2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 jalview.util.MessageManager;
22 import java.awt.BorderLayout;
23 import java.awt.Color;
24 import java.awt.Component;
25 import java.awt.Dimension;
27 import java.awt.GridLayout;
28 import java.awt.datatransfer.DataFlavor;
29 import java.awt.datatransfer.Transferable;
30 import java.awt.dnd.DnDConstants;
31 import java.awt.dnd.DropTarget;
32 import java.awt.dnd.DropTargetDragEvent;
33 import java.awt.dnd.DropTargetDropEvent;
34 import java.awt.dnd.DropTargetEvent;
35 import java.awt.dnd.DropTargetListener;
36 import java.awt.event.ActionEvent;
37 import java.awt.event.ActionListener;
38 import java.awt.event.ComponentEvent;
39 import java.awt.event.MouseEvent;
40 import java.awt.event.MouseListener;
42 import java.util.ArrayList;
43 import java.util.Collection;
44 import java.util.List;
46 import javax.swing.DefaultListModel;
47 import javax.swing.DefaultListSelectionModel;
48 import javax.swing.JButton;
49 import javax.swing.JLabel;
50 import javax.swing.JList;
51 import javax.swing.JPanel;
52 import javax.swing.JScrollPane;
53 import javax.swing.JTextField;
54 import javax.swing.ListModel;
55 import javax.swing.ListSelectionModel;
56 import javax.swing.event.ListSelectionEvent;
57 import javax.swing.event.ListSelectionListener;
59 import fr.orsay.lri.varna.VARNAPanel;
60 import fr.orsay.lri.varna.components.ReorderableJList;
61 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
62 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
63 import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
64 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
65 import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
66 import fr.orsay.lri.varna.models.FullBackup;
67 import fr.orsay.lri.varna.models.VARNAConfig;
68 import fr.orsay.lri.varna.models.rna.Mapping;
69 import fr.orsay.lri.varna.models.rna.RNA;
71 public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
72 implements DropTargetListener, InterfaceVARNAListener,
79 // private static final long serialVersionUID = -790155708306987257L;
81 private String DEFAULT_SEQUENCE = "CAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIA";
83 private String DEFAULT_STRUCTURE1 = "..(((((...(((((...(((((...(((((.....)))))...))))).....(((((...(((((.....)))))...))))).....)))))...)))))..";
85 private String DEFAULT_STRUCTURE2 = "..(((((...(((((...(((((........(((((...(((((.....)))))...)))))..................))))).....)))))...)))))..";
89 protected JPanel _tools = new JPanel();
91 private JPanel _input = new JPanel();
93 private JPanel _seqPanel = new JPanel();
95 private JPanel _strPanel = new JPanel();
97 private JLabel _info = new JLabel();
99 private JTextField _str = new JTextField();
101 private JTextField _seq = new JTextField();
103 private JLabel _strLabel = new JLabel(MessageManager.getString("label.str"));
105 private JLabel _seqLabel = new JLabel(MessageManager.getString("label.seq"));
107 private JButton _createButton = new JButton(MessageManager.getString("action.create"));
109 private JButton _updateButton = new JButton(MessageManager.getString("action.update"));
111 private JButton _deleteButton = new JButton(MessageManager.getString("action.delete"));
113 private JButton _duplicateButton = new JButton(MessageManager.getString("action.snapshot"));
115 protected JPanel _listPanel = new JPanel();
117 private ReorderableJList _sideList = null;
119 private static String errorOpt = "error";
121 @SuppressWarnings("unused")
122 private boolean _error;
124 private Color _backgroundColor = Color.white;
126 private static int _nextID = 1;
128 @SuppressWarnings("unused")
129 private int _algoCode;
131 private BackupHolder _rnaList;
134 * public AppVarnaBinding() { //super("VARNA in Jalview");
135 * //this.set_seq("ATGC"); //this.set_str(".()."); //RNAPanelDemoInit();
137 * //initVarna("ATGCATGATATATATATAT","....((((...))))....");
138 * initVarna(this.DEFAULT_SEQUENCE,this.DEFAULT_STRUCTURE1); }
141 public AppVarnaBinding(String seq, String struc)
143 // super("VARNA in Jalview");
144 initVarna(seq, struc);
148 public AppVarnaBinding(ArrayList<RNA> rnaList)
151 // super("VARNA in Jalview");
152 initVarnaEdit(rnaList);
155 private void initVarna(String seq, String str)
158 DefaultListModel dlm = new DefaultListModel();
160 DefaultListSelectionModel m = new DefaultListSelectionModel();
161 m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
162 m.setLeadAnchorNotificationEnabled(false);
164 _sideList = new ReorderableJList();
165 _sideList.setModel(dlm);
166 _sideList.addMouseListener(this);
167 _sideList.setSelectionModel(m);
168 _sideList.setPreferredSize(new Dimension(100, 0));
169 _sideList.addListSelectionListener(new ListSelectionListener()
171 public void valueChanged(ListSelectionEvent arg0)
173 if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
175 FullBackup sel = (FullBackup) _sideList.getSelectedValue();
176 Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA()
177 .getSize(), sel.rna.getSize());
178 vp.showRNAInterpolated(sel.rna, sel.config, map);
179 _seq.setText(sel.rna.getSeq());
180 _str.setText(sel.rna.getStructDBN());
185 _rnaList = new BackupHolder(dlm, _sideList);
186 RNA _RNA1 = new RNA("User defined 1");
191 vp = new VARNAPanel("0", ".");
192 _RNA1.setRNA(seq, str);
193 _RNA1.drawRNARadiate(vp.getConfig());
194 } catch (ExceptionNonEqualLength e)
197 } catch (ExceptionUnmatchedClosingParentheses e2)
199 e2.printStackTrace();
200 } catch (ExceptionFileFormatOrSyntax e3)
202 e3.printStackTrace();
204 vp.setPreferredSize(new Dimension(400, 400));
205 _rnaList.add(vp.getConfig().clone(), _RNA1, generateDefaultName(), true);
207 // TODO setBackground(_backgroundColor);
208 vp.setBackground(_backgroundColor);
210 // TODO getContentPane().setLayout(new BorderLayout());
211 // TODO getContentPane().add(vp, BorderLayout.CENTER);
214 vp.addVARNAListener(this);
217 private void initVarnaEdit(ArrayList<RNA> rnaInList)
220 DefaultListModel dlm = new DefaultListModel();
222 int marginTools = 40;
224 DefaultListSelectionModel m = new DefaultListSelectionModel();
225 m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
226 m.setLeadAnchorNotificationEnabled(false);
228 _sideList = new ReorderableJList();
229 _sideList.setModel(dlm);
230 _sideList.addMouseListener(this);
231 _sideList.setSelectionModel(m);
232 _sideList.setPreferredSize(new Dimension(100, 0));
233 _sideList.addListSelectionListener(new ListSelectionListener()
235 public void valueChanged(ListSelectionEvent arg0)
237 // System.out.println(arg0);
238 if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
240 FullBackup sel = (FullBackup) _sideList.getSelectedValue();
241 Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA()
242 .getSize(), sel.rna.getSize());
243 //vp.showRNAInterpolated(sel.rna, sel.config, map);
244 vp.showRNA(sel.rna, sel.config);
245 // _seq.setText(sel.rna.getSeq());
246 _str.setText(sel.rna.getStructDBN());
250 _rnaList = new BackupHolder(dlm, _sideList);
255 vp = new VARNAPanel("0", ".");
256 for (int i = 0; i < rnaInList.size(); i++)
258 rnaInList.get(i).drawRNARadiate(vp.getConfig());
261 } catch (ExceptionNonEqualLength e)
265 vp.setPreferredSize(new Dimension(400, 400));
266 for (int i = 0; i < rnaInList.size(); i++)
268 if (i < rnaInList.size() - 1)
270 _rnaList.add(vp.getConfig().clone(), rnaInList.get(i), rnaInList
275 _rnaList.add(vp.getConfig().clone(), rnaInList.get(i), rnaInList
276 .get(i).getName(), true);
281 * _rnaList.add(vp.getConfig().clone(),_RNA2,generateDefaultName());
282 * _rnaList.add(vp.getConfig().clone(),_RNA1,generateDefaultName(),true);
285 JScrollPane listScroller = new JScrollPane(_sideList);
286 listScroller.setPreferredSize(new Dimension(150, 0));
288 vp.setBackground(_backgroundColor);
290 Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
292 // _seqLabel.setHorizontalTextPosition(JLabel.LEFT);
293 // _seqLabel.setPreferredSize(new Dimension(marginTools, 15));
294 _seq.setFont(textFieldsFont);
295 _seq.setText(rnaInList.get(0).getSeq());
297 _updateButton.addActionListener(new ActionListener()
299 public void actionPerformed(ActionEvent e)
301 FullBackup sel = (FullBackup) _sideList.getSelectedValue();
302 sel.rna.setSequence("A");
306 // _seqPanel.setLayout(new BorderLayout());
307 // _seqPanel.add(_seqLabel, BorderLayout.WEST);
308 // _seqPanel.add(_seq, BorderLayout.CENTER);
310 _strLabel.setPreferredSize(new Dimension(marginTools, 15));
311 _strLabel.setHorizontalTextPosition(JLabel.LEFT);
312 _str.setFont(textFieldsFont);
313 _strPanel.setLayout(new BorderLayout());
314 _strPanel.add(_strLabel, BorderLayout.WEST);
315 _strPanel.add(_str, BorderLayout.CENTER);
317 _input.setLayout(new GridLayout(1, 0));
318 // _input.add(_seqPanel);
319 _input.add(_strPanel);
321 JPanel goPanel = new JPanel();
322 goPanel.setLayout(new BorderLayout());
324 _tools.setLayout(new BorderLayout());
325 _tools.add(_input, BorderLayout.CENTER);
326 // _tools.add(_info, BorderLayout.SOUTH);
327 _tools.add(goPanel, BorderLayout.EAST);
330 * _deleteButton.addActionListener(new ActionListener() { public void
331 * actionPerformed(ActionEvent e) { _rnaList.removeSelected(); } });
332 * _duplicateButton.addActionListener(new ActionListener() { public void
333 * actionPerformed(ActionEvent e) {
334 * _rnaList.add((VARNAConfig)vp.getConfig().
335 * clone(),vp.getRNA().clone(),vp.getRNA
336 * ().getName()+"-"+DateFormat.getTimeInstance(DateFormat.LONG).format(new
337 * Date()),true); }});
339 goPanel.add(_updateButton, BorderLayout.CENTER);
341 JPanel ops = new JPanel();
342 ops.setLayout(new GridLayout(1, 2));
343 ops.add(_deleteButton);
344 ops.add(_duplicateButton);
346 JLabel j = new JLabel(MessageManager.getString("label.structures_manager"), JLabel.CENTER);
347 _listPanel.setLayout(new BorderLayout());
349 // _listPanel.add(ops, BorderLayout.SOUTH);
350 _listPanel.add(j, BorderLayout.NORTH);
351 _listPanel.add(listScroller, BorderLayout.CENTER);
353 // JSplitPane split = new
354 // JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,vp);
356 * TODO getContentPane().setLayout(new BorderLayout());
357 * getContentPane().add(split, BorderLayout.CENTER);
358 * getContentPane().add(_tools, BorderLayout.NORTH);
361 // TODO setVisible(true);
362 DropTarget dt = new DropTarget(vp, this);
364 vp.addVARNAListener(this);
367 public JPanel getTools()
372 public JPanel getListPanel()
378 * TODO: Is it effective to transfer the whole RNA?
380 * @return Currently selected RNA
382 public RNA getSelectedRNA()
384 return _rnaList.getElementAt(_sideList.getSelectedIndex()).rna;
388 * Substitute currently selected RNA with the edited one
392 public void updateSelectedRNA(RNA rnaEdit)
399 * private void RNAPanelDemoInit() { DefaultListModel dlm = new
400 * DefaultListModel();
403 * int marginTools = 40;
405 * DefaultListSelectionModel m = new DefaultListSelectionModel();
406 * m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
407 * m.setLeadAnchorNotificationEnabled(false);
410 * _sideList = new ReorderableJList(); _sideList.setModel(dlm);
411 * _sideList.addMouseListener(this); _sideList.setSelectionModel(m);
412 * _sideList.setPreferredSize(new Dimension(100, 0));
413 * _sideList.addListSelectionListener( new ListSelectionListener(){ public
414 * void valueChanged(ListSelectionEvent arg0) { //System.out.println(arg0); if
415 * (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting()) { FullBackup
416 * sel = (FullBackup) _sideList.getSelectedValue(); Mapping map =
417 * Mapping.DefaultOutermostMapping(vp.getRNA().getSize(), sel.rna.getSize());
418 * vp.showRNAInterpolated(sel.rna,sel.config,map);
419 * _seq.setText(sel.rna.getSeq()); _str.setText(sel.rna.getStructDBN()); } }
422 * _rnaList = new BackupHolder(dlm,_sideList); RNA _RNA1 = new
423 * RNA("User defined 1"); RNA _RNA2 = new RNA("User defined 2"); try { vp =
424 * new VARNAPanel("0","."); _RNA1.setRNA(DEFAULT_SEQUENCE,
425 * DEFAULT_STRUCTURE1); _RNA1.drawRNARadiate(vp.getConfig());
426 * _RNA2.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE2);
427 * _RNA2.drawRNARadiate(vp.getConfig()); } catch (ExceptionNonEqualLength e) {
428 * vp.errorDialog(e); } catch (ExceptionUnmatchedClosingParentheses e2) {
429 * e2.printStackTrace(); } catch (ExceptionFileFormatOrSyntax e3) {
430 * e3.printStackTrace(); } vp.setPreferredSize(new Dimension(400, 400));
431 * _rnaList.add(vp.getConfig().clone(),_RNA2,generateDefaultName());
432 * _rnaList.add(vp.getConfig().clone(),_RNA1,generateDefaultName(),true);
434 * JScrollPane listScroller = new JScrollPane(_sideList);
435 * listScroller.setPreferredSize(new Dimension(150, 0));
437 * setBackground(_backgroundColor); vp.setBackground(_backgroundColor);
440 * Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
442 * _seqLabel.setHorizontalTextPosition(JLabel.LEFT);
443 * _seqLabel.setPreferredSize(new Dimension(marginTools, 15));
444 * _seq.setFont(textFieldsFont); _seq.setText(DEFAULT_SEQUENCE);
446 * _createButton.addActionListener(new ActionListener() { public void
447 * actionPerformed(ActionEvent e) { try { RNA nRNA = new
448 * RNA(generateDefaultName()); nRNA.setRNA(_seq.getText(), _str.getText());
449 * nRNA.drawRNARadiate(vp.getConfig()); _rnaList.add(new
450 * VARNAConfig(),nRNA,true); } catch (ExceptionUnmatchedClosingParentheses e1)
451 * { JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error",
452 * JOptionPane.ERROR_MESSAGE); } catch (ExceptionFileFormatOrSyntax e1) {
453 * JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error",
454 * JOptionPane.ERROR_MESSAGE); } } });
457 * _seqPanel.setLayout(new BorderLayout()); _seqPanel.add(_seqLabel,
458 * BorderLayout.WEST); _seqPanel.add(_seq, BorderLayout.CENTER);
460 * _strLabel.setPreferredSize(new Dimension(marginTools, 15));
461 * _strLabel.setHorizontalTextPosition(JLabel.LEFT);
462 * _str.setFont(textFieldsFont); _strPanel.setLayout(new BorderLayout());
463 * _strPanel.add(_strLabel, BorderLayout.WEST); _strPanel.add(_str,
464 * BorderLayout.CENTER);
466 * _input.setLayout(new GridLayout(2, 0)); _input.add(_seqPanel);
467 * _input.add(_strPanel);
469 * JPanel goPanel = new JPanel(); goPanel.setLayout(new BorderLayout());
471 * _tools.setLayout(new BorderLayout()); _tools.add(_input,
472 * BorderLayout.CENTER); _tools.add(_info, BorderLayout.SOUTH);
473 * _tools.add(goPanel, BorderLayout.EAST);
475 * _deleteButton.addActionListener(new ActionListener() { public void
476 * actionPerformed(ActionEvent e) { _rnaList.removeSelected(); } });
477 * _duplicateButton.addActionListener(new ActionListener() { public void
478 * actionPerformed(ActionEvent e) {
479 * _rnaList.add((VARNAConfig)vp.getConfig().clone
480 * (),vp.getRNA().clone(),vp.getRNA
481 * ().getName()+"-"+DateFormat.getTimeInstance(DateFormat.LONG).format(new
482 * Date()),true); }});
484 * JPanel ops = new JPanel(); ops.setLayout(new GridLayout(1,2));
485 * ops.add(_deleteButton); ops.add(_duplicateButton);
487 * JLabel j = new JLabel("Structures Manager",JLabel.CENTER);
488 * _listPanel.setLayout(new BorderLayout());
490 * _listPanel.add(ops,BorderLayout.SOUTH);
491 * _listPanel.add(j,BorderLayout.NORTH);
492 * _listPanel.add(listScroller,BorderLayout.CENTER);
494 * goPanel.add(_createButton, BorderLayout.CENTER);
496 * JSplitPane split = new
497 * JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,vp);
498 * getContentPane().setLayout(new BorderLayout()); getContentPane().add(split,
499 * BorderLayout.CENTER); getContentPane().add(_tools, BorderLayout.NORTH);
501 * setVisible(true); DropTarget dt = new DropTarget(vp, this);
503 * vp.addVARNAListener(this); }
505 public static String generateDefaultName()
507 return "User file #" + _nextID++;
512 return (RNA) _sideList.getSelectedValue();
515 public String[][] getParameterInfo()
519 // Parameter Name Kind of Value Description,
520 { "sequenceDBN", "String", "A raw RNA sequence" },
521 { "structureDBN", "String",
522 "An RNA structure in dot bracket notation (DBN)" },
523 { errorOpt, "boolean", "To show errors" }, };
529 vp.setBackground(_backgroundColor);
533 @SuppressWarnings("unused")
534 private Color getSafeColor(String col, Color def)
539 result = Color.decode(col);
540 } catch (Exception e)
544 result = Color.getColor(col, def);
545 } catch (Exception e2)
553 public VARNAPanel get_varnaPanel()
558 public void set_varnaPanel(VARNAPanel surface)
563 public String get_seq()
565 return _seq.getText();
568 public void set_seq(String _seq)
570 this._seq.setText(_seq);
573 public String get_str()
575 return _str.getText();
578 public void set_str(String _str)
580 this._str.setText(_str);
583 public JLabel get_info()
588 public void set_info(JLabel _info)
594 * public static void main(String[] args) { AppVarnaBinding d = new
595 * AppVarnaBinding(); d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
596 * d.pack(); d.setVisible(true); }
599 public void dragEnter(DropTargetDragEvent arg0)
601 // TODO Auto-generated method stub
605 public void dragExit(DropTargetEvent arg0)
607 // TODO Auto-generated method stub
611 public void dragOver(DropTargetDragEvent arg0)
613 // TODO Auto-generated method stub
617 public void drop(DropTargetDropEvent dtde)
621 Transferable tr = dtde.getTransferable();
622 DataFlavor[] flavors = tr.getTransferDataFlavors();
623 for (int i = 0; i < flavors.length; i++)
625 if (flavors[i].isFlavorJavaFileListType())
627 dtde.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
628 Object ob = tr.getTransferData(flavors[i]);
629 if (ob instanceof List)
631 List list = (List) ob;
632 for (int j = 0; j < list.size(); j++)
634 Object o = list.get(j);
636 if (dtde.getSource() instanceof DropTarget)
638 DropTarget dt = (DropTarget) dtde.getSource();
639 Component c = dt.getComponent();
640 if (c instanceof VARNAPanel)
642 String path = o.toString();
643 VARNAPanel vp = (VARNAPanel) c;
646 FullBackup bck = VARNAPanel.importSession(path);
647 _rnaList.add(bck.config, bck.rna, bck.name, true);
648 } catch (ExceptionLoadingFailed e3)
651 Collection<RNA> mdls = fr.orsay.lri.varna.factories.RNAFactory
655 r.drawRNA(vp.getConfig());
656 String name = r.getName();
659 name = path.substring(path
660 .lastIndexOf(File.separatorChar) + 1);
664 name += " (Model " + mn++ + ")";
666 _rnaList.add(vp.getConfig().clone(), r, name, true);
673 // If we made it this far, everything worked.
674 dtde.dropComplete(true);
678 // Hmm, the user must not have dropped a file list
680 } catch (Exception e)
688 public void dropActionChanged(DropTargetDragEvent arg0)
692 private class BackupHolder
694 private DefaultListModel _rnaList;
696 private ArrayList<RNA> _rnas = new ArrayList<RNA>();
700 public BackupHolder(DefaultListModel rnaList, JList l)
706 public void add(VARNAConfig c, RNA r)
708 add(c, r, r.getName(), false);
711 public void add(VARNAConfig c, RNA r, boolean select)
713 add(c, r, r.getName(), select);
716 public void add(VARNAConfig c, RNA r, String name)
718 add(c, r, name, false);
721 public void add(VARNAConfig c, RNA r, String name, boolean select)
725 _l.removeSelectionInterval(0, _rnaList.size());
729 name = generateDefaultName();
731 FullBackup bck = new FullBackup(c, r, name);
733 _rnaList.add(0, bck);
736 _l.setSelectedIndex(0);
740 public void remove(int i)
747 public DefaultListModel getModel()
752 public boolean contains(RNA r)
754 return _rnas.contains(r);
758 * public int getSize() { return _rnaList.getSize(); }
760 public FullBackup getElementAt(int i)
762 return (FullBackup) _rnaList.getElementAt(i);
765 public void removeSelected()
767 int i = _l.getSelectedIndex();
770 if (_rnaList.getSize() == 1)
776 } catch (ExceptionUnmatchedClosingParentheses e1)
778 } catch (ExceptionFileFormatOrSyntax e1)
787 if (newi == _rnaList.getSize())
789 newi = _rnaList.getSize() - 2;
791 FullBackup bck = (FullBackup) _rnaList.getElementAt(newi);
792 _l.setSelectedValue(bck, true);
800 public void onLayoutChanged()
802 // TODO Auto-generated method stub
806 public void onUINewStructure(VARNAConfig v, RNA r)
808 // patch to fix infinite loop
809 // The problem is that onUINewStructure is called when user clicks
810 // check with Yann about whether Jalview should do anything with this event.
811 // e.g. if user has used VARNA's menu to import a structure .. Jalview may need to be told which structure is displayed.
813 // _rnaList.add(v, r, "", true);
816 public void onWarningEmitted(String s)
818 // TODO Auto-generated method stub
822 public void mouseClicked(MouseEvent e)
824 if (e.getClickCount() == 2)
826 int index = _sideList.locationToIndex(e.getPoint());
827 ListModel dlm = _sideList.getModel();
828 FullBackup item = (FullBackup) dlm.getElementAt(index);
830 _sideList.ensureIndexIsVisible(index);
832 * TODO Object newName = JOptionPane.showInputDialog( this,
833 * "Specify a new name for this RNA", "Rename RNA",
834 * JOptionPane.QUESTION_MESSAGE, (Icon)null, null, item.toString()); if
835 * (newName!=null) { item.name = newName.toString();
836 * this._sideList.repaint(); }
841 public void mouseEntered(MouseEvent arg0)
843 // TODO Auto-generated method stub
847 public void mouseExited(MouseEvent arg0)
849 // TODO Auto-generated method stub
853 public void mousePressed(MouseEvent arg0)
855 // TODO Auto-generated method stub
859 public void mouseReleased(MouseEvent arg0)
861 // TODO Auto-generated method stub
866 public Color getColour(int atomIndex, int pdbResNum, String chain,
869 // TODO Auto-generated method stub
874 public String[] getPdbFile()
876 // TODO Auto-generated method stub
881 public void highlightAtom(int atomIndex, int pdbResNum, String chain,
884 // TODO Auto-generated method stub
889 public void mouseOverStructure(int atomIndex, String strInfo)
891 // TODO Auto-generated method stub
896 public void releaseReferences(Object svl)
898 // TODO Auto-generated method stub
903 public void updateColours(Object source)
905 // TODO Auto-generated method stub
910 public void componentHidden(ComponentEvent e)
912 // TODO Auto-generated method stub
917 public void componentMoved(ComponentEvent e)
919 // TODO Auto-generated method stub
924 public void componentResized(ComponentEvent e)
926 // TODO Auto-generated method stub
931 public void componentShown(ComponentEvent e)
933 // TODO Auto-generated method stub
938 public void onStructureRedrawn()
940 // TODO Auto-generated method stub
945 public void onZoomLevelChanged()
947 // TODO Auto-generated method stub
952 public void onTranslationChanged()
954 // TODO Auto-generated method stub
960 * public static void main(String[] args) { JTextField str = new
961 * JTextField("ATGC");
963 * AppVarnaBinding vab = new AppVarnaBinding(); vab.varnagui.set_seq(str);
964 * vab.varnagui.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
965 * vab.varnagui.pack(); vab.varnagui.setVisible(true); } }