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  1. Project Clover database Wed Nov 5 2025 13:15:40 GMT
  2. Package jalview.gui

File AlignmentPanel.java

 

Coverage histogram

../../img/srcFileCovDistChart7.png
30% of files have more coverage

Code metrics

216
559
74
1
1,936
1,216
200
0.36
7.55
74
2.7

Classes

Class Line # Actions
AlignmentPanel 82 559 200
0.644287464.4%
 

Contributing tests

This file is covered by 249 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 java.awt.BorderLayout;
24    import java.awt.Color;
25    import java.awt.Container;
26    import java.awt.Dimension;
27    import java.awt.Font;
28    import java.awt.FontMetrics;
29    import java.awt.Graphics;
30    import java.awt.Graphics2D;
31    import java.awt.event.AdjustmentEvent;
32    import java.awt.event.AdjustmentListener;
33    import java.awt.event.ComponentAdapter;
34    import java.awt.event.ComponentEvent;
35    import java.awt.print.PageFormat;
36    import java.awt.print.Printable;
37    import java.awt.print.PrinterException;
38    import java.beans.PropertyChangeEvent;
39    import java.beans.PropertyChangeListener;
40    import java.io.File;
41    import java.io.FileWriter;
42    import java.io.PrintWriter;
43    import java.util.List;
44   
45    import javax.swing.BoundedRangeModel;
46    import javax.swing.SwingUtilities;
47   
48    import jalview.analysis.AnnotationSorter;
49    import jalview.api.AlignViewportI;
50    import jalview.api.AlignmentViewPanel;
51    import jalview.bin.Cache;
52    import jalview.bin.Console;
53    import jalview.bin.Jalview;
54    import jalview.datamodel.AlignmentAnnotation;
55    import jalview.datamodel.AlignmentI;
56    import jalview.datamodel.HiddenColumns;
57    import jalview.datamodel.SearchResultsI;
58    import jalview.datamodel.SequenceFeature;
59    import jalview.datamodel.SequenceGroup;
60    import jalview.datamodel.SequenceI;
61    import jalview.gui.ImageExporter.ImageWriterI;
62    import jalview.io.HTMLOutput;
63    import jalview.io.exceptions.ImageOutputException;
64    import jalview.jbgui.GAlignmentPanel;
65    import jalview.math.AlignmentDimension;
66    import jalview.schemes.ResidueProperties;
67    import jalview.structure.StructureSelectionManager;
68    import jalview.util.Comparison;
69    import jalview.util.ImageMaker;
70    import jalview.util.MessageManager;
71    import jalview.util.imagemaker.BitmapImageSizing;
72    import jalview.viewmodel.ViewportListenerI;
73    import jalview.viewmodel.ViewportRanges;
74   
75    /**
76    * DOCUMENT ME!
77    *
78    * @author $author$
79    * @version $Revision: 1.161 $
80    */
81    @SuppressWarnings("serial")
 
82    public class AlignmentPanel extends GAlignmentPanel implements
83    AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI
84    {
85    /*
86    * spare space in pixels between sequence id and alignment panel
87    */
88    private static final int ID_WIDTH_PADDING = 4;
89   
90    public AlignViewport av;
91   
92    OverviewPanel overviewPanel;
93   
94    private SeqPanel seqPanel;
95   
96    private IdPanel idPanel;
97   
98    IdwidthAdjuster idwidthAdjuster;
99   
100    public AlignFrame alignFrame;
101   
102    private ScalePanel scalePanel;
103   
104    private AnnotationPanel annotationPanel;
105   
106    private AnnotationLabels alabels;
107   
108    private int hextent = 0;
109   
110    private int vextent = 0;
111   
112    /*
113    * Flag set while scrolling to follow complementary cDNA/protein scroll. When
114    * false, suppresses invoking the same method recursively.
115    */
116    private boolean scrollComplementaryPanel = true;
117   
118    private PropertyChangeListener propertyChangeListener;
119   
120    private CalculationChooser calculationDialog;
121   
122    /**
123    * Creates a new AlignmentPanel object.
124    *
125    * @param af
126    * @param av
127    */
 
128  501 toggle public AlignmentPanel(AlignFrame af, final AlignViewport av)
129    {
130    // setBackground(Color.white); // BH 2019
131  501 alignFrame = af;
132  501 this.av = av;
133  501 setSeqPanel(new SeqPanel(av, this));
134  501 setIdPanel(new IdPanel(av, this));
135   
136  501 setScalePanel(new ScalePanel(av, this));
137   
138  501 idPanelHolder.add(getIdPanel(), BorderLayout.CENTER);
139  501 idwidthAdjuster = new IdwidthAdjuster(this);
140  501 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
141   
142  501 setAnnotationPanel(new AnnotationPanel(this));
143  501 setAlabels(new AnnotationLabels(this));
144   
145  501 annotationScroller.setViewportView(getAnnotationPanel());
146  501 annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER);
147   
148  501 scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER);
149  501 seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER);
150   
151  501 setScrollValues(0, 0);
152   
153  501 hscroll.addAdjustmentListener(this);
154  501 vscroll.addAdjustmentListener(this);
155   
156  501 addComponentListener(new ComponentAdapter()
157    {
 
158  924 toggle @Override
159    public void componentResized(ComponentEvent evt)
160    {
161    // reset the viewport ranges when the alignment panel is resized
162    // in particular, this initialises the end residue value when Jalview
163    // is initialised
164  924 ViewportRanges ranges = av.getRanges();
165  924 if (av.getWrapAlignment())
166    {
167  17 int widthInRes = getSeqPanel().seqCanvas.getWrappedCanvasWidth(
168    getSeqPanel().seqCanvas.getWidth());
169  17 ranges.setViewportWidth(widthInRes);
170    }
171    else
172    {
173  907 int widthInRes = getSeqPanel().seqCanvas.getWidth()
174    / av.getCharWidth();
175  907 int heightInSeq = getSeqPanel().seqCanvas.getHeight()
176    / av.getCharHeight();
177   
178  907 ranges.setViewportWidth(widthInRes);
179  907 ranges.setViewportHeight(heightInSeq);
180    }
181    }
182   
183    });
184   
185  501 final AlignmentPanel ap = this;
186  501 propertyChangeListener = new PropertyChangeListener()
187    {
 
188  67 toggle @Override
189    public void propertyChange(PropertyChangeEvent evt)
190    {
191  67 if (evt.getPropertyName().equals("alignment"))
192    {
193  67 PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
194  67 alignmentChanged();
195    }
196    }
197    };
198  501 av.addPropertyChangeListener(propertyChangeListener);
199   
200  501 av.getRanges().addPropertyChangeListener(this);
201  501 fontChanged();
202  501 adjustAnnotationHeight();
203  501 updateLayout();
204    }
205   
 
206  853 toggle @Override
207    public AlignViewportI getAlignViewport()
208    {
209  853 return av;
210    }
211   
 
212  883 toggle public void alignmentChanged()
213    {
214  883 av.alignmentChanged(this);
215   
216  883 if (getCalculationDialog() != null)
217    {
218  0 getCalculationDialog().validateCalcTypes();
219    }
220   
221  883 alignFrame.updateEditMenuBar();
222   
223    // no idea if we need to update structure
224  883 paintAlignment(true, true);
225   
226    }
227   
228    /**
229    * DOCUMENT ME!
230    */
 
231  1571 toggle public void fontChanged()
232    {
233    // set idCanvas bufferedImage to null
234    // to prevent drawing old image
235  1571 FontMetrics fm = getFontMetrics(av.getFont());
236   
237    // update the flag controlling whether the grid is too small to render the
238    // font
239  1571 av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
240   
241  1571 scalePanelHolder.setPreferredSize(
242    new Dimension(10, av.getCharHeight() + fm.getDescent()));
243  1571 idSpaceFillerPanel1.setPreferredSize(
244    new Dimension(10, av.getCharHeight() + fm.getDescent()));
245  1571 idwidthAdjuster.invalidate();
246  1571 scalePanelHolder.invalidate();
247    // BH 2018 getIdPanel().getIdCanvas().gg = null;
248  1571 getSeqPanel().seqCanvas.img = null;
249  1571 getAnnotationPanel().adjustPanelHeight();
250   
251  1571 Dimension d = calculateIdWidth();
252  1571 getIdPanel().getIdCanvas().setPreferredSize(d);
253  1571 hscrollFillerPanel.setPreferredSize(d);
254   
255  1571 repaint();
256    }
257   
258    /**
259    * Calculates the width of the alignment labels based on the displayed names
260    * and any bounds on label width set in preferences.
261    *
262    * The calculated width is set as a property of the viewport and the layout is
263    * updated.
264    *
265    * @return Dimension giving the maximum width of the alignment label panel
266    * that should be used.
267    */
 
268  1574 toggle public Dimension calculateIdWidth()
269    {
270  1574 int oldWidth = av.getIdWidth();
271   
272    // calculate sensible default width when no preference is available
273  1574 Dimension r = null;
274  1574 if (av.getIdWidth() < 0)
275    {
276  472 r = calculateDefaultAlignmentIdWidth();
277  472 av.setIdWidth(r.width);
278    }
279    else
280    {
281  1102 r = new Dimension();
282  1102 r.width = av.getIdWidth();
283  1102 r.height = 0;
284    }
285   
286    /*
287    * fudge: if desired width has changed, update layout
288    * (see also paintComponent - updates layout on a repaint)
289    */
290  1574 if (r.width != oldWidth)
291    {
292  472 idPanelHolder.setPreferredSize(r);
293  472 validate();
294    }
295  1574 return r;
296    }
297   
 
298  2902 toggle public Dimension calculateDefaultAlignmentIdWidth()
299    {
300  2902 return calculateIdWidth(-1, false, false);
301    }
302   
303    /**
304    * pre 2.11.3 Id width calculation - used when importing old projects only
305    *
306    * @return
307    */
 
308  43 toggle public int getLegacyIdWidth()
309    {
310  43 int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
311  43 int idWidth = Math.min(afwidth - 200, 2 * afwidth / 3);
312  43 int maxwidth = Math.max(IdwidthAdjuster.MIN_ID_WIDTH, idWidth);
313  43 Dimension w = calculateIdWidthOrLegacy(true, maxwidth, false, false);
314  43 return w.width;
315    }
316   
317    /**
318    * Calculate the width of the alignment labels based on the displayed names
319    * and any bounds on label width set in preferences. Also includes annotations
320    * not actually visible.
321    *
322    * FIXME JAL-244 JAL-4091 - doesn't include sequence associated annotation
323    * label decorators and only called during tests
324    *
325    * @param maxwidth
326    * -1 or maximum width allowed for IdWidth
327    * @return Dimension giving the maximum width of the alignment label panel
328    * that should be used.
329    */
 
330  0 toggle protected Dimension calculateIdWidth(int maxwidth)
331    {
332  0 return calculateIdWidth(maxwidth, true, false);
333    }
334   
335    /**
336    * Calculate the width of the alignment labels based on the displayed names
337    * and any bounds on label width set in preferences.
338    *
339    * @param maxwidth
340    * -1 or maximum width allowed for IdWidth
341    * @param includeAnnotations
342    * - when true includes width of any additional marks in annotation
343    * id panel
344    * @param visibleOnly
345    * - when true, ignore label widths for hidden annotation rows
346    * @return Dimension giving the maximum width of the alignment label panel
347    * that should be used.
348    */
 
349  2978 toggle public Dimension calculateIdWidth(int maxwidth,
350    boolean includeAnnotations, boolean visibleOnly)
351    {
352  2978 return calculateIdWidthOrLegacy(false, maxwidth, includeAnnotations,
353    visibleOnly);
354    }
355   
356    /**
357    * legacy mode or post 2.11.3 ID width calculation
358    *
359    * @param legacy
360    * - uses annotation labels, not rendered label width (excludes
361    * additional decorators)
362    * @param maxwidth
363    * @param includeAnnotations
364    * @param visibleOnly
365    * @return
366    */
 
367  3021 toggle private Dimension calculateIdWidthOrLegacy(boolean legacy, int maxwidth,
368    boolean includeAnnotations, boolean visibleOnly)
369    {
370  3021 Container c = new Container();
371   
372  3021 FontMetrics fm = c.getFontMetrics(
373    new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
374   
375  3021 AlignmentI al = av.getAlignment();
376  3021 int i = 0;
377  3021 int idWidth = 0;
378   
379  33304 while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
380    {
381  30283 SequenceI s = al.getSequenceAt(i);
382  30283 String id = s.getDisplayId(av.getShowJVSuffix());
383  30283 int stringWidth = fm.stringWidth(id);
384  30283 idWidth = Math.max(idWidth, stringWidth);
385  30283 i++;
386    }
387   
388    // Also check annotation label widths
389  3021 if (includeAnnotations && al.getAlignmentAnnotation() != null)
390    {
391  76 if (legacy)
392    {
393  0 fm = c.getFontMetrics(getAlabels().getFont());
394    }
395   
396  76 if (!legacy || Jalview.isHeadlessMode())
397    {
398  76 AnnotationLabels aal = getAlabels();
399  76 int stringWidth = aal.drawLabels(null, false, idWidth, false, false,
400    fm, !visibleOnly);
401  76 idWidth = Math.max(idWidth, stringWidth);
402    }
403    else
404    {
405  0 for (i = 0; i < al.getAlignmentAnnotation().length; i++)
406    {
407  0 AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
408  0 if (visibleOnly && !aa.isForDisplay())
409    {
410  0 continue;
411    }
412  0 String label = aa.label;
413  0 int stringWidth = fm.stringWidth(label);
414  0 idWidth = Math.max(idWidth, stringWidth);
415    }
416    }
417    }
418   
419  3021 int w = maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth);
420  3021 w += ID_WIDTH_PADDING;
421   
422  3021 return new Dimension(w, 12);
423    }
424   
425    /**
426    * Highlight the given results on the alignment
427    *
428    */
 
429  1 toggle public void highlightSearchResults(SearchResultsI results)
430    {
431  1 boolean scrolled = scrollToPosition(results, 0, false);
432   
433  1 boolean fastPaint = !(scrolled && av.getWrapAlignment());
434   
435  1 getSeqPanel().seqCanvas.highlightSearchResults(results, fastPaint);
436    }
437   
438    /**
439    * Scroll the view to show the position of the highlighted region in results
440    * (if any)
441    *
442    * @param searchResults
443    * @return
444    */
 
445  2 toggle public boolean scrollToPosition(SearchResultsI searchResults)
446    {
447  2 return scrollToPosition(searchResults, 0, false);
448    }
449   
450    /**
451    * Scrolls the view (if necessary) to show the position of the first
452    * highlighted region in results (if any). Answers true if the view was
453    * scrolled, or false if no matched region was found, or it is already
454    * visible.
455    *
456    * @param results
457    * @param verticalOffset
458    * if greater than zero, allows scrolling to a position below the
459    * first displayed sequence
460    * @param centre
461    * if true, try to centre the search results horizontally in the view
462    * @return
463    */
 
464  7 toggle protected boolean scrollToPosition(SearchResultsI results,
465    int verticalOffset, boolean centre)
466    {
467  7 int startv, endv, starts, ends;
468  7 ViewportRanges ranges = av.getRanges();
469   
470  7 if (results == null || results.isEmpty() || av == null
471    || av.getAlignment() == null)
472    {
473  0 return false;
474    }
475  7 int seqIndex = av.getAlignment().findIndex(results);
476  7 if (seqIndex == -1)
477    {
478  0 return false;
479    }
480  7 SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
481   
482  7 int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
483  7 if (r == null)
484    {
485  0 return false;
486    }
487  7 int start = r[0];
488  7 int end = r[1];
489   
490    /*
491    * To centre results, scroll to positions half the visible width
492    * left/right of the start/end positions
493    */
494  7 if (centre)
495    {
496  4 int offset = (ranges.getEndRes() - ranges.getStartRes() + 1) / 2 - 1;
497  4 start = Math.max(start - offset, 0);
498  4 end = end + offset - 1;
499    }
500  7 if (start < 0)
501    {
502  0 return false;
503    }
504  7 if (end == seq.getEnd())
505    {
506  0 return false;
507    }
508   
509  7 if (av.hasHiddenColumns())
510    {
511  0 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
512  0 start = hidden.absoluteToVisibleColumn(start);
513  0 end = hidden.absoluteToVisibleColumn(end);
514  0 if (start == end)
515    {
516  0 if (!hidden.isVisible(r[0]))
517    {
518    // don't scroll - position isn't visible
519  0 return false;
520    }
521    }
522    }
523   
524    /*
525    * allow for offset of target sequence (actually scroll to one above it)
526    */
527  7 seqIndex = Math.max(0, seqIndex - verticalOffset);
528  7 boolean scrollNeeded = true;
529   
530  7 if (!av.getWrapAlignment())
531    {
532  ? if ((startv = ranges.getStartRes()) >= start)
533    {
534    /*
535    * Scroll left to make start of search results visible
536    */
537  4 setScrollValues(start, seqIndex);
538    }
539  ? else if ((endv = ranges.getEndRes()) <= end)
540    {
541    /*
542    * Scroll right to make end of search results visible
543    */
544  2 setScrollValues(startv + end - endv, seqIndex);
545    }
546  0 else if ((starts = ranges.getStartSeq()) > seqIndex)
547    {
548    /*
549    * Scroll up to make start of search results visible
550    */
551  0 setScrollValues(ranges.getStartRes(), seqIndex);
552    }
553  0 else if ((ends = ranges.getEndSeq()) <= seqIndex)
554    {
555    /*
556    * Scroll down to make end of search results visible
557    */
558  0 setScrollValues(ranges.getStartRes(), starts + seqIndex - ends + 1);
559    }
560    /*
561    * Else results are already visible - no need to scroll
562    */
563  6 scrollNeeded = false;
564    }
565    else
566    {
567  1 scrollNeeded = ranges.scrollToWrappedVisible(start);
568    }
569   
570  7 paintAlignment(false, false);
571   
572  7 return scrollNeeded;
573    }
574   
575    /**
576    * DOCUMENT ME!
577    *
578    * @return DOCUMENT ME!
579    */
 
580  56 toggle public OverviewPanel getOverviewPanel()
581    {
582  56 return overviewPanel;
583    }
584   
585    /**
586    * DOCUMENT ME!
587    *
588    * @param op
589    * DOCUMENT ME!
590    */
 
591  82 toggle public void setOverviewPanel(OverviewPanel op)
592    {
593  82 overviewPanel = op;
594    }
595   
596    /**
597    *
598    * @param b
599    * Hide or show annotation panel
600    *
601    */
 
602  653 toggle public void setAnnotationVisible(boolean b)
603    {
604  653 if (!av.getWrapAlignment())
605    {
606  623 annotationSpaceFillerHolder.setVisible(b);
607  623 annotationScroller.setVisible(b);
608    }
609  653 repaint();
610    }
611   
612    /**
613    * automatically adjust annotation panel height for new annotation whilst
614    * ensuring the alignment is still visible.
615    */
 
616  2155 toggle @Override
617    public void adjustAnnotationHeight()
618    {
619    // TODO: display vertical annotation scrollbar if necessary
620    // this is called after loading new annotation onto alignment
621  2155 if (alignFrame.getHeight() == 0)
622    {
623  10 jalview.bin.Console.error(
624    "adjustAnnotationHeight called with zero height alignment window");
625    }
626  2155 validateAnnotationDimensions(true);
627  2155 addNotify();
628    // TODO: many places call this method and also paintAlignment with various
629    // different settings. this means multiple redraws are triggered...
630  2155 paintAlignment(true, av.needToUpdateStructureViews());
631    }
632   
633    /**
634    * calculate the annotation dimensions and refresh slider values accordingly.
635    * need to do repaints/notifys afterwards.
636    */
 
637  3098 toggle protected void validateAnnotationDimensions(boolean adjustPanelHeight)
638    {
639    // BH 2018.04.18 comment: addNotify() is not appropriate here. We
640    // are not changing ancestors, and keyboard action listeners do
641    // not need to be reset. addNotify() is a very expensive operation,
642    // requiring a full re-layout of all parents and children.
643    // Note in JComponent:
644    // This method is called by the toolkit internally and should
645    // not be called directly by programs.
646    // I note that addNotify() is called in several areas of Jalview.
647   
648  3098 AnnotationPanel ap = getAnnotationPanel();
649  3098 int annotationHeight = ap.adjustPanelHeight();
650  3098 annotationHeight = ap.adjustForAlignFrame(adjustPanelHeight,
651    annotationHeight);
652   
653  3098 hscroll.addNotify();
654  3098 Dimension e = idPanel.getSize();
655  3098 int idWidth = e.width;
656  3098 boolean manuallyAdjusted = this.getIdPanel().getIdCanvas()
657    .isManuallyAdjusted();
658  3098 annotationScroller.setPreferredSize(new Dimension(
659  3098 manuallyAdjusted ? idWidth : annotationScroller.getWidth(),
660    annotationHeight));
661   
662  3098 alabels.setPreferredSize(new Dimension(idWidth, annotationHeight));
663   
664  3098 annotationSpaceFillerHolder.setPreferredSize(new Dimension(
665  3098 manuallyAdjusted ? idWidth
666    : annotationSpaceFillerHolder.getWidth(),
667    annotationHeight));
668  3098 annotationScroller.validate();
669  3098 annotationScroller.addNotify();
670  3098 ap.validate();
671    }
672   
673    /**
674    * update alignment layout for viewport settings
675    *
676    * @param wrap
677    * DOCUMENT ME!
678    */
 
679  653 toggle public void updateLayout()
680    {
681  653 fontChanged();
682  653 setAnnotationVisible(av.isShowAnnotation());
683  653 boolean wrap = av.getWrapAlignment();
684  653 ViewportRanges ranges = av.getRanges();
685  653 ranges.setStartSeq(0);
686    // scalePanelHolder.setVisible(!wrap);
687  653 hscroll.setVisible(!wrap);
688    // Allow idPanel width adjustment in wrap mode
689  653 idwidthAdjuster.setVisible(true);
690   
691  653 if (wrap)
692    {
693  30 annotationScroller.setVisible(false);
694  30 annotationSpaceFillerHolder.setVisible(false);
695    }
696  623 else if (av.isShowAnnotation())
697    {
698  613 annotationScroller.setVisible(true);
699  613 annotationSpaceFillerHolder.setVisible(true);
700  613 validateAnnotationDimensions(false);
701    }
702   
703  653 int canvasWidth = getSeqPanel().seqCanvas.getWidth();
704  653 if (canvasWidth > 0)
705    { // may not yet be laid out
706  31 if (wrap)
707    {
708  10 int widthInRes = getSeqPanel().seqCanvas
709    .getWrappedCanvasWidth(canvasWidth);
710  10 ranges.setViewportWidth(widthInRes);
711    }
712    else
713    {
714  21 int widthInRes = (canvasWidth / av.getCharWidth());
715  21 int heightInSeq = (getSeqPanel().seqCanvas.getHeight()
716    / av.getCharHeight());
717   
718  21 ranges.setViewportWidth(widthInRes);
719  21 ranges.setViewportHeight(heightInSeq);
720    }
721    }
722   
723    // idSpaceFillerPanel1.setVisible(!wrap);
724   
725  653 repaint();
726    }
727   
728    /**
729    * Adjust row/column scrollers to show a visible position in the alignment.
730    *
731    * @param x
732    * visible column to scroll to
733    * @param y
734    * visible row to scroll to
735    *
736    */
 
737  4194 toggle public void setScrollValues(int xpos, int ypos)
738    {
739  4194 int x = xpos;
740  4194 int y = ypos;
741   
742  4194 if (av == null || av.getAlignment() == null)
743    {
744  0 return;
745    }
746   
747  4194 if (av.getWrapAlignment())
748    {
749  276 setScrollingForWrappedPanel(x);
750    }
751    else
752    {
753  3918 int width = av.getAlignment().getVisibleWidth();
754  3918 int height = av.getAlignment().getHeight();
755   
756  3918 hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
757  3918 vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
758   
759  3918 if (hextent > width)
760    {
761  977 hextent = width;
762    }
763   
764  3918 if (vextent > height)
765    {
766  1085 vextent = height;
767    }
768   
769  3918 if ((hextent + x) > width)
770    {
771  2 x = width - hextent;
772    }
773   
774  3918 if ((vextent + y) > height)
775    {
776  30 y = height - vextent;
777    }
778   
779  3918 if (y < 0)
780    {
781  0 y = 0;
782    }
783   
784  3918 if (x < 0)
785    {
786  1 x = 0;
787    }
788   
789    // update the scroll values
790  3918 hscroll.setValues(x, hextent, 0, width);
791  3918 vscroll.setValues(y, vextent, 0, height);
792    }
793    }
794   
795    /**
796    * Answers true if the panel has no horizontal scrollbar, or the scrollbar is
797    * at its rightmost position, else false.
798    *
799    * @return
800    */
 
801  0 toggle boolean isScrolledFullyRight()
802    {
803  0 if (hscroll == null)
804    {
805  0 return true;
806    }
807  0 BoundedRangeModel model = hscroll.getModel();
808  0 return (model.getExtent() + model.getValue() >= model.getMaximum());
809    }
810   
811    /**
812    * Respond to adjustment event when horizontal or vertical scrollbar is
813    * changed
814    *
815    * @param evt
816    * adjustment event encoding whether hscroll or vscroll changed
817    */
 
818  875 toggle @Override
819    public void adjustmentValueChanged(AdjustmentEvent evt)
820    {
821  875 if (av.getWrapAlignment())
822    {
823  25 adjustScrollingWrapped(evt);
824  25 return;
825    }
826   
827  850 ViewportRanges ranges = av.getRanges();
828   
829  850 if (evt.getSource() == hscroll)
830    {
831  341 int oldX = ranges.getStartRes();
832  341 int oldwidth = ranges.getViewportWidth();
833  341 int x = hscroll.getValue();
834  341 int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
835   
836    // if we're scrolling to the position we're already at, stop
837    // this prevents infinite recursion of events when the scroll/viewport
838    // ranges values are the same
839  341 if ((x == oldX) && (width == oldwidth))
840    {
841  59 return;
842    }
843  282 ranges.setViewportStartAndWidth(x, width);
844    }
845  509 else if (evt.getSource() == vscroll)
846    {
847  509 int oldY = ranges.getStartSeq();
848  509 int oldheight = ranges.getViewportHeight();
849  509 int y = vscroll.getValue();
850  509 int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
851   
852    // if we're scrolling to the position we're already at, stop
853    // this prevents infinite recursion of events when the scroll/viewport
854    // ranges values are the same
855  509 if ((y == oldY) && (height == oldheight))
856    {
857  49 return;
858    }
859  460 ranges.setViewportStartAndHeight(y, height);
860    }
861  742 repaint();
862    }
863   
864    /**
865    * Responds to a scroll change by setting the start position of the viewport.
866    * Does
867    *
868    * @param evt
869    */
 
870  25 toggle protected void adjustScrollingWrapped(AdjustmentEvent evt)
871    {
872  25 if (evt.getSource() == hscroll)
873    {
874  0 return; // no horizontal scroll when wrapped
875    }
876  25 final ViewportRanges ranges = av.getRanges();
877   
878  25 if (evt.getSource() == vscroll)
879    {
880  25 int newY = vscroll.getValue();
881   
882    /*
883    * if we're scrolling to the position we're already at, stop
884    * this prevents infinite recursion of events when the scroll/viewport
885    * ranges values are the same
886    */
887  25 int oldX = ranges.getStartRes();
888  25 int oldY = ranges.getWrappedScrollPosition(oldX);
889  25 if (oldY == newY)
890    {
891  25 return;
892    }
893  0 if (newY > -1)
894    {
895    /*
896    * limit page up/down to one width's worth of positions
897    */
898  0 int rowSize = ranges.getViewportWidth();
899  0 int newX = newY > oldY ? oldX + rowSize : oldX - rowSize;
900  0 ranges.setViewportStartAndWidth(Math.max(0, newX), rowSize);
901    }
902    }
903    else
904    {
905    // This is only called if file loaded is a jar file that
906    // was wrapped when saved and user has wrap alignment true
907    // as preference setting
908  0 SwingUtilities.invokeLater(new Runnable()
909    {
 
910  0 toggle @Override
911    public void run()
912    {
913    // When updating scrolling to use ViewportChange events, this code
914    // could not be validated and it is not clear if it is now being
915    // called. Log warning here in case it is called and unforeseen
916    // problems occur
917  0 Console.warn(
918    "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
919   
920    // scroll to start of panel
921  0 ranges.setStartRes(0);
922  0 ranges.setStartSeq(0);
923    }
924    });
925    }
926  0 repaint();
927    }
928   
929    /* (non-Javadoc)
930    * @see jalview.api.AlignmentViewPanel#paintAlignment(boolean)
931    */
 
932  7620 toggle @Override
933    public void paintAlignment(boolean updateOverview,
934    boolean updateStructures)
935    {
936  7620 final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
937    av.isShowAutocalculatedAbove());
938  7618 sorter.sort(getAlignment().getAlignmentAnnotation(),
939    av.getSortAnnotationsBy());
940  7618 repaint();
941   
942  7618 if (updateStructures)
943    {
944  5304 av.getStructureSelectionManager().sequenceColoursChanged(this);
945    }
946  7612 if (updateOverview)
947    {
948   
949  7574 if (overviewPanel != null)
950    {
951  496 overviewPanel.updateOverviewImage();
952    }
953    }
954    }
955   
 
956  2913 toggle @Override
957    public void paintComponent(Graphics g)
958    {
959  2913 invalidate(); // needed so that the id width adjuster works correctly
960  2913 Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
961  2913 int idWidth = d.width;
962   
963    // check wrapped alignment as at least 1 residue width
964  2911 if (av.getWrapAlignment())
965    {
966  250 SeqCanvas sc = this.getSeqPanel().seqCanvas;
967  250 if (sc != null && sc.getWidth() < sc.getMinimumWrappedCanvasWidth())
968    {
969    // need to make some adjustments
970  0 idWidth -= (sc.getMinimumWrappedCanvasWidth() - sc.getWidth());
971  0 av.setIdWidth(idWidth);
972  0 av.getAlignPanel().getIdPanel().getIdCanvas()
973    .setManuallyAdjusted(true);
974   
975  0 validateAnnotationDimensions(false);
976    }
977    }
978   
979  2911 idPanelHolder.setPreferredSize(new Dimension(idWidth, d.height));
980  2911 hscrollFillerPanel.setPreferredSize(new Dimension(idWidth, 12));
981   
982  2911 validate(); // needed so that the id width adjuster works correctly
983   
984    /*
985    * set scroll bar positions - tried to remove but necessary for split panel to resize correctly
986    * though I still think this call should be elsewhere.
987    */
988  2911 ViewportRanges ranges = av.getRanges();
989  2911 setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
990  2911 super.paintComponent(g);
991    }
992   
993    /**
994    * Set vertical scroll bar position, and number of increments, for wrapped
995    * panel
996    *
997    * @param topLeftColumn
998    * the column position at top left (0..)
999    */
 
1000  276 toggle private void setScrollingForWrappedPanel(int topLeftColumn)
1001    {
1002  276 ViewportRanges ranges = av.getRanges();
1003  276 int scrollPosition = ranges.getWrappedScrollPosition(topLeftColumn);
1004  276 int maxScroll = ranges.getWrappedMaxScroll(topLeftColumn);
1005   
1006    /*
1007    * a scrollbar's value can be set to at most (maximum-extent)
1008    * so we add extent (1) to the maxScroll value
1009    */
1010  276 vscroll.setUnitIncrement(1);
1011  276 vscroll.setValues(scrollPosition, 1, 0, maxScroll + 1);
1012    }
1013   
1014    /**
1015    * DOCUMENT ME!
1016    *
1017    * @param pg
1018    * DOCUMENT ME!
1019    * @param pf
1020    * DOCUMENT ME!
1021    * @param pi
1022    * DOCUMENT ME!
1023    *
1024    * @return DOCUMENT ME!
1025    *
1026    * @throws PrinterException
1027    * DOCUMENT ME!
1028    */
 
1029  0 toggle @Override
1030    public int print(Graphics pg, PageFormat pf, int pi)
1031    throws PrinterException
1032    {
1033  0 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
1034   
1035  0 int pwidth = (int) pf.getImageableWidth();
1036  0 int pheight = (int) pf.getImageableHeight();
1037   
1038  0 if (av.getWrapAlignment())
1039    {
1040  0 return printWrappedAlignment(pwidth, pheight, pi, pg);
1041    }
1042    else
1043    {
1044  0 return printUnwrapped(pwidth, pheight, pi, pg, pg);
1045    }
1046    }
1047   
1048    /**
1049    * Draws the alignment image, including sequence ids, sequences, and
1050    * annotation labels and annotations if shown, on either one or two Graphics
1051    * contexts.
1052    *
1053    * @param pageWidth
1054    * in pixels
1055    * @param pageHeight
1056    * in pixels
1057    * @param pageIndex
1058    * (0, 1, ...)
1059    * @param idGraphics
1060    * the graphics context for sequence ids and annotation labels
1061    * @param alignmentGraphics
1062    * the graphics context for sequences and annotations (may or may not
1063    * be the same context as idGraphics)
1064    * @return
1065    * @throws PrinterException
1066    */
 
1067  38 toggle public int printUnwrapped(int pageWidth, int pageHeight, int pageIndex,
1068    Graphics idGraphics, Graphics alignmentGraphics)
1069    throws PrinterException
1070    {
1071  38 final int idWidth, idWidthForGui;
1072    // otherwise calculate it
1073  38 idWidth = getVisibleIdWidth(false);
1074    // if (getIdPanel()!=null && getIdPanel().getWidth()>0)
1075    // {
1076    // // use the current IdPanel's width, if its set and non-zero
1077    // idWidthForGui = getIdPanel().getWidth();
1078    // } else {
1079    // idWidthForGui=0;
1080    // }
1081    /*
1082    * Get the horizontal offset to where we draw the sequences.
1083    * This is idWidth if using a single Graphics context, else zero.
1084    */
1085  38 final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0
1086    : idWidth;
1087   
1088  38 FontMetrics fm = getFontMetrics(av.getFont());
1089  38 final int charHeight = av.getCharHeight();
1090  38 final int scaleHeight = charHeight + fm.getDescent();
1091   
1092  38 idGraphics.setColor(Color.white);
1093  38 idGraphics.fillRect(0, 0, pageWidth, pageHeight);
1094  38 idGraphics.setFont(av.getFont());
1095   
1096    /*
1097    * How many sequences and residues can we fit on a printable page?
1098    */
1099  38 final int totalRes = (pageWidth - idWidth) / av.getCharWidth();
1100   
1101  38 final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
1102   
1103  38 final int alignmentWidth = av.getAlignment().getVisibleWidth();
1104  38 int pagesWide = (alignmentWidth / totalRes) + 1;
1105   
1106  38 final int startRes = (pageIndex % pagesWide) * totalRes;
1107  38 final int endRes = Math.min(startRes + totalRes - 1,
1108    alignmentWidth - 1);
1109   
1110  38 final int startSeq = (pageIndex / pagesWide) * totalSeq;
1111  38 final int alignmentHeight = av.getAlignment().getHeight();
1112  38 final int endSeq = Math.min(startSeq + totalSeq, alignmentHeight);
1113   
1114  38 int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight;
1115   
1116  38 if (av.isShowAnnotation())
1117    {
1118  38 pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
1119    }
1120   
1121  38 pagesHigh /= pageHeight;
1122   
1123  38 if (pageIndex >= (pagesWide * pagesHigh))
1124    {
1125  0 return Printable.NO_SUCH_PAGE;
1126    }
1127  38 final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3;
1128   
1129  38 alignmentGraphics.setColor(Color.white);
1130  38 alignmentGraphics.fillRect(0, 0, pageWidth, pageHeight + scaleHeight);
1131   
1132    /*
1133    * draw the Scale at horizontal offset, then reset to top left (0, 0)
1134    */
1135  38 alignmentGraphics.translate(alignmentGraphicsOffset, 0);
1136  38 getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
1137    pageWidth - idWidth, scaleHeight);
1138  38 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1139   
1140    /*
1141    * Draw the sequence ids, offset for scale height,
1142    * then reset to top left (0, 0)
1143    */
1144  38 idGraphics.translate(0, scaleHeight);
1145  38 IdCanvas idCanvas = getIdPanel().getIdCanvas();
1146  38 List<SequenceI> selection = av.getSelectionGroup() == null ? null
1147    : av.getSelectionGroup().getSequences(null);
1148   
1149  38 idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1,
1150    selection, false, idWidth);
1151   
1152  38 idGraphics.setFont(av.getFont());
1153  38 idGraphics.translate(0, -scaleHeight);
1154   
1155    /*
1156    * draw the sequences, offset for scale height, and id width (if using a
1157    * single graphics context), then reset to (0, scale height)
1158    */
1159  38 alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
1160  38 getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics,
1161    startRes, endRes, startSeq, endSeq - 1);
1162  38 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1163   
1164  38 if (av.isShowAnnotation() && (endSeq == alignmentHeight))
1165    {
1166    /*
1167    * draw annotation labels; drawComponent() translates by
1168    * getScrollOffset(), so compensate for that first;
1169    * then reset to (0, scale height)
1170    */
1171  38 int offset = getAlabels().getScrollOffset();
1172  38 idGraphics.translate(0, -offset);
1173  38 idGraphics.translate(0, alignmentDrawnHeight);
1174  38 getAlabels().drawComponentNotGUI(idGraphics, idWidth);
1175  38 idGraphics.translate(0, -alignmentDrawnHeight);
1176   
1177    /*
1178    * draw the annotations starting at
1179    * (idOffset, alignmentHeight) from (0, scaleHeight)
1180    */
1181  38 alignmentGraphics.translate(alignmentGraphicsOffset,
1182    alignmentDrawnHeight);
1183  38 updateLayout();
1184  38 getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
1185    alignmentGraphics, -1, startRes, endRes + 1);
1186    }
1187   
1188  33 return Printable.PAGE_EXISTS;
1189    }
1190   
1191    /**
1192    * Prints one page of an alignment in wrapped mode. Returns
1193    * Printable.PAGE_EXISTS (0) if a page was drawn, or Printable.NO_SUCH_PAGE if
1194    * no page could be drawn (page number out of range).
1195    *
1196    * @param pageWidth
1197    * @param pageHeight
1198    * @param pageNumber
1199    * (0, 1, ...)
1200    * @param g
1201    *
1202    * @return
1203    *
1204    * @throws PrinterException
1205    */
 
1206  0 toggle public int printWrappedAlignment(int pageWidth, int pageHeight,
1207    int pageNumber, Graphics g) throws PrinterException
1208    {
1209  0 getSeqPanel().seqCanvas.calculateWrappedGeometry(getWidth(),
1210    getHeight());
1211  0 int annotationHeight = 0;
1212  0 if (av.isShowAnnotation())
1213    {
1214  0 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1215    }
1216   
1217  0 int hgap = av.getCharHeight();
1218  0 if (av.getScaleAboveWrapped())
1219    {
1220  0 hgap += av.getCharHeight();
1221    }
1222   
1223  0 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1224    + annotationHeight;
1225   
1226  0 int idWidth = getVisibleIdWidth(false);
1227   
1228  0 int maxwidth = av.getAlignment().getVisibleWidth();
1229   
1230  0 int resWidth = getSeqPanel().seqCanvas
1231    .getWrappedCanvasWidth(pageWidth - idWidth);
1232  0 av.getRanges().setViewportStartAndWidth(0, resWidth);
1233   
1234  0 int totalHeight = cHeight * (maxwidth / resWidth + 1);
1235   
1236  0 g.setColor(Color.white);
1237  0 g.fillRect(0, 0, pageWidth, pageHeight);
1238  0 g.setFont(av.getFont());
1239  0 g.setColor(Color.black);
1240   
1241    /*
1242    * method: print the whole wrapped alignment, but with a clip region that
1243    * is restricted to the requested page; this supports selective print of
1244    * single pages or ranges, (at the cost of repeated processing in the
1245    * 'normal' case, when all pages are printed)
1246    */
1247  0 g.translate(0, -pageNumber * pageHeight);
1248   
1249  0 g.setClip(0, pageNumber * pageHeight, pageWidth, pageHeight);
1250   
1251    /*
1252    * draw sequence ids and annotation labels (if shown)
1253    */
1254  0 IdCanvas idCanvas = getIdPanel().getIdCanvas();
1255  0 idCanvas.drawIdsWrappedNoGUI((Graphics2D) g, av, 0, totalHeight);
1256   
1257  0 g.translate(idWidth, 0);
1258   
1259  0 getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g,
1260    pageWidth - idWidth, totalHeight, 0);
1261   
1262  0 if ((pageNumber * pageHeight) < totalHeight)
1263    {
1264  0 return Printable.PAGE_EXISTS;
1265    }
1266    else
1267    {
1268  0 return Printable.NO_SUCH_PAGE;
1269    }
1270    }
1271   
1272    /**
1273    * get current sequence ID panel width, or nominal value if panel were to be
1274    * displayed using default settings
1275    *
1276    * @return
1277    */
 
1278  0 toggle public int getVisibleIdWidth()
1279    {
1280  0 return getVisibleIdWidth(true);
1281    }
1282   
1283    /**
1284    * get current sequence ID panel width, or nominal value if panel were to be
1285    * displayed using default settings
1286    *
1287    * @param onscreen
1288    * indicate if the Id width for onscreen or offscreen display should
1289    * be returned
1290    * @return
1291    */
 
1292  76 toggle protected int getVisibleIdWidth(boolean onscreen)
1293    {
1294    // see if rendering offscreen - check preferences and calc width accordingly
1295  76 if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
1296    {
1297  0 return calculateIdWidth(-1, true, true).width;
1298    }
1299  76 Integer idwidth = onscreen ? null
1300    : Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
1301  76 if (idwidth != null)
1302    {
1303  0 return idwidth.intValue() + ID_WIDTH_PADDING;
1304    }
1305   
1306    // int w = getIdPanel().getWidth();
1307    // w = calculateIdWidth(-1, true, true).width;
1308  76 int w = calculateIdWidth(-1, true, true).width;
1309  76 return (w > 0 ? w : calculateIdWidth().width);
1310    }
1311   
 
1312  12 toggle void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer)
1313    throws ImageOutputException
1314    {
1315  12 makeAlignmentImage(type, file, renderer,
1316    BitmapImageSizing.defaultBitmapImageSizing());
1317    }
1318   
1319    /**
1320    * Builds an image of the alignment of the specified type (EPS/PNG/SVG) and
1321    * writes it to the specified file
1322    *
1323    * @param type
1324    * @param file
1325    * @param textrenderer
1326    * @param bitmapscale
1327    */
 
1328  36 toggle void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer,
1329    BitmapImageSizing userBis) throws ImageOutputException
1330    {
1331  36 final int borderBottomOffset = 5;
1332   
1333  36 AlignmentDimension aDimension = getAlignmentDimension();
1334   
1335    // todo use a lambda function in place of callback here?
1336  36 ImageWriterI writer = new ImageWriterI()
1337    {
 
1338  36 toggle @Override
1339    public void exportImage(Graphics graphics) throws Exception
1340    {
1341  36 if (av.getWrapAlignment())
1342    {
1343  0 printWrappedAlignment(aDimension.getWidth(),
1344    aDimension.getHeight() + borderBottomOffset, 0, graphics);
1345    }
1346    else
1347    {
1348  36 printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
1349    graphics, graphics);
1350    }
1351    }
1352    };
1353   
1354  36 String fileTitle = alignFrame.getTitle();
1355  36 ImageExporter exporter = new ImageExporter(writer, alignFrame, type,
1356    fileTitle);
1357  36 int imageWidth = aDimension.getWidth();
1358  36 int imageHeight = aDimension.getHeight() + borderBottomOffset;
1359  36 String of = MessageManager.getString("label.alignment");
1360  36 exporter.doExport(file, this, imageWidth, imageHeight, of, renderer,
1361    userBis);
1362    }
1363   
1364    /**
1365    * Calculates and returns a suitable width and height (in pixels) for an
1366    * exported image
1367    *
1368    * @return
1369    */
 
1370  38 toggle public AlignmentDimension getAlignmentDimension()
1371    {
1372  38 int maxwidth = av.getAlignment().getVisibleWidth();
1373   
1374  38 int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
1375    + getScalePanel().getHeight();
1376  38 int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
1377   
1378  38 if (av.getWrapAlignment())
1379    {
1380  0 height = getWrappedHeight();
1381  0 if (Jalview.isHeadlessMode())
1382    {
1383    // need to obtain default alignment width and then add in any
1384    // additional allowance for id margin
1385    // this duplicates the calculation in getWrappedHeight but adjusts for
1386    // offscreen idWidth
1387  0 width = alignFrame.getWidth() - vscroll.getPreferredSize().width
1388    - alignFrame.getInsets().left - alignFrame.getInsets().right
1389    - getVisibleIdWidth() + getVisibleIdWidth(false);
1390    }
1391    else
1392    {
1393  0 width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
1394    }
1395   
1396    }
1397  38 else if (av.isShowAnnotation())
1398    {
1399  38 height += getAnnotationPanel().adjustPanelHeight() + 3;
1400    }
1401  38 return new AlignmentDimension(width, height);
1402   
1403    }
1404   
 
1405  0 toggle public void makePNGImageMap(File imgMapFile, String imageName)
1406    throws ImageOutputException
1407    {
1408    // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
1409    // ////////////////////////////////////////////
1410  0 int idWidth = getVisibleIdWidth(false);
1411  0 FontMetrics fm = getFontMetrics(av.getFont());
1412  0 int scaleHeight = av.getCharHeight() + fm.getDescent();
1413   
1414    // Gen image map
1415    // ////////////////////////////////
1416  0 if (imgMapFile != null)
1417    {
1418  0 try
1419    {
1420  0 int sSize = av.getAlignment().getHeight();
1421  0 int alwidth = av.getAlignment().getWidth();
1422  0 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
1423  0 out.println(HTMLOutput.getImageMapHTML());
1424  0 out.println("<img src=\"" + imageName
1425    + "\" border=\"0\" usemap=\"#Map\" >"
1426    + "<map name=\"Map\">");
1427   
1428  0 for (int s = 0; s < sSize; s++)
1429    {
1430  0 int sy = s * av.getCharHeight() + scaleHeight;
1431   
1432  0 SequenceI seq = av.getAlignment().getSequenceAt(s);
1433  0 SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
1434  0 for (int column = 0; column < alwidth; column++)
1435    {
1436  0 StringBuilder text = new StringBuilder(512);
1437  0 String triplet = null;
1438  0 if (av.getAlignment().isNucleotide())
1439    {
1440  0 triplet = ResidueProperties.nucleotideName
1441    .get(seq.getCharAt(column) + "");
1442    }
1443    else
1444    {
1445  0 triplet = ResidueProperties.aa2Triplet
1446    .get(seq.getCharAt(column) + "");
1447    }
1448   
1449  0 if (triplet == null)
1450    {
1451  0 continue;
1452    }
1453   
1454  0 int seqPos = seq.findPosition(column);
1455  0 int gSize = groups.length;
1456  0 for (int g = 0; g < gSize; g++)
1457    {
1458  0 if (text.length() < 1)
1459    {
1460  0 text.append("<area shape=\"rect\" coords=\"")
1461    .append((idWidth + column * av.getCharWidth()))
1462    .append(",").append(sy).append(",")
1463    .append((idWidth
1464    + (column + 1) * av.getCharWidth()))
1465    .append(",").append((av.getCharHeight() + sy))
1466    .append("\"").append(" onMouseOver=\"toolTip('")
1467    .append(seqPos).append(" ").append(triplet);
1468    }
1469   
1470  0 if (groups[g].getStartRes() < column
1471    && groups[g].getEndRes() > column)
1472    {
1473  0 text.append("<br><em>").append(groups[g].getName())
1474    .append("</em>");
1475    }
1476    }
1477   
1478  0 if (text.length() < 1)
1479    {
1480  0 text.append("<area shape=\"rect\" coords=\"")
1481    .append((idWidth + column * av.getCharWidth()))
1482    .append(",").append(sy).append(",")
1483    .append((idWidth + (column + 1) * av.getCharWidth()))
1484    .append(",").append((av.getCharHeight() + sy))
1485    .append("\"").append(" onMouseOver=\"toolTip('")
1486    .append(seqPos).append(" ").append(triplet);
1487    }
1488  0 if (!Comparison.isGap(seq.getCharAt(column)))
1489    {
1490  0 List<SequenceFeature> features = seq.findFeatures(column,
1491    column);
1492  0 for (SequenceFeature sf : features)
1493    {
1494  0 if (sf.isContactFeature())
1495    {
1496  0 text.append("<br>").append(sf.getType()).append(" ")
1497    .append(sf.getBegin()).append(":")
1498    .append(sf.getEnd());
1499    }
1500    else
1501    {
1502  0 text.append("<br>");
1503  0 text.append(sf.getType());
1504  0 String description = sf.getDescription();
1505  0 if (description != null
1506    && !sf.getType().equals(description))
1507    {
1508  0 description = description.replace("\"", "&quot;");
1509  0 text.append(" ").append(description);
1510    }
1511    }
1512  0 String status = sf.getStatus();
1513  0 if (status != null && !"".equals(status))
1514    {
1515  0 text.append(" (").append(status).append(")");
1516    }
1517    }
1518  0 if (text.length() > 1)
1519    {
1520  0 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
1521  0 out.println(text.toString());
1522    }
1523    }
1524    }
1525    }
1526  0 out.println("</map></body></html>");
1527  0 out.close();
1528   
1529    } catch (Exception ex)
1530    {
1531  0 throw new ImageOutputException(
1532    "couldn't write ImageMap due to unexpected error", ex);
1533    }
1534    } // /////////END OF IMAGE MAP
1535   
1536    }
1537   
1538    /**
1539    * Answers the height of the entire alignment in pixels, assuming it is in
1540    * wrapped mode
1541    *
1542    * @return
1543    */
 
1544  0 toggle int getWrappedHeight()
1545    {
1546  0 int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
1547   
1548  0 if (Jalview.isHeadlessMode())
1549    {
1550  0 seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
1551    - vscroll.getPreferredSize().width
1552    - alignFrame.getInsets().left - alignFrame.getInsets().right;
1553    }
1554   
1555  0 int chunkWidth = getSeqPanel().seqCanvas
1556    .getWrappedCanvasWidth(seqPanelWidth);
1557   
1558  0 int hgap = av.getCharHeight();
1559  0 if (av.getScaleAboveWrapped())
1560    {
1561  0 hgap += av.getCharHeight();
1562    }
1563   
1564  0 int annotationHeight = 0;
1565  0 if (av.isShowAnnotation())
1566    {
1567  0 hgap += SeqCanvas.SEQS_ANNOTATION_GAP;
1568  0 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1569    }
1570   
1571  0 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1572    + annotationHeight;
1573   
1574  0 int maxwidth = av.getAlignment().getWidth();
1575  0 if (av.hasHiddenColumns())
1576    {
1577  0 maxwidth = av.getAlignment().getHiddenColumns()
1578    .absoluteToVisibleColumn(maxwidth) - 1;
1579    }
1580   
1581  0 int height = ((maxwidth / chunkWidth) + 1) * cHeight;
1582   
1583  0 return height;
1584    }
1585   
1586    /**
1587    * close the panel - deregisters all listeners and nulls any references to
1588    * alignment data.
1589    */
 
1590  270 toggle public void closePanel()
1591    {
1592  270 PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
1593  270 PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
1594  270 PaintRefresher.RemoveComponent(this);
1595   
1596  270 closeChildFrames();
1597   
1598    /*
1599    * try to ensure references are nulled
1600    */
1601  270 if (annotationPanel != null)
1602    {
1603  270 annotationPanel.dispose();
1604  270 annotationPanel = null;
1605    }
1606   
1607  270 if (av != null)
1608    {
1609  270 av.removePropertyChangeListener(propertyChangeListener);
1610  270 propertyChangeListener = null;
1611  270 StructureSelectionManager ssm = av.getStructureSelectionManager();
1612  270 ssm.removeStructureViewerListener(getSeqPanel(), null);
1613  269 ssm.removeSelectionListener(getSeqPanel());
1614  269 ssm.removeCommandListener(av);
1615  269 ssm.removeStructureViewerListener(getSeqPanel(), null);
1616  269 ssm.removeSelectionListener(getSeqPanel());
1617  269 av.dispose();
1618  269 av = null;
1619    }
1620    else
1621    {
1622  0 if (Console.isDebugEnabled())
1623    {
1624  0 Console.warn("Closing alignment panel which is already closed.");
1625    }
1626    }
1627    }
1628   
1629    /**
1630    * Close any open dialogs that would be orphaned when this one is closed
1631    */
 
1632  270 toggle protected void closeChildFrames()
1633    {
1634  270 if (overviewPanel != null)
1635    {
1636  1 overviewPanel.dispose();
1637  1 overviewPanel = null;
1638    }
1639  270 if (calculationDialog != null)
1640    {
1641  0 calculationDialog.closeFrame();
1642  0 calculationDialog = null;
1643    }
1644    }
1645   
1646    /**
1647    * hides or shows dynamic annotation rows based on groups and av state flags
1648    */
 
1649  46 toggle public void updateAnnotation()
1650    {
1651  46 updateAnnotation(false, false);
1652    }
1653   
 
1654  0 toggle public void updateAnnotation(boolean applyGlobalSettings)
1655    {
1656  0 updateAnnotation(applyGlobalSettings, false);
1657    }
1658   
 
1659  135 toggle public void updateAnnotation(boolean applyGlobalSettings,
1660    boolean preserveNewGroupSettings)
1661    {
1662  135 av.updateGroupAnnotationSettings(applyGlobalSettings,
1663    preserveNewGroupSettings);
1664  135 adjustAnnotationHeight();
1665    }
1666   
 
1667  16408 toggle @Override
1668    public AlignmentI getAlignment()
1669    {
1670  16409 return av == null ? null : av.getAlignment();
1671    }
1672   
 
1673  3253 toggle @Override
1674    public String getViewName()
1675    {
1676  3253 return av.getViewName();
1677    }
1678   
1679    /**
1680    * Make/Unmake this alignment panel the current input focus
1681    *
1682    * @param b
1683    */
 
1684  0 toggle public void setSelected(boolean b)
1685    {
1686  0 try
1687    {
1688  0 if (alignFrame.getSplitViewContainer() != null)
1689    {
1690    /*
1691    * bring enclosing SplitFrame to front first if there is one
1692    */
1693  0 ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b);
1694    }
1695  0 alignFrame.setSelected(b);
1696    } catch (Exception ex)
1697    {
1698    }
1699  0 if (b)
1700    {
1701  0 setAlignFrameView();
1702    }
1703    }
1704   
 
1705  0 toggle public void setAlignFrameView()
1706    {
1707  0 alignFrame.setDisplayedView(this);
1708    }
1709   
 
1710  143 toggle @Override
1711    public StructureSelectionManager getStructureSelectionManager()
1712    {
1713  143 return av.getStructureSelectionManager();
1714    }
1715   
 
1716  0 toggle @Override
1717    public void raiseOOMWarning(String string, OutOfMemoryError error)
1718    {
1719  0 new OOMWarning(string, error, this);
1720    }
1721   
 
1722  20 toggle @Override
1723    public jalview.api.FeatureRenderer cloneFeatureRenderer()
1724    {
1725   
1726  20 return new FeatureRenderer(this);
1727    }
1728   
 
1729  611 toggle @Override
1730    public jalview.api.FeatureRenderer getFeatureRenderer()
1731    {
1732  611 return seqPanel.seqCanvas.getFeatureRenderer();
1733    }
1734   
 
1735  0 toggle public void updateFeatureRenderer(
1736    jalview.renderer.seqfeatures.FeatureRenderer fr)
1737    {
1738  0 fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
1739    }
1740   
 
1741  0 toggle public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
1742    {
1743  0 if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
1744    {
1745  0 getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr);
1746    }
1747    }
1748   
 
1749  580 toggle public ScalePanel getScalePanel()
1750    {
1751  580 return scalePanel;
1752    }
1753   
 
1754  501 toggle public void setScalePanel(ScalePanel scalePanel)
1755    {
1756  501 this.scalePanel = scalePanel;
1757    }
1758   
 
1759  16715 toggle public SeqPanel getSeqPanel()
1760    {
1761  16715 return seqPanel;
1762    }
1763   
 
1764  501 toggle public void setSeqPanel(SeqPanel seqPanel)
1765    {
1766  501 this.seqPanel = seqPanel;
1767    }
1768   
 
1769  15934 toggle public AnnotationPanel getAnnotationPanel()
1770    {
1771  15934 return annotationPanel;
1772    }
1773   
 
1774  501 toggle public void setAnnotationPanel(AnnotationPanel annotationPanel)
1775    {
1776  501 this.annotationPanel = annotationPanel;
1777    }
1778   
 
1779  16194 toggle public AnnotationLabels getAlabels()
1780    {
1781  16194 return alabels;
1782    }
1783   
 
1784  501 toggle public void setAlabels(AnnotationLabels alabels)
1785    {
1786  501 this.alabels = alabels;
1787    }
1788   
 
1789  11557 toggle public IdPanel getIdPanel()
1790    {
1791  11557 return idPanel;
1792    }
1793   
 
1794  501 toggle public void setIdPanel(IdPanel idPanel)
1795    {
1796  501 this.idPanel = idPanel;
1797    }
1798   
1799    /**
1800    * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
1801    * The aim is to keep the two alignments 'lined up' on their centre columns.
1802    *
1803    * @param sr
1804    * holds mapped region(s) of this alignment that we are scrolling
1805    * 'to'; may be modified for sequence offset by this method
1806    * @param verticalOffset
1807    * the number of visible sequences to show above the mapped region
1808    */
 
1809  4 toggle protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
1810    {
1811  4 scrollToPosition(sr, verticalOffset, true);
1812    }
1813   
1814    /**
1815    * Set a flag to say do not scroll any (cDNA/protein) complement.
1816    *
1817    * @param b
1818    */
 
1819  1536 toggle protected void setToScrollComplementPanel(boolean b)
1820    {
1821  1536 this.scrollComplementaryPanel = b;
1822    }
1823   
1824    /**
1825    * Get whether to scroll complement panel
1826    *
1827    * @return true if cDNA/protein complement panels should be scrolled
1828    */
 
1829  768 toggle protected boolean isSetToScrollComplementPanel()
1830    {
1831  768 return this.scrollComplementaryPanel;
1832    }
1833   
1834    /**
1835    * Redraw sensibly.
1836    *
1837    * @adjustHeight if true, try to recalculate panel height for visible
1838    * annotations
1839    */
 
1840  0 toggle protected void refresh(boolean adjustHeight)
1841    {
1842  0 validateAnnotationDimensions(adjustHeight);
1843  0 addNotify();
1844  0 if (adjustHeight)
1845    {
1846    // sort, repaint, update overview
1847  0 paintAlignment(true, false);
1848    }
1849    else
1850    {
1851    // lightweight repaint
1852  0 repaint();
1853    }
1854    }
1855   
 
1856  768 toggle @Override
1857    /**
1858    * Property change event fired when a change is made to the viewport ranges
1859    * object associated with this alignment panel's viewport
1860    */
1861    public void propertyChange(PropertyChangeEvent evt)
1862    {
1863    // update this panel's scroll values based on the new viewport ranges values
1864  768 ViewportRanges ranges = av.getRanges();
1865  768 int x = ranges.getStartRes();
1866  768 int y = ranges.getStartSeq();
1867  768 setScrollValues(x, y);
1868   
1869    // now update any complementary alignment (its viewport ranges object
1870    // is different so does not get automatically updated)
1871  768 if (isSetToScrollComplementPanel())
1872    {
1873  763 setToScrollComplementPanel(false);
1874  763 av.scrollComplementaryAlignment();
1875  763 setToScrollComplementPanel(true);
1876    }
1877    }
1878   
1879    /**
1880    * Set the reference to the PCA/Tree chooser dialog for this panel. This
1881    * reference should be nulled when the dialog is closed.
1882    *
1883    * @param calculationChooser
1884    */
 
1885  0 toggle public void setCalculationDialog(CalculationChooser calculationChooser)
1886    {
1887  0 calculationDialog = calculationChooser;
1888    }
1889   
1890    /**
1891    * Returns the reference to the PCA/Tree chooser dialog for this panel (null
1892    * if none is open)
1893    */
 
1894  991 toggle public CalculationChooser getCalculationDialog()
1895    {
1896  991 return calculationDialog;
1897    }
1898   
1899    /**
1900    * Constructs and sets the title for the Overview window (if there is one),
1901    * including the align frame's title, and view name (if applicable). Returns
1902    * the title, or null if this panel has no Overview window open.
1903    *
1904    * @param alignFrame
1905    * @return
1906    */
 
1907  484 toggle public String setOverviewTitle(AlignFrame alignFrame)
1908    {
1909  484 if (this.overviewPanel == null)
1910    {
1911  382 return null;
1912    }
1913  102 String overviewTitle = MessageManager
1914    .formatMessage("label.overview_params", new Object[]
1915    { alignFrame.getTitle() });
1916  102 String viewName = getViewName();
1917  102 if (viewName != null)
1918    {
1919  65 overviewTitle += (" " + viewName);
1920    }
1921  102 overviewPanel.setTitle(overviewTitle);
1922  102 return overviewTitle;
1923    }
1924   
1925    /**
1926    * If this alignment panel has an Overview panel open, closes it
1927    */
 
1928  36 toggle public void closeOverviewPanel()
1929    {
1930  36 if (overviewPanel != null)
1931    {
1932  12 overviewPanel.close();
1933  12 overviewPanel = null;
1934    }
1935    }
1936    }
  • Report generated by OpenClover v 4.4.1 on Wed Nov 5 2025 13:25:38 GMT using coverage data from Wed Nov 5 2025 13:25:23 GMT.
  • OpenClover is free and open-source software.