Clover icon

jalviewX

  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.gui

File SeqPanel.java

 

Coverage histogram

../../img/srcFileCovDistChart1.png
53% of files have more coverage

Code metrics

458
769
54
2
2,430
1,688
351
0.46
14.24
27
6.5

Classes

Class Line # Actions
SeqPanel 82 747 338 1,124
0.093548399.4%
SeqPanel.ScrollThread 2119 22 13 41
0.00%
 

Contributing tests

This file is covered by 76 tests. .

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.api.AlignViewportI;
24    import jalview.bin.Cache;
25    import jalview.bin.Jalview;
26    import jalview.commands.EditCommand;
27    import jalview.commands.EditCommand.Action;
28    import jalview.commands.EditCommand.Edit;
29    import jalview.datamodel.AlignmentI;
30    import jalview.datamodel.ColumnSelection;
31    import jalview.datamodel.HiddenColumns;
32    import jalview.datamodel.SearchResultMatchI;
33    import jalview.datamodel.SearchResults;
34    import jalview.datamodel.SearchResultsI;
35    import jalview.datamodel.Sequence;
36    import jalview.datamodel.SequenceFeature;
37    import jalview.datamodel.SequenceGroup;
38    import jalview.datamodel.SequenceI;
39    import jalview.io.SequenceAnnotationReport;
40    import jalview.renderer.ResidueShaderI;
41    import jalview.schemes.ResidueProperties;
42    import jalview.structure.SelectionListener;
43    import jalview.structure.SelectionSource;
44    import jalview.structure.SequenceListener;
45    import jalview.structure.StructureSelectionManager;
46    import jalview.structure.VamsasSource;
47    import jalview.util.Comparison;
48    import jalview.util.MappingUtils;
49    import jalview.util.MessageManager;
50    import jalview.util.Platform;
51    import jalview.viewmodel.AlignmentViewport;
52    import jalview.viewmodel.ViewportRanges;
53   
54    import java.awt.BorderLayout;
55    import java.awt.Color;
56    import java.awt.Font;
57    import java.awt.FontMetrics;
58    import java.awt.Point;
59    import java.awt.event.ActionEvent;
60    import java.awt.event.ActionListener;
61    import java.awt.event.MouseEvent;
62    import java.awt.event.MouseListener;
63    import java.awt.event.MouseMotionListener;
64    import java.awt.event.MouseWheelEvent;
65    import java.awt.event.MouseWheelListener;
66    import java.util.Collections;
67    import java.util.List;
68   
69    import javax.swing.JLabel;
70    import javax.swing.JPanel;
71    import javax.swing.JToolTip;
72    import javax.swing.SwingUtilities;
73    import javax.swing.Timer;
74    import javax.swing.ToolTipManager;
75   
76    /**
77    * DOCUMENT ME!
78    *
79    * @author $author$
80    * @version $Revision: 1.130 $
81    */
 
82    public class SeqPanel extends JPanel
83    implements MouseListener, MouseMotionListener, MouseWheelListener,
84    SequenceListener, SelectionListener
85    {
86    private static final int MAX_TOOLTIP_LENGTH = 300;
87   
88    public SeqCanvas seqCanvas;
89   
90    public AlignmentPanel ap;
91   
92    /*
93    * last column position for mouseMoved event
94    */
95    private int lastMouseColumn;
96   
97    /*
98    * last sequence offset for mouseMoved event
99    */
100    private int lastMouseSeq;
101   
102    protected int lastres;
103   
104    protected int startseq;
105   
106    protected AlignViewport av;
107   
108    ScrollThread scrollThread = null;
109   
110    boolean mouseDragging = false;
111   
112    boolean editingSeqs = false;
113   
114    boolean groupEditing = false;
115   
116    // ////////////////////////////////////////
117    // ///Everything below this is for defining the boundary of the rubberband
118    // ////////////////////////////////////////
119    int oldSeq = -1;
120   
121    boolean changeEndSeq = false;
122   
123    boolean changeStartSeq = false;
124   
125    boolean changeEndRes = false;
126   
127    boolean changeStartRes = false;
128   
129    SequenceGroup stretchGroup = null;
130   
131    boolean remove = false;
132   
133    Point lastMousePress;
134   
135    boolean mouseWheelPressed = false;
136   
137    StringBuffer keyboardNo1;
138   
139    StringBuffer keyboardNo2;
140   
141    java.net.URL linkImageURL;
142   
143    private final SequenceAnnotationReport seqARep;
144   
145    StringBuilder tooltipText = new StringBuilder();
146   
147    String tmpString;
148   
149    EditCommand editCommand;
150   
151    StructureSelectionManager ssm;
152   
153    SearchResultsI lastSearchResults;
154   
155    /**
156    * Creates a new SeqPanel object
157    *
158    * @param viewport
159    * @param alignPanel
160    */
 
161  217 toggle public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel)
162    {
163  217 linkImageURL = getClass().getResource("/images/link.gif");
164  217 seqARep = new SequenceAnnotationReport(linkImageURL.toString());
165  217 ToolTipManager.sharedInstance().registerComponent(this);
166  217 ToolTipManager.sharedInstance().setInitialDelay(0);
167  217 ToolTipManager.sharedInstance().setDismissDelay(10000);
168   
169   
170  217 this.av = viewport;
171  217 setBackground(Color.white);
172   
173  217 seqCanvas = new SeqCanvas(alignPanel);
174  217 setLayout(new BorderLayout());
175  217 add(seqCanvas, BorderLayout.CENTER);
176   
177  217 this.ap = alignPanel;
178   
179  217 if (!viewport.isDataset())
180    {
181  217 addMouseMotionListener(this);
182  217 addMouseListener(this);
183  217 addMouseWheelListener(this);
184  217 ssm = viewport.getStructureSelectionManager();
185  217 ssm.addStructureViewerListener(this);
186  217 ssm.addSelectionListener(this);
187    }
188   
189  217 lastMouseColumn = -1;
190  217 lastMouseSeq = -1;
191    }
192   
193    int startWrapBlock = -1;
194   
195    int wrappedBlock = -1;
196   
197    /**
198    * Returns the aligned sequence position (base 0) at the mouse position, or
199    * the closest visible one
200    *
201    * @param evt
202    * @return
203    */
 
204  0 toggle int findColumn(MouseEvent evt)
205    {
206  0 int res = 0;
207  0 int x = evt.getX();
208   
209  0 int startRes = av.getRanges().getStartRes();
210  0 if (av.getWrapAlignment())
211    {
212   
213  0 int hgap = av.getCharHeight();
214  0 if (av.getScaleAboveWrapped())
215    {
216  0 hgap += av.getCharHeight();
217    }
218   
219  0 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
220    + hgap + seqCanvas.getAnnotationHeight();
221   
222  0 int y = evt.getY();
223  0 y = Math.max(0, y - hgap);
224  0 x = Math.max(0, x - seqCanvas.getLabelWidthWest());
225   
226  0 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
227  0 if (cwidth < 1)
228    {
229  0 return 0;
230    }
231   
232  0 wrappedBlock = y / cHeight;
233  0 wrappedBlock += startRes / cwidth;
234    // allow for wrapped view scrolled right (possible from Overview)
235  0 int startOffset = startRes % cwidth;
236  0 res = wrappedBlock * cwidth + startOffset
237    + +Math.min(cwidth - 1, x / av.getCharWidth());
238    }
239    else
240    {
241  0 if (x > seqCanvas.getX() + seqCanvas.getWidth())
242    {
243    // make sure we calculate relative to visible alignment, rather than
244    // right-hand gutter
245  0 x = seqCanvas.getX() + seqCanvas.getWidth();
246    }
247  0 res = (x / av.getCharWidth()) + startRes;
248  0 if (res > av.getRanges().getEndRes())
249    {
250    // moused off right
251  0 res = av.getRanges().getEndRes();
252    }
253    }
254   
255  0 if (av.hasHiddenColumns())
256    {
257  0 res = av.getAlignment().getHiddenColumns()
258    .visibleToAbsoluteColumn(res);
259    }
260   
261  0 return res;
262   
263    }
264   
 
265  0 toggle int findSeq(MouseEvent evt)
266    {
267  0 int seq = 0;
268  0 int y = evt.getY();
269   
270  0 if (av.getWrapAlignment())
271    {
272  0 int hgap = av.getCharHeight();
273  0 if (av.getScaleAboveWrapped())
274    {
275  0 hgap += av.getCharHeight();
276    }
277   
278  0 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
279    + hgap + seqCanvas.getAnnotationHeight();
280   
281  0 y -= hgap;
282   
283  0 seq = Math.min((y % cHeight) / av.getCharHeight(),
284    av.getAlignment().getHeight() - 1);
285    }
286    else
287    {
288  0 seq = Math.min(
289    (y / av.getCharHeight()) + av.getRanges().getStartSeq(),
290    av.getAlignment().getHeight() - 1);
291    }
292   
293  0 return seq;
294    }
295   
296    /**
297    * When all of a sequence of edits are complete, put the resulting edit list
298    * on the history stack (undo list), and reset flags for editing in progress.
299    */
 
300  0 toggle void endEditing()
301    {
302  0 try
303    {
304  0 if (editCommand != null && editCommand.getSize() > 0)
305    {
306  0 ap.alignFrame.addHistoryItem(editCommand);
307  0 av.firePropertyChange("alignment", null,
308    av.getAlignment().getSequences());
309    }
310    } finally
311    {
312    /*
313    * Tidy up come what may...
314    */
315  0 startseq = -1;
316  0 lastres = -1;
317  0 editingSeqs = false;
318  0 groupEditing = false;
319  0 keyboardNo1 = null;
320  0 keyboardNo2 = null;
321  0 editCommand = null;
322    }
323    }
324   
 
325  0 toggle void setCursorRow()
326    {
327  0 seqCanvas.cursorY = getKeyboardNo1() - 1;
328  0 scrollToVisible(true);
329    }
330   
 
331  0 toggle void setCursorColumn()
332    {
333  0 seqCanvas.cursorX = getKeyboardNo1() - 1;
334  0 scrollToVisible(true);
335    }
336   
 
337  0 toggle void setCursorRowAndColumn()
338    {
339  0 if (keyboardNo2 == null)
340    {
341  0 keyboardNo2 = new StringBuffer();
342    }
343    else
344    {
345  0 seqCanvas.cursorX = getKeyboardNo1() - 1;
346  0 seqCanvas.cursorY = getKeyboardNo2() - 1;
347  0 scrollToVisible(true);
348    }
349    }
350   
 
351  0 toggle void setCursorPosition()
352    {
353  0 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
354   
355  0 seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
356  0 scrollToVisible(true);
357    }
358   
 
359  0 toggle void moveCursor(int dx, int dy)
360    {
361  0 seqCanvas.cursorX += dx;
362  0 seqCanvas.cursorY += dy;
363   
364  0 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
365   
366  0 if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX))
367    {
368  0 int original = seqCanvas.cursorX - dx;
369  0 int maxWidth = av.getAlignment().getWidth();
370   
371  0 if (!hidden.isVisible(seqCanvas.cursorX))
372    {
373  0 int visx = hidden.absoluteToVisibleColumn(seqCanvas.cursorX - dx);
374  0 int[] region = hidden.getRegionWithEdgeAtRes(visx);
375   
376  0 if (region != null) // just in case
377    {
378  0 if (dx == 1)
379    {
380    // moving right
381  0 seqCanvas.cursorX = region[1] + 1;
382    }
383  0 else if (dx == -1)
384    {
385    // moving left
386  0 seqCanvas.cursorX = region[0] - 1;
387    }
388    }
389  0 seqCanvas.cursorX = (seqCanvas.cursorX < 0) ? 0 : seqCanvas.cursorX;
390    }
391   
392  0 if (seqCanvas.cursorX >= maxWidth
393    || !hidden.isVisible(seqCanvas.cursorX))
394    {
395  0 seqCanvas.cursorX = original;
396    }
397    }
398   
399  0 scrollToVisible(false);
400    }
401   
402    /**
403    * Scroll to make the cursor visible in the viewport.
404    *
405    * @param jump
406    * just jump to the location rather than scrolling
407    */
 
408  0 toggle void scrollToVisible(boolean jump)
409    {
410  0 if (seqCanvas.cursorX < 0)
411    {
412  0 seqCanvas.cursorX = 0;
413    }
414  0 else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
415    {
416  0 seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
417    }
418   
419  0 if (seqCanvas.cursorY < 0)
420    {
421  0 seqCanvas.cursorY = 0;
422    }
423  0 else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
424    {
425  0 seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
426    }
427   
428  0 endEditing();
429   
430  0 boolean repaintNeeded = true;
431  0 if (jump)
432    {
433    // only need to repaint if the viewport did not move, as otherwise it will
434    // get a repaint
435  0 repaintNeeded = !av.getRanges().setViewportLocation(seqCanvas.cursorX,
436    seqCanvas.cursorY);
437    }
438    else
439    {
440  0 if (av.getWrapAlignment())
441    {
442    // scrollToWrappedVisible expects x-value to have hidden cols subtracted
443  0 int x = av.getAlignment().getHiddenColumns()
444    .absoluteToVisibleColumn(seqCanvas.cursorX);
445  0 av.getRanges().scrollToWrappedVisible(x);
446    }
447    else
448    {
449  0 av.getRanges().scrollToVisible(seqCanvas.cursorX,
450    seqCanvas.cursorY);
451    }
452    }
453   
454  0 if (av.getAlignment().getHiddenColumns().isVisible(seqCanvas.cursorX))
455    {
456  0 setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
457    seqCanvas.cursorX, seqCanvas.cursorY);
458    }
459   
460  0 if (repaintNeeded)
461    {
462  0 seqCanvas.repaint();
463    }
464    }
465   
466   
 
467  0 toggle void setSelectionAreaAtCursor(boolean topLeft)
468    {
469  0 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
470   
471  0 if (av.getSelectionGroup() != null)
472    {
473  0 SequenceGroup sg = av.getSelectionGroup();
474    // Find the top and bottom of this group
475  0 int min = av.getAlignment().getHeight(), max = 0;
476  0 for (int i = 0; i < sg.getSize(); i++)
477    {
478  0 int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
479  0 if (index > max)
480    {
481  0 max = index;
482    }
483  0 if (index < min)
484    {
485  0 min = index;
486    }
487    }
488   
489  0 max++;
490   
491  0 if (topLeft)
492    {
493  0 sg.setStartRes(seqCanvas.cursorX);
494  0 if (sg.getEndRes() < seqCanvas.cursorX)
495    {
496  0 sg.setEndRes(seqCanvas.cursorX);
497    }
498   
499  0 min = seqCanvas.cursorY;
500    }
501    else
502    {
503  0 sg.setEndRes(seqCanvas.cursorX);
504  0 if (sg.getStartRes() > seqCanvas.cursorX)
505    {
506  0 sg.setStartRes(seqCanvas.cursorX);
507    }
508   
509  0 max = seqCanvas.cursorY + 1;
510    }
511   
512  0 if (min > max)
513    {
514    // Only the user can do this
515  0 av.setSelectionGroup(null);
516    }
517    else
518    {
519    // Now add any sequences between min and max
520  0 sg.getSequences(null).clear();
521  0 for (int i = min; i < max; i++)
522    {
523  0 sg.addSequence(av.getAlignment().getSequenceAt(i), false);
524    }
525    }
526    }
527   
528  0 if (av.getSelectionGroup() == null)
529    {
530  0 SequenceGroup sg = new SequenceGroup();
531  0 sg.setStartRes(seqCanvas.cursorX);
532  0 sg.setEndRes(seqCanvas.cursorX);
533  0 sg.addSequence(sequence, false);
534  0 av.setSelectionGroup(sg);
535    }
536   
537  0 ap.paintAlignment(false, false);
538  0 av.sendSelection();
539    }
540   
 
541  0 toggle void insertGapAtCursor(boolean group)
542    {
543  0 groupEditing = group;
544  0 startseq = seqCanvas.cursorY;
545  0 lastres = seqCanvas.cursorX;
546  0 editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
547  0 endEditing();
548    }
549   
 
550  0 toggle void deleteGapAtCursor(boolean group)
551    {
552  0 groupEditing = group;
553  0 startseq = seqCanvas.cursorY;
554  0 lastres = seqCanvas.cursorX + getKeyboardNo1();
555  0 editSequence(false, false, seqCanvas.cursorX);
556  0 endEditing();
557    }
558   
 
559  0 toggle void insertNucAtCursor(boolean group, String nuc)
560    {
561    // TODO not called - delete?
562  0 groupEditing = group;
563  0 startseq = seqCanvas.cursorY;
564  0 lastres = seqCanvas.cursorX;
565  0 editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
566  0 endEditing();
567    }
568   
 
569  0 toggle void numberPressed(char value)
570    {
571  0 if (keyboardNo1 == null)
572    {
573  0 keyboardNo1 = new StringBuffer();
574    }
575   
576  0 if (keyboardNo2 != null)
577    {
578  0 keyboardNo2.append(value);
579    }
580    else
581    {
582  0 keyboardNo1.append(value);
583    }
584    }
585   
 
586  0 toggle int getKeyboardNo1()
587    {
588  0 try
589    {
590  0 if (keyboardNo1 != null)
591    {
592  0 int value = Integer.parseInt(keyboardNo1.toString());
593  0 keyboardNo1 = null;
594  0 return value;
595    }
596    } catch (Exception x)
597    {
598    }
599  0 keyboardNo1 = null;
600  0 return 1;
601    }
602   
 
603  0 toggle int getKeyboardNo2()
604    {
605  0 try
606    {
607  0 if (keyboardNo2 != null)
608    {
609  0 int value = Integer.parseInt(keyboardNo2.toString());
610  0 keyboardNo2 = null;
611  0 return value;
612    }
613    } catch (Exception x)
614    {
615    }
616  0 keyboardNo2 = null;
617  0 return 1;
618    }
619   
620    /**
621    * DOCUMENT ME!
622    *
623    * @param evt
624    * DOCUMENT ME!
625    */
 
626  0 toggle @Override
627    public void mouseReleased(MouseEvent evt)
628    {
629  0 boolean didDrag = mouseDragging; // did we come here after a drag
630  0 mouseDragging = false;
631  0 mouseWheelPressed = false;
632   
633  0 if (evt.isPopupTrigger()) // Windows: mouseReleased
634    {
635  0 showPopupMenu(evt);
636  0 evt.consume();
637  0 return;
638    }
639   
640  0 if (editingSeqs)
641    {
642  0 endEditing();
643    }
644    else
645    {
646  0 doMouseReleasedDefineMode(evt, didDrag);
647    }
648    }
649   
650    /**
651    * DOCUMENT ME!
652    *
653    * @param evt
654    * DOCUMENT ME!
655    */
 
656  0 toggle @Override
657    public void mousePressed(MouseEvent evt)
658    {
659  0 lastMousePress = evt.getPoint();
660   
661  0 if (SwingUtilities.isMiddleMouseButton(evt))
662    {
663  0 mouseWheelPressed = true;
664  0 return;
665    }
666   
667  0 boolean isControlDown = Platform.isControlDown(evt);
668  0 if (evt.isShiftDown() || isControlDown)
669    {
670  0 editingSeqs = true;
671  0 if (isControlDown)
672    {
673  0 groupEditing = true;
674    }
675    }
676    else
677    {
678  0 doMousePressedDefineMode(evt);
679  0 return;
680    }
681   
682  0 int seq = findSeq(evt);
683  0 int res = findColumn(evt);
684   
685  0 if (seq < 0 || res < 0)
686    {
687  0 return;
688    }
689   
690  0 if ((seq < av.getAlignment().getHeight())
691    && (res < av.getAlignment().getSequenceAt(seq).getLength()))
692    {
693  0 startseq = seq;
694  0 lastres = res;
695    }
696    else
697    {
698  0 startseq = -1;
699  0 lastres = -1;
700    }
701   
702  0 return;
703    }
704   
705    String lastMessage;
706   
707    private String formattedTooltipText;
708   
 
709  0 toggle @Override
710    public void mouseOverSequence(SequenceI sequence, int index, int pos)
711    {
712  0 String tmp = sequence.hashCode() + " " + index + " " + pos;
713   
714  0 if (lastMessage == null || !lastMessage.equals(tmp))
715    {
716    // System.err.println("mouseOver Sequence: "+tmp);
717  0 ssm.mouseOverSequence(sequence, index, pos, av);
718    }
719  0 lastMessage = tmp;
720    }
721   
722    /**
723    * Highlight the mapped region described by the search results object (unless
724    * unchanged). This supports highlight of protein while mousing over linked
725    * cDNA and vice versa. The status bar is also updated to show the location of
726    * the start of the highlighted region.
727    */
 
728  3 toggle @Override
729    public void highlightSequence(SearchResultsI results)
730    {
731  3 if (results == null || results.equals(lastSearchResults))
732    {
733  0 return;
734    }
735  3 lastSearchResults = results;
736   
737  3 boolean wasScrolled = false;
738   
739  3 if (av.isFollowHighlight())
740    {
741    // don't allow highlight of protein/cDNA to also scroll a complementary
742    // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
743    // over residue to change abruptly, causing highlighted residue in panel 2
744    // to change, causing a scroll in panel 1 etc)
745  3 ap.setToScrollComplementPanel(false);
746  3 wasScrolled = ap.scrollToPosition(results, false);
747  3 if (wasScrolled)
748    {
749  0 seqCanvas.revalidate();
750    }
751  3 ap.setToScrollComplementPanel(true);
752    }
753   
754  3 boolean fastPaint = !(wasScrolled && av.getWrapAlignment());
755  3 if (seqCanvas.highlightSearchResults(results, fastPaint))
756    {
757  0 setStatusMessage(results);
758    }
759    }
760   
 
761  0 toggle @Override
762    public VamsasSource getVamsasSource()
763    {
764  0 return this.ap == null ? null : this.ap.av;
765    }
766   
 
767  0 toggle @Override
768    public void updateColours(SequenceI seq, int index)
769    {
770  0 System.out.println("update the seqPanel colours");
771    // repaint();
772    }
773   
774    /**
775    * Action on mouse movement is to update the status bar to show the current
776    * sequence position, and (if features are shown) to show any features at the
777    * position in a tooltip. Does nothing if the mouse move does not change
778    * residue position.
779    *
780    * @param evt
781    */
 
782  0 toggle @Override
783    public void mouseMoved(MouseEvent evt)
784    {
785  0 if (editingSeqs)
786    {
787    // This is because MacOSX creates a mouseMoved
788    // If control is down, other platforms will not.
789  0 mouseDragged(evt);
790    }
791   
792  0 final int column = findColumn(evt);
793  0 final int seq = findSeq(evt);
794   
795  0 if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
796    {
797  0 lastMouseSeq = -1;
798  0 return;
799    }
800  0 if (column == lastMouseColumn && seq == lastMouseSeq)
801    {
802    /*
803    * just a pixel move without change of residue
804    */
805  0 return;
806    }
807  0 lastMouseColumn = column;
808  0 lastMouseSeq = seq;
809   
810  0 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
811   
812  0 if (column >= sequence.getLength())
813    {
814  0 return;
815    }
816   
817    /*
818    * set status bar message, returning residue position in sequence
819    */
820  0 boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
821  0 final int pos = setStatusMessage(sequence, column, seq);
822  0 if (ssm != null && !isGapped)
823    {
824  0 mouseOverSequence(sequence, column, pos);
825    }
826   
827  0 tooltipText.setLength(6); // Cuts the buffer back to <html>
828   
829  0 SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
830  0 if (groups != null)
831    {
832  0 for (int g = 0; g < groups.length; g++)
833    {
834  0 if (groups[g].getStartRes() <= column
835    && groups[g].getEndRes() >= column)
836    {
837  0 if (!groups[g].getName().startsWith("JTreeGroup")
838    && !groups[g].getName().startsWith("JGroup"))
839    {
840  0 tooltipText.append(groups[g].getName());
841    }
842   
843  0 if (groups[g].getDescription() != null)
844    {
845  0 tooltipText.append(": " + groups[g].getDescription());
846    }
847    }
848    }
849    }
850   
851    /*
852    * add any features at the position to the tooltip; if over a gap, only
853    * add features that straddle the gap (pos may be the residue before or
854    * after the gap)
855    */
856  0 if (av.isShowSequenceFeatures())
857    {
858  0 List<SequenceFeature> features = ap.getFeatureRenderer()
859    .findFeaturesAtColumn(sequence, column + 1);
860  0 seqARep.appendFeatures(tooltipText, pos, features,
861    this.ap.getSeqPanel().seqCanvas.fr);
862    }
863  0 if (tooltipText.length() == 6) // <html>
864    {
865  0 setToolTipText(null);
866  0 lastTooltip = null;
867    }
868    else
869    {
870  0 if (tooltipText.length() > MAX_TOOLTIP_LENGTH) // constant
871    {
872  0 tooltipText.setLength(MAX_TOOLTIP_LENGTH);
873  0 tooltipText.append("...");
874    }
875  0 String textString = tooltipText.toString();
876  0 if (lastTooltip == null || !lastTooltip.equals(textString))
877    {
878  0 formattedTooltipText = JvSwingUtils.wrapTooltip(true,
879    textString);
880  0 setToolTipText(formattedTooltipText);
881   
882  0 lastTooltip = textString;
883    }
884    }
885    }
886   
887   
888    private Point lastp = null;
889   
890    private JToolTip tempTip = new JLabel().createToolTip();
891   
892    /*
893    * (non-Javadoc)
894    *
895    * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
896    */
 
897  0 toggle @Override
898    public Point getToolTipLocation(MouseEvent event)
899    {
900    // BH 2018
901   
902  0 if (tooltipText == null || tooltipText.length() == 6)
903  0 return null;
904   
905  0 if (lastp != null && event.isShiftDown())
906  0 return lastp;
907   
908  0 Point p = lastp;
909  0 int x = event.getX();
910  0 int y = event.getY();
911  0 int w = getWidth();
912   
913  0 tempTip.setTipText(formattedTooltipText);
914  0 int tipWidth = (int) tempTip.getPreferredSize().getWidth();
915   
916    // was x += (w - x < 200) ? -(w / 2) : 5;
917  0 x = (x + tipWidth < w ? x + 10 : w - tipWidth);
918  0 p = new Point(x, y + 20); // BH 2018 was - 20?
919    /*
920    * TODO: try to modify position region is not obcured by tooltip
921    *
922    * Done?
923    */
924   
925  0 return lastp = p;
926    }
927   
928    String lastTooltip;
929   
930    /**
931    * set when the current UI interaction has resulted in a change that requires
932    * shading in overviews and structures to be recalculated. this could be
933    * changed to a something more expressive that indicates what actually has
934    * changed, so selective redraws can be applied (ie. only structures, only
935    * overview, etc)
936    */
937    private boolean updateOverviewAndStructs = false; // TODO: refactor to avcontroller
938   
939    /**
940    * set if av.getSelectionGroup() refers to a group that is defined on the
941    * alignment view, rather than a transient selection
942    */
943    // private boolean editingDefinedGroup = false; // TODO: refactor to
944    // avcontroller or viewModel
945   
946    /**
947    * Sets the status message in alignment panel, showing the sequence number
948    * (index) and id, and residue and residue position if not at a gap, for the
949    * given sequence and column position. Returns the residue position returned
950    * by Sequence.findPosition. Note this may be for the nearest adjacent residue
951    * if at a gapped position.
952    *
953    * @param sequence
954    * aligned sequence object
955    * @param column
956    * alignment column
957    * @param seqIndex
958    * index of sequence in alignment
959    * @return sequence position of residue at column, or adjacent residue if at a
960    * gap
961    */
 
962  5 toggle int setStatusMessage(SequenceI sequence, final int column, int seqIndex)
963    {
964  5 char sequenceChar = sequence.getCharAt(column);
965  5 int pos = sequence.findPosition(column);
966  5 setStatusMessage(sequence, seqIndex, sequenceChar, pos);
967   
968  5 return pos;
969    }
970   
971    /**
972    * Builds the status message for the current cursor location and writes it to
973    * the status bar, for example
974    *
975    * <pre>
976    * Sequence 3 ID: FER1_SOLLC
977    * Sequence 5 ID: FER1_PEA Residue: THR (4)
978    * Sequence 5 ID: FER1_PEA Residue: B (3)
979    * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
980    * </pre>
981    *
982    * @param sequence
983    * @param seqIndex
984    * sequence position in the alignment (1..)
985    * @param sequenceChar
986    * the character under the cursor
987    * @param residuePos
988    * the sequence residue position (if not over a gap)
989    */
 
990  5 toggle protected void setStatusMessage(SequenceI sequence, int seqIndex,
991    char sequenceChar, int residuePos)
992    {
993  5 StringBuilder text = new StringBuilder(32);
994   
995    /*
996    * Sequence number (if known), and sequence name.
997    */
998  5 String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
999  5 text.append("Sequence").append(seqno).append(" ID: ")
1000    .append(sequence.getName());
1001   
1002  5 String residue = null;
1003   
1004    /*
1005    * Try to translate the display character to residue name (null for gap).
1006    */
1007  5 boolean isGapped = Comparison.isGap(sequenceChar);
1008   
1009  5 if (!isGapped)
1010    {
1011  3 boolean nucleotide = av.getAlignment().isNucleotide();
1012  3 String displayChar = String.valueOf(sequenceChar);
1013  3 if (nucleotide)
1014    {
1015  0 residue = ResidueProperties.nucleotideName.get(displayChar);
1016    }
1017    else
1018    {
1019  3 residue = "X".equalsIgnoreCase(displayChar) ? "X"
1020  3 : ("*".equals(displayChar) ? "STOP"
1021    : ResidueProperties.aa2Triplet.get(displayChar));
1022    }
1023  3 text.append(" ").append(nucleotide ? "Nucleotide" : "Residue")
1024  3 .append(": ").append(residue == null ? displayChar : residue);
1025   
1026  3 text.append(" (").append(Integer.toString(residuePos)).append(")");
1027    }
1028  5 ap.alignFrame.setStatus(text.toString());
1029    }
1030   
1031    /**
1032    * Set the status bar message to highlight the first matched position in
1033    * search results.
1034    *
1035    * @param results
1036    */
 
1037  0 toggle private void setStatusMessage(SearchResultsI results)
1038    {
1039  0 AlignmentI al = this.av.getAlignment();
1040  0 int sequenceIndex = al.findIndex(results);
1041  0 if (sequenceIndex == -1)
1042    {
1043  0 return;
1044    }
1045  0 SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
1046  0 for (SearchResultMatchI m : results.getResults())
1047    {
1048  0 SequenceI seq = m.getSequence();
1049  0 if (seq.getDatasetSequence() != null)
1050    {
1051  0 seq = seq.getDatasetSequence();
1052    }
1053   
1054  0 if (seq == ds)
1055    {
1056  0 int start = m.getStart();
1057  0 setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
1058    start);
1059  0 return;
1060    }
1061    }
1062    }
1063   
1064    /**
1065    * {@inheritDoc}
1066    */
 
1067  0 toggle @Override
1068    public void mouseDragged(MouseEvent evt)
1069    {
1070  0 if (mouseWheelPressed)
1071    {
1072  0 boolean inSplitFrame = ap.av.getCodingComplement() != null;
1073  0 boolean copyChanges = inSplitFrame && av.isProteinFontAsCdna();
1074   
1075  0 int oldWidth = av.getCharWidth();
1076   
1077    // Which is bigger, left-right or up-down?
1078  0 if (Math.abs(evt.getY() - lastMousePress.getY()) > Math
1079    .abs(evt.getX() - lastMousePress.getX()))
1080    {
1081    /*
1082    * on drag up or down, decrement or increment font size
1083    */
1084  0 int fontSize = av.font.getSize();
1085  0 boolean fontChanged = false;
1086   
1087  0 if (evt.getY() < lastMousePress.getY())
1088    {
1089  0 fontChanged = true;
1090  0 fontSize--;
1091    }
1092  0 else if (evt.getY() > lastMousePress.getY())
1093    {
1094  0 fontChanged = true;
1095  0 fontSize++;
1096    }
1097   
1098  0 if (fontSize < 1)
1099    {
1100  0 fontSize = 1;
1101    }
1102   
1103  0 if (fontChanged)
1104    {
1105  0 Font newFont = new Font(av.font.getName(), av.font.getStyle(),
1106    fontSize);
1107  0 av.setFont(newFont, true);
1108  0 av.setCharWidth(oldWidth);
1109  0 ap.fontChanged();
1110  0 if (copyChanges)
1111    {
1112  0 ap.av.getCodingComplement().setFont(newFont, true);
1113  0 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1114    .getSplitViewContainer();
1115  0 splitFrame.adjustLayout();
1116  0 splitFrame.repaint();
1117    }
1118    }
1119    }
1120    else
1121    {
1122    /*
1123    * on drag left or right, decrement or increment character width
1124    */
1125  0 int newWidth = 0;
1126  0 if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
1127    {
1128  0 newWidth = av.getCharWidth() - 1;
1129  0 av.setCharWidth(newWidth);
1130    }
1131  0 else if (evt.getX() > lastMousePress.getX())
1132    {
1133  0 newWidth = av.getCharWidth() + 1;
1134  0 av.setCharWidth(newWidth);
1135    }
1136  0 if (newWidth > 0)
1137    {
1138  0 ap.paintAlignment(false, false);
1139  0 if (copyChanges)
1140    {
1141    /*
1142    * need to ensure newWidth is set on cdna, regardless of which
1143    * panel the mouse drag happened in; protein will compute its
1144    * character width as 1:1 or 3:1
1145    */
1146  0 av.getCodingComplement().setCharWidth(newWidth);
1147  0 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1148    .getSplitViewContainer();
1149  0 splitFrame.adjustLayout();
1150  0 splitFrame.repaint();
1151    }
1152    }
1153    }
1154   
1155  0 FontMetrics fm = getFontMetrics(av.getFont());
1156  0 av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
1157   
1158  0 lastMousePress = evt.getPoint();
1159   
1160  0 return;
1161    }
1162   
1163  0 if (!editingSeqs)
1164    {
1165  0 doMouseDraggedDefineMode(evt);
1166  0 return;
1167    }
1168   
1169  0 int res = findColumn(evt);
1170   
1171  0 if (res < 0)
1172    {
1173  0 res = 0;
1174    }
1175   
1176  0 if ((lastres == -1) || (lastres == res))
1177    {
1178  0 return;
1179    }
1180   
1181  0 if ((res < av.getAlignment().getWidth()) && (res < lastres))
1182    {
1183    // dragLeft, delete gap
1184  0 editSequence(false, false, res);
1185    }
1186    else
1187    {
1188  0 editSequence(true, false, res);
1189    }
1190   
1191  0 mouseDragging = true;
1192  0 if (scrollThread != null)
1193    {
1194  0 scrollThread.setMousePosition(evt.getPoint());
1195    }
1196    }
1197   
1198    // TODO: Make it more clever than many booleans
 
1199  0 toggle synchronized void editSequence(boolean insertGap, boolean editSeq,
1200    int startres)
1201    {
1202  0 int fixedLeft = -1;
1203  0 int fixedRight = -1;
1204  0 boolean fixedColumns = false;
1205  0 SequenceGroup sg = av.getSelectionGroup();
1206   
1207  0 SequenceI seq = av.getAlignment().getSequenceAt(startseq);
1208   
1209    // No group, but the sequence may represent a group
1210  0 if (!groupEditing && av.hasHiddenRows())
1211    {
1212  0 if (av.isHiddenRepSequence(seq))
1213    {
1214  0 sg = av.getRepresentedSequences(seq);
1215  0 groupEditing = true;
1216    }
1217    }
1218   
1219  0 StringBuilder message = new StringBuilder(64);
1220  0 if (groupEditing)
1221    {
1222  0 message.append("Edit group:");
1223  0 if (editCommand == null)
1224    {
1225  0 editCommand = new EditCommand(
1226    MessageManager.getString("action.edit_group"));
1227    }
1228    }
1229    else
1230    {
1231  0 message.append("Edit sequence: " + seq.getName());
1232  0 String label = seq.getName();
1233  0 if (label.length() > 10)
1234    {
1235  0 label = label.substring(0, 10);
1236    }
1237  0 if (editCommand == null)
1238    {
1239  0 editCommand = new EditCommand(MessageManager
1240    .formatMessage("label.edit_params", new String[]
1241    { label }));
1242    }
1243    }
1244   
1245  0 if (insertGap)
1246    {
1247  0 message.append(" insert ");
1248    }
1249    else
1250    {
1251  0 message.append(" delete ");
1252    }
1253   
1254  0 message.append(Math.abs(startres - lastres) + " gaps.");
1255  0 ap.alignFrame.setStatus(message.toString());
1256   
1257    // Are we editing within a selection group?
1258  0 if (groupEditing || (sg != null
1259    && sg.getSequences(av.getHiddenRepSequences()).contains(seq)))
1260    {
1261  0 fixedColumns = true;
1262   
1263    // sg might be null as the user may only see 1 sequence,
1264    // but the sequence represents a group
1265  0 if (sg == null)
1266    {
1267  0 if (!av.isHiddenRepSequence(seq))
1268    {
1269  0 endEditing();
1270  0 return;
1271    }
1272  0 sg = av.getRepresentedSequences(seq);
1273    }
1274   
1275  0 fixedLeft = sg.getStartRes();
1276  0 fixedRight = sg.getEndRes();
1277   
1278  0 if ((startres < fixedLeft && lastres >= fixedLeft)
1279    || (startres >= fixedLeft && lastres < fixedLeft)
1280    || (startres > fixedRight && lastres <= fixedRight)
1281    || (startres <= fixedRight && lastres > fixedRight))
1282    {
1283  0 endEditing();
1284  0 return;
1285    }
1286   
1287  0 if (fixedLeft > startres)
1288    {
1289  0 fixedRight = fixedLeft - 1;
1290  0 fixedLeft = 0;
1291    }
1292  0 else if (fixedRight < startres)
1293    {
1294  0 fixedLeft = fixedRight;
1295  0 fixedRight = -1;
1296    }
1297    }
1298   
1299  0 if (av.hasHiddenColumns())
1300    {
1301  0 fixedColumns = true;
1302  0 int y1 = av.getAlignment().getHiddenColumns()
1303    .getNextHiddenBoundary(true, startres);
1304  0 int y2 = av.getAlignment().getHiddenColumns()
1305    .getNextHiddenBoundary(false, startres);
1306   
1307  0 if ((insertGap && startres > y1 && lastres < y1)
1308    || (!insertGap && startres < y2 && lastres > y2))
1309    {
1310  0 endEditing();
1311  0 return;
1312    }
1313   
1314    // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1315    // Selection spans a hidden region
1316  0 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1317    {
1318  0 if (startres >= y2)
1319    {
1320  0 fixedLeft = y2;
1321    }
1322    else
1323    {
1324  0 fixedRight = y2 - 1;
1325    }
1326    }
1327    }
1328   
1329  0 if (groupEditing)
1330    {
1331  0 List<SequenceI> vseqs = sg.getSequences(av.getHiddenRepSequences());
1332  0 int g, groupSize = vseqs.size();
1333  0 SequenceI[] groupSeqs = new SequenceI[groupSize];
1334  0 for (g = 0; g < groupSeqs.length; g++)
1335    {
1336  0 groupSeqs[g] = vseqs.get(g);
1337    }
1338   
1339    // drag to right
1340  0 if (insertGap)
1341    {
1342    // If the user has selected the whole sequence, and is dragging to
1343    // the right, we can still extend the alignment and selectionGroup
1344  0 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1345    && sg.getEndRes() == av.getAlignment().getWidth() - 1)
1346    {
1347  0 sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
1348  0 fixedRight = sg.getEndRes();
1349    }
1350   
1351    // Is it valid with fixed columns??
1352    // Find the next gap before the end
1353    // of the visible region boundary
1354  0 boolean blank = false;
1355  0 for (; fixedRight > lastres; fixedRight--)
1356    {
1357  0 blank = true;
1358   
1359  0 for (g = 0; g < groupSize; g++)
1360    {
1361  0 for (int j = 0; j < startres - lastres; j++)
1362    {
1363  0 if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j)))
1364    {
1365  0 blank = false;
1366  0 break;
1367    }
1368    }
1369    }
1370  0 if (blank)
1371    {
1372  0 break;
1373    }
1374    }
1375   
1376  0 if (!blank)
1377    {
1378  0 if (sg.getSize() == av.getAlignment().getHeight())
1379    {
1380  0 if ((av.hasHiddenColumns() && startres < av.getAlignment()
1381    .getHiddenColumns()
1382    .getNextHiddenBoundary(false, startres)))
1383    {
1384  0 endEditing();
1385  0 return;
1386    }
1387   
1388  0 int alWidth = av.getAlignment().getWidth();
1389  0 if (av.hasHiddenRows())
1390    {
1391  0 int hwidth = av.getAlignment().getHiddenSequences()
1392    .getWidth();
1393  0 if (hwidth > alWidth)
1394    {
1395  0 alWidth = hwidth;
1396    }
1397    }
1398    // We can still insert gaps if the selectionGroup
1399    // contains all the sequences
1400  0 sg.setEndRes(sg.getEndRes() + startres - lastres);
1401  0 fixedRight = alWidth + startres - lastres;
1402    }
1403    else
1404    {
1405  0 endEditing();
1406  0 return;
1407    }
1408    }
1409    }
1410   
1411    // drag to left
1412  0 else if (!insertGap)
1413    {
1414    // / Are we able to delete?
1415    // ie are all columns blank?
1416   
1417  0 for (g = 0; g < groupSize; g++)
1418    {
1419  0 for (int j = startres; j < lastres; j++)
1420    {
1421  0 if (groupSeqs[g].getLength() <= j)
1422    {
1423  0 continue;
1424    }
1425   
1426  0 if (!Comparison.isGap(groupSeqs[g].getCharAt(j)))
1427    {
1428    // Not a gap, block edit not valid
1429  0 endEditing();
1430  0 return;
1431    }
1432    }
1433    }
1434    }
1435   
1436  0 if (insertGap)
1437    {
1438    // dragging to the right
1439  0 if (fixedColumns && fixedRight != -1)
1440    {
1441  0 for (int j = lastres; j < startres; j++)
1442    {
1443  0 insertChar(j, groupSeqs, fixedRight);
1444    }
1445    }
1446    else
1447    {
1448  0 appendEdit(Action.INSERT_GAP, groupSeqs, startres,
1449    startres - lastres);
1450    }
1451    }
1452    else
1453    {
1454    // dragging to the left
1455  0 if (fixedColumns && fixedRight != -1)
1456    {
1457  0 for (int j = lastres; j > startres; j--)
1458    {
1459  0 deleteChar(startres, groupSeqs, fixedRight);
1460    }
1461    }
1462    else
1463    {
1464  0 appendEdit(Action.DELETE_GAP, groupSeqs, startres,
1465    lastres - startres);
1466    }
1467   
1468    }
1469    }
1470    else
1471    // ///Editing a single sequence///////////
1472    {
1473  0 if (insertGap)
1474    {
1475    // dragging to the right
1476  0 if (fixedColumns && fixedRight != -1)
1477    {
1478  0 for (int j = lastres; j < startres; j++)
1479    {
1480  0 insertChar(j, new SequenceI[] { seq }, fixedRight);
1481    }
1482    }
1483    else
1484    {
1485  0 appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres,
1486    startres - lastres);
1487    }
1488    }
1489    else
1490    {
1491  0 if (!editSeq)
1492    {
1493    // dragging to the left
1494  0 if (fixedColumns && fixedRight != -1)
1495    {
1496  0 for (int j = lastres; j > startres; j--)
1497    {
1498  0 if (!Comparison.isGap(seq.getCharAt(startres)))
1499    {
1500  0 endEditing();
1501  0 break;
1502    }
1503  0 deleteChar(startres, new SequenceI[] { seq }, fixedRight);
1504    }
1505    }
1506    else
1507    {
1508    // could be a keyboard edit trying to delete none gaps
1509  0 int max = 0;
1510  0 for (int m = startres; m < lastres; m++)
1511    {
1512  0 if (!Comparison.isGap(seq.getCharAt(m)))
1513    {
1514  0 break;
1515    }
1516  0 max++;
1517    }
1518   
1519  0 if (max > 0)
1520    {
1521  0 appendEdit(Action.DELETE_GAP, new SequenceI[] { seq },
1522    startres, max);
1523    }
1524    }
1525    }
1526    else
1527    {// insertGap==false AND editSeq==TRUE;
1528  0 if (fixedColumns && fixedRight != -1)
1529    {
1530  0 for (int j = lastres; j < startres; j++)
1531    {
1532  0 insertChar(j, new SequenceI[] { seq }, fixedRight);
1533    }
1534    }
1535    else
1536    {
1537  0 appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres,
1538    startres - lastres);
1539    }
1540    }
1541    }
1542    }
1543   
1544  0 lastres = startres;
1545  0 seqCanvas.repaint();
1546    }
1547   
 
1548  0 toggle void insertChar(int j, SequenceI[] seq, int fixedColumn)
1549    {
1550  0 int blankColumn = fixedColumn;
1551  0 for (int s = 0; s < seq.length; s++)
1552    {
1553    // Find the next gap before the end of the visible region boundary
1554    // If lastCol > j, theres a boundary after the gap insertion
1555   
1556  0 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1557    {
1558  0 if (Comparison.isGap(seq[s].getCharAt(blankColumn)))
1559    {
1560    // Theres a space, so break and insert the gap
1561  0 break;
1562    }
1563    }
1564   
1565  0 if (blankColumn <= j)
1566    {
1567  0 blankColumn = fixedColumn;
1568  0 endEditing();
1569  0 return;
1570    }
1571    }
1572   
1573  0 appendEdit(Action.DELETE_GAP, seq, blankColumn, 1);
1574   
1575  0 appendEdit(Action.INSERT_GAP, seq, j, 1);
1576   
1577    }
1578   
1579    /**
1580    * Helper method to add and perform one edit action.
1581    *
1582    * @param action
1583    * @param seq
1584    * @param pos
1585    * @param count
1586    */
 
1587  0 toggle protected void appendEdit(Action action, SequenceI[] seq, int pos,
1588    int count)
1589    {
1590   
1591  0 final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
1592    av.getAlignment().getGapCharacter());
1593   
1594  0 editCommand.appendEdit(edit, av.getAlignment(), true, null);
1595    }
1596   
 
1597  0 toggle void deleteChar(int j, SequenceI[] seq, int fixedColumn)
1598    {
1599   
1600  0 appendEdit(Action.DELETE_GAP, seq, j, 1);
1601   
1602  0 appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1);
1603    }
1604   
1605    /**
1606    * On reentering the panel, stops any scrolling that was started on dragging
1607    * out of the panel
1608    *
1609    * @param e
1610    */
 
1611  0 toggle @Override
1612    public void mouseEntered(MouseEvent e)
1613    {
1614  0 if (oldSeq < 0)
1615    {
1616  0 oldSeq = 0;
1617    }
1618  0 stopScrolling();
1619    }
1620   
1621    /**
1622    * On leaving the panel, if the mouse is being dragged, starts a thread to
1623    * scroll it until the mouse is released (in unwrapped mode only)
1624    *
1625    * @param e
1626    */
 
1627  0 toggle @Override
1628    public void mouseExited(MouseEvent e)
1629    {
1630  0 if (mouseDragging)
1631    {
1632  0 startScrolling(e.getPoint());
1633    }
1634    }
1635   
1636    /**
1637    * Handler for double-click on a position with one or more sequence features.
1638    * Opens the Amend Features dialog to allow feature details to be amended, or
1639    * the feature deleted.
1640    */
 
1641  0 toggle @Override
1642    public void mouseClicked(MouseEvent evt)
1643    {
1644  0 SequenceGroup sg = null;
1645  0 SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
1646  0 if (evt.getClickCount() > 1)
1647    {
1648  0 sg = av.getSelectionGroup();
1649  0 if (sg != null && sg.getSize() == 1
1650    && sg.getEndRes() - sg.getStartRes() < 2)
1651    {
1652  0 av.setSelectionGroup(null);
1653    }
1654   
1655  0 int column = findColumn(evt);
1656   
1657    /*
1658    * find features at the position (if not gapped), or straddling
1659    * the position (if at a gap)
1660    */
1661  0 List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
1662    .findFeaturesAtColumn(sequence, column + 1);
1663   
1664  0 if (!features.isEmpty())
1665    {
1666    /*
1667    * highlight the first feature at the position on the alignment
1668    */
1669  0 SearchResultsI highlight = new SearchResults();
1670  0 highlight.addResult(sequence, features.get(0).getBegin(), features
1671    .get(0).getEnd());
1672  0 seqCanvas.highlightSearchResults(highlight, true);
1673   
1674    /*
1675    * open the Amend Features dialog
1676    */
1677  0 new FeatureEditor(ap, Collections.singletonList(sequence), features,
1678    false).showDialog();
1679    }
1680    }
1681    }
1682   
 
1683  0 toggle @Override
1684    public void mouseWheelMoved(MouseWheelEvent e)
1685    {
1686  0 e.consume();
1687  0 double wheelRotation = e.getPreciseWheelRotation();
1688  0 if (wheelRotation > 0)
1689    {
1690  0 if (e.isShiftDown())
1691    {
1692  0 av.getRanges().scrollRight(true);
1693   
1694    }
1695    else
1696    {
1697  0 av.getRanges().scrollUp(false);
1698    }
1699    }
1700  0 else if (wheelRotation < 0)
1701    {
1702  0 if (e.isShiftDown())
1703    {
1704  0 av.getRanges().scrollRight(false);
1705    }
1706    else
1707    {
1708  0 av.getRanges().scrollUp(true);
1709    }
1710    }
1711   
1712    /*
1713    * update status bar and tooltip for new position
1714    * (need to synthesize a mouse movement to refresh tooltip)
1715    */
1716  0 mouseMoved(e);
1717  0 ToolTipManager.sharedInstance().mouseMoved(e);
1718    }
1719   
1720    /**
1721    * DOCUMENT ME!
1722    *
1723    * @param evt
1724    * DOCUMENT ME!
1725    */
 
1726  0 toggle public void doMousePressedDefineMode(MouseEvent evt)
1727    {
1728  0 final int res = findColumn(evt);
1729  0 final int seq = findSeq(evt);
1730  0 oldSeq = seq;
1731  0 updateOverviewAndStructs = false;
1732   
1733  0 startWrapBlock = wrappedBlock;
1734   
1735  0 if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
1736    {
1737  0 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1738    MessageManager.getString(
1739    "label.cannot_edit_annotations_in_wrapped_view"),
1740    MessageManager.getString("label.wrapped_view_no_edit"),
1741    JvOptionPane.WARNING_MESSAGE);
1742  0 return;
1743    }
1744   
1745  0 if (seq < 0 || res < 0)
1746    {
1747  0 return;
1748    }
1749   
1750  0 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1751   
1752  0 if ((sequence == null) || (res > sequence.getLength()))
1753    {
1754  0 return;
1755    }
1756   
1757  0 stretchGroup = av.getSelectionGroup();
1758   
1759  0 if (stretchGroup == null || !stretchGroup.contains(sequence, res))
1760    {
1761  0 stretchGroup = av.getAlignment().findGroup(sequence, res);
1762  0 if (stretchGroup != null)
1763    {
1764    // only update the current selection if the popup menu has a group to
1765    // focus on
1766  0 av.setSelectionGroup(stretchGroup);
1767    }
1768    }
1769   
1770  0 if (evt.isPopupTrigger()) // Mac: mousePressed
1771    {
1772  0 showPopupMenu(evt);
1773  0 return;
1774    }
1775   
1776    /*
1777    * defer right-mouse click handling to mouseReleased on Windows
1778    * (where isPopupTrigger() will answer true)
1779    * NB isRightMouseButton is also true for Cmd-click on Mac
1780    */
1781  0 if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac())
1782    {
1783  0 return;
1784    }
1785   
1786  0 if (av.cursorMode)
1787    {
1788  0 seqCanvas.cursorX = findColumn(evt);
1789  0 seqCanvas.cursorY = findSeq(evt);
1790  0 seqCanvas.repaint();
1791  0 return;
1792    }
1793   
1794  0 if (stretchGroup == null)
1795    {
1796  0 createStretchGroup(res, sequence);
1797    }
1798   
1799  0 if (stretchGroup != null)
1800    {
1801  0 stretchGroup.addPropertyChangeListener(seqCanvas);
1802    }
1803   
1804  0 seqCanvas.repaint();
1805    }
1806   
 
1807  0 toggle private void createStretchGroup(int res, SequenceI sequence)
1808    {
1809    // Only if left mouse button do we want to change group sizes
1810    // define a new group here
1811  0 SequenceGroup sg = new SequenceGroup();
1812  0 sg.setStartRes(res);
1813  0 sg.setEndRes(res);
1814  0 sg.addSequence(sequence, false);
1815  0 av.setSelectionGroup(sg);
1816  0 stretchGroup = sg;
1817   
1818  0 if (av.getConservationSelected())
1819    {
1820  0 SliderPanel.setConservationSlider(ap, av.getResidueShading(),
1821    ap.getViewName());
1822    }
1823   
1824  0 if (av.getAbovePIDThreshold())
1825    {
1826  0 SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
1827    ap.getViewName());
1828    }
1829    // TODO: stretchGroup will always be not null. Is this a merge error ?
1830    // or is there a threading issue here?
1831  0 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
1832    {
1833    // Edit end res position of selected group
1834  0 changeEndRes = true;
1835    }
1836  0 else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
1837    {
1838    // Edit end res position of selected group
1839  0 changeStartRes = true;
1840    }
1841  0 stretchGroup.getWidth();
1842   
1843    }
1844   
1845    /**
1846    * Build and show a pop-up menu at the right-click mouse position
1847    *
1848    * @param evt
1849    * @param res
1850    * @param sequences
1851    */
 
1852  0 toggle void showPopupMenu(MouseEvent evt)
1853    {
1854  0 final int column = findColumn(evt);
1855  0 final int seq = findSeq(evt);
1856  0 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1857  0 List<SequenceFeature> features = ap.getFeatureRenderer()
1858    .findFeaturesAtColumn(sequence, column + 1);
1859   
1860  0 PopupMenu pop = new PopupMenu(ap, null, features);
1861  0 pop.show(this, evt.getX(), evt.getY());
1862    }
1863   
1864    /**
1865    * Update the display after mouse up on a selection or group
1866    *
1867    * @param evt
1868    * mouse released event details
1869    * @param afterDrag
1870    * true if this event is happening after a mouse drag (rather than a
1871    * mouse down)
1872    */
 
1873  0 toggle public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
1874    {
1875  0 if (stretchGroup == null)
1876    {
1877  0 return;
1878    }
1879   
1880  0 stretchGroup.removePropertyChangeListener(seqCanvas);
1881   
1882    // always do this - annotation has own state
1883    // but defer colourscheme update until hidden sequences are passed in
1884  0 boolean vischange = stretchGroup.recalcConservation(true);
1885  0 updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup()
1886    && afterDrag;
1887  0 if (stretchGroup.cs != null)
1888    {
1889  0 stretchGroup.cs.alignmentChanged(stretchGroup,
1890    av.getHiddenRepSequences());
1891   
1892  0 ResidueShaderI groupColourScheme = stretchGroup
1893    .getGroupColourScheme();
1894  0 String name = stretchGroup.getName();
1895  0 if (stretchGroup.cs.conservationApplied())
1896    {
1897  0 SliderPanel.setConservationSlider(ap, groupColourScheme, name);
1898    }
1899  0 if (stretchGroup.cs.getThreshold() > 0)
1900    {
1901  0 SliderPanel.setPIDSliderSource(ap, groupColourScheme, name);
1902    }
1903    }
1904  0 PaintRefresher.Refresh(this, av.getSequenceSetId());
1905    // TODO: structure colours only need updating if stretchGroup used to or now
1906    // does contain sequences with structure views
1907  0 ap.paintAlignment(updateOverviewAndStructs, updateOverviewAndStructs);
1908  0 updateOverviewAndStructs = false;
1909  0 changeEndRes = false;
1910  0 changeStartRes = false;
1911  0 stretchGroup = null;
1912  0 av.sendSelection();
1913    }
1914   
1915    /**
1916    * DOCUMENT ME!
1917    *
1918    * @param evt
1919    * DOCUMENT ME!
1920    */
 
1921  0 toggle public void doMouseDraggedDefineMode(MouseEvent evt)
1922    {
1923  0 int res = findColumn(evt);
1924  0 int y = findSeq(evt);
1925   
1926  0 if (wrappedBlock != startWrapBlock)
1927    {
1928  0 return;
1929    }
1930   
1931  0 if (stretchGroup == null)
1932    {
1933  0 return;
1934    }
1935   
1936  0 res = Math.min(res, av.getAlignment().getWidth()-1);
1937   
1938  0 if (stretchGroup.getEndRes() == res)
1939    {
1940    // Edit end res position of selected group
1941  0 changeEndRes = true;
1942    }
1943  0 else if (stretchGroup.getStartRes() == res)
1944    {
1945    // Edit start res position of selected group
1946  0 changeStartRes = true;
1947    }
1948   
1949  0 if (res < av.getRanges().getStartRes())
1950    {
1951  0 res = av.getRanges().getStartRes();
1952    }
1953   
1954  0 if (changeEndRes)
1955    {
1956  0 if (res > (stretchGroup.getStartRes() - 1))
1957    {
1958  0 stretchGroup.setEndRes(res);
1959  0 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1960    }
1961    }
1962  0 else if (changeStartRes)
1963    {
1964  0 if (res < (stretchGroup.getEndRes() + 1))
1965    {
1966  0 stretchGroup.setStartRes(res);
1967  0 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1968    }
1969    }
1970   
1971  0 int dragDirection = 0;
1972   
1973  0 if (y > oldSeq)
1974    {
1975  0 dragDirection = 1;
1976    }
1977  0 else if (y < oldSeq)
1978    {
1979  0 dragDirection = -1;
1980    }
1981   
1982  0 while ((y != oldSeq) && (oldSeq > -1)
1983    && (y < av.getAlignment().getHeight()))
1984    {
1985    // This routine ensures we don't skip any sequences, as the
1986    // selection is quite slow.
1987  0 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1988   
1989  0 oldSeq += dragDirection;
1990   
1991  0 if (oldSeq < 0)
1992    {
1993  0 break;
1994    }
1995   
1996  0 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1997   
1998  0 if (stretchGroup.getSequences(null).contains(nextSeq))
1999    {
2000  0 stretchGroup.deleteSequence(seq, false);
2001  0 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
2002    }
2003    else
2004    {
2005  0 if (seq != null)
2006    {
2007  0 stretchGroup.addSequence(seq, false);
2008    }
2009   
2010  0 stretchGroup.addSequence(nextSeq, false);
2011  0 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
2012    }
2013    }
2014   
2015  0 if (oldSeq < 0)
2016    {
2017  0 oldSeq = -1;
2018    }
2019   
2020  0 mouseDragging = true;
2021   
2022  0 if (scrollThread != null)
2023    {
2024  0 scrollThread.setMousePosition(evt.getPoint());
2025    }
2026    }
2027   
2028    /**
2029    * Stops the scroll thread if it is running
2030    */
 
2031  0 toggle void stopScrolling()
2032    {
2033  0 if (scrollThread != null)
2034    {
2035  0 scrollThread.stopScrolling();
2036  0 scrollThread = null;
2037    }
2038  0 mouseDragging = false;
2039    }
2040   
2041    /**
2042    * Starts a thread to scroll the alignment, towards a given mouse position
2043    * outside the panel bounds, unless the alignment is in wrapped mode
2044    *
2045    * @param mousePos
2046    */
 
2047  0 toggle void startScrolling(Point mousePos)
2048    {
2049    /*
2050    * set this.mouseDragging in case this was called from
2051    * a drag in ScalePanel or AnnotationPanel
2052    */
2053  0 mouseDragging = true;
2054  0 if (!av.getWrapAlignment() && scrollThread == null)
2055    {
2056  0 scrollThread = new ScrollThread();
2057  0 scrollThread.setMousePosition(mousePos);
2058  0 if (!Jalview.isJS())
2059    {
2060    /*
2061    * Java - run in a new thread
2062    */
2063  0 scrollThread.start();
2064    }
2065    else
2066    {
2067    /*
2068    * Javascript - run every 20ms until scrolling stopped
2069    * or reaches the limit of scrollable alignment
2070    */
2071    // java.util.Timer version:
2072    // Timer t = new Timer("ScrollThreadTimer", true);
2073    // TimerTask task = new TimerTask()
2074    // {
2075    // @Override
2076    // public void run()
2077    // {
2078    // if (!scrollThread.scrollOnce())
2079    // {
2080    // cancel();
2081    // }
2082    // }
2083    // };
2084    // t.schedule(task, 20, 20);
2085  0 Timer t = new Timer(20, new ActionListener()
2086    {
 
2087  0 toggle @Override
2088    public void actionPerformed(ActionEvent e)
2089    {
2090  0 if (scrollThread != null)
2091    {
2092    // if (!scrollOnce() {t.stop();}) gives compiler error :-(
2093  0 scrollThread.scrollOnce();
2094    }
2095    }
2096    });
2097  0 t.addActionListener(new ActionListener()
2098    {
 
2099  0 toggle @Override
2100    public void actionPerformed(ActionEvent e)
2101    {
2102  0 if (scrollThread == null)
2103    {
2104    // finished and nulled itself
2105  0 t.stop();
2106    }
2107    }
2108    });
2109  0 t.start();
2110    }
2111    }
2112    }
2113   
2114    /**
2115    * Performs scrolling of the visible alignment left, right, up or down, until
2116    * scrolling is stopped by calling stopScrolling, mouse drag is ended, or the
2117    * limit of the alignment is reached
2118    */
 
2119    class ScrollThread extends Thread
2120    {
2121    private Point mousePos;
2122   
2123    private volatile boolean keepRunning = true;
2124   
2125    /**
2126    * Constructor
2127    */
 
2128  0 toggle public ScrollThread()
2129    {
2130  0 setName("SeqPanel$ScrollThread");
2131    }
2132   
2133    /**
2134    * Sets the position of the mouse that determines the direction of the
2135    * scroll to perform. If this is called as the mouse moves, scrolling should
2136    * respond accordingly. For example, if the mouse is dragged right, scroll
2137    * right should start; if the drag continues down, scroll down should also
2138    * happen.
2139    *
2140    * @param p
2141    */
 
2142  0 toggle public void setMousePosition(Point p)
2143    {
2144  0 mousePos = p;
2145    }
2146   
2147    /**
2148    * Sets a flag that will cause the thread to exit
2149    */
 
2150  0 toggle public void stopScrolling()
2151    {
2152  0 keepRunning = false;
2153    }
2154   
2155    /**
2156    * Scrolls the alignment left or right, and/or up or down, depending on the
2157    * last notified mouse position, until the limit of the alignment is
2158    * reached, or a flag is set to stop the scroll
2159    */
 
2160  0 toggle @Override
2161    public void run()
2162    {
2163  0 while (keepRunning)
2164    {
2165  0 if (mousePos != null)
2166    {
2167  0 keepRunning = scrollOnce();
2168    }
2169  0 try
2170    {
2171  0 Thread.sleep(20);
2172    } catch (Exception ex)
2173    {
2174    }
2175    }
2176  0 SeqPanel.this.scrollThread = null;
2177    }
2178   
2179    /**
2180    * Scrolls
2181    * <ul>
2182    * <li>one row up, if the mouse is above the panel</li>
2183    * <li>one row down, if the mouse is below the panel</li>
2184    * <li>one column left, if the mouse is left of the panel</li>
2185    * <li>one column right, if the mouse is right of the panel</li>
2186    * </ul>
2187    * Answers true if a scroll was performed, false if not - meaning either
2188    * that the mouse position is within the panel, or the edge of the alignment
2189    * has been reached.
2190    */
 
2191  0 toggle boolean scrollOnce()
2192    {
2193    /*
2194    * quit after mouseUp ensures interrupt in JalviewJS
2195    */
2196  0 if (!mouseDragging)
2197    {
2198  0 return false;
2199    }
2200   
2201  0 boolean scrolled = false;
2202  0 ViewportRanges ranges = SeqPanel.this.av.getRanges();
2203   
2204    /*
2205    * scroll up or down
2206    */
2207  0 if (mousePos.y < 0)
2208    {
2209    // mouse is above this panel - try scroll up
2210  0 scrolled = ranges.scrollUp(true);
2211    }
2212  0 else if (mousePos.y >= getHeight())
2213    {
2214    // mouse is below this panel - try scroll down
2215  0 scrolled = ranges.scrollUp(false);
2216    }
2217   
2218    /*
2219    * scroll left or right
2220    */
2221  0 if (mousePos.x < 0)
2222    {
2223  0 scrolled |= ranges.scrollRight(false);
2224    }
2225  0 else if (mousePos.x >= getWidth())
2226    {
2227  0 scrolled |= ranges.scrollRight(true);
2228    }
2229  0 return scrolled;
2230    }
2231    }
2232   
2233    /**
2234    * modify current selection according to a received message.
2235    */
 
2236  204 toggle @Override
2237    public void selection(SequenceGroup seqsel, ColumnSelection colsel,
2238    HiddenColumns hidden, SelectionSource source)
2239    {
2240    // TODO: fix this hack - source of messages is align viewport, but SeqPanel
2241    // handles selection messages...
2242    // TODO: extend config options to allow user to control if selections may be
2243    // shared between viewports.
2244  204 boolean iSentTheSelection = (av == source
2245    || (source instanceof AlignViewport
2246    && ((AlignmentViewport) source).getSequenceSetId()
2247    .equals(av.getSequenceSetId())));
2248   
2249  204 if (iSentTheSelection)
2250    {
2251    // respond to our own event by updating dependent dialogs
2252  14 if (ap.getCalculationDialog() != null)
2253    {
2254  0 ap.getCalculationDialog().validateCalcTypes();
2255    }
2256   
2257  14 return;
2258    }
2259   
2260    // process further ?
2261  190 if (!av.followSelection)
2262    {
2263  0 return;
2264    }
2265   
2266    /*
2267    * Ignore the selection if there is one of our own pending.
2268    */
2269  190 if (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
2270    {
2271  126 return;
2272    }
2273   
2274    /*
2275    * Check for selection in a view of which this one is a dna/protein
2276    * complement.
2277    */
2278  64 if (selectionFromTranslation(seqsel, colsel, hidden, source))
2279    {
2280  0 return;
2281    }
2282   
2283    // do we want to thread this ? (contention with seqsel and colsel locks, I
2284    // suspect)
2285    /*
2286    * only copy colsel if there is a real intersection between
2287    * sequence selection and this panel's alignment
2288    */
2289  64 boolean repaint = false;
2290  64 boolean copycolsel = false;
2291   
2292  64 SequenceGroup sgroup = null;
2293  64 if (seqsel != null && seqsel.getSize() > 0)
2294    {
2295  10 if (av.getAlignment() == null)
2296    {
2297  0 Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
2298    + " ViewId=" + av.getViewId()
2299    + " 's alignment is NULL! returning immediately.");
2300  0 return;
2301    }
2302  10 sgroup = seqsel.intersect(av.getAlignment(),
2303  10 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
2304  10 if ((sgroup != null && sgroup.getSize() > 0))
2305    {
2306  0 copycolsel = true;
2307    }
2308    }
2309  64 if (sgroup != null && sgroup.getSize() > 0)
2310    {
2311  0 av.setSelectionGroup(sgroup);
2312    }
2313    else
2314    {
2315  64 av.setSelectionGroup(null);
2316    }
2317  64 av.isSelectionGroupChanged(true);
2318  64 repaint = true;
2319   
2320  64 if (copycolsel)
2321    {
2322    // the current selection is unset or from a previous message
2323    // so import the new colsel.
2324  0 if (colsel == null || colsel.isEmpty())
2325    {
2326  0 if (av.getColumnSelection() != null)
2327    {
2328  0 av.getColumnSelection().clear();
2329  0 repaint = true;
2330    }
2331    }
2332    else
2333    {
2334    // TODO: shift colSel according to the intersecting sequences
2335  0 if (av.getColumnSelection() == null)
2336    {
2337  0 av.setColumnSelection(new ColumnSelection(colsel));
2338    }
2339    else
2340    {
2341  0 av.getColumnSelection().setElementsFrom(colsel,
2342    av.getAlignment().getHiddenColumns());
2343    }
2344    }
2345  0 av.isColSelChanged(true);
2346  0 repaint = true;
2347    }
2348   
2349  64 if (copycolsel && av.hasHiddenColumns()
2350    && (av.getAlignment().getHiddenColumns() == null))
2351    {
2352  0 System.err.println("Bad things");
2353    }
2354  64 if (repaint) // always true!
2355    {
2356    // probably finessing with multiple redraws here
2357  64 PaintRefresher.Refresh(this, av.getSequenceSetId());
2358    // ap.paintAlignment(false);
2359    }
2360   
2361    // lastly, update dependent dialogs
2362  64 if (ap.getCalculationDialog() != null)
2363    {
2364  0 ap.getCalculationDialog().validateCalcTypes();
2365    }
2366   
2367    }
2368   
2369    /**
2370    * If this panel is a cdna/protein translation view of the selection source,
2371    * tries to map the source selection to a local one, and returns true. Else
2372    * returns false.
2373    *
2374    * @param seqsel
2375    * @param colsel
2376    * @param source
2377    */
 
2378  64 toggle protected boolean selectionFromTranslation(SequenceGroup seqsel,
2379    ColumnSelection colsel, HiddenColumns hidden,
2380    SelectionSource source)
2381    {
2382  64 if (!(source instanceof AlignViewportI))
2383    {
2384  0 return false;
2385    }
2386  64 final AlignViewportI sourceAv = (AlignViewportI) source;
2387  64 if (sourceAv.getCodingComplement() != av
2388    && av.getCodingComplement() != sourceAv)
2389    {
2390  64 return false;
2391    }
2392   
2393    /*
2394    * Map sequence selection
2395    */
2396  0 SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
2397  0 av.setSelectionGroup(sg);
2398  0 av.isSelectionGroupChanged(true);
2399   
2400    /*
2401    * Map column selection
2402    */
2403    // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
2404    // av);
2405  0 ColumnSelection cs = new ColumnSelection();
2406  0 HiddenColumns hs = new HiddenColumns();
2407  0 MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
2408  0 av.setColumnSelection(cs);
2409  0 av.getAlignment().setHiddenColumns(hs);
2410   
2411    // lastly, update any dependent dialogs
2412  0 if (ap.getCalculationDialog() != null)
2413    {
2414  0 ap.getCalculationDialog().validateCalcTypes();
2415    }
2416   
2417  0 PaintRefresher.Refresh(this, av.getSequenceSetId());
2418   
2419  0 return true;
2420    }
2421   
2422    /**
2423    *
2424    * @return null or last search results handled by this panel
2425    */
 
2426  1 toggle public SearchResultsI getLastSearchResults()
2427    {
2428  1 return lastSearchResults;
2429    }
2430    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.