
837 // TODO Auto-generated method stub
844 public static void main(String[] args)
846 JTextField str = new JTextField("ATGC");
848 AppVarnaBinding vab = new AppVarnaBinding();
849 vab.varnagui.set_seq(str);
850 vab.varnagui.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
852 vab.varnagui.setVisible(true);