2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.appletgui;
24 import java.awt.event.*;
26 import jalview.api.AlignmentViewPanel;
27 import jalview.datamodel.*;
28 import jalview.structure.StructureSelectionManager;
30 public class AlignmentPanel extends Panel implements AdjustmentListener,
34 public AlignViewport av;
36 OverviewPanel overviewPanel;
42 IdwidthAdjuster idwidthAdjuster;
44 public AlignFrame alignFrame;
46 ScalePanel scalePanel;
48 AnnotationPanel annotationPanel;
50 AnnotationLabels alabels;
52 // this value is set false when selection area being dragged
53 boolean fastPaint = true;
55 public void finalize()
60 seqPanelHolder = null;
61 sequenceHolderPanel = null;
63 scalePanelHolder = null;
64 annotationPanel = null;
65 annotationPanelHolder = null;
66 annotationSpaceFillerHolder = null;
69 public AlignmentPanel(AlignFrame af, final AlignViewport av)
81 seqPanel = new SeqPanel(av, this);
82 idPanel = new IdPanel(av, this);
83 scalePanel = new ScalePanel(av, this);
84 idwidthAdjuster = new IdwidthAdjuster(this);
85 annotationPanel = new AnnotationPanel(this);
86 annotationPanelHolder.add(annotationPanel, BorderLayout.CENTER);
88 sequenceHolderPanel.add(annotationPanelHolder, BorderLayout.SOUTH);
89 alabels = new AnnotationLabels(this);
91 setAnnotationVisible(av.showAnnotation);
93 idPanelHolder.add(idPanel, BorderLayout.CENTER);
94 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
95 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
96 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
97 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
100 setScrollValues(0, 0);
102 apvscroll.addAdjustmentListener(this);
103 hscroll.addAdjustmentListener(this);
104 vscroll.addAdjustmentListener(this);
106 addComponentListener(new ComponentAdapter()
108 public void componentResized(ComponentEvent evt)
110 setScrollValues(av.getStartRes(), av.getStartSeq());
111 if (getSize().height > 0
112 && annotationPanelHolder.getSize().height > 0)
114 validateAnnotationDimensions(false);
121 Dimension d = calculateIdWidth();
122 idPanel.idCanvas.setSize(d);
124 hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
126 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
127 annotationSpaceFillerHolder.setSize(d.width,
128 annotationPanel.getSize().height);
129 alabels.setSize(d.width, annotationPanel.getSize().height);
130 final AlignmentPanel ap = this;
131 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
133 public void propertyChange(java.beans.PropertyChangeEvent evt)
135 if (evt.getPropertyName().equals("alignment"))
137 PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
144 public SequenceRenderer getSequenceRenderer()
146 return seqPanel.seqCanvas.sr;
149 public jalview.api.FeatureRenderer getFeatureRenderer()
151 return seqPanel.seqCanvas.fr;
154 public jalview.api.FeatureRenderer cloneFeatureRenderer()
156 FeatureRenderer nfr = new FeatureRenderer(av);
157 nfr.transferSettings(seqPanel.seqCanvas.fr);
160 public void alignmentChanged()
162 av.alignmentChanged(this);
164 if (overviewPanel != null)
166 overviewPanel.updateOverviewImage();
169 alignFrame.updateEditMenuBar();
174 public void fontChanged()
176 // set idCanvas bufferedImage to null
177 // to prevent drawing old image
178 idPanel.idCanvas.image = null;
179 FontMetrics fm = getFontMetrics(av.getFont());
181 scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
182 idwidthAdjuster.setSize(new Dimension(10, av.charHeight
184 av.updateSequenceIdColours();
185 annotationPanel.image = null;
186 int ap = annotationPanel.adjustPanelHeight(false);
187 Dimension d = calculateIdWidth();
188 d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
189 alabels.setSize(d.width + 4, ap);
191 idPanel.idCanvas.setSize(d);
192 hscrollFillerPanel.setSize(d);
194 validateAnnotationDimensions(false);
195 annotationPanel.repaint();
199 if (overviewPanel != null)
201 overviewPanel.updateOverviewImage();
205 public void setIdWidth(int w, int h)
207 idPanel.idCanvas.setSize(w, h);
208 idPanelHolder.setSize(w, idPanelHolder.getSize().height);
209 annotationSpaceFillerHolder.setSize(w,
210 annotationSpaceFillerHolder.getSize().height);
211 alabels.setSize(w, alabels.getSize().height);
215 Dimension calculateIdWidth()
217 if (av.nullFrame == null)
219 av.nullFrame = new Frame();
220 av.nullFrame.addNotify();
223 Graphics g = av.nullFrame.getGraphics();
225 FontMetrics fm = g.getFontMetrics(av.font);
226 AlignmentI al = av.getAlignment();
231 while (i < al.getHeight() && al.getSequenceAt(i) != null)
233 SequenceI s = al.getSequenceAt(i);
234 id = s.getDisplayId(av.getShowJVSuffix());
236 if (fm.stringWidth(id) > idWidth)
238 idWidth = fm.stringWidth(id);
243 // Also check annotation label widths
245 if (al.getAlignmentAnnotation() != null)
247 fm = g.getFontMetrics(av.nullFrame.getFont());
248 while (i < al.getAlignmentAnnotation().length)
250 String label = al.getAlignmentAnnotation()[i].label;
251 if (fm.stringWidth(label) > idWidth)
253 idWidth = fm.stringWidth(label);
259 return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
263 * Highlight the given results on the alignment.
266 public void highlightSearchResults(SearchResults results)
268 scrollToPosition(results);
269 seqPanel.seqCanvas.highlightSearchResults(results);
273 * scroll the view to show the position of the highlighted region in results
274 * (if any) and redraw the overview
277 * @return false if results were not found
279 public boolean scrollToPosition(SearchResults results)
281 return scrollToPosition(results, true);
285 * scroll the view to show the position of the highlighted region in results
289 * @param redrawOverview
290 * - when set, the overview will be recalculated (takes longer)
291 * @return false if results were not found
293 public boolean scrollToPosition(SearchResults results,
294 boolean redrawOverview)
297 // do we need to scroll the panel?
298 if (results != null && results.getSize() > 0)
300 AlignmentI alignment = av.getAlignment();
301 int seqIndex = alignment.findIndex(results);
306 SequenceI seq = alignment.getSequenceAt(seqIndex);
307 int[] r = results.getResults(seq, 0, alignment.getWidth());
313 .println("DEBUG: scroll didn't happen - results not within alignment : "
314 + seq.getStart() + "," + seq.getEnd());
322 * System.out.println("DEBUG: scroll: start=" + r[0] +
323 * " av.getStartRes()=" + av.getStartRes() + " end=" + r[1] +
324 * " seq.end=" + seq.getEnd() + " av.getEndRes()=" + av.getEndRes() +
325 * " hextent=" + hextent);
334 if (end == seq.getEnd())
338 return scrollTo(start, end, seqIndex, false, redrawOverview);
343 public boolean scrollTo(int ostart, int end, int seqIndex,
344 boolean scrollToNearest, boolean redrawOverview)
346 int startv, endv, starts, ends, width;
349 if (av.hasHiddenColumns())
351 start = av.getColumnSelection().findColumnPosition(ostart);
352 end = av.getColumnSelection().findColumnPosition(end);
355 if (!scrollToNearest && !av.getColumnSelection().isVisible(ostart))
357 // don't scroll - position isn't visible
366 if (!av.wrapAlignment)
369 * int spos=av.getStartRes(),sqpos=av.getStartSeq(); if ((startv =
370 * av.getStartRes()) >= start) { spos=start-1; // seqIn //
371 * setScrollValues(start - 1, seqIndex); } else if ((endv =
372 * av.getEndRes()) <= end) { // setScrollValues(spos=startv + 1 + end -
373 * endv, seqIndex); spos=startv + 1 + end - endv; } else if ((starts =
374 * av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(),
375 * seqIndex); } else if ((ends = av.getEndSeq()) <= seqIndex) {
376 * setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); }
380 if ((av.getStartRes() > end)
381 || (av.getEndRes() < start)
382 || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
384 if (start > av.getAlignment().getWidth() - hextent)
386 start = av.getAlignment().getWidth() - hextent;
393 if (seqIndex > av.getAlignment().getHeight() - vextent)
395 seqIndex = av.getAlignment().getHeight() - vextent;
401 // System.out.println("trying to scroll to: "+start+" "+seqIndex);
402 setScrollValues(start, seqIndex);
407 scrollToWrappedVisible(start);
409 if (redrawOverview && overviewPanel != null)
411 overviewPanel.setBoxPosition();
413 paintAlignment(redrawOverview);
417 void scrollToWrappedVisible(int res)
419 int cwidth = seqPanel.seqCanvas
420 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
421 if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
423 vscroll.setValue(res / cwidth);
424 av.startRes = vscroll.getValue() * cwidth;
428 public OverviewPanel getOverviewPanel()
430 return overviewPanel;
433 public void setOverviewPanel(OverviewPanel op)
438 public void setAnnotationVisible(boolean b)
440 if (!av.wrapAlignment)
442 annotationSpaceFillerHolder.setVisible(b);
443 annotationPanelHolder.setVisible(b);
447 annotationSpaceFillerHolder.setVisible(false);
448 annotationPanelHolder.setVisible(false);
455 * automatically adjust annotation panel height for new annotation whilst
456 * ensuring the alignment is still visible.
458 public void adjustAnnotationHeight()
460 // TODO: display vertical annotation scrollbar if necessary
461 // this is called after loading new annotation onto alignment
462 if (alignFrame.getSize().height == 0)
464 System.out.println("NEEDS FIXING");
467 validateAnnotationDimensions(true);
468 apvscroll.addNotify();
471 paintAlignment(true);
475 * calculate the annotation dimensions and refresh slider values accordingly.
476 * need to do repaints/notifys afterwards.
478 protected void validateAnnotationDimensions(boolean adjustPanelHeight)
480 boolean modified = false;
481 int height = av.calcPanelHeight();
483 if (hscroll.isVisible())
485 height += (minsize = hscroll.getPreferredSize().height);
487 if (apvscroll.isVisible())
489 minsize += apvscroll.getPreferredSize().height;
491 int mheight = height;
492 Dimension d = sequenceHolderPanel.getSize(), e = idPanel.getSize();
493 int seqandannot = d.height - scalePanelHolder.getSize().height;
495 if (adjustPanelHeight)
497 // NOTE: this logic is different in the application. Need a better
498 // algorithm to define behaviour
499 // sets initial preferred height
500 // try and set height according to alignment
501 float sscaling = (float) ((av.getCharHeight() * av.getAlignment()
502 .getHeight()) / (1.0 * mheight));
505 // if the alignment is too big then
506 // default is 0.5 split
507 height = seqandannot / 2;
511 // otherwise just set the panel so that one row of sequence is visible
512 height = -av.getCharHeight() * 1
513 + (int) (seqandannot * (1 - sscaling));
518 // maintain same window layout whilst updating sliders
519 height = annotationPanelHolder.getSize().height;
522 if (seqandannot - height < 5)
524 height = seqandannot;
526 annotationPanel.setSize(new Dimension(d.width, height));
527 alabels.setSize(new Dimension(e.width, height));
528 annotationSpaceFillerHolder.setSize(new Dimension(e.width, height));
529 annotationPanelHolder.setSize(new Dimension(d.width, height));
530 // seqPanelHolder.setSize(d.width, seqandannot - height);
532 .setSize(d.width, seqPanel.seqCanvas.getSize().height);
533 int s = apvscroll.getValue();
534 if (s > mheight - height)
538 apvscroll.setValues(s, height, 0, mheight);
539 annotationPanel.setScrollOffset(apvscroll.getValue(), false);
540 alabels.setScrollOffset(apvscroll.getValue(), false);
543 public void setWrapAlignment(boolean wrap)
547 scalePanelHolder.setVisible(!wrap);
549 hscroll.setVisible(!wrap);
550 idwidthAdjuster.setVisible(!wrap);
554 annotationPanelHolder.setVisible(false);
555 annotationSpaceFillerHolder.setVisible(false);
557 else if (av.showAnnotation)
559 annotationPanelHolder.setVisible(true);
560 annotationSpaceFillerHolder.setVisible(true);
563 idSpaceFillerPanel1.setVisible(!wrap);
565 fontChanged(); // This is so that the scalePanel is resized correctly
568 sequenceHolderPanel.validate();
577 // return value is true if the scroll is valid
578 public boolean scrollUp(boolean up)
582 if (vscroll.getValue() < 1)
586 setScrollValues(hscroll.getValue(), vscroll.getValue() - 1);
590 if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())
594 setScrollValues(hscroll.getValue(), vscroll.getValue() + 1);
601 public boolean scrollRight(boolean right)
605 if (hscroll.getValue() < 1)
609 setScrollValues(hscroll.getValue() - 1, vscroll.getValue());
613 if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
617 setScrollValues(hscroll.getValue() + 1, vscroll.getValue());
624 public void setScrollValues(int x, int y)
626 int width = av.getAlignment().getWidth();
627 int height = av.getAlignment().getHeight();
629 if (av.hasHiddenColumns())
631 width = av.getColumnSelection().findColumnPosition(width);
639 hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
640 vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
647 if (vextent > height)
652 if ((hextent + x) > width)
654 System.err.println("hextent was " + hextent + " and x was " + x);
659 if ((vextent + y) > height)
661 y = height - vextent;
671 System.err.println("x was " + x);
677 int endSeq = y + vextent;
678 if (endSeq > av.getAlignment().getHeight())
680 endSeq = av.getAlignment().getHeight();
683 av.setEndSeq(endSeq);
685 av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
687 hscroll.setValues(x, hextent, 0, width);
688 vscroll.setValues(y, vextent, 0, height);
690 if (overviewPanel != null)
692 overviewPanel.setBoxPosition();
698 public void adjustmentValueChanged(AdjustmentEvent evt)
700 int oldX = av.getStartRes();
701 int oldY = av.getStartSeq();
703 if (evt == null || evt.getSource() == apvscroll)
705 annotationPanel.setScrollOffset(apvscroll.getValue(), false);
706 alabels.setScrollOffset(apvscroll.getValue(), false);
707 // annotationPanel.image=null;
708 // alabels.image=null;
709 // alabels.repaint();
710 // annotationPanel.repaint();
712 if (evt == null || evt.getSource() == hscroll)
714 int x = hscroll.getValue();
716 av.setEndRes(x + seqPanel.seqCanvas.getSize().width
717 / av.getCharWidth() - 1);
720 if (evt == null || evt.getSource() == vscroll)
722 int offy = vscroll.getValue();
723 if (av.getWrapAlignment())
725 int rowSize = seqPanel.seqCanvas
726 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
727 av.setStartRes(vscroll.getValue() * rowSize);
728 av.setEndRes((vscroll.getValue() + 1) * rowSize);
732 av.setStartSeq(offy);
733 av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
734 / av.getCharHeight());
738 if (overviewPanel != null)
740 overviewPanel.setBoxPosition();
743 int scrollX = av.startRes - oldX;
744 int scrollY = av.startSeq - oldY;
746 if (av.getWrapAlignment() || !fastPaint || av.MAC)
752 // Make sure we're not trying to draw a panel
753 // larger than the visible window
754 if (scrollX > av.endRes - av.startRes)
756 scrollX = av.endRes - av.startRes;
758 else if (scrollX < av.startRes - av.endRes)
760 scrollX = av.startRes - av.endRes;
763 idPanel.idCanvas.fastPaint(scrollY);
764 seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
766 scalePanel.repaint();
767 if (av.getShowAnnotation())
769 annotationPanel.fastPaint(av.getStartRes() - oldX);
776 private void sendViewPosition()
778 StructureSelectionManager.getStructureSelectionManager(av.applet)
779 .sendViewPosition(this, av.startRes, av.endRes, av.startSeq,
783 public void paintAlignment(boolean updateOverview)
789 jalview.structure.StructureSelectionManager
790 .getStructureSelectionManager(av.applet)
791 .sequenceColoursChanged(this);
793 if (overviewPanel != null)
795 overviewPanel.updateOverviewImage();
800 public void update(Graphics g)
805 public void paint(Graphics g)
808 Dimension d = idPanel.idCanvas.getSize();
809 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
811 if (av.getWrapAlignment())
813 int maxwidth = av.getAlignment().getWidth();
815 if (av.hasHiddenColumns())
817 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
820 int canvasWidth = seqPanel.seqCanvas
821 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
825 int max = maxwidth / canvasWidth;
826 vscroll.setMaximum(1 + max);
827 vscroll.setUnitIncrement(1);
828 vscroll.setVisibleAmount(1);
833 setScrollValues(av.getStartRes(), av.getStartSeq());
836 seqPanel.seqCanvas.repaint();
837 idPanel.idCanvas.repaint();
838 if (!av.wrapAlignment)
840 if (av.showAnnotation)
843 annotationPanel.repaint();
845 scalePanel.repaint();
850 protected Panel sequenceHolderPanel = new Panel();
852 protected Scrollbar vscroll = new Scrollbar();
854 protected Scrollbar hscroll = new Scrollbar();
856 protected Panel seqPanelHolder = new Panel();
858 BorderLayout borderLayout1 = new BorderLayout();
860 BorderLayout borderLayout3 = new BorderLayout();
862 protected Panel scalePanelHolder = new Panel();
864 protected Panel idPanelHolder = new Panel();
866 BorderLayout borderLayout5 = new BorderLayout();
868 protected Panel idSpaceFillerPanel1 = new Panel();
870 public Panel annotationSpaceFillerHolder = new Panel();
872 BorderLayout borderLayout6 = new BorderLayout();
874 BorderLayout borderLayout7 = new BorderLayout();
876 Panel hscrollHolder = new Panel();
878 BorderLayout borderLayout10 = new BorderLayout();
880 protected Panel hscrollFillerPanel = new Panel();
882 BorderLayout borderLayout11 = new BorderLayout();
884 BorderLayout borderLayout4 = new BorderLayout();
886 BorderLayout borderLayout2 = new BorderLayout();
888 Panel annotationPanelHolder = new Panel();
890 protected Scrollbar apvscroll = new Scrollbar();
892 BorderLayout borderLayout12 = new BorderLayout();
894 private void jbInit() throws Exception
896 // idPanelHolder.setPreferredSize(new Dimension(70, 10));
897 this.setLayout(borderLayout7);
899 // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
900 sequenceHolderPanel.setLayout(borderLayout3);
901 seqPanelHolder.setLayout(borderLayout1);
902 scalePanelHolder.setBackground(Color.white);
904 // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
905 scalePanelHolder.setLayout(borderLayout6);
906 idPanelHolder.setLayout(borderLayout5);
907 idSpaceFillerPanel1.setBackground(Color.white);
909 // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
910 idSpaceFillerPanel1.setLayout(borderLayout11);
911 annotationSpaceFillerHolder.setBackground(Color.white);
913 // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
914 annotationSpaceFillerHolder.setLayout(borderLayout4);
915 hscroll.setOrientation(Scrollbar.HORIZONTAL);
916 hscrollHolder.setLayout(borderLayout10);
917 hscrollFillerPanel.setBackground(Color.white);
918 apvscroll.setOrientation(Scrollbar.VERTICAL);
919 apvscroll.setVisible(true);
920 apvscroll.addAdjustmentListener(this);
922 annotationPanelHolder.setBackground(Color.white);
923 annotationPanelHolder.setLayout(borderLayout12);
924 annotationPanelHolder.add(apvscroll, BorderLayout.EAST);
925 // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
926 hscrollHolder.setBackground(Color.white);
928 // annotationScroller.setPreferredSize(new Dimension(10, 80));
929 // this.setPreferredSize(new Dimension(220, 166));
930 seqPanelHolder.setBackground(Color.white);
931 idPanelHolder.setBackground(Color.white);
932 sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
933 sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
934 seqPanelHolder.add(vscroll, BorderLayout.EAST);
936 // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
937 this.add(idPanelHolder, BorderLayout.WEST);
938 idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
939 idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
940 this.add(hscrollHolder, BorderLayout.SOUTH);
941 hscrollHolder.add(hscroll, BorderLayout.CENTER);
942 hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
943 this.add(sequenceHolderPanel, BorderLayout.CENTER);
947 * hides or shows dynamic annotation rows based on groups and av state flags
949 public void updateAnnotation()
951 updateAnnotation(false);
954 public void updateAnnotation(boolean applyGlobalSettings)
956 updateAnnotation(applyGlobalSettings, false);
959 public void updateAnnotation(boolean applyGlobalSettings,
960 boolean preserveNewGroupSettings)
962 av.updateGroupAnnotationSettings(applyGlobalSettings,
963 preserveNewGroupSettings);
964 adjustAnnotationHeight();
968 public AlignmentI getAlignment()
970 return av.getAlignment();
974 public StructureSelectionManager getStructureSelectionManager()
976 return StructureSelectionManager
977 .getStructureSelectionManager(av.applet);
981 public void raiseOOMWarning(String string, OutOfMemoryError error)
984 System.err.println("Out of memory whilst '" + string + "'");
985 error.printStackTrace();