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 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);
439 annotationSpaceFillerHolder.setVisible(false);
440 annotationPanelHolder.setVisible(false);
447 * automatically adjust annotation panel height for new annotation whilst
448 * ensuring the alignment is still visible.
450 public void adjustAnnotationHeight()
452 // TODO: display vertical annotation scrollbar if necessary
453 // this is called after loading new annotation onto alignment
454 if (alignFrame.getSize().height == 0)
456 System.out.println("NEEDS FIXING");
459 validateAnnotationDimensions(true);
460 apvscroll.addNotify();
463 paintAlignment(true);
467 * calculate the annotation dimensions and refresh slider values accordingly.
468 * need to do repaints/notifys afterwards.
470 protected void validateAnnotationDimensions(boolean adjustPanelHeight)
472 boolean modified = false;
473 int height = av.calcPanelHeight();
475 if (hscroll.isVisible())
477 height += (minsize = hscroll.getPreferredSize().height);
479 if (apvscroll.isVisible())
481 minsize += apvscroll.getPreferredSize().height;
483 int mheight = height;
484 Dimension d = sequenceHolderPanel.getSize(), e = idPanel.getSize();
485 int seqandannot = d.height - scalePanelHolder.getSize().height;
487 if (adjustPanelHeight)
489 // NOTE: this logic is different in the application. Need a better algorithm to define behaviour
490 // sets initial preferred height
491 // try and set height according to alignment
492 float sscaling = (float) ((av.getCharHeight() * av.getAlignment().getHeight())/(1.0*mheight));
495 // if the alignment is too big then
496 // default is 0.5 split
497 height = seqandannot / 2;
501 // otherwise just set the panel so that one row of sequence is visible
502 height = -av.getCharHeight() * 1
503 + (int) (seqandannot * (1 - sscaling));
508 // maintain same window layout whilst updating sliders
509 height = annotationPanelHolder.getSize().height;
512 if (seqandannot - height < 5)
514 height = seqandannot;
516 annotationPanel.setSize(new Dimension(d.width, height));
517 alabels.setSize(new Dimension(e.width, height));
518 annotationSpaceFillerHolder.setSize(new Dimension(e.width, height));
519 annotationPanelHolder.setSize(new Dimension(d.width, height));
520 // seqPanelHolder.setSize(d.width, seqandannot - height);
522 .setSize(d.width, seqPanel.seqCanvas.getSize().height);
523 int s = apvscroll.getValue();
524 if (s > mheight - height)
528 apvscroll.setValues(s, height, 0, mheight);
529 annotationPanel.setScrollOffset(apvscroll.getValue(), false);
530 alabels.setScrollOffset(apvscroll.getValue(), false);
533 public void setWrapAlignment(boolean wrap)
537 scalePanelHolder.setVisible(!wrap);
539 hscroll.setVisible(!wrap);
540 idwidthAdjuster.setVisible(!wrap);
544 annotationPanelHolder.setVisible(false);
545 annotationSpaceFillerHolder.setVisible(false);
547 else if (av.showAnnotation)
549 annotationPanelHolder.setVisible(true);
550 annotationSpaceFillerHolder.setVisible(true);
553 idSpaceFillerPanel1.setVisible(!wrap);
555 fontChanged(); // This is so that the scalePanel is resized correctly
558 sequenceHolderPanel.revalidate();
567 // return value is true if the scroll is valid
568 public boolean scrollUp(boolean up)
572 if (vscroll.getValue() < 1)
576 setScrollValues(hscroll.getValue(), vscroll.getValue() - 1);
580 if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())
584 setScrollValues(hscroll.getValue(), vscroll.getValue() + 1);
591 public boolean scrollRight(boolean right)
595 if (hscroll.getValue() < 1)
599 setScrollValues(hscroll.getValue() - 1, vscroll.getValue());
603 if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
607 setScrollValues(hscroll.getValue() + 1, vscroll.getValue());
614 public void setScrollValues(int x, int y)
616 int width = av.getAlignment().getWidth();
617 int height = av.getAlignment().getHeight();
619 if (av.hasHiddenColumns())
621 width = av.getColumnSelection().findColumnPosition(width);
629 hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
630 vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
637 if (vextent > height)
642 if ((hextent + x) > width)
644 System.err.println("hextent was " + hextent + " and x was " + x);
649 if ((vextent + y) > height)
651 y = height - vextent;
661 System.err.println("x was " + x);
667 int endSeq = y + vextent;
668 if (endSeq > av.getAlignment().getHeight())
670 endSeq = av.getAlignment().getHeight();
673 av.setEndSeq(endSeq);
675 av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
677 hscroll.setValues(x, hextent, 0, width);
678 vscroll.setValues(y, vextent, 0, height);
680 if (overviewPanel != null)
682 overviewPanel.setBoxPosition();
688 public void adjustmentValueChanged(AdjustmentEvent evt)
690 int oldX = av.getStartRes();
691 int oldY = av.getStartSeq();
693 if (evt == null || evt.getSource() == apvscroll)
695 annotationPanel.setScrollOffset(apvscroll.getValue(), false);
696 alabels.setScrollOffset(apvscroll.getValue(), false);
697 // annotationPanel.image=null;
698 // alabels.image=null;
699 // alabels.repaint();
700 // annotationPanel.repaint();
702 if (evt == null || evt.getSource() == hscroll)
704 int x = hscroll.getValue();
706 av.setEndRes(x + seqPanel.seqCanvas.getSize().width
707 / av.getCharWidth() - 1);
710 if (evt == null || evt.getSource() == vscroll)
712 int offy = vscroll.getValue();
713 if (av.getWrapAlignment())
715 int rowSize = seqPanel.seqCanvas
716 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
717 av.setStartRes(vscroll.getValue() * rowSize);
718 av.setEndRes((vscroll.getValue() + 1) * rowSize);
722 av.setStartSeq(offy);
723 av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
724 / av.getCharHeight());
728 if (overviewPanel != null)
730 overviewPanel.setBoxPosition();
733 int scrollX = av.startRes - oldX;
734 int scrollY = av.startSeq - oldY;
736 if (av.getWrapAlignment() || !fastPaint || av.MAC)
742 // Make sure we're not trying to draw a panel
743 // larger than the visible window
744 if (scrollX > av.endRes - av.startRes)
746 scrollX = av.endRes - av.startRes;
748 else if (scrollX < av.startRes - av.endRes)
750 scrollX = av.startRes - av.endRes;
753 idPanel.idCanvas.fastPaint(scrollY);
754 seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
756 scalePanel.repaint();
757 if (av.getShowAnnotation())
759 annotationPanel.fastPaint(av.getStartRes() - oldX);
766 private void sendViewPosition()
768 StructureSelectionManager.getStructureSelectionManager(av.applet)
769 .sendViewPosition(this, av.startRes, av.endRes, av.startSeq,
773 public void paintAlignment(boolean updateOverview)
779 jalview.structure.StructureSelectionManager
780 .getStructureSelectionManager(av.applet)
781 .sequenceColoursChanged(this);
783 if (overviewPanel != null)
785 overviewPanel.updateOverviewImage();
790 public void update(Graphics g)
795 public void paint(Graphics g)
798 Dimension d = idPanel.idCanvas.getSize();
799 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
801 if (av.getWrapAlignment())
803 int maxwidth = av.getAlignment().getWidth();
805 if (av.hasHiddenColumns())
807 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
810 int canvasWidth = seqPanel.seqCanvas
811 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
815 int max = maxwidth / canvasWidth;
816 vscroll.setMaximum(1 + max);
817 vscroll.setUnitIncrement(1);
818 vscroll.setVisibleAmount(1);
823 setScrollValues(av.getStartRes(), av.getStartSeq());
826 seqPanel.seqCanvas.repaint();
827 idPanel.idCanvas.repaint();
828 if (!av.wrapAlignment)
830 if (av.showAnnotation)
833 annotationPanel.repaint();
835 scalePanel.repaint();
840 protected Panel sequenceHolderPanel = new Panel();
842 protected Scrollbar vscroll = new Scrollbar();
844 protected Scrollbar hscroll = new Scrollbar();
846 protected Panel seqPanelHolder = new Panel();
848 BorderLayout borderLayout1 = new BorderLayout();
850 BorderLayout borderLayout3 = new BorderLayout();
852 protected Panel scalePanelHolder = new Panel();
854 protected Panel idPanelHolder = new Panel();
856 BorderLayout borderLayout5 = new BorderLayout();
858 protected Panel idSpaceFillerPanel1 = new Panel();
860 public Panel annotationSpaceFillerHolder = new Panel();
862 BorderLayout borderLayout6 = new BorderLayout();
864 BorderLayout borderLayout7 = new BorderLayout();
866 Panel hscrollHolder = new Panel();
868 BorderLayout borderLayout10 = new BorderLayout();
870 protected Panel hscrollFillerPanel = new Panel();
872 BorderLayout borderLayout11 = new BorderLayout();
874 BorderLayout borderLayout4 = new BorderLayout();
876 BorderLayout borderLayout2 = new BorderLayout();
878 Panel annotationPanelHolder = new Panel();
880 protected Scrollbar apvscroll = new Scrollbar();
882 BorderLayout borderLayout12 = new BorderLayout();
884 private void jbInit() throws Exception
886 // idPanelHolder.setPreferredSize(new Dimension(70, 10));
887 this.setLayout(borderLayout7);
889 // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
890 sequenceHolderPanel.setLayout(borderLayout3);
891 seqPanelHolder.setLayout(borderLayout1);
892 scalePanelHolder.setBackground(Color.white);
894 // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
895 scalePanelHolder.setLayout(borderLayout6);
896 idPanelHolder.setLayout(borderLayout5);
897 idSpaceFillerPanel1.setBackground(Color.white);
899 // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
900 idSpaceFillerPanel1.setLayout(borderLayout11);
901 annotationSpaceFillerHolder.setBackground(Color.white);
903 // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
904 annotationSpaceFillerHolder.setLayout(borderLayout4);
905 hscroll.setOrientation(Scrollbar.HORIZONTAL);
906 hscrollHolder.setLayout(borderLayout10);
907 hscrollFillerPanel.setBackground(Color.white);
908 apvscroll.setOrientation(Scrollbar.VERTICAL);
909 apvscroll.setVisible(true);
910 apvscroll.addAdjustmentListener(this);
912 annotationPanelHolder.setBackground(Color.white);
913 annotationPanelHolder.setLayout(borderLayout12);
914 annotationPanelHolder.add(apvscroll, BorderLayout.EAST);
915 // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
916 hscrollHolder.setBackground(Color.white);
918 // annotationScroller.setPreferredSize(new Dimension(10, 80));
919 // this.setPreferredSize(new Dimension(220, 166));
920 seqPanelHolder.setBackground(Color.white);
921 idPanelHolder.setBackground(Color.white);
922 sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
923 sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
924 seqPanelHolder.add(vscroll, BorderLayout.EAST);
926 // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
927 this.add(idPanelHolder, BorderLayout.WEST);
928 idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
929 idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
930 this.add(hscrollHolder, BorderLayout.SOUTH);
931 hscrollHolder.add(hscroll, BorderLayout.CENTER);
932 hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
933 this.add(sequenceHolderPanel, BorderLayout.CENTER);
937 * hides or shows dynamic annotation rows based on groups and av state flags
939 public void updateAnnotation()
941 updateAnnotation(false);
944 public void updateAnnotation(boolean applyGlobalSettings)
946 updateAnnotation(applyGlobalSettings, false);
949 public void updateAnnotation(boolean applyGlobalSettings,
950 boolean preserveNewGroupSettings)
952 av.updateGroupAnnotationSettings(applyGlobalSettings,
953 preserveNewGroupSettings);
954 adjustAnnotationHeight();
958 public AlignmentI getAlignment()
960 return av.getAlignment();
964 public StructureSelectionManager getStructureSelectionManager()
966 return StructureSelectionManager
967 .getStructureSelectionManager(av.applet);
971 public void raiseOOMWarning(String string, OutOfMemoryError error)
974 System.err.println("Out of memory whilst '" + string + "'");
975 error.printStackTrace();