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.MouseEvent;
37 import java.awt.event.MouseListener;
39 import java.text.DateFormat;
40 import java.util.ArrayList;
41 import java.util.Date;
42 import java.util.List;
44 import javax.swing.DefaultListModel;
45 import javax.swing.DefaultListSelectionModel;
46 import javax.swing.Icon;
47 import javax.swing.JButton;
48 import javax.swing.JFrame;
49 import javax.swing.JLabel;
50 import javax.swing.JList;
51 import javax.swing.JOptionPane;
52 import javax.swing.JPanel;
53 import javax.swing.JScrollPane;
54 import javax.swing.JSplitPane;
55 import javax.swing.JTextField;
56 import javax.swing.ListModel;
57 import javax.swing.ListSelectionModel;
58 import javax.swing.UIManager;
59 import javax.swing.UnsupportedLookAndFeelException;
60 import javax.swing.event.ListSelectionEvent;
61 import javax.swing.event.ListSelectionListener;
63 import fr.orsay.lri.varna.VARNAPanel;
64 import fr.orsay.lri.varna.components.ReorderableJList;
65 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
66 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
67 import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
68 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
69 import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
70 import fr.orsay.lri.varna.models.FullBackup;
71 import fr.orsay.lri.varna.models.VARNAConfig;
72 import fr.orsay.lri.varna.models.rna.Mapping;
73 import fr.orsay.lri.varna.models.rna.RNA;
75 public class AppVarnaBinding extends JFrame implements DropTargetListener, InterfaceVARNAListener, MouseListener {
80 //private static final long serialVersionUID = -790155708306987257L;
82 private String DEFAULT_SEQUENCE = "CAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIA";
84 private String DEFAULT_STRUCTURE1 = "..(((((...(((((...(((((...(((((.....)))))...))))).....(((((...(((((.....)))))...))))).....)))))...)))))..";
85 private String DEFAULT_STRUCTURE2 = "..(((((...(((((...(((((........(((((...(((((.....)))))...)))))..................))))).....)))))...)))))..";
86 // private static final String DEFAULT_STRUCTURE1 = "((((....))))";
87 // private static final String DEFAULT_STRUCTURE2 =
88 // "((((..(((....)))..))))";
92 private JPanel _tools = new JPanel();
93 private JPanel _input = new JPanel();
95 private JPanel _seqPanel = new JPanel();
96 private JPanel _strPanel = new JPanel();
97 private JLabel _info = new JLabel();
98 private JTextField _str = new JTextField();
99 private JTextField _seq = new JTextField();
100 private JLabel _strLabel = new JLabel(" Str:");
101 private JLabel _seqLabel = new JLabel(" Seq:");
102 private JButton _createButton = new JButton("Create");
103 private JButton _deleteButton = new JButton("Delete");
104 private JButton _duplicateButton = new JButton("Snapshot");
106 private JPanel _listPanel = new JPanel();
107 private ReorderableJList _sideList = null;
110 private static String errorOpt = "error";
111 @SuppressWarnings("unused")
112 private boolean _error;
114 private Color _backgroundColor = Color.white;
116 private static int _nextID = 1;
117 @SuppressWarnings("unused")
118 private int _algoCode;
120 private BackupHolder _rnaList;
123 public AppVarnaBinding() {
124 super("VARNA in Jalview");
125 //this.set_seq("ATGC");
126 //this.set_str(".().");
127 //RNAPanelDemoInit();
129 //initVarna("ATGCATGATATATATATAT","....((((...))))....");
130 initVarna(this.DEFAULT_SEQUENCE,this.DEFAULT_STRUCTURE1);
133 public AppVarnaBinding(String seq){
134 super("VARNA in Jalview");
135 initVarna(seq,this.DEFAULT_STRUCTURE1);
140 private void initVarna(String seq, String str){
141 DefaultListModel dlm = new DefaultListModel();
144 DefaultListSelectionModel m = new DefaultListSelectionModel();
145 m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
146 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 setBackground(_backgroundColor);
185 vp.setBackground(_backgroundColor);
187 getContentPane().setLayout(new BorderLayout());
188 getContentPane().add(vp, BorderLayout.CENTER);
191 vp.addVARNAListener(this);
194 private void RNAPanelDemoInit()
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);
226 RNA _RNA1 = new RNA("User defined 1");
227 RNA _RNA2 = new RNA("User defined 2");
229 vp = new VARNAPanel("0",".");
230 _RNA1.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE1);
231 _RNA1.drawRNARadiate(vp.getConfig());
232 _RNA2.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE2);
233 _RNA2.drawRNARadiate(vp.getConfig());
234 } catch (ExceptionNonEqualLength e) {
236 } catch (ExceptionUnmatchedClosingParentheses e2) {
237 e2.printStackTrace();
238 } catch (ExceptionFileFormatOrSyntax e3) {
239 e3.printStackTrace();
241 vp.setPreferredSize(new Dimension(400, 400));
242 _rnaList.add(vp.getConfig().clone(),_RNA2,generateDefaultName());
243 _rnaList.add(vp.getConfig().clone(),_RNA1,generateDefaultName(),true);
245 JScrollPane listScroller = new JScrollPane(_sideList);
246 listScroller.setPreferredSize(new Dimension(150, 0));
248 setBackground(_backgroundColor);
249 vp.setBackground(_backgroundColor);
252 Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
254 _seqLabel.setHorizontalTextPosition(JLabel.LEFT);
255 _seqLabel.setPreferredSize(new Dimension(marginTools, 15));
256 _seq.setFont(textFieldsFont);
257 _seq.setText(DEFAULT_SEQUENCE);
259 _createButton.addActionListener(new ActionListener() {
260 public void actionPerformed(ActionEvent e) {
262 RNA nRNA = new RNA(generateDefaultName());
263 nRNA.setRNA(_seq.getText(), _str.getText());
264 nRNA.drawRNARadiate(vp.getConfig());
265 _rnaList.add(new VARNAConfig(),nRNA,true);
266 } catch (ExceptionUnmatchedClosingParentheses e1) {
267 JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
268 } catch (ExceptionFileFormatOrSyntax e1) {
269 JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
275 _seqPanel.setLayout(new BorderLayout());
276 _seqPanel.add(_seqLabel, BorderLayout.WEST);
277 _seqPanel.add(_seq, BorderLayout.CENTER);
279 _strLabel.setPreferredSize(new Dimension(marginTools, 15));
280 _strLabel.setHorizontalTextPosition(JLabel.LEFT);
281 _str.setFont(textFieldsFont);
282 _strPanel.setLayout(new BorderLayout());
283 _strPanel.add(_strLabel, BorderLayout.WEST);
284 _strPanel.add(_str, BorderLayout.CENTER);
286 _input.setLayout(new GridLayout(2, 0));
287 _input.add(_seqPanel);
288 _input.add(_strPanel);
290 JPanel goPanel = new JPanel();
291 goPanel.setLayout(new BorderLayout());
293 _tools.setLayout(new BorderLayout());
294 _tools.add(_input, BorderLayout.CENTER);
295 _tools.add(_info, BorderLayout.SOUTH);
296 _tools.add(goPanel, BorderLayout.EAST);
298 _deleteButton.addActionListener(new ActionListener() {
299 public void actionPerformed(ActionEvent e) {
300 _rnaList.removeSelected();
303 _duplicateButton.addActionListener(new ActionListener() {
304 public void actionPerformed(ActionEvent e) {
305 _rnaList.add((VARNAConfig)vp.getConfig().clone(),vp.getRNA().clone(),vp.getRNA().getName()+"-"+DateFormat.getTimeInstance(DateFormat.LONG).format(new Date()),true);
308 JPanel ops = new JPanel();
309 ops.setLayout(new GridLayout(1,2));
310 ops.add(_deleteButton);
311 ops.add(_duplicateButton);
313 JLabel j = new JLabel("Structures Manager",JLabel.CENTER);
314 _listPanel.setLayout(new BorderLayout());
316 _listPanel.add(ops,BorderLayout.SOUTH);
317 _listPanel.add(j,BorderLayout.NORTH);
318 _listPanel.add(listScroller,BorderLayout.CENTER);
320 goPanel.add(_createButton, BorderLayout.CENTER);
322 JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,vp);
323 getContentPane().setLayout(new BorderLayout());
324 getContentPane().add(split, BorderLayout.CENTER);
325 getContentPane().add(_tools, BorderLayout.NORTH);
328 DropTarget dt = new DropTarget(vp, this);
330 vp.addVARNAListener(this);
333 public static String generateDefaultName()
335 return "User file #"+_nextID++;
338 public RNA getRNA() {
339 return (RNA)_sideList.getSelectedValue();
344 public String[][] getParameterInfo() {
346 // Parameter Name Kind of Value Description,
347 { "sequenceDBN", "String", "A raw RNA sequence" },
348 { "structureDBN", "String",
349 "An RNA structure in dot bracket notation (DBN)" },
350 { errorOpt, "boolean", "To show errors" }, };
355 vp.setBackground(_backgroundColor);
359 @SuppressWarnings("unused")
360 private Color getSafeColor(String col, Color def) {
363 result = Color.decode(col);
364 } catch (Exception e) {
366 result = Color.getColor(col, def);
367 } catch (Exception e2) {
374 public VARNAPanel get_varnaPanel() {
378 public void set_varnaPanel(VARNAPanel surface) {
383 public String get_seq() {
384 return _seq.getText();
387 public void set_seq(String _seq) {
388 this._seq.setText(_seq);
391 public String get_str(){
392 return _str.getText();
395 public void set_str(String _str){
396 this._str.setText(_str);
399 public JLabel get_info() {
403 public void set_info(JLabel _info) {
407 public static void main(String[] args) {
408 AppVarnaBinding d = new AppVarnaBinding();
409 d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
415 public void dragEnter(DropTargetDragEvent arg0) {
416 // TODO Auto-generated method stub
420 public void dragExit(DropTargetEvent arg0) {
421 // TODO Auto-generated method stub
425 public void dragOver(DropTargetDragEvent arg0) {
426 // TODO Auto-generated method stub
430 public void drop(DropTargetDropEvent dtde) {
432 Transferable tr = dtde.getTransferable();
433 DataFlavor[] flavors = tr.getTransferDataFlavors();
434 for (int i = 0; i < flavors.length; i++) {
435 if (flavors[i].isFlavorJavaFileListType()) {
436 dtde.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
437 Object ob = tr.getTransferData(flavors[i]);
438 if (ob instanceof List)
440 List list = (List) ob;
441 for (int j = 0; j < list.size(); j++) {
442 Object o = list.get(j);
444 if (dtde.getSource() instanceof DropTarget)
446 DropTarget dt = (DropTarget) dtde.getSource();
447 Component c = dt.getComponent();
448 if (c instanceof VARNAPanel)
450 String path = o.toString();
451 VARNAPanel vp = (VARNAPanel) c;
453 FullBackup bck = VARNAPanel.importSession(path);
454 _rnaList.add(bck.config, bck.rna,bck.name,true);
456 catch (ExceptionLoadingFailed e3)
460 r.drawRNA(vp.getConfig());
461 String name =r.getName();
464 name = path.substring(path.lastIndexOf(File.separatorChar)+1);
466 _rnaList.add(vp.getConfig().clone(),r,name,true);
472 // If we made it this far, everything worked.
473 dtde.dropComplete(true);
477 // Hmm, the user must not have dropped a file list
479 } catch (Exception e) {
486 public void dropActionChanged(DropTargetDragEvent arg0) {
489 private class BackupHolder{
490 private DefaultListModel _rnaList;
491 private ArrayList<RNA> _rnas = new ArrayList<RNA>();
494 public BackupHolder(DefaultListModel rnaList, JList l)
500 public void add(VARNAConfig c, RNA r)
502 add(c, r, r.getName(),false);
505 public void add(VARNAConfig c, RNA r,boolean select)
507 add(c, r, r.getName(),select);
510 public void add(VARNAConfig c, RNA r, String name)
512 add(c, r, name,false);
514 public void add(VARNAConfig c, RNA r, String name, boolean select)
517 _l.removeSelectionInterval(0, _rnaList.size());
521 name = generateDefaultName();
523 FullBackup bck = new FullBackup(c,r,name);
527 _l.setSelectedIndex(0);
531 public void remove(int i)
537 public DefaultListModel getModel()
541 public boolean contains(RNA r)
543 return _rnas.contains(r);
545 /*public int getSize()
547 return _rnaList.getSize();
549 public FullBackup getElementAt(int i)
551 return (FullBackup) _rnaList.getElementAt(i);
554 public void removeSelected()
556 int i = _l.getSelectedIndex();
559 if (_rnaList.getSize()==1)
564 } catch (ExceptionUnmatchedClosingParentheses e1) {
565 } catch (ExceptionFileFormatOrSyntax e1) {
573 if (newi==_rnaList.getSize())
575 newi = _rnaList.getSize()-2;
577 FullBackup bck = (FullBackup) _rnaList.getElementAt(newi);
578 _l.setSelectedValue(bck,true);
586 public void onLayoutChanged() {
587 // TODO Auto-generated method stub
591 public void onUINewStructure(VARNAConfig v, RNA r) {
592 _rnaList.add(v, r,"",true);
595 public void onWarningEmitted(String s) {
596 // TODO Auto-generated method stub
600 public void mouseClicked(MouseEvent e) {
601 if(e.getClickCount() == 2){
602 int index = _sideList.locationToIndex(e.getPoint());
603 ListModel dlm = _sideList.getModel();
604 FullBackup item = (FullBackup) dlm.getElementAt(index);;
605 _sideList.ensureIndexIsVisible(index);
606 Object newName = JOptionPane.showInputDialog(
608 "Specify a new name for this RNA",
610 JOptionPane.QUESTION_MESSAGE,
616 item.name = newName.toString();
617 this._sideList.repaint();
622 public void mouseEntered(MouseEvent arg0) {
623 // TODO Auto-generated method stub
627 public void mouseExited(MouseEvent arg0) {
628 // TODO Auto-generated method stub
632 public void mousePressed(MouseEvent arg0) {
633 // TODO Auto-generated method stub
637 public void mouseReleased(MouseEvent arg0) {
638 // TODO Auto-generated method stub
645 public static void main(String[] args)
647 JTextField str = new JTextField("ATGC");
649 AppVarnaBinding vab = new AppVarnaBinding();
650 vab.varnagui.set_seq(str);
651 vab.varnagui.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
653 vab.varnagui.setVisible(true);