2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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/>.
18 package jalview.appletgui;
21 import java.awt.event.*;
22 import java.util.Hashtable;
23 import java.util.Vector;
25 import jalview.api.AlignmentViewPanel;
26 import jalview.datamodel.*;
27 import jalview.structure.StructureSelectionManager;
29 public class AlignmentPanel extends Panel implements AdjustmentListener, AlignmentViewPanel
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 sequenceHolderPanel=null;
60 scalePanelHolder=null;
62 annotationPanelHolder=null;
63 annotationSpaceFillerHolder=null;
65 public AlignmentPanel(AlignFrame af, final AlignViewport av)
77 seqPanel = new SeqPanel(av, this);
78 idPanel = new IdPanel(av, this);
79 scalePanel = new ScalePanel(av, this);
80 idwidthAdjuster = new IdwidthAdjuster(this);
81 annotationPanel = new AnnotationPanel(this);
82 annotationPanelHolder.add(annotationPanel, BorderLayout.CENTER);
84 sequenceHolderPanel.add(annotationPanelHolder, BorderLayout.SOUTH);
86 alabels = new AnnotationLabels(this);
88 setAnnotationVisible(av.showAnnotation);
90 idPanelHolder.add(idPanel, BorderLayout.CENTER);
91 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
92 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
93 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
94 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
97 setScrollValues(0, 0);
99 apvscroll.addAdjustmentListener(this);
100 hscroll.addAdjustmentListener(this);
101 vscroll.addAdjustmentListener(this);
103 addComponentListener(new ComponentAdapter()
105 public void componentResized(ComponentEvent evt)
107 setScrollValues(av.getStartRes(), av.getStartSeq());
108 if (getSize().height>0 && annotationPanelHolder.getSize().height>0) {
109 validateAnnotationDimensions(false);
116 Dimension d = calculateIdWidth();
117 idPanel.idCanvas.setSize(d);
119 hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
121 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
122 annotationSpaceFillerHolder.setSize(d.width,
123 annotationPanel.getSize().height);
124 alabels.setSize(d.width, annotationPanel.getSize().height);
125 final AlignmentPanel ap = this;
126 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
128 public void propertyChange(java.beans.PropertyChangeEvent evt)
130 if (evt.getPropertyName().equals("alignment"))
132 PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
140 public SequenceRenderer getSequenceRenderer()
142 return seqPanel.seqCanvas.sr;
145 public FeatureRenderer getFeatureRenderer()
147 return seqPanel.seqCanvas.fr;
150 public void alignmentChanged()
152 av.alignmentChanged(this);
154 if (overviewPanel != null)
156 overviewPanel.updateOverviewImage();
159 alignFrame.updateEditMenuBar();
164 public void fontChanged()
166 // set idCanvas bufferedImage to null
167 // to prevent drawing old image
168 idPanel.idCanvas.image = null;
169 FontMetrics fm = getFontMetrics(av.getFont());
171 scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
172 idwidthAdjuster.setSize(new Dimension(10, av.charHeight
174 av.updateSequenceIdColours();
175 annotationPanel.image = null;
176 int ap = annotationPanel.adjustPanelHeight(false);
177 Dimension d = calculateIdWidth();
178 d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
179 alabels.setSize(d.width + 4, ap);
180 idPanel.idCanvas.setSize(d);
181 hscrollFillerPanel.setSize(d);
183 validateAnnotationDimensions(false);
184 annotationPanel.repaint();
188 if (overviewPanel != null)
190 overviewPanel.updateOverviewImage();
194 public void setIdWidth(int w, int h)
196 idPanel.idCanvas.setSize(w, h);
197 idPanelHolder.setSize(w, idPanelHolder.getSize().height);
198 annotationSpaceFillerHolder.setSize(w,annotationSpaceFillerHolder.getSize().height);
199 alabels.setSize(w, alabels.getSize().height);
203 Dimension calculateIdWidth()
205 if (av.nullFrame == null)
207 av.nullFrame = new Frame();
208 av.nullFrame.addNotify();
211 Graphics g = av.nullFrame.getGraphics();
213 FontMetrics fm = g.getFontMetrics(av.font);
214 AlignmentI al = av.getAlignment();
219 while (i < al.getHeight() && al.getSequenceAt(i) != null)
221 SequenceI s = al.getSequenceAt(i);
222 id = s.getDisplayId(av.getShowJVSuffix());
224 if (fm.stringWidth(id) > idWidth)
226 idWidth = fm.stringWidth(id);
231 // Also check annotation label widths
233 if (al.getAlignmentAnnotation() != null)
235 fm = g.getFontMetrics(av.nullFrame.getFont());
236 while (i < al.getAlignmentAnnotation().length)
238 String label = al.getAlignmentAnnotation()[i].label;
239 if (fm.stringWidth(label) > idWidth)
241 idWidth = fm.stringWidth(label);
247 return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
251 * Highlight the given results on the alignment.
254 public void highlightSearchResults(SearchResults results)
256 scrollToPosition(results);
257 seqPanel.seqCanvas.highlightSearchResults(results);
261 * scroll the view to show the position of the highlighted region in results
262 * (if any) and redraw the overview
265 * @return false if results were not found
267 public boolean scrollToPosition(SearchResults results)
269 return scrollToPosition(results, true);
273 * scroll the view to show the position of the highlighted region in results
277 * @param redrawOverview
278 * - when set, the overview will be recalculated (takes longer)
279 * @return false if results were not found
281 public boolean scrollToPosition(SearchResults results,
282 boolean redrawOverview)
284 // do we need to scroll the panel?
285 if (results != null && results.getSize() > 0)
287 int seqIndex = av.alignment.findIndex(results);
292 SequenceI seq = av.alignment.getSequenceAt(seqIndex);
293 int[] r = results.getResults(seq, 0,av.alignment.getWidth());
296 if (av.applet.debug) {// DEBUG
297 System.out.println("DEBUG: scroll didn't happen - results not within alignment : "+seq.getStart()+","+seq.getEnd());
301 if (av.applet.debug) {
303 System.out.println("DEBUG: scroll: start=" + r[0]
304 + " av.getStartRes()=" + av.getStartRes() + " end=" + r[1]
305 + " seq.end=" + seq.getEnd() + " av.getEndRes()="
306 + av.getEndRes() + " hextent=" + hextent);
314 if (end == seq.getEnd())
318 return scrollTo(start, end, seqIndex, false, redrawOverview);
322 public boolean scrollTo(int ostart, int end, int seqIndex, boolean scrollToNearest, boolean redrawOverview)
325 if (av.hasHiddenColumns)
327 start = av.getColumnSelection().findColumnPosition(ostart);
328 end = av.getColumnSelection().findColumnPosition(end);
331 if (!scrollToNearest && !av.colSel.isVisible(ostart))
333 // don't scroll - position isn't visible
338 if (!av.wrapAlignment)
340 if ((av.getStartRes() > end)
341 || (av.getEndRes() < start)
342 || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
344 if (start > av.alignment.getWidth() - hextent)
346 start = av.alignment.getWidth() - hextent;
353 if (seqIndex > av.alignment.getHeight() - vextent)
355 seqIndex = av.alignment.getHeight() - vextent;
361 setScrollValues(start, seqIndex);
366 scrollToWrappedVisible(start);
368 if (redrawOverview && overviewPanel != null)
370 overviewPanel.setBoxPosition();
372 paintAlignment(redrawOverview);
376 void scrollToWrappedVisible(int res)
378 int cwidth = seqPanel.seqCanvas
379 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
380 if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
382 vscroll.setValue(res / cwidth);
383 av.startRes = vscroll.getValue() * cwidth;
387 public OverviewPanel getOverviewPanel()
389 return overviewPanel;
392 public void setOverviewPanel(OverviewPanel op)
397 public void setAnnotationVisible(boolean b)
399 if (!av.wrapAlignment)
401 annotationSpaceFillerHolder.setVisible(b);
402 annotationPanelHolder.setVisible(b);
409 * automatically adjust annotation panel height for new annotation whilst
410 * ensuring the alignment is still visible.
412 public void adjustAnnotationHeight()
414 // TODO: display vertical annotation scrollbar if necessary
415 // this is called after loading new annotation onto alignment
416 if (alignFrame.getSize().height == 0)
418 System.out.println("NEEDS FIXING");
421 validateAnnotationDimensions(true);
422 apvscroll.addNotify();
428 * calculate the annotation dimensions and refresh slider values accordingly.
429 * need to do repaints/notifys afterwards.
431 protected void validateAnnotationDimensions(boolean adjustPanelHeight) {
432 boolean modified=false;
433 int height = annotationPanel.calcPanelHeight();
435 if (hscroll.isVisible())
437 height += (minsize=hscroll.getPreferredSize().height);
439 if (apvscroll.isVisible()) {
440 minsize+=apvscroll.getPreferredSize().height;
442 int mheight = height;
443 Dimension d=sequenceHolderPanel.getSize(),e=idPanel.getSize();
444 int seqandannot=d.height-scalePanelHolder.getSize().height;
445 // sets initial preferred height
446 if ((height+40) > seqandannot / 2)
448 height = seqandannot / 2;
450 if (!adjustPanelHeight)
452 // maintain same window layout whilst updating sliders
453 height=annotationPanelHolder.getSize().height;
456 if (seqandannot-height<5)
458 height = seqandannot;
460 annotationPanel.setSize(new Dimension(d.width,height));
461 alabels.setSize(new Dimension(e.width,height));
462 annotationSpaceFillerHolder.setSize(new Dimension(e.width, height));
463 annotationPanelHolder.setSize(new Dimension(d.width, height));
464 seqPanelHolder.setSize(d.width,seqandannot-height);
465 int s=apvscroll.getValue();
466 if (s>mheight-height)
470 apvscroll.setValues(s, height, 0, mheight);
471 annotationPanel.setScrollOffset(apvscroll.getValue());
472 alabels.setScrollOffset(apvscroll.getValue());
475 public void setWrapAlignment(boolean wrap)
479 scalePanelHolder.setVisible(!wrap);
481 hscroll.setVisible(!wrap);
482 idwidthAdjuster.setVisible(!wrap);
486 annotationPanelHolder.setVisible(false);
487 annotationSpaceFillerHolder.setVisible(false);
489 else if (av.showAnnotation)
491 annotationPanelHolder.setVisible(true);
492 annotationSpaceFillerHolder.setVisible(true);
495 idSpaceFillerPanel1.setVisible(!wrap);
497 fontChanged(); // This is so that the scalePanel is resized correctly
508 // return value is true if the scroll is valid
509 public boolean scrollUp(boolean up)
513 if (vscroll.getValue() < 1)
517 setScrollValues(hscroll.getValue(), vscroll.getValue() - 1);
521 if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())
525 setScrollValues(hscroll.getValue(), vscroll.getValue() + 1);
532 public boolean scrollRight(boolean right)
536 if (hscroll.getValue() < 1)
540 setScrollValues(hscroll.getValue() - 1, vscroll.getValue());
544 if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
548 setScrollValues(hscroll.getValue() + 1, vscroll.getValue());
555 public void setScrollValues(int x, int y)
557 int width = av.alignment.getWidth();
558 int height = av.alignment.getHeight();
560 if (av.hasHiddenColumns)
562 width = av.getColumnSelection().findColumnPosition(width);
566 av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
568 hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
569 vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
576 if (vextent > height)
581 if ((hextent + x) > width)
586 if ((vextent + y) > height)
588 y = height - vextent;
603 int endSeq = y + vextent;
604 if (endSeq > av.alignment.getHeight())
606 endSeq = av.alignment.getHeight();
609 av.setEndSeq(endSeq);
610 hscroll.setValues(x, hextent, 0, width);
611 vscroll.setValues(y, vextent, 0, height);
613 if (overviewPanel != null)
615 overviewPanel.setBoxPosition();
622 public void adjustmentValueChanged(AdjustmentEvent evt)
624 int oldX = av.getStartRes();
625 int oldY = av.getStartSeq();
627 if (evt == null || evt.getSource() == apvscroll)
629 annotationPanel.setScrollOffset(apvscroll.getValue());
630 alabels.setScrollOffset(apvscroll.getValue());
631 // annotationPanel.image=null;
632 // alabels.image=null;
633 // alabels.repaint();
634 // annotationPanel.repaint();
636 if (evt == null || evt.getSource() == hscroll)
638 int x = hscroll.getValue();
640 av.setEndRes(x + seqPanel.seqCanvas.getSize().width
641 / av.getCharWidth() - 1);
644 if (evt == null || evt.getSource() == vscroll)
646 int offy = vscroll.getValue();
647 if (av.getWrapAlignment())
649 int rowSize = seqPanel.seqCanvas
650 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
651 av.setStartRes(vscroll.getValue() * rowSize);
652 av.setEndRes((vscroll.getValue() + 1) * rowSize);
656 av.setStartSeq(offy);
657 av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
658 / av.getCharHeight());
662 if (overviewPanel != null)
664 overviewPanel.setBoxPosition();
667 int scrollX = av.startRes - oldX;
668 int scrollY = av.startSeq - oldY;
670 if (av.getWrapAlignment() || !fastPaint || av.MAC)
676 // Make sure we're not trying to draw a panel
677 // larger than the visible window
678 if (scrollX > av.endRes - av.startRes)
680 scrollX = av.endRes - av.startRes;
682 else if (scrollX < av.startRes - av.endRes)
684 scrollX = av.startRes - av.endRes;
687 idPanel.idCanvas.fastPaint(scrollY);
688 seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
690 scalePanel.repaint();
691 if (av.getShowAnnotation())
693 annotationPanel.fastPaint(av.getStartRes() - oldX);
699 private void sendViewPosition()
701 StructureSelectionManager.getStructureSelectionManager(av.applet).sendViewPosition(this, av.startRes, av.endRes, av.startSeq, av.endSeq);
704 public void paintAlignment(boolean updateOverview)
710 jalview.structure.StructureSelectionManager
711 .getStructureSelectionManager(av.applet).sequenceColoursChanged(this);
713 if (overviewPanel != null)
715 overviewPanel.updateOverviewImage();
720 public void update(Graphics g)
725 public void paint(Graphics g)
728 Dimension d = idPanel.idCanvas.getSize();
729 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
731 if (av.getWrapAlignment())
733 int maxwidth = av.alignment.getWidth();
735 if (av.hasHiddenColumns)
737 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
740 int canvasWidth = seqPanel.seqCanvas
741 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
745 int max = maxwidth / canvasWidth;
746 vscroll.setMaximum(1 + max);
747 vscroll.setUnitIncrement(1);
748 vscroll.setVisibleAmount(1);
753 setScrollValues(av.getStartRes(), av.getStartSeq());
758 seqPanel.seqCanvas.repaint();
759 scalePanel.repaint();
760 annotationPanel.repaint();
761 idPanel.idCanvas.repaint();
764 protected Panel sequenceHolderPanel = new Panel();
766 protected Scrollbar vscroll = new Scrollbar();
768 protected Scrollbar hscroll = new Scrollbar();
770 protected Panel seqPanelHolder = new Panel();
772 BorderLayout borderLayout1 = new BorderLayout();
774 BorderLayout borderLayout3 = new BorderLayout();
776 protected Panel scalePanelHolder = new Panel();
778 protected Panel idPanelHolder = new Panel();
780 BorderLayout borderLayout5 = new BorderLayout();
782 protected Panel idSpaceFillerPanel1 = new Panel();
784 public Panel annotationSpaceFillerHolder = new Panel();
786 BorderLayout borderLayout6 = new BorderLayout();
788 BorderLayout borderLayout7 = new BorderLayout();
790 Panel hscrollHolder = new Panel();
792 BorderLayout borderLayout10 = new BorderLayout();
794 protected Panel hscrollFillerPanel = new Panel();
796 BorderLayout borderLayout11 = new BorderLayout();
798 BorderLayout borderLayout4 = new BorderLayout();
800 BorderLayout borderLayout2 = new BorderLayout();
802 Panel annotationPanelHolder = new Panel();
804 protected Scrollbar apvscroll = new Scrollbar();
806 BorderLayout borderLayout12 = new BorderLayout();
808 private void jbInit() throws Exception
810 // idPanelHolder.setPreferredSize(new Dimension(70, 10));
811 this.setLayout(borderLayout7);
813 //sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
814 sequenceHolderPanel.setLayout(borderLayout3);
815 seqPanelHolder.setLayout(borderLayout1);
816 scalePanelHolder.setBackground(Color.white);
818 // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
819 scalePanelHolder.setLayout(borderLayout6);
820 idPanelHolder.setLayout(borderLayout5);
821 idSpaceFillerPanel1.setBackground(Color.white);
823 // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
824 idSpaceFillerPanel1.setLayout(borderLayout11);
825 annotationSpaceFillerHolder.setBackground(Color.white);
827 // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
828 annotationSpaceFillerHolder.setLayout(borderLayout4);
829 hscroll.setOrientation(Scrollbar.HORIZONTAL);
830 hscrollHolder.setLayout(borderLayout10);
831 hscrollFillerPanel.setBackground(Color.white);
832 apvscroll.setOrientation(Scrollbar.VERTICAL);
833 apvscroll.setVisible(true);
834 apvscroll.addAdjustmentListener(this);
836 annotationPanelHolder.setBackground(Color.white);
837 annotationPanelHolder.setLayout(borderLayout12);
838 annotationPanelHolder.add(apvscroll, BorderLayout.EAST);
839 // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
840 hscrollHolder.setBackground(Color.white);
842 // annotationScroller.setPreferredSize(new Dimension(10, 80));
843 // this.setPreferredSize(new Dimension(220, 166));
844 seqPanelHolder.setBackground(Color.white);
845 idPanelHolder.setBackground(Color.white);
846 sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
847 sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
848 seqPanelHolder.add(vscroll, BorderLayout.EAST);
850 // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
851 this.add(idPanelHolder, BorderLayout.WEST);
852 idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
853 idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
854 this.add(hscrollHolder, BorderLayout.SOUTH);
855 hscrollHolder.add(hscroll, BorderLayout.CENTER);
856 hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
857 this.add(sequenceHolderPanel, BorderLayout.CENTER);
861 * hides or shows dynamic annotation rows based on groups and av state flags
863 public void updateAnnotation()
865 updateAnnotation(false);
868 public void updateAnnotation(boolean applyGlobalSettings)
870 // TODO: this should be merged with other annotation update stuff - that
871 // sits on AlignViewport
872 boolean updateCalcs = false;
873 boolean conv = av.isShowGroupConservation();
874 boolean cons = av.isShowGroupConsensus();
875 boolean showprf = av.isShowSequenceLogo();
876 boolean showConsHist = av.isShowConsensusHistogram();
878 boolean sortg = true;
880 // remove old automatic annotation
881 // add any new annotation
883 Vector gr = av.alignment.getGroups(); // OrderedBy(av.alignment.getSequencesArray());
884 // intersect alignment annotation with alignment groups
886 AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation();
887 Hashtable oldrfs = new Hashtable();
890 for (int an = 0; an < aan.length; an++)
892 if (aan[an].autoCalculated && aan[an].groupRef != null)
894 oldrfs.put(aan[an].groupRef, aan[an].groupRef);
895 av.alignment.deleteAnnotation(aan[an]);
903 for (int g = 0; g < gr.size(); g++)
906 sg = (SequenceGroup) gr.elementAt(g);
907 if (applyGlobalSettings || !oldrfs.containsKey(sg))
909 // set defaults for this group's conservation/consensus
910 sg.setshowSequenceLogo(showprf);
911 sg.setShowConsensusHistogram(showConsHist);
916 av.alignment.addAnnotation(sg.getConservationRow(), 0);
921 av.alignment.addAnnotation(sg.getConsensus(), 0);
923 // refresh the annotation rows
926 sg.recalcConservation();
931 adjustAnnotationHeight();
935 public AlignmentI getAlignment()
940 public StructureSelectionManager getStructureSelectionManager()
942 return StructureSelectionManager.getStructureSelectionManager(av.applet);