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Coverage Report

  1. Project Clover database Tue Nov 18 2025 10:51:49 GMT
  2. Package jalview.appletgui

File SeqCanvas.java

 

Coverage histogram

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

Code metrics

188
334
21
1
930
698
140
0.42
15.9
21
6.67

Classes

Class Line # Actions
SeqCanvas 44 334 140
0.00%
 

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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.AlignmentI;
24    import jalview.datamodel.HiddenColumns;
25    import jalview.datamodel.SearchResultsI;
26    import jalview.datamodel.SequenceGroup;
27    import jalview.datamodel.SequenceI;
28    import jalview.datamodel.VisibleContigsIterator;
29    import jalview.renderer.ScaleRenderer;
30    import jalview.renderer.ScaleRenderer.ScaleMark;
31    import jalview.viewmodel.AlignmentViewport;
32    import jalview.viewmodel.ViewportListenerI;
33    import jalview.viewmodel.ViewportRanges;
34   
35    import java.awt.Color;
36    import java.awt.FontMetrics;
37    import java.awt.Graphics;
38    import java.awt.Image;
39    import java.awt.Panel;
40    import java.beans.PropertyChangeEvent;
41    import java.util.Iterator;
42   
43    @SuppressWarnings("serial")
 
44    public class SeqCanvas extends Panel implements ViewportListenerI
45    {
46    FeatureRenderer fr;
47   
48    SequenceRenderer sr;
49   
50    Image img;
51   
52    Graphics gg;
53   
54    int imgWidth;
55   
56    int imgHeight;
57   
58    AlignViewport av;
59   
60    boolean fastPaint = false;
61   
62    int cursorX = 0;
63   
64    int cursorY = 0;
65   
 
66  0 toggle public SeqCanvas(AlignViewport av)
67    {
68  0 this.av = av;
69  0 fr = new FeatureRenderer(av);
70  0 sr = new SequenceRenderer(av);
71  0 PaintRefresher.Register(this, av.getSequenceSetId());
72  0 updateViewport();
73   
74  0 av.getRanges().addPropertyChangeListener(this);
75    }
76   
77    int avcharHeight = 0, avcharWidth = 0;
78   
 
79  0 toggle private void updateViewport()
80    {
81  0 avcharHeight = av.getCharHeight();
82  0 avcharWidth = av.getCharWidth();
83    }
84   
 
85  0 toggle public AlignmentViewport getViewport()
86    {
87  0 return av;
88    }
89   
 
90  0 toggle public FeatureRenderer getFeatureRenderer()
91    {
92  0 return fr;
93    }
94   
 
95  0 toggle public SequenceRenderer getSequenceRenderer()
96    {
97  0 return sr;
98    }
99   
 
100  0 toggle private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
101    {
102  0 updateViewport();
103  0 g.setColor(Color.black);
104  0 for (ScaleMark mark : new ScaleRenderer().calculateMarks(av, startx,
105    endx))
106    {
107  0 int mpos = mark.column; // (i - startx - 1)
108  0 if (mpos < 0)
109    {
110  0 continue;
111    }
112  0 String mstring = mark.text;
113   
114  0 if (mark.major)
115    {
116  0 if (mstring != null)
117    {
118  0 g.drawString(mstring, mpos * avcharWidth,
119    ypos - (avcharHeight / 2));
120    }
121  0 g.drawLine((mpos * avcharWidth) + (avcharWidth / 2),
122    (ypos + 2) - (avcharHeight / 2),
123    (mpos * avcharWidth) + (avcharWidth / 2), ypos - 2);
124    }
125    }
126    }
127   
 
128  0 toggle private void drawWestScale(Graphics g, int startx, int endx, int ypos)
129    {
130  0 FontMetrics fm = getFontMetrics(av.getFont());
131  0 ypos += avcharHeight;
132  0 if (av.hasHiddenColumns())
133    {
134  0 startx = av.getAlignment().getHiddenColumns()
135    .visibleToAbsoluteColumn(startx);
136  0 endx = av.getAlignment().getHiddenColumns()
137    .visibleToAbsoluteColumn(endx);
138    }
139   
140    // WEST SCALE
141  0 for (int i = 0; i < av.getAlignment().getHeight(); i++)
142    {
143  0 SequenceI seq = av.getAlignment().getSequenceAt(i);
144  0 int index = startx;
145  0 int value = -1;
146   
147  0 while (index < endx)
148    {
149  0 if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
150    {
151  0 index++;
152   
153  0 continue;
154    }
155   
156  0 value = av.getAlignment().getSequenceAt(i).findPosition(index);
157   
158  0 break;
159    }
160   
161  0 if (value != -1)
162    {
163  0 int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
164    - avcharWidth / 2;
165  0 g.drawString(value + "", x,
166    (ypos + (i * avcharHeight)) - (avcharHeight / 5));
167    }
168    }
169    }
170   
 
171  0 toggle private void drawEastScale(Graphics g, int startx, int endx, int ypos)
172    {
173  0 ypos += avcharHeight;
174   
175  0 if (av.hasHiddenColumns())
176    {
177  0 endx = av.getAlignment().getHiddenColumns()
178    .visibleToAbsoluteColumn(endx);
179    }
180   
181  0 SequenceI seq;
182    // EAST SCALE
183  0 for (int i = 0; i < av.getAlignment().getHeight(); i++)
184    {
185  0 seq = av.getAlignment().getSequenceAt(i);
186  0 int index = endx;
187  0 int value = -1;
188   
189  0 while (index > startx)
190    {
191  0 if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
192    {
193  0 index--;
194   
195  0 continue;
196    }
197   
198  0 value = seq.findPosition(index);
199   
200  0 break;
201    }
202   
203  0 if (value != -1)
204    {
205  0 g.drawString(String.valueOf(value), 0,
206    (ypos + (i * avcharHeight)) - (avcharHeight / 5));
207    }
208    }
209    }
210   
211    int lastsr = 0;
212   
 
213  0 toggle void fastPaint(int horizontal, int vertical)
214    {
215  0 if (fastPaint || gg == null)
216    {
217  0 return;
218    }
219   
220  0 ViewportRanges ranges = av.getRanges();
221   
222  0 updateViewport();
223   
224    // Its possible on certain browsers that the call to fastpaint
225    // is faster than it can paint, so this check here catches
226    // this possibility
227  0 if (lastsr + horizontal != ranges.getStartRes())
228    {
229  0 horizontal = ranges.getStartRes() - lastsr;
230    }
231   
232  0 lastsr = ranges.getStartRes();
233   
234  0 fastPaint = true;
235  0 gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight,
236    imgWidth - horizontal * avcharWidth,
237    imgHeight - vertical * avcharHeight, -horizontal * avcharWidth,
238    -vertical * avcharHeight);
239   
240  0 int sr = ranges.getStartRes(), er = ranges.getEndRes(),
241    ss = ranges.getStartSeq(), es = ranges.getEndSeq(), transX = 0,
242    transY = 0;
243   
244  0 if (horizontal > 0) // scrollbar pulled right, image to the left
245    {
246  0 transX = (er - sr - horizontal) * avcharWidth;
247  0 sr = er - horizontal;
248    }
249  0 else if (horizontal < 0)
250    {
251  0 er = sr - horizontal;
252    }
253   
254  0 else if (vertical > 0) // scroll down
255    {
256  0 ss = es - vertical;
257  0 if (ss < ranges.getStartSeq()) // ie scrolling too fast, more than a page
258    // at a
259    // time
260    {
261  0 ss = ranges.getStartSeq();
262    }
263    else
264    {
265  0 transY = imgHeight - ((vertical + 1) * avcharHeight);
266    }
267    }
268  0 else if (vertical < 0)
269    {
270  0 es = ss - vertical;
271  0 if (es > ranges.getEndSeq())
272    {
273  0 es = ranges.getEndSeq();
274    }
275    }
276   
277  0 gg.translate(transX, transY);
278   
279  0 drawPanel(gg, sr, er, ss, es, 0);
280  0 gg.translate(-transX, -transY);
281   
282  0 repaint();
283   
284    }
285   
286    /**
287    * Definitions of startx and endx (hopefully): SMJS This is what I'm working
288    * towards! startx is the first residue (starting at 0) to display. endx is
289    * the last residue to display (starting at 0). starty is the first sequence
290    * to display (starting at 0). endy is the last sequence to display (starting
291    * at 0). NOTE 1: The av limits are set in setFont in this class and in the
292    * adjustment listener in SeqPanel when the scrollbars move.
293    */
 
294  0 toggle @Override
295    public void update(Graphics g)
296    {
297  0 paint(g);
298    }
299   
 
300  0 toggle @Override
301    public void paint(Graphics g)
302    {
303   
304  0 if (img != null
305    && (fastPaint || (getSize().width != g.getClipBounds().width)
306    || (getSize().height != g.getClipBounds().height)))
307    {
308  0 g.drawImage(img, 0, 0, this);
309  0 fastPaint = false;
310  0 return;
311    }
312   
313  0 if (fastPaint)
314    {
315  0 g.drawImage(img, 0, 0, this);
316  0 fastPaint = false;
317  0 return;
318    }
319   
320  0 updateViewport();
321    // this draws the whole of the alignment
322  0 imgWidth = this.getSize().width;
323  0 imgHeight = this.getSize().height;
324   
325  0 imgWidth -= imgWidth % avcharWidth;
326  0 imgHeight -= imgHeight % avcharHeight;
327   
328  0 if (imgWidth < 1 || imgHeight < 1)
329    {
330  0 return;
331    }
332   
333  0 if (img == null || imgWidth != img.getWidth(this)
334    || imgHeight != img.getHeight(this))
335    {
336  0 img = createImage(imgWidth, imgHeight);
337  0 gg = img.getGraphics();
338  0 gg.setFont(av.getFont());
339    }
340   
341  0 gg.setColor(Color.white);
342  0 gg.fillRect(0, 0, imgWidth, imgHeight);
343   
344  0 ViewportRanges ranges = av.getRanges();
345   
346  0 if (av.getWrapAlignment())
347    {
348  0 drawWrappedPanel(gg, imgWidth, imgHeight, ranges.getStartRes());
349    }
350    else
351    {
352  0 drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
353    ranges.getStartSeq(), ranges.getEndSeq(), 0);
354    }
355   
356  0 g.drawImage(img, 0, 0, this);
357   
358    }
359   
360    int LABEL_WEST, LABEL_EAST;
361   
 
362  0 toggle public int getWrappedCanvasWidth(int cwidth)
363    {
364  0 cwidth -= cwidth % av.getCharWidth();
365   
366  0 FontMetrics fm = getFontMetrics(av.getFont());
367   
368  0 LABEL_EAST = 0;
369  0 LABEL_WEST = 0;
370   
371  0 if (av.getScaleRightWrapped())
372    {
373  0 LABEL_EAST = fm.stringWidth(getMask());
374    }
375   
376  0 if (av.getScaleLeftWrapped())
377    {
378  0 LABEL_WEST = fm.stringWidth(getMask());
379    }
380   
381  0 return (cwidth - LABEL_EAST - LABEL_WEST) / av.getCharWidth();
382    }
383   
384    /**
385    * Generates a string of zeroes.
386    *
387    * @return String
388    */
 
389  0 toggle String getMask()
390    {
391  0 String mask = "0";
392  0 int maxWidth = 0;
393  0 int tmp;
394  0 AlignmentI alignment = av.getAlignment();
395  0 for (int i = 0; i < alignment.getHeight(); i++)
396    {
397  0 tmp = alignment.getSequenceAt(i).getEnd();
398  0 if (tmp > maxWidth)
399    {
400  0 maxWidth = tmp;
401    }
402    }
403   
404  0 for (int i = maxWidth; i > 0; i /= 10)
405    {
406  0 mask += "0";
407    }
408  0 return mask;
409    }
410   
 
411  0 toggle private void drawWrappedPanel(Graphics g, int canvasWidth,
412    int canvasHeight, int startRes)
413    {
414  0 AlignmentI al = av.getAlignment();
415   
416  0 FontMetrics fm = getFontMetrics(av.getFont());
417   
418  0 LABEL_EAST = 0;
419  0 LABEL_WEST = 0;
420   
421  0 if (av.getScaleRightWrapped())
422    {
423  0 LABEL_EAST = fm.stringWidth(getMask());
424    }
425   
426  0 if (av.getScaleLeftWrapped())
427    {
428  0 LABEL_WEST = fm.stringWidth(getMask());
429    }
430   
431  0 int hgap = avcharHeight;
432  0 if (av.getScaleAboveWrapped())
433    {
434  0 hgap += avcharHeight;
435    }
436   
437  0 int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / avcharWidth;
438  0 int cHeight = av.getAlignment().getHeight() * avcharHeight;
439   
440  0 av.setWrappedWidth(cWidth);
441   
442  0 av.getRanges().setViewportStartAndWidth(startRes, cWidth);
443   
444  0 int endx;
445  0 int ypos = hgap;
446   
447  0 int maxwidth = av.getAlignment().getVisibleWidth();
448   
449  0 while ((ypos <= canvasHeight) && (startRes < maxwidth))
450    {
451  0 endx = startRes + cWidth - 1;
452   
453  0 if (endx > maxwidth)
454    {
455  0 endx = maxwidth;
456    }
457   
458  0 g.setColor(Color.black);
459   
460  0 if (av.getScaleLeftWrapped())
461    {
462  0 drawWestScale(g, startRes, endx, ypos);
463    }
464   
465  0 if (av.getScaleRightWrapped())
466    {
467  0 g.translate(canvasWidth - LABEL_EAST, 0);
468  0 drawEastScale(g, startRes, endx, ypos);
469  0 g.translate(-(canvasWidth - LABEL_EAST), 0);
470    }
471   
472  0 g.translate(LABEL_WEST, 0);
473   
474  0 if (av.getScaleAboveWrapped())
475    {
476  0 drawNorthScale(g, startRes, endx, ypos);
477    }
478  0 if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
479    {
480  0 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
481  0 g.setColor(Color.blue);
482  0 int res;
483  0 Iterator<Integer> it = hidden.getStartRegionIterator(startRes,
484    endx + 1);
485  0 while (it.hasNext())
486    {
487  0 res = it.next() - startRes;
488  0 gg.fillPolygon(
489    new int[]
490    { res * avcharWidth - avcharHeight / 4,
491    res * avcharWidth + avcharHeight / 4,
492    res * avcharWidth },
493    new int[]
494    { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2),
495    ypos - (avcharHeight / 2) + 8 },
496    3);
497    }
498    }
499   
500  0 if (g.getClip() == null)
501    {
502  0 g.setClip(0, 0, cWidth * avcharWidth, canvasHeight);
503    }
504   
505  0 drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos);
506  0 g.setClip(null);
507   
508  0 if (av.isShowAnnotation())
509    {
510  0 g.translate(0, cHeight + ypos + 4);
511  0 if (annotations == null)
512    {
513  0 annotations = new AnnotationPanel(av);
514    }
515   
516  0 annotations.drawComponent(g, startRes, endx + 1);
517  0 g.translate(0, -cHeight - ypos - 4);
518    }
519  0 g.translate(-LABEL_WEST, 0);
520   
521  0 ypos += cHeight + getAnnotationHeight() + hgap;
522   
523  0 startRes += cWidth;
524    }
525   
526    }
527   
528    AnnotationPanel annotations;
529   
 
530  0 toggle int getAnnotationHeight()
531    {
532  0 if (!av.isShowAnnotation())
533    {
534  0 return 0;
535    }
536   
537  0 if (annotations == null)
538    {
539  0 annotations = new AnnotationPanel(av);
540    }
541   
542  0 return annotations.adjustPanelHeight();
543    }
544   
 
545  0 toggle private void drawPanel(Graphics g1, final int startRes, final int endRes,
546    final int startSeq, final int endSeq, final int offset)
547    {
548   
549  0 if (!av.hasHiddenColumns())
550    {
551  0 draw(g1, startRes, endRes, startSeq, endSeq, offset);
552    }
553    else
554    {
555  0 int screenY = 0;
556  0 int blockStart;
557  0 int blockEnd;
558   
559  0 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
560  0 VisibleContigsIterator regions = hidden
561    .getVisContigsIterator(startRes, endRes + 1, true);
562   
563  0 while (regions.hasNext())
564    {
565  0 int[] region = regions.next();
566  0 blockEnd = region[1];
567  0 blockStart = region[0];
568   
569    /*
570    * draw up to just before the next hidden region, or the end of
571    * the visible region, whichever comes first
572    */
573  0 g1.translate(screenY * avcharWidth, 0);
574   
575  0 draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
576   
577    /*
578    * draw the downline of the hidden column marker (ScalePanel draws the
579    * triangle on top) if we reached it
580    */
581  0 if (av.getShowHiddenMarkers()
582    && (regions.hasNext() || regions.endsAtHidden()))
583    {
584  0 g1.setColor(Color.blue);
585  0 g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
586    0 + offset, (blockEnd - blockStart + 1) * avcharWidth - 1,
587    (endSeq - startSeq + 1) * avcharHeight + offset);
588    }
589   
590  0 g1.translate(-screenY * avcharWidth, 0);
591  0 screenY += blockEnd - blockStart + 1;
592    }
593    }
594    }
595   
596    // int startRes, int endRes, int startSeq, int endSeq, int x, int y,
597    // int x1, int x2, int y1, int y2, int startx, int starty,
 
598  0 toggle void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq,
599    int offset)
600    {
601  0 g.setFont(av.getFont());
602  0 sr.prepare(g, av.isRenderGaps());
603  0 updateViewport();
604  0 SequenceI nextSeq;
605   
606    // / First draw the sequences
607    // ///////////////////////////
608  0 for (int i = startSeq; i <= endSeq; i++)
609    {
610  0 nextSeq = av.getAlignment().getSequenceAt(i);
611   
612  0 if (nextSeq == null)
613    {
614  0 continue;
615    }
616   
617  0 sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
618    startRes, endRes, offset + ((i - startSeq) * avcharHeight));
619   
620  0 if (av.isShowSequenceFeatures())
621    {
622  0 fr.drawSequence(g, nextSeq, startRes, endRes,
623    offset + ((i - startSeq) * avcharHeight), false);
624    }
625   
626    // / Highlight search Results once all sequences have been drawn
627    // ////////////////////////////////////////////////////////
628  0 if (av.hasSearchResults())
629    {
630  0 int[] visibleResults = av.getSearchResults().getResults(nextSeq,
631    startRes, endRes);
632  0 if (visibleResults != null)
633    {
634  0 for (int r = 0; r < visibleResults.length; r += 2)
635    {
636  0 sr.drawHighlightedText(nextSeq, visibleResults[r],
637    visibleResults[r + 1],
638    (visibleResults[r] - startRes) * avcharWidth,
639    offset + ((i - startSeq) * avcharHeight));
640    }
641    }
642    }
643   
644  0 if (av.cursorMode && cursorY == i && cursorX >= startRes
645    && cursorX <= endRes)
646    {
647  0 char s = nextSeq.getCharAt(cursorX);
648   
649  0 sr.drawCursor(g, s, (cursorX - startRes) * avcharWidth,
650    offset + ((i - startSeq) * avcharHeight));
651    }
652    }
653   
654  0 if (av.getSelectionGroup() != null
655    || av.getAlignment().getGroups().size() > 0)
656    {
657  0 drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
658    }
659   
660    }
661   
 
662  0 toggle private void drawGroupsBoundaries(Graphics g, int startRes, int endRes,
663    int startSeq, int endSeq, int offset)
664    {
665    //
666    // ///////////////////////////////////
667    // Now outline any areas if necessary
668    // ///////////////////////////////////
669  0 SequenceGroup group = av.getSelectionGroup();
670   
671  0 int sx = -1;
672  0 int sy = -1;
673  0 int ex = -1;
674  0 int groupIndex = -1;
675   
676  0 if ((group == null) && (av.getAlignment().getGroups().size() > 0))
677    {
678  0 group = av.getAlignment().getGroups().get(0);
679  0 groupIndex = 0;
680    }
681   
682  0 if (group != null)
683    {
684  0 do
685    {
686  0 int oldY = -1;
687  0 int i = 0;
688  0 boolean inGroup = false;
689  0 int top = -1;
690  0 int bottom = -1;
691  0 int alHeight = av.getAlignment().getHeight() - 1;
692   
693  0 for (i = startSeq; i <= endSeq; i++)
694    {
695  0 sx = (group.getStartRes() - startRes) * avcharWidth;
696  0 sy = offset + ((i - startSeq) * avcharHeight);
697  0 ex = (((group.getEndRes() + 1) - group.getStartRes())
698    * avcharWidth) - 1;
699   
700  0 if (sx + ex < 0 || sx > imgWidth)
701    {
702  0 continue;
703    }
704   
705  0 if ((sx <= (endRes - startRes) * avcharWidth)
706    && group.getSequences(null)
707    .contains(av.getAlignment().getSequenceAt(i)))
708    {
709  0 if ((bottom == -1)
710    && (i >= alHeight || !group.getSequences(null).contains(
711    av.getAlignment().getSequenceAt(i + 1))))
712    {
713  0 bottom = sy + avcharHeight;
714    }
715   
716  0 if (!inGroup)
717    {
718  0 if (((top == -1) && (i == 0)) || !group.getSequences(null)
719    .contains(av.getAlignment().getSequenceAt(i - 1)))
720    {
721  0 top = sy;
722    }
723   
724  0 oldY = sy;
725  0 inGroup = true;
726   
727  0 if (group == av.getSelectionGroup())
728    {
729  0 g.setColor(Color.red);
730    }
731    else
732    {
733  0 g.setColor(group.getOutlineColour());
734    }
735    }
736    }
737    else
738    {
739  0 if (inGroup)
740    {
741  0 if (sx >= 0 && sx < imgWidth)
742    {
743  0 g.drawLine(sx, oldY, sx, sy);
744    }
745   
746  0 if (sx + ex < imgWidth)
747    {
748  0 g.drawLine(sx + ex, oldY, sx + ex, sy);
749    }
750   
751  0 if (sx < 0)
752    {
753  0 ex += sx;
754  0 sx = 0;
755    }
756   
757  0 if (sx + ex > imgWidth)
758    {
759  0 ex = imgWidth;
760    }
761   
762  0 else if (sx + ex >= (endRes - startRes + 1) * avcharWidth)
763    {
764  0 ex = (endRes - startRes + 1) * avcharWidth;
765    }
766   
767  0 if (top != -1)
768    {
769  0 g.drawLine(sx, top, sx + ex, top);
770  0 top = -1;
771    }
772   
773  0 if (bottom != -1)
774    {
775  0 g.drawLine(sx, bottom, sx + ex, bottom);
776  0 bottom = -1;
777    }
778   
779  0 inGroup = false;
780    }
781    }
782    }
783   
784  0 if (inGroup)
785    {
786  0 sy = offset + ((i - startSeq) * avcharHeight);
787  0 if (sx >= 0 && sx < imgWidth)
788    {
789  0 g.drawLine(sx, oldY, sx, sy);
790    }
791   
792  0 if (sx + ex < imgWidth)
793    {
794  0 g.drawLine(sx + ex, oldY, sx + ex, sy);
795    }
796   
797  0 if (sx < 0)
798    {
799  0 ex += sx;
800  0 sx = 0;
801    }
802   
803  0 if (sx + ex > imgWidth)
804    {
805  0 ex = imgWidth;
806    }
807  0 else if (sx + ex >= (endRes - startRes + 1) * avcharWidth)
808    {
809  0 ex = (endRes - startRes + 1) * avcharWidth;
810    }
811   
812  0 if (top != -1)
813    {
814  0 g.drawLine(sx, top, sx + ex, top);
815  0 top = -1;
816    }
817   
818  0 if (bottom != -1)
819    {
820  0 g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
821  0 bottom = -1;
822    }
823   
824  0 inGroup = false;
825    }
826   
827  0 groupIndex++;
828   
829  0 if (groupIndex >= av.getAlignment().getGroups().size())
830    {
831  0 break;
832    }
833   
834  0 group = av.getAlignment().getGroups().get(groupIndex);
835  0 } while (groupIndex < av.getAlignment().getGroups().size());
836   
837    }
838    }
839   
 
840  0 toggle public void highlightSearchResults(SearchResultsI results)
841    {
842  0 av.setSearchResults(results);
843  0 repaint();
844    }
845   
 
846  0 toggle @Override
847    public void propertyChange(PropertyChangeEvent evt)
848    {
849  0 String eventName = evt.getPropertyName();
850   
851  0 if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED))
852    {
853  0 fastPaint = true;
854  0 repaint();
855  0 return;
856    }
857  0 else if (eventName.equals(ViewportRanges.MOVE_VIEWPORT))
858    {
859  0 fastPaint = false;
860  0 repaint();
861  0 return;
862    }
863   
864  0 if (!av.getWrapAlignment())
865    {
866  0 int scrollX = 0;
867  0 if (eventName.equals(ViewportRanges.STARTRES)
868    || eventName.equals(ViewportRanges.STARTRESANDSEQ))
869    {
870    // Make sure we're not trying to draw a panel
871    // larger than the visible window
872  0 if (eventName.equals(ViewportRanges.STARTRES))
873    {
874  0 scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
875    }
876    else
877    {
878  0 scrollX = ((int[]) evt.getNewValue())[0]
879    - ((int[]) evt.getOldValue())[0];
880    }
881  0 ViewportRanges vpRanges = av.getRanges();
882  0 int range = vpRanges.getEndRes() - vpRanges.getStartRes();
883  0 if (scrollX > range)
884    {
885  0 scrollX = range;
886    }
887  0 else if (scrollX < -range)
888    {
889  0 scrollX = -range;
890    }
891    }
892   
893    // Both scrolling and resizing change viewport ranges: scrolling changes
894    // both start and end points, but resize only changes end values.
895    // Here we only want to fastpaint on a scroll, with resize using a normal
896    // paint, so scroll events are identified as changes to the horizontal or
897    // vertical start value.
898  0 if (eventName.equals(ViewportRanges.STARTRES))
899    {
900    // scroll - startres and endres both change
901  0 fastPaint(scrollX, 0);
902    }
903  0 else if (eventName.equals(ViewportRanges.STARTSEQ))
904    {
905    // scroll
906  0 fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
907    }
908  0 else if (eventName.equals(ViewportRanges.STARTRESANDSEQ))
909    {
910  0 fastPaint(scrollX, 0);
911    }
912    }
913    }
914   
915    /**
916    * Ensure that a full paint is done next, for whatever reason. This was
917    * necessary for JavaScript; apparently in Java the timing is just right on
918    * multiple threads (EventQueue-0, Consensus, Conservation) that we can get
919    * away with one fast paint before the others, but this ensures that in the
920    * end we get a full paint. Problem arose in relation to copy/paste, where the
921    * paste was not finalized with a full paint.
922    *
923    * @author hansonr 2019.04.17
924    */
 
925  0 toggle public void clearFastPaint()
926    {
927  0 fastPaint = false;
928    }
929   
930    }
  • Report generated by OpenClover v 4.4.1 on Tue Nov 18 2025 11:02:12 GMT using coverage data from Tue Nov 18 2025 11:01:58 GMT.
  • OpenClover is free and open-source software.