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Coverage Report

  1. Project Clover database Wed Nov 12 2025 09:00:47 GMT
  2. Package jalview.appletgui

File IdPanel.java

 

Coverage histogram

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

Code metrics

88
165
14
2
472
374
73
0.44
11.79
7
5.21

Classes

Class Line # Actions
IdPanel 41 147 63
0.00%
IdPanel.ScrollThread 414 18 10
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.appletgui;
22   
23    import jalview.datamodel.SequenceFeature;
24    import jalview.datamodel.SequenceGroup;
25    import jalview.datamodel.SequenceI;
26    import jalview.urls.api.UrlProviderFactoryI;
27    import jalview.urls.api.UrlProviderI;
28    import jalview.urls.applet.AppletUrlProviderFactory;
29    import jalview.viewmodel.AlignmentViewport;
30   
31    import java.awt.BorderLayout;
32    import java.awt.Panel;
33    import java.awt.event.InputEvent;
34    import java.awt.event.MouseEvent;
35    import java.awt.event.MouseListener;
36    import java.awt.event.MouseMotionListener;
37    import java.util.ArrayList;
38    import java.util.HashMap;
39    import java.util.List;
40   
 
41    public class IdPanel extends Panel
42    implements MouseListener, MouseMotionListener
43    {
44   
45    protected IdCanvas idCanvas;
46   
47    protected AlignmentViewport av;
48   
49    protected AlignmentPanel alignPanel;
50   
51    ScrollThread scrollThread = null;
52   
53    int lastid = -1;
54   
55    boolean mouseDragging = false;
56   
57    UrlProviderI urlProvider = null;
58   
 
59  0 toggle public IdPanel(AlignViewport viewport, AlignmentPanel parent)
60    {
61  0 this.av = viewport;
62  0 alignPanel = parent;
63  0 idCanvas = new IdCanvas(viewport);
64  0 setLayout(new BorderLayout());
65  0 add(idCanvas, BorderLayout.CENTER);
66  0 idCanvas.addMouseListener(this);
67  0 idCanvas.addMouseMotionListener(this);
68   
69  0 String label, url;
70    // TODO: add in group link parameter
71   
72    // make a list of label,url pairs
73  0 HashMap<String, String> urlList = new HashMap<>();
74  0 if (viewport.applet != null)
75    {
76  0 for (int i = 1; i < 10; i++)
77    {
78  0 label = viewport.applet.getParameter("linkLabel_" + i);
79  0 url = viewport.applet.getParameter("linkURL_" + i);
80   
81    // only add non-null parameters
82  0 if (label != null)
83    {
84  0 urlList.put(label, url);
85    }
86    }
87   
88  0 if (!urlList.isEmpty())
89    {
90    // set default as first entry in list
91  0 String defaultUrl = viewport.applet.getParameter("linkLabel_1");
92  0 UrlProviderFactoryI factory = new AppletUrlProviderFactory(
93    defaultUrl, urlList);
94  0 urlProvider = factory.createUrlProvider();
95    }
96    }
97    }
98   
99    Tooltip tooltip;
100   
 
101  0 toggle @Override
102    public void mouseMoved(MouseEvent e)
103    {
104  0 int seq = alignPanel.seqPanel.findSeq(e);
105   
106  0 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
107   
108  0 StringBuffer tooltiptext = new StringBuffer();
109  0 if (sequence == null)
110    {
111  0 return;
112    }
113  0 if (sequence.getDescription() != null)
114    {
115  0 tooltiptext.append(sequence.getDescription());
116  0 tooltiptext.append("\n");
117    }
118   
119  0 for (SequenceFeature sf : sequence.getFeatures()
120    .getNonPositionalFeatures())
121    {
122  0 boolean nl = false;
123  0 if (sf.getFeatureGroup() != null)
124    {
125  0 tooltiptext.append(sf.getFeatureGroup());
126  0 nl = true;
127    }
128  0 if (sf.getType() != null)
129    {
130  0 tooltiptext.append(" ");
131  0 tooltiptext.append(sf.getType());
132  0 nl = true;
133    }
134  0 if (sf.getDescription() != null)
135    {
136  0 tooltiptext.append(" ");
137  0 tooltiptext.append(sf.getDescription());
138  0 nl = true;
139    }
140  0 if (!Float.isNaN(sf.getScore()) && sf.getScore() != 0f)
141    {
142  0 tooltiptext.append(" Score = ");
143  0 tooltiptext.append(sf.getScore());
144  0 nl = true;
145    }
146  0 if (sf.getStatus() != null && sf.getStatus().length() > 0)
147    {
148  0 tooltiptext.append(" (");
149  0 tooltiptext.append(sf.getStatus());
150  0 tooltiptext.append(")");
151  0 nl = true;
152    }
153  0 if (nl)
154    {
155  0 tooltiptext.append("\n");
156    }
157    }
158   
159  0 if (tooltiptext.length() == 0)
160    {
161    // nothing to display - so clear tooltip if one is visible
162  0 if (tooltip != null)
163    {
164  0 tooltip.setVisible(false);
165    }
166  0 tooltip = null;
167  0 tooltiptext = null;
168  0 return;
169    }
170  0 if (tooltip == null)
171    {
172  0 tooltip = new Tooltip(
173    sequence.getDisplayId(true) + "\n" + tooltiptext.toString(),
174    idCanvas);
175    }
176    else
177    {
178  0 tooltip.setTip(
179    sequence.getDisplayId(true) + "\n" + tooltiptext.toString());
180    }
181  0 tooltiptext = null;
182    }
183   
 
184  0 toggle @Override
185    public void mouseDragged(MouseEvent e)
186    {
187  0 mouseDragging = true;
188   
189  0 int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
190   
191  0 if (seq < lastid)
192    {
193  0 selectSeqs(lastid - 1, seq);
194    }
195  0 else if (seq > lastid)
196    {
197  0 selectSeqs(lastid + 1, seq);
198    }
199   
200  0 lastid = seq;
201  0 alignPanel.paintAlignment(false, false);
202    }
203   
 
204  0 toggle @Override
205    public void mouseClicked(MouseEvent e)
206    {
207  0 if (e.getClickCount() < 2)
208    {
209  0 return;
210    }
211   
212    // get the sequence details
213  0 int seq = alignPanel.seqPanel.findSeq(e);
214  0 SequenceI sq = av.getAlignment().getSequenceAt(seq);
215  0 if (sq == null)
216    {
217  0 return;
218    }
219  0 String id = sq.getName();
220   
221    // get the default url with the sequence details filled in
222  0 if (urlProvider == null)
223    {
224  0 return;
225    }
226  0 String url = urlProvider.getPrimaryUrl(id);
227  0 String target = urlProvider.getPrimaryTarget(id);
228  0 try
229    {
230  0 alignPanel.alignFrame.showURL(url, target);
231    } catch (Exception ex)
232    {
233  0 ex.printStackTrace();
234    }
235    }
236   
 
237  0 toggle @Override
238    public void mouseEntered(MouseEvent e)
239    {
240  0 if (scrollThread != null)
241    {
242  0 scrollThread.running = false;
243    }
244    }
245   
 
246  0 toggle @Override
247    public void mouseExited(MouseEvent e)
248    {
249  0 if (av.getWrapAlignment())
250    {
251  0 return;
252    }
253   
254  0 if (mouseDragging && e.getY() < 0 && av.getRanges().getStartSeq() > 0)
255    {
256  0 scrollThread = new ScrollThread(true);
257    }
258   
259  0 if (mouseDragging && e.getY() >= getSize().height
260    && av.getAlignment().getHeight() > av.getRanges().getEndSeq())
261    {
262  0 scrollThread = new ScrollThread(false);
263    }
264    }
265   
 
266  0 toggle @Override
267    public void mousePressed(MouseEvent e)
268    {
269  0 if (e.getClickCount() > 1)
270    {
271  0 return;
272    }
273   
274  0 int y = e.getY();
275  0 if (av.getWrapAlignment())
276    {
277  0 y -= 2 * av.getCharHeight();
278    }
279   
280  0 int seq = alignPanel.seqPanel.findSeq(e);
281   
282  0 if ((e.getModifiersEx()
283    & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
284    {
285  0 SequenceI sq = av.getAlignment().getSequenceAt(seq);
286   
287    /*
288    * build a new links menu based on the current links
289    * and any non-positional features
290    */
291  0 List<String> nlinks;
292  0 if (urlProvider != null)
293    {
294  0 nlinks = urlProvider.getLinksForMenu();
295    }
296    else
297    {
298  0 nlinks = new ArrayList<>();
299    }
300   
301  0 for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
302    {
303  0 if (sf.links != null)
304    {
305  0 for (String link : sf.links)
306    {
307  0 nlinks.add(link);
308    }
309    }
310    }
311   
312  0 APopupMenu popup = new APopupMenu(alignPanel, sq, nlinks);
313  0 this.add(popup);
314  0 popup.show(this, e.getX(), e.getY());
315  0 return;
316    }
317   
318  0 if ((av.getSelectionGroup() == null)
319    || ((!jalview.util.Platform.isControlDown(e)
320    && !e.isShiftDown()) && av.getSelectionGroup() != null))
321    {
322  0 av.setSelectionGroup(new SequenceGroup());
323  0 av.getSelectionGroup().setStartRes(0);
324  0 av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
325    }
326   
327  0 if (e.isShiftDown() && lastid != -1)
328    {
329  0 selectSeqs(lastid, seq);
330    }
331    else
332    {
333  0 selectSeq(seq);
334    }
335   
336  0 alignPanel.paintAlignment(false, false);
337    }
338   
 
339  0 toggle void selectSeq(int seq)
340    {
341  0 lastid = seq;
342  0 SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
343  0 av.getSelectionGroup().addOrRemove(pickedSeq, true);
344    }
345   
 
346  0 toggle void selectSeqs(int start, int end)
347    {
348   
349  0 lastid = start;
350   
351  0 if (end >= av.getAlignment().getHeight())
352    {
353  0 end = av.getAlignment().getHeight() - 1;
354    }
355   
356  0 if (end < start)
357    {
358  0 int tmp = start;
359  0 start = end;
360  0 end = tmp;
361  0 lastid = end;
362    }
363  0 if (av.getSelectionGroup() == null)
364    {
365  0 av.setSelectionGroup(new SequenceGroup());
366    }
367  0 for (int i = start; i <= end; i++)
368    {
369  0 av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
370    i == end);
371    }
372   
373    }
374   
 
375  0 toggle @Override
376    public void mouseReleased(MouseEvent e)
377    {
378  0 if (scrollThread != null)
379    {
380  0 scrollThread.running = false;
381    }
382   
383  0 if (av.getSelectionGroup() != null)
384    {
385  0 av.getSelectionGroup().recalcConservation();
386    }
387   
388  0 mouseDragging = false;
389  0 PaintRefresher.Refresh(this, av.getSequenceSetId());
390    // always send selection message when mouse is released
391  0 av.sendSelection();
392    }
393   
 
394  0 toggle public void highlightSearchResults(List<SequenceI> list)
395    {
396  0 idCanvas.setHighlighted(list);
397   
398  0 if (list == null || list.isEmpty())
399    {
400  0 return;
401    }
402   
403  0 int index = av.getAlignment().findIndex(list.get(0));
404   
405    // do we need to scroll the panel?
406  0 if (av.getRanges().getStartSeq() > index
407    || av.getRanges().getEndSeq() < index)
408    {
409  0 av.getRanges().setStartSeq(index);
410    }
411    }
412   
413    // this class allows scrolling off the bottom of the visible alignment
 
414    class ScrollThread extends Thread
415    {
416    boolean running = false;
417   
418    boolean up = true;
419   
 
420  0 toggle public ScrollThread(boolean isUp)
421    {
422  0 this.up = isUp;
423  0 start();
424    }
425   
 
426  0 toggle public void stopScrolling()
427    {
428  0 running = false;
429    }
430   
 
431  0 toggle @Override
432    public void run()
433    {
434  0 running = true;
435  0 while (running)
436    {
437  0 if (av.getRanges().scrollUp(up))
438    {
439    // scroll was ok, so add new sequence to selection
440  0 int seq = av.getRanges().getStartSeq();
441  0 if (!up)
442    {
443  0 seq = av.getRanges().getEndSeq();
444    }
445   
446  0 if (seq < lastid)
447    {
448  0 selectSeqs(lastid - 1, seq);
449    }
450  0 else if (seq > lastid && seq < av.getAlignment().getHeight())
451    {
452  0 selectSeqs(lastid + 1, seq);
453    }
454   
455  0 lastid = seq;
456    }
457    else
458    {
459  0 running = false;
460    }
461   
462  0 alignPanel.paintAlignment(true, false);
463  0 try
464    {
465  0 Thread.sleep(100);
466    } catch (Exception ex)
467    {
468    }
469    }
470    }
471    }
472    }
  • Report generated by OpenClover v 4.4.1 on Wed Nov 12 2025 09:10:40 GMT using coverage data from Wed Nov 12 2025 09:10:27 GMT.
  • OpenClover is free and open-source software.