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Coverage Report

  1. Project Clover database Mon Nov 11 2024 15:05:32 GMT
  2. Package jalview.gui

File AppVarnaBinding.java

 

Coverage histogram

../../img/srcFileCovDistChart0.png
60% of files have more coverage

Code metrics

38
137
36
2
581
403
62
0.45
3.81
18
1.72

Classes

Class Line # Actions
AppVarnaBinding 67 124 55
0.00%
AppVarnaBinding.BackupHolder 316 13 7
0.00%
 

Contributing tests

No tests hitting this source file were found.

Source view

1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.gui;
22   
23    import jalview.datamodel.SequenceI;
24    import jalview.ext.varna.JalviewVarnaBinding;
25    import jalview.structure.AtomSpec;
26    import jalview.util.MessageManager;
27   
28    import java.awt.BorderLayout;
29    import java.awt.Color;
30    import java.awt.Component;
31    import java.awt.Dimension;
32    import java.awt.datatransfer.DataFlavor;
33    import java.awt.datatransfer.Transferable;
34    import java.awt.dnd.DnDConstants;
35    import java.awt.dnd.DropTarget;
36    import java.awt.dnd.DropTargetAdapter;
37    import java.awt.dnd.DropTargetDropEvent;
38    import java.awt.event.ComponentEvent;
39    import java.awt.event.MouseAdapter;
40    import java.awt.event.MouseEvent;
41    import java.io.File;
42    import java.io.IOException;
43    import java.util.ArrayList;
44    import java.util.Collection;
45    import java.util.List;
46   
47    import javax.swing.DefaultListModel;
48    import javax.swing.DefaultListSelectionModel;
49    import javax.swing.JLabel;
50    import javax.swing.JList;
51    import javax.swing.JPanel;
52    import javax.swing.JScrollPane;
53    import javax.swing.ListModel;
54    import javax.swing.ListSelectionModel;
55    import javax.swing.event.ListSelectionEvent;
56    import javax.swing.event.ListSelectionListener;
57   
58    import fr.orsay.lri.varna.VARNAPanel;
59    import fr.orsay.lri.varna.components.ReorderableJList;
60    import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
61    import fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm;
62    import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
63    import fr.orsay.lri.varna.models.FullBackup;
64    import fr.orsay.lri.varna.models.VARNAConfig;
65    import fr.orsay.lri.varna.models.rna.RNA;
66   
 
67    public class AppVarnaBinding extends JalviewVarnaBinding
68    {
69    public VARNAPanel vp;
70   
71    protected JPanel _listPanel = new JPanel();
72   
73    private ReorderableJList _sideList = null;
74   
75    private static String errorOpt = "error";
76   
77    @SuppressWarnings("unused")
78    private boolean _error;
79   
80    private Color _backgroundColor = Color.white;
81   
82    private static int _nextID = 1;
83   
84    @SuppressWarnings("unused")
85    private int _algoCode;
86   
87    private BackupHolder _rnaList;
88   
89    /**
90    * Constructor
91    */
 
92  0 toggle public AppVarnaBinding()
93    {
94  0 init();
95    }
96   
97    /**
98    * Constructs the VARNAPanel and an (empty) selection list of structures to
99    * show in it
100    */
 
101  0 toggle private void init()
102    {
103  0 DefaultListModel<FullBackup> dlm = new DefaultListModel<FullBackup>();
104   
105  0 int marginTools = 40;
106   
107  0 DefaultListSelectionModel m = new DefaultListSelectionModel();
108  0 m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
109  0 m.setLeadAnchorNotificationEnabled(false);
110   
111  0 _sideList = new ReorderableJList();
112  0 _sideList.setModel(dlm);
113  0 _sideList.addMouseListener(new MouseAdapter()
114    {
 
115  0 toggle @Override
116    public void mouseClicked(MouseEvent e)
117    {
118  0 AppVarnaBinding.this.mouseClicked(e);
119    }
120    });
121  0 _sideList.setSelectionModel(m);
122  0 _sideList.setPreferredSize(new Dimension(100, 0));
123  0 _sideList.addListSelectionListener(new ListSelectionListener()
124    {
 
125  0 toggle public void valueChanged(ListSelectionEvent evt)
126    {
127  0 changeSelectedStructure_actionPerformed(evt);
128    }
129    });
130  0 _rnaList = new BackupHolder(dlm, _sideList);
131   
132  0 try
133    {
134  0 vp = new VARNAPanel("0", ".");
135    } catch (ExceptionNonEqualLength e)
136    {
137  0 vp.errorDialog(e);
138    }
139  0 vp.setPreferredSize(new Dimension(400, 400));
140   
141  0 JScrollPane listScroller = new JScrollPane(_sideList);
142  0 listScroller.setPreferredSize(new Dimension(150, 0));
143   
144  0 vp.setBackground(_backgroundColor);
145   
146  0 JLabel j = new JLabel(
147    MessageManager.getString("label.structures_manager"),
148    JLabel.CENTER);
149  0 _listPanel.setLayout(new BorderLayout());
150   
151  0 _listPanel.add(j, BorderLayout.NORTH);
152  0 _listPanel.add(listScroller, BorderLayout.CENTER);
153   
154  0 new DropTarget(vp, new DropTargetAdapter()
155    {
 
156  0 toggle @Override
157    public void drop(DropTargetDropEvent dtde)
158    {
159  0 AppVarnaBinding.this.drop(dtde);
160    }
161    });
162    }
163   
 
164  0 toggle public JPanel getListPanel()
165    {
166  0 return _listPanel;
167    }
168   
169    /**
170    * Returns the currently selected RNA, or null if none selected
171    *
172    * @return
173    */
 
174  0 toggle public RNA getSelectedRNA()
175    {
176  0 int selectedIndex = _sideList.getSelectedIndex();
177  0 if (selectedIndex < 0)
178    {
179  0 return null;
180    }
181  0 FullBackup selected = _rnaList.getElementAt(selectedIndex);
182  0 return selected.rna;
183    }
184   
185    /**
186    * Substitute currently selected RNA with the edited one
187    *
188    * @param rnaEdit
189    */
 
190  0 toggle public void updateSelectedRNA(RNA rnaEdit)
191    {
192  0 vp.repaint();
193  0 vp.showRNA(rnaEdit);
194    }
195   
 
196  0 toggle public static String generateDefaultName()
197    {
198  0 return "User file #" + _nextID++;
199    }
200   
 
201  0 toggle public String[][] getParameterInfo()
202    {
203  0 String[][] info = {
204    // Parameter Name Kind of Value Description,
205    { "sequenceDBN", "String", "A raw RNA sequence" },
206    { "structureDBN", "String",
207    "An RNA structure in dot bracket notation (DBN)" },
208    { errorOpt, "boolean", "To show errors" }, };
209  0 return info;
210    }
211   
 
212  0 toggle @SuppressWarnings("unused")
213    private Color getSafeColor(String col, Color def)
214    {
215  0 Color result;
216  0 try
217    {
218  0 result = Color.decode(col);
219    } catch (Exception e)
220    {
221  0 try
222    {
223  0 result = Color.getColor(col, def);
224    } catch (Exception e2)
225    {
226  0 return def;
227    }
228    }
229  0 return result;
230    }
231   
 
232  0 toggle public VARNAPanel get_varnaPanel()
233    {
234  0 return vp;
235    }
236   
 
237  0 toggle public void set_varnaPanel(VARNAPanel surface)
238    {
239  0 vp = surface;
240    }
241   
 
242  0 toggle public void drop(DropTargetDropEvent dtde)
243    {
244  0 try
245    {
246  0 Transferable tr = dtde.getTransferable();
247  0 DataFlavor[] flavors = tr.getTransferDataFlavors();
248  0 for (int i = 0; i < flavors.length; i++)
249    {
250  0 if (flavors[i].isFlavorJavaFileListType())
251    {
252  0 dtde.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
253  0 Object ob = tr.getTransferData(flavors[i]);
254  0 if (ob instanceof List)
255    {
256  0 List list = (List) ob;
257  0 for (int j = 0; j < list.size(); j++)
258    {
259  0 Object o = list.get(j);
260   
261  0 if (dtde.getSource() instanceof DropTarget)
262    {
263  0 DropTarget dt = (DropTarget) dtde.getSource();
264  0 Component c = dt.getComponent();
265  0 if (c instanceof VARNAPanel)
266    {
267  0 String path = o.toString();
268  0 VARNAPanel varnaPanel = (VARNAPanel) c;
269  0 try
270    {
271  0 FullBackup bck = VARNAPanel.importSession(path);
272  0 _rnaList.add(bck.config, bck.rna, bck.name, true);
273    } catch (ExceptionLoadingFailed e3)
274    {
275  0 int mn = 1;
276  0 Collection<RNA> mdls = fr.orsay.lri.varna.factories.RNAFactory
277    .loadSecStr(path);
278  0 for (RNA r : mdls)
279    {
280  0 r.drawRNA(varnaPanel.getConfig());
281  0 String name = r.getName();
282  0 if (name.equals(""))
283    {
284  0 name = path.substring(
285    path.lastIndexOf(File.separatorChar) + 1);
286    }
287  0 if (mdls.size() > 1)
288    {
289  0 name += " (Model " + mn++ + ")";
290    }
291  0 _rnaList.add(varnaPanel.getConfig().clone(), r, name,
292    true);
293    // BH 2018 SwingJS clone of varnaPanel or its config will
294    // be the object itself, not a clone
295    }
296    }
297    }
298    }
299    }
300    }
301    // If we made it this far, everything worked.
302  0 dtde.dropComplete(true);
303  0 return;
304    }
305    }
306    // Hmm, the user must not have dropped a file list
307  0 dtde.rejectDrop();
308    } catch (Exception e)
309    {
310  0 e.printStackTrace();
311  0 dtde.rejectDrop();
312    }
313   
314    }
315   
 
316    private class BackupHolder
317    {
318    private DefaultListModel<FullBackup> _rnalist;
319   
320    private List<RNA> _rnas = new ArrayList<RNA>();
321   
322    JList _l;
323   
 
324  0 toggle public BackupHolder(DefaultListModel<FullBackup> rnaList, JList l)
325    {
326  0 _rnalist = rnaList;
327  0 _l = l;
328    }
329   
 
330  0 toggle public void add(VARNAConfig c, RNA r, String name)
331    {
332  0 add(c, r, name, false);
333    }
334   
335    /**
336    * Adds an entry to the end of the selection list and (optionally) sets it
337    * as selected
338    *
339    * @param c
340    * @param r
341    * @param name
342    * @param select
343    */
 
344  0 toggle public void add(VARNAConfig c, RNA r, String name, boolean select)
345    {
346  0 if (select)
347    {
348  0 _l.removeSelectionInterval(0, _rnalist.size());
349    }
350  0 if (name.equals(""))
351    {
352  0 name = generateDefaultName();
353    }
354  0 FullBackup bck = new FullBackup(c, r, name);
355  0 _rnas.add(r);
356  0 _rnalist.addElement(bck);
357  0 if (select)
358    {
359  0 _l.setSelectedIndex(0);
360    }
361    }
362   
 
363  0 toggle public FullBackup getElementAt(int i)
364    {
365  0 return _rnalist.getElementAt(i);
366    }
367    }
368   
 
369  0 toggle public void mouseClicked(MouseEvent e)
370    {
371  0 if (e.getClickCount() == 2)
372    {
373  0 int index = _sideList.locationToIndex(e.getPoint());
374  0 ListModel<FullBackup> dlm = _sideList.getModel();
375    // FullBackup item = dlm.getElementAt(index);
376   
377  0 _sideList.ensureIndexIsVisible(index);
378    /*
379    * TODO Object newName = JvOptionPane.showInputDialog( this,
380    * "Specify a new name for this RNA", "Rename RNA",
381    * JvOptionPane.QUESTION_MESSAGE, (Icon)null, null, item.toString()); if
382    * (newName!=null) { item.name = newName.toString();
383    * this._sideList.repaint(); }
384    */
385    }
386    }
387   
 
388  0 toggle @Override
389    public String[] getStructureFiles()
390    {
391  0 return null;
392    }
393   
 
394  0 toggle @Override
395    public void releaseReferences(Object svl)
396    {
397    }
398   
 
399  0 toggle @Override
400    public void updateColours(Object source)
401    {
402    }
403   
 
404  0 toggle @Override
405    public void componentHidden(ComponentEvent e)
406    {
407    }
408   
 
409  0 toggle @Override
410    public void componentMoved(ComponentEvent e)
411    {
412    }
413   
 
414  0 toggle @Override
415    public void componentResized(ComponentEvent e)
416    {
417    }
418   
 
419  0 toggle @Override
420    public void componentShown(ComponentEvent e)
421    {
422    }
423   
 
424  0 toggle @Override
425    public void highlightAtoms(List<AtomSpec> atoms)
426    {
427    }
428   
 
429  0 toggle @Override
430    public boolean isListeningFor(SequenceI seq)
431    {
432  0 return true;
433    }
434   
435    /**
436    * Returns the path to a temporary file containing a representation of the
437    * state of the Varna display, or null on any error
438    *
439    * @param rna
440    * @param jds
441    *
442    * @return
443    */
 
444  0 toggle public String getStateInfo(RNA rna)
445    {
446  0 if (vp == null)
447    {
448  0 return null;
449    }
450   
451    /*
452    * we have to show the RNA we want to save in the viewer; get the currently
453    * displayed model first so we can restore it
454    */
455  0 FullBackup sel = (FullBackup) _sideList.getSelectedValue();
456   
457  0 FullBackup model = null;
458  0 ListModel models = _sideList.getModel();
459  0 for (int i = 0; i < models.getSize(); i++)
460    {
461  0 model = (FullBackup) models.getElementAt(i);
462  0 if (model.rna == rna)
463    {
464  0 break;
465    }
466    }
467  0 if (model == null)
468    {
469  0 return null;
470    }
471   
472    /*
473    * switch display
474    */
475  0 vp.showRNA(model.rna, model.config);
476   
477  0 try
478    {
479  0 File temp;
480  0 temp = File.createTempFile("varna", null);
481  0 temp.deleteOnExit();
482  0 String filePath = temp.getAbsolutePath();
483  0 vp.toXML(filePath);
484   
485    /*
486    * restore the previous display
487    */
488  0 vp.showRNA(sel.rna, sel.config);
489   
490  0 return filePath;
491    } catch (IOException e)
492    {
493  0 return null;
494    }
495    }
496   
 
497  0 toggle public int getSelectedIndex()
498    {
499  0 return _sideList.getSelectedIndex();
500    }
501   
502    /**
503    * Switch the Varna display to the structure selected in the left hand panel
504    *
505    * @param evt
506    */
 
507  0 toggle protected void changeSelectedStructure_actionPerformed(
508    ListSelectionEvent evt)
509    {
510  0 if (!evt.getValueIsAdjusting())
511    {
512  0 showSelectedStructure();
513    }
514    }
515   
516    /**
517    *
518    */
 
519  0 toggle protected void showSelectedStructure()
520    {
521  0 FullBackup sel = (FullBackup) _sideList.getSelectedValue();
522  0 if (sel != null)
523    {
524  0 vp.showRNA(sel.rna, sel.config);
525    }
526    }
527   
528    /**
529    * Set and display the selected item in the list of structures
530    *
531    * @param selectedRna
532    */
 
533  0 toggle public void setSelectedIndex(final int selectedRna)
534    {
535    /*
536    * note this does nothing if, say, selecting item 3 when only 1 has been
537    * added on load
538    */
539  0 _sideList.setSelectedIndex(selectedRna);
540    // TODO ? need a worker thread to get this to happen properly
541    }
542   
543    /**
544    * Add an RNA structure to the selection list
545    *
546    * @param rna
547    */
 
548  0 toggle public void addStructure(RNA rna)
549    {
550  0 VARNAConfig config = vp.getConfig().clone(); // BH 2018 this will NOT be a
551    // clone in SwingJS
552  0 addStructure(rna, config);
553    }
554   
555    /**
556    * @param rna
557    * @param config
558    */
 
559  0 toggle protected void addStructure(final RNA rna, final VARNAConfig config)
560    {
561  0 drawRna(rna, config);
562  0 _rnaList.add(config, rna, rna.getName());
563    }
564   
565    /**
566    * @param rna
567    * @param config
568    */
 
569  0 toggle protected void drawRna(final RNA rna, final VARNAConfig config)
570    {
571  0 try
572    {
573  0 rna.drawRNA(rna.getDrawMode(), config);
574    } catch (ExceptionNAViewAlgorithm e)
575    {
576    // only throwable for draw mode = 3 NAView
577  0 jalview.bin.Console
578    .errPrintln("Error drawing RNA: " + e.getMessage());
579    }
580    }
581    }
  • Report generated by OpenClover v 4.4.1 on Mon Nov 11 2024 15:12:36 GMT using coverage data from Mon Nov 11 2024 15:12:26 GMT.
  • OpenClover is free and open-source software.