2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.appletgui;
22 import java.awt.event.*;
24 import jalview.api.AlignmentViewPanel;
25 import jalview.datamodel.*;
26 import jalview.structure.StructureSelectionManager;
28 public class AlignmentPanel extends Panel implements AdjustmentListener,
32 public AlignViewport av;
34 OverviewPanel overviewPanel;
40 IdwidthAdjuster idwidthAdjuster;
42 public AlignFrame alignFrame;
44 ScalePanel scalePanel;
46 AnnotationPanel annotationPanel;
48 AnnotationLabels alabels;
50 // this value is set false when selection area being dragged
51 boolean fastPaint = true;
53 public void finalize()
58 seqPanelHolder = null;
59 sequenceHolderPanel = null;
61 scalePanelHolder = null;
62 annotationPanel = null;
63 annotationPanelHolder = null;
64 annotationSpaceFillerHolder = null;
67 public AlignmentPanel(AlignFrame af, final AlignViewport av)
79 seqPanel = new SeqPanel(av, this);
80 idPanel = new IdPanel(av, this);
81 scalePanel = new ScalePanel(av, this);
82 idwidthAdjuster = new IdwidthAdjuster(this);
83 annotationPanel = new AnnotationPanel(this);
84 annotationPanelHolder.add(annotationPanel, BorderLayout.CENTER);
86 sequenceHolderPanel.add(annotationPanelHolder, BorderLayout.SOUTH);
88 alabels = new AnnotationLabels(this);
90 setAnnotationVisible(av.showAnnotation);
92 idPanelHolder.add(idPanel, BorderLayout.CENTER);
93 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
94 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
95 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
96 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
99 setScrollValues(0, 0);
101 apvscroll.addAdjustmentListener(this);
102 hscroll.addAdjustmentListener(this);
103 vscroll.addAdjustmentListener(this);
105 addComponentListener(new ComponentAdapter()
107 public void componentResized(ComponentEvent evt)
109 setScrollValues(av.getStartRes(), av.getStartSeq());
110 if (getSize().height > 0
111 && annotationPanelHolder.getSize().height > 0)
113 validateAnnotationDimensions(false);
120 Dimension d = calculateIdWidth();
121 idPanel.idCanvas.setSize(d);
123 hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
125 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
126 annotationSpaceFillerHolder.setSize(d.width,
127 annotationPanel.getSize().height);
128 alabels.setSize(d.width, annotationPanel.getSize().height);
129 final AlignmentPanel ap = this;
130 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
132 public void propertyChange(java.beans.PropertyChangeEvent evt)
134 if (evt.getPropertyName().equals("alignment"))
136 PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
144 public SequenceRenderer getSequenceRenderer()
146 return seqPanel.seqCanvas.sr;
149 public FeatureRenderer getFeatureRenderer()
151 return seqPanel.seqCanvas.fr;
154 public void alignmentChanged()
156 av.alignmentChanged(this);
158 if (overviewPanel != null)
160 overviewPanel.updateOverviewImage();
163 alignFrame.updateEditMenuBar();
168 public void fontChanged()
170 // set idCanvas bufferedImage to null
171 // to prevent drawing old image
172 idPanel.idCanvas.image = null;
173 FontMetrics fm = getFontMetrics(av.getFont());
175 scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
176 idwidthAdjuster.setSize(new Dimension(10, av.charHeight
178 av.updateSequenceIdColours();
179 annotationPanel.image = null;
180 int ap = annotationPanel.adjustPanelHeight(false);
181 Dimension d = calculateIdWidth();
182 d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
183 alabels.setSize(d.width + 4, ap);
185 idPanel.idCanvas.setSize(d);
186 hscrollFillerPanel.setSize(d);
188 validateAnnotationDimensions(false);
189 annotationPanel.repaint();
193 if (overviewPanel != null)
195 overviewPanel.updateOverviewImage();
199 public void setIdWidth(int w, int h)
201 idPanel.idCanvas.setSize(w, h);
202 idPanelHolder.setSize(w, idPanelHolder.getSize().height);
203 annotationSpaceFillerHolder.setSize(w,
204 annotationSpaceFillerHolder.getSize().height);
205 alabels.setSize(w, alabels.getSize().height);
209 Dimension calculateIdWidth()
211 if (av.nullFrame == null)
213 av.nullFrame = new Frame();
214 av.nullFrame.addNotify();
217 Graphics g = av.nullFrame.getGraphics();
219 FontMetrics fm = g.getFontMetrics(av.font);
220 AlignmentI al = av.getAlignment();
225 while (i < al.getHeight() && al.getSequenceAt(i) != null)
227 SequenceI s = al.getSequenceAt(i);
228 id = s.getDisplayId(av.getShowJVSuffix());
230 if (fm.stringWidth(id) > idWidth)
232 idWidth = fm.stringWidth(id);
237 // Also check annotation label widths
239 if (al.getAlignmentAnnotation() != null)
241 fm = g.getFontMetrics(av.nullFrame.getFont());
242 while (i < al.getAlignmentAnnotation().length)
244 String label = al.getAlignmentAnnotation()[i].label;
245 if (fm.stringWidth(label) > idWidth)
247 idWidth = fm.stringWidth(label);
253 return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
257 * Highlight the given results on the alignment.
260 public void highlightSearchResults(SearchResults results)
262 scrollToPosition(results);
263 seqPanel.seqCanvas.highlightSearchResults(results);
267 * scroll the view to show the position of the highlighted region in results
268 * (if any) and redraw the overview
271 * @return false if results were not found
273 public boolean scrollToPosition(SearchResults results)
275 return scrollToPosition(results, true);
279 * scroll the view to show the position of the highlighted region in results
283 * @param redrawOverview
284 * - when set, the overview will be recalculated (takes longer)
285 * @return false if results were not found
287 public boolean scrollToPosition(SearchResults results,
288 boolean redrawOverview)
291 // do we need to scroll the panel?
292 if (results != null && results.getSize() > 0)
294 AlignmentI alignment = av.getAlignment();
295 int seqIndex = alignment.findIndex(results);
300 SequenceI seq = alignment.getSequenceAt(seqIndex);
301 int[] r = results.getResults(seq, 0, alignment.getWidth());
307 .println("DEBUG: scroll didn't happen - results not within alignment : "
308 + seq.getStart() + "," + seq.getEnd());
316 * System.out.println("DEBUG: scroll: start=" + r[0] +
317 * " av.getStartRes()=" + av.getStartRes() + " end=" + r[1] +
318 * " seq.end=" + seq.getEnd() + " av.getEndRes()=" + av.getEndRes() +
319 * " hextent=" + hextent);
328 if (end == seq.getEnd())
332 return scrollTo(start, end, seqIndex, false, redrawOverview);
337 public boolean scrollTo(int ostart, int end, int seqIndex,
338 boolean scrollToNearest, boolean redrawOverview)
340 int startv, endv, starts, ends, width;
343 if (av.hasHiddenColumns())
345 start = av.getColumnSelection().findColumnPosition(ostart);
346 end = av.getColumnSelection().findColumnPosition(end);
349 if (!scrollToNearest && !av.getColumnSelection().isVisible(ostart))
351 // don't scroll - position isn't visible
360 if (!av.wrapAlignment)
363 * int spos=av.getStartRes(),sqpos=av.getStartSeq(); if ((startv =
364 * av.getStartRes()) >= start) { spos=start-1; // seqIn //
365 * setScrollValues(start - 1, seqIndex); } else if ((endv =
366 * av.getEndRes()) <= end) { // setScrollValues(spos=startv + 1 + end -
367 * endv, seqIndex); spos=startv + 1 + end - endv; } else if ((starts =
368 * av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(),
369 * seqIndex); } else if ((ends = av.getEndSeq()) <= seqIndex) {
370 * setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); }
374 if ((av.getStartRes() > end)
375 || (av.getEndRes() < start)
376 || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
378 if (start > av.getAlignment().getWidth() - hextent)
380 start = av.getAlignment().getWidth() - hextent;
387 if (seqIndex > av.getAlignment().getHeight() - vextent)
389 seqIndex = av.getAlignment().getHeight() - vextent;
395 // System.out.println("trying to scroll to: "+start+" "+seqIndex);
396 setScrollValues(start, seqIndex);
401 scrollToWrappedVisible(start);
403 if (redrawOverview && overviewPanel != null)
405 overviewPanel.setBoxPosition();
407 paintAlignment(redrawOverview);
411 void scrollToWrappedVisible(int res)
413 int cwidth = seqPanel.seqCanvas
414 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
415 if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
417 vscroll.setValue(res / cwidth);
418 av.startRes = vscroll.getValue() * cwidth;
422 public OverviewPanel getOverviewPanel()
424 return overviewPanel;
427 public void setOverviewPanel(OverviewPanel op)
432 public void setAnnotationVisible(boolean b)
434 if (!av.wrapAlignment)
436 annotationSpaceFillerHolder.setVisible(b);
437 annotationPanelHolder.setVisible(b);
444 * automatically adjust annotation panel height for new annotation whilst
445 * ensuring the alignment is still visible.
447 public void adjustAnnotationHeight()
449 // TODO: display vertical annotation scrollbar if necessary
450 // this is called after loading new annotation onto alignment
451 if (alignFrame.getSize().height == 0)
453 System.out.println("NEEDS FIXING");
456 validateAnnotationDimensions(true);
457 apvscroll.addNotify();
460 paintAlignment(true);
464 * calculate the annotation dimensions and refresh slider values accordingly.
465 * need to do repaints/notifys afterwards.
467 protected void validateAnnotationDimensions(boolean adjustPanelHeight)
469 boolean modified = false;
470 int height = av.calcPanelHeight();
472 if (hscroll.isVisible())
474 height += (minsize = hscroll.getPreferredSize().height);
476 if (apvscroll.isVisible())
478 minsize += apvscroll.getPreferredSize().height;
480 int mheight = height;
481 Dimension d = sequenceHolderPanel.getSize(), e = idPanel.getSize();
482 int seqandannot = d.height - scalePanelHolder.getSize().height;
483 // sets initial preferred height
484 if ((height + 40) > seqandannot / 2)
486 height = seqandannot / 2;
488 if (!adjustPanelHeight)
490 // maintain same window layout whilst updating sliders
491 height = annotationPanelHolder.getSize().height;
494 if (seqandannot - height < 5)
496 height = seqandannot;
498 annotationPanel.setSize(new Dimension(d.width, height));
499 alabels.setSize(new Dimension(e.width, height));
500 annotationSpaceFillerHolder.setSize(new Dimension(e.width, height));
501 annotationPanelHolder.setSize(new Dimension(d.width, height));
502 seqPanelHolder.setSize(d.width, seqandannot - height);
504 .setSize(d.width, seqPanel.seqCanvas.getSize().height);
505 int s = apvscroll.getValue();
506 if (s > mheight - height)
510 apvscroll.setValues(s, height, 0, mheight);
511 annotationPanel.setScrollOffset(apvscroll.getValue());
512 alabels.setScrollOffset(apvscroll.getValue());
515 public void setWrapAlignment(boolean wrap)
519 scalePanelHolder.setVisible(!wrap);
521 hscroll.setVisible(!wrap);
522 idwidthAdjuster.setVisible(!wrap);
526 annotationPanelHolder.setVisible(false);
527 annotationSpaceFillerHolder.setVisible(false);
529 else if (av.showAnnotation)
531 annotationPanelHolder.setVisible(true);
532 annotationSpaceFillerHolder.setVisible(true);
535 idSpaceFillerPanel1.setVisible(!wrap);
537 fontChanged(); // This is so that the scalePanel is resized correctly
548 // return value is true if the scroll is valid
549 public boolean scrollUp(boolean up)
553 if (vscroll.getValue() < 1)
557 setScrollValues(hscroll.getValue(), vscroll.getValue() - 1);
561 if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())
565 setScrollValues(hscroll.getValue(), vscroll.getValue() + 1);
572 public boolean scrollRight(boolean right)
576 if (hscroll.getValue() < 1)
580 setScrollValues(hscroll.getValue() - 1, vscroll.getValue());
584 if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
588 setScrollValues(hscroll.getValue() + 1, vscroll.getValue());
595 public void setScrollValues(int x, int y)
597 int width = av.getAlignment().getWidth();
598 int height = av.getAlignment().getHeight();
600 if (av.hasHiddenColumns())
602 width = av.getColumnSelection().findColumnPosition(width);
610 hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
611 vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
618 if (vextent > height)
623 if ((hextent + x) > width)
625 System.err.println("hextent was " + hextent + " and x was " + x);
630 if ((vextent + y) > height)
632 y = height - vextent;
642 System.err.println("x was " + x);
648 int endSeq = y + vextent;
649 if (endSeq > av.getAlignment().getHeight())
651 endSeq = av.getAlignment().getHeight();
654 av.setEndSeq(endSeq);
656 av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
658 hscroll.setValues(x, hextent, 0, width);
659 vscroll.setValues(y, vextent, 0, height);
661 if (overviewPanel != null)
663 overviewPanel.setBoxPosition();
669 public void adjustmentValueChanged(AdjustmentEvent evt)
671 int oldX = av.getStartRes();
672 int oldY = av.getStartSeq();
674 if (evt == null || evt.getSource() == apvscroll)
676 annotationPanel.setScrollOffset(apvscroll.getValue());
677 alabels.setScrollOffset(apvscroll.getValue());
678 // annotationPanel.image=null;
679 // alabels.image=null;
680 // alabels.repaint();
681 // annotationPanel.repaint();
683 if (evt == null || evt.getSource() == hscroll)
685 int x = hscroll.getValue();
687 av.setEndRes(x + seqPanel.seqCanvas.getSize().width
688 / av.getCharWidth() - 1);
691 if (evt == null || evt.getSource() == vscroll)
693 int offy = vscroll.getValue();
694 if (av.getWrapAlignment())
696 int rowSize = seqPanel.seqCanvas
697 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
698 av.setStartRes(vscroll.getValue() * rowSize);
699 av.setEndRes((vscroll.getValue() + 1) * rowSize);
703 av.setStartSeq(offy);
704 av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
705 / av.getCharHeight());
709 if (overviewPanel != null)
711 overviewPanel.setBoxPosition();
714 int scrollX = av.startRes - oldX;
715 int scrollY = av.startSeq - oldY;
717 if (av.getWrapAlignment() || !fastPaint || av.MAC)
723 // Make sure we're not trying to draw a panel
724 // larger than the visible window
725 if (scrollX > av.endRes - av.startRes)
727 scrollX = av.endRes - av.startRes;
729 else if (scrollX < av.startRes - av.endRes)
731 scrollX = av.startRes - av.endRes;
734 idPanel.idCanvas.fastPaint(scrollY);
735 seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
737 scalePanel.repaint();
738 if (av.getShowAnnotation())
740 annotationPanel.fastPaint(av.getStartRes() - oldX);
747 private void sendViewPosition()
749 StructureSelectionManager.getStructureSelectionManager(av.applet)
750 .sendViewPosition(this, av.startRes, av.endRes, av.startSeq,
754 public void paintAlignment(boolean updateOverview)
760 jalview.structure.StructureSelectionManager
761 .getStructureSelectionManager(av.applet)
762 .sequenceColoursChanged(this);
764 if (overviewPanel != null)
766 overviewPanel.updateOverviewImage();
771 public void update(Graphics g)
776 public void paint(Graphics g)
779 Dimension d = idPanel.idCanvas.getSize();
780 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
782 if (av.getWrapAlignment())
784 int maxwidth = av.getAlignment().getWidth();
786 if (av.hasHiddenColumns())
788 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
791 int canvasWidth = seqPanel.seqCanvas
792 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
796 int max = maxwidth / canvasWidth;
797 vscroll.setMaximum(1 + max);
798 vscroll.setUnitIncrement(1);
799 vscroll.setVisibleAmount(1);
804 setScrollValues(av.getStartRes(), av.getStartSeq());
809 seqPanel.seqCanvas.repaint();
810 scalePanel.repaint();
811 annotationPanel.repaint();
812 idPanel.idCanvas.repaint();
815 protected Panel sequenceHolderPanel = new Panel();
817 protected Scrollbar vscroll = new Scrollbar();
819 protected Scrollbar hscroll = new Scrollbar();
821 protected Panel seqPanelHolder = new Panel();
823 BorderLayout borderLayout1 = new BorderLayout();
825 BorderLayout borderLayout3 = new BorderLayout();
827 protected Panel scalePanelHolder = new Panel();
829 protected Panel idPanelHolder = new Panel();
831 BorderLayout borderLayout5 = new BorderLayout();
833 protected Panel idSpaceFillerPanel1 = new Panel();
835 public Panel annotationSpaceFillerHolder = new Panel();
837 BorderLayout borderLayout6 = new BorderLayout();
839 BorderLayout borderLayout7 = new BorderLayout();
841 Panel hscrollHolder = new Panel();
843 BorderLayout borderLayout10 = new BorderLayout();
845 protected Panel hscrollFillerPanel = new Panel();
847 BorderLayout borderLayout11 = new BorderLayout();
849 BorderLayout borderLayout4 = new BorderLayout();
851 BorderLayout borderLayout2 = new BorderLayout();
853 Panel annotationPanelHolder = new Panel();
855 protected Scrollbar apvscroll = new Scrollbar();
857 BorderLayout borderLayout12 = new BorderLayout();
859 private void jbInit() throws Exception
861 // idPanelHolder.setPreferredSize(new Dimension(70, 10));
862 this.setLayout(borderLayout7);
864 // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
865 sequenceHolderPanel.setLayout(borderLayout3);
866 seqPanelHolder.setLayout(borderLayout1);
867 scalePanelHolder.setBackground(Color.white);
869 // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
870 scalePanelHolder.setLayout(borderLayout6);
871 idPanelHolder.setLayout(borderLayout5);
872 idSpaceFillerPanel1.setBackground(Color.white);
874 // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
875 idSpaceFillerPanel1.setLayout(borderLayout11);
876 annotationSpaceFillerHolder.setBackground(Color.white);
878 // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
879 annotationSpaceFillerHolder.setLayout(borderLayout4);
880 hscroll.setOrientation(Scrollbar.HORIZONTAL);
881 hscrollHolder.setLayout(borderLayout10);
882 hscrollFillerPanel.setBackground(Color.white);
883 apvscroll.setOrientation(Scrollbar.VERTICAL);
884 apvscroll.setVisible(true);
885 apvscroll.addAdjustmentListener(this);
887 annotationPanelHolder.setBackground(Color.white);
888 annotationPanelHolder.setLayout(borderLayout12);
889 annotationPanelHolder.add(apvscroll, BorderLayout.EAST);
890 // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
891 hscrollHolder.setBackground(Color.white);
893 // annotationScroller.setPreferredSize(new Dimension(10, 80));
894 // this.setPreferredSize(new Dimension(220, 166));
895 seqPanelHolder.setBackground(Color.white);
896 idPanelHolder.setBackground(Color.white);
897 sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
898 sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
899 seqPanelHolder.add(vscroll, BorderLayout.EAST);
901 // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
902 this.add(idPanelHolder, BorderLayout.WEST);
903 idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
904 idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
905 this.add(hscrollHolder, BorderLayout.SOUTH);
906 hscrollHolder.add(hscroll, BorderLayout.CENTER);
907 hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
908 this.add(sequenceHolderPanel, BorderLayout.CENTER);
912 * hides or shows dynamic annotation rows based on groups and av state flags
914 public void updateAnnotation()
916 updateAnnotation(false);
919 public void updateAnnotation(boolean applyGlobalSettings)
921 updateAnnotation(applyGlobalSettings, false);
924 public void updateAnnotation(boolean applyGlobalSettings,
925 boolean preserveNewGroupSettings)
927 av.updateGroupAnnotationSettings(applyGlobalSettings,
928 preserveNewGroupSettings);
929 adjustAnnotationHeight();
933 public AlignmentI getAlignment()
935 return av.getAlignment();
939 public StructureSelectionManager getStructureSelectionManager()
941 return StructureSelectionManager
942 .getStructureSelectionManager(av.applet);
946 public void raiseOOMWarning(String string, OutOfMemoryError error)
949 System.err.println("Out of memory whilst '" + string + "'");
950 error.printStackTrace();