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.datamodel.*;
27 public class AlignmentPanel extends Panel implements AdjustmentListener
30 public AlignViewport av;
32 OverviewPanel overviewPanel;
38 IdwidthAdjuster idwidthAdjuster;
40 public AlignFrame alignFrame;
42 ScalePanel scalePanel;
44 AnnotationPanel annotationPanel;
46 AnnotationLabels alabels;
48 // this value is set false when selection area being dragged
49 boolean fastPaint = true;
51 public AlignmentPanel(AlignFrame af, final AlignViewport av)
63 seqPanel = new SeqPanel(av, this);
64 idPanel = new IdPanel(av, this);
65 scalePanel = new ScalePanel(av, this);
66 idwidthAdjuster = new IdwidthAdjuster(this);
67 annotationPanel = new AnnotationPanel(this);
68 annotationPanelHolder.add(annotationPanel, BorderLayout.CENTER);
70 sequenceHolderPanel.add(annotationPanelHolder, BorderLayout.SOUTH);
72 alabels = new AnnotationLabels(this);
74 setAnnotationVisible(av.showAnnotation);
76 idPanelHolder.add(idPanel, BorderLayout.CENTER);
77 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
78 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
79 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
80 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
83 setScrollValues(0, 0);
85 apvscroll.addAdjustmentListener(this);
86 hscroll.addAdjustmentListener(this);
87 vscroll.addAdjustmentListener(this);
89 addComponentListener(new ComponentAdapter()
91 public void componentResized(ComponentEvent evt)
93 setScrollValues(av.getStartRes(), av.getStartSeq());
98 Dimension d = calculateIdWidth();
99 idPanel.idCanvas.setSize(d);
101 hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
103 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
104 annotationSpaceFillerHolder.setSize(d.width,
105 annotationPanel.getSize().height);
106 alabels.setSize(d.width, annotationPanel.getSize().height);
107 final AlignmentPanel ap = this;
108 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
110 public void propertyChange(java.beans.PropertyChangeEvent evt)
112 if (evt.getPropertyName().equals("alignment"))
114 PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
122 public SequenceRenderer getSequenceRenderer()
124 return seqPanel.seqCanvas.sr;
127 public FeatureRenderer getFeatureRenderer()
129 return seqPanel.seqCanvas.fr;
132 public void alignmentChanged()
134 av.alignmentChanged(this);
136 if (overviewPanel != null)
138 overviewPanel.updateOverviewImage();
141 alignFrame.updateEditMenuBar();
146 public void fontChanged()
148 // set idCanvas bufferedImage to null
149 // to prevent drawing old image
150 idPanel.idCanvas.image = null;
151 FontMetrics fm = getFontMetrics(av.getFont());
153 scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
154 idwidthAdjuster.setSize(new Dimension(10, av.charHeight
156 av.updateSequenceIdColours();
157 annotationPanel.image = null;
158 int ap = annotationPanel.adjustPanelHeight(false);
159 Dimension d = calculateIdWidth();
160 d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
161 alabels.setSize(d.width + 4, ap);
162 idPanel.idCanvas.setSize(d);
163 hscrollFillerPanel.setSize(d);
165 validateAnnotationDimensions(false);
166 annotationPanel.repaint();
170 if (overviewPanel != null)
172 overviewPanel.updateOverviewImage();
176 public void setIdWidth(int w, int h)
178 idPanel.idCanvas.setSize(w, h);
179 idPanelHolder.setSize(w, idPanelHolder.getSize().height);
180 annotationSpaceFillerHolder.setSize(w,annotationSpaceFillerHolder.getSize().height);
181 alabels.setSize(w, alabels.getSize().height);
185 Dimension calculateIdWidth()
187 if (av.nullFrame == null)
189 av.nullFrame = new Frame();
190 av.nullFrame.addNotify();
193 Graphics g = av.nullFrame.getGraphics();
195 FontMetrics fm = g.getFontMetrics(av.font);
196 AlignmentI al = av.getAlignment();
201 while (i < al.getHeight() && al.getSequenceAt(i) != null)
203 SequenceI s = al.getSequenceAt(i);
204 id = s.getDisplayId(av.getShowJVSuffix());
206 if (fm.stringWidth(id) > idWidth)
208 idWidth = fm.stringWidth(id);
213 // Also check annotation label widths
215 if (al.getAlignmentAnnotation() != null)
217 fm = g.getFontMetrics(av.nullFrame.getFont());
218 while (i < al.getAlignmentAnnotation().length)
220 String label = al.getAlignmentAnnotation()[i].label;
221 if (fm.stringWidth(label) > idWidth)
223 idWidth = fm.stringWidth(label);
229 return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
233 * Highlight the given results on the alignment.
236 public void highlightSearchResults(SearchResults results)
238 scrollToPosition(results);
239 seqPanel.seqCanvas.highlightSearchResults(results);
243 * scroll the view to show the position of the highlighted region in results
244 * (if any) and redraw the overview
247 * @return false if results were not found
249 public boolean scrollToPosition(SearchResults results)
251 return scrollToPosition(results, true);
255 * scroll the view to show the position of the highlighted region in results
259 * @param redrawOverview
260 * - when set, the overview will be recalculated (takes longer)
261 * @return false if results were not found
263 public boolean scrollToPosition(SearchResults results,
264 boolean redrawOverview)
266 // do we need to scroll the panel?
267 if (results != null && results.getSize() > 0)
269 int seqIndex = av.alignment.findIndex(results);
274 SequenceI seq = av.alignment.getSequenceAt(seqIndex);
275 int[] r = results.getResults(seq, seq.getStart(), seq.getEnd());
278 if (av.applet.debug) {// DEBUG
279 System.out.println("DEBUG: scroll didn't happen - results not within alignment : "+seq.getStart()+","+seq.getEnd());
283 if (av.applet.debug) {
285 System.out.println("DEBUG: scroll didn't happen: start=" + r[0]
286 + " av.getStartRes()=" + av.getStartRes() + " end=" + r[1]
287 + " seq.end=" + seq.getEnd() + " av.getEndRes()="
288 + av.getEndRes() + " hextent=" + hextent);
296 if (end == seq.getEnd())
300 if (av.hasHiddenColumns)
302 start = av.getColumnSelection().findColumnPosition(start);
303 end = av.getColumnSelection().findColumnPosition(end);
306 if (!av.colSel.isVisible(r[0]))
308 // don't scroll - position isn't visible
313 if (!av.wrapAlignment)
315 if ((av.getStartRes() > end)
316 || (av.getEndRes() < start)
317 || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
319 if (start > av.alignment.getWidth() - hextent)
321 start = av.alignment.getWidth() - hextent;
328 if (seqIndex > av.alignment.getHeight() - vextent)
330 seqIndex = av.alignment.getHeight() - vextent;
336 setScrollValues(start, seqIndex);
341 scrollToWrappedVisible(start);
344 if (redrawOverview && overviewPanel != null)
346 overviewPanel.setBoxPosition();
348 paintAlignment(redrawOverview);
352 void scrollToWrappedVisible(int res)
354 int cwidth = seqPanel.seqCanvas
355 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
356 if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
358 vscroll.setValue(res / cwidth);
359 av.startRes = vscroll.getValue() * cwidth;
363 public OverviewPanel getOverviewPanel()
365 return overviewPanel;
368 public void setOverviewPanel(OverviewPanel op)
373 public void setAnnotationVisible(boolean b)
375 if (!av.wrapAlignment)
377 annotationSpaceFillerHolder.setVisible(b);
378 annotationPanelHolder.setVisible(b);
384 public void setWrapAlignment(boolean wrap)
388 scalePanelHolder.setVisible(!wrap);
390 hscroll.setVisible(!wrap);
391 idwidthAdjuster.setVisible(!wrap);
395 annotationPanelHolder.setVisible(false);
396 annotationSpaceFillerHolder.setVisible(false);
398 else if (av.showAnnotation)
400 annotationPanelHolder.setVisible(true);
401 annotationSpaceFillerHolder.setVisible(true);
404 idSpaceFillerPanel1.setVisible(!wrap);
406 fontChanged(); // This is so that the scalePanel is resized correctly
417 // return value is true if the scroll is valid
418 public boolean scrollUp(boolean up)
422 if (vscroll.getValue() < 1)
426 setScrollValues(hscroll.getValue(), vscroll.getValue() - 1);
430 if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())
434 setScrollValues(hscroll.getValue(), vscroll.getValue() + 1);
441 public boolean scrollRight(boolean right)
445 if (hscroll.getValue() < 1)
449 setScrollValues(hscroll.getValue() - 1, vscroll.getValue());
453 if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
457 setScrollValues(hscroll.getValue() + 1, vscroll.getValue());
464 public void setScrollValues(int x, int y)
466 int width = av.alignment.getWidth();
467 int height = av.alignment.getHeight();
469 if (av.hasHiddenColumns)
471 width = av.getColumnSelection().findColumnPosition(width);
475 av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
477 hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
478 vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
485 if (vextent > height)
490 if ((hextent + x) > width)
495 if ((vextent + y) > height)
497 y = height - vextent;
512 int endSeq = y + vextent;
513 if (endSeq > av.alignment.getHeight())
515 endSeq = av.alignment.getHeight();
518 av.setEndSeq(endSeq);
519 hscroll.setValues(x, hextent, 0, width);
520 vscroll.setValues(y, vextent, 0, height);
522 if (overviewPanel != null)
524 overviewPanel.setBoxPosition();
529 public void adjustmentValueChanged(AdjustmentEvent evt)
531 int oldX = av.getStartRes();
532 int oldY = av.getStartSeq();
534 if (evt == null || evt.getSource() == apvscroll)
536 annotationPanel.setScrollOffset(apvscroll.getValue());
537 alabels.setScrollOffset(apvscroll.getValue());
538 // annotationPanel.image=null;
539 // alabels.image=null;
540 // alabels.repaint();
541 // annotationPanel.repaint();
543 if (evt == null || evt.getSource() == hscroll)
545 int x = hscroll.getValue();
547 av.setEndRes(x + seqPanel.seqCanvas.getSize().width
548 / av.getCharWidth() - 1);
551 if (evt == null || evt.getSource() == vscroll)
553 int offy = vscroll.getValue();
554 if (av.getWrapAlignment())
556 int rowSize = seqPanel.seqCanvas
557 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
558 av.setStartRes(vscroll.getValue() * rowSize);
559 av.setEndRes((vscroll.getValue() + 1) * rowSize);
563 av.setStartSeq(offy);
564 av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
565 / av.getCharHeight());
569 if (overviewPanel != null)
571 overviewPanel.setBoxPosition();
574 int scrollX = av.startRes - oldX;
575 int scrollY = av.startSeq - oldY;
577 if (av.getWrapAlignment() || !fastPaint || av.MAC)
583 // Make sure we're not trying to draw a panel
584 // larger than the visible window
585 if (scrollX > av.endRes - av.startRes)
587 scrollX = av.endRes - av.startRes;
589 else if (scrollX < av.startRes - av.endRes)
591 scrollX = av.startRes - av.endRes;
594 idPanel.idCanvas.fastPaint(scrollY);
595 seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
597 scalePanel.repaint();
598 if (av.getShowAnnotation())
600 annotationPanel.fastPaint(av.getStartRes() - oldX);
606 public void paintAlignment(boolean updateOverview)
612 jalview.structure.StructureSelectionManager
613 .getStructureSelectionManager().sequenceColoursChanged(this);
615 if (overviewPanel != null)
617 overviewPanel.updateOverviewImage();
622 public void update(Graphics g)
627 public void paint(Graphics g)
630 Dimension d = idPanel.idCanvas.getSize();
631 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
633 if (av.getWrapAlignment())
635 int maxwidth = av.alignment.getWidth();
637 if (av.hasHiddenColumns)
639 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
642 int canvasWidth = seqPanel.seqCanvas
643 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
647 int max = maxwidth / canvasWidth;
648 vscroll.setMaximum(1 + max);
649 vscroll.setUnitIncrement(1);
650 vscroll.setVisibleAmount(1);
655 setScrollValues(av.getStartRes(), av.getStartSeq());
660 seqPanel.seqCanvas.repaint();
661 scalePanel.repaint();
662 annotationPanel.repaint();
663 idPanel.idCanvas.repaint();
666 protected Panel sequenceHolderPanel = new Panel();
668 protected Scrollbar vscroll = new Scrollbar();
670 protected Scrollbar hscroll = new Scrollbar();
672 protected Panel seqPanelHolder = new Panel();
674 BorderLayout borderLayout1 = new BorderLayout();
676 BorderLayout borderLayout3 = new BorderLayout();
678 protected Panel scalePanelHolder = new Panel();
680 protected Panel idPanelHolder = new Panel();
682 BorderLayout borderLayout5 = new BorderLayout();
684 protected Panel idSpaceFillerPanel1 = new Panel();
686 public Panel annotationSpaceFillerHolder = new Panel();
688 BorderLayout borderLayout6 = new BorderLayout();
690 BorderLayout borderLayout7 = new BorderLayout();
692 Panel hscrollHolder = new Panel();
694 BorderLayout borderLayout10 = new BorderLayout();
696 protected Panel hscrollFillerPanel = new Panel();
698 BorderLayout borderLayout11 = new BorderLayout();
700 BorderLayout borderLayout4 = new BorderLayout();
702 BorderLayout borderLayout2 = new BorderLayout();
704 Panel annotationPanelHolder = new Panel();
706 protected Scrollbar apvscroll = new Scrollbar();
708 BorderLayout borderLayout12 = new BorderLayout();
710 private void jbInit() throws Exception
712 // idPanelHolder.setPreferredSize(new Dimension(70, 10));
713 this.setLayout(borderLayout7);
715 //sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
716 sequenceHolderPanel.setLayout(borderLayout3);
717 seqPanelHolder.setLayout(borderLayout1);
718 scalePanelHolder.setBackground(Color.white);
720 // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
721 scalePanelHolder.setLayout(borderLayout6);
722 idPanelHolder.setLayout(borderLayout5);
723 idSpaceFillerPanel1.setBackground(Color.white);
725 // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
726 idSpaceFillerPanel1.setLayout(borderLayout11);
727 annotationSpaceFillerHolder.setBackground(Color.white);
729 // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
730 annotationSpaceFillerHolder.setLayout(borderLayout4);
731 hscroll.setOrientation(Scrollbar.HORIZONTAL);
732 hscrollHolder.setLayout(borderLayout10);
733 hscrollFillerPanel.setBackground(Color.white);
734 apvscroll.setOrientation(Scrollbar.VERTICAL);
735 apvscroll.setVisible(true);
736 apvscroll.addAdjustmentListener(this);
738 annotationPanelHolder.setBackground(Color.white);
739 annotationPanelHolder.setLayout(borderLayout12);
740 annotationPanelHolder.add(apvscroll, BorderLayout.EAST);
741 // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
742 hscrollHolder.setBackground(Color.white);
744 // annotationScroller.setPreferredSize(new Dimension(10, 80));
745 // this.setPreferredSize(new Dimension(220, 166));
746 seqPanelHolder.setBackground(Color.white);
747 idPanelHolder.setBackground(Color.white);
748 sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
749 sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
750 seqPanelHolder.add(vscroll, BorderLayout.EAST);
752 // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
753 this.add(idPanelHolder, BorderLayout.WEST);
754 idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
755 idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
756 this.add(hscrollHolder, BorderLayout.SOUTH);
757 hscrollHolder.add(hscroll, BorderLayout.CENTER);
758 hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
759 this.add(sequenceHolderPanel, BorderLayout.CENTER);
763 * hides or shows dynamic annotation rows based on groups and av state flags
765 public void updateAnnotation()
767 updateAnnotation(false);
770 public void updateAnnotation(boolean applyGlobalSettings)
772 // TODO: this should be merged with other annotation update stuff - that
773 // sits on AlignViewport
774 boolean updateCalcs = false;
775 boolean conv = av.isShowGroupConservation();
776 boolean cons = av.isShowGroupConsensus();
777 boolean showprf = av.isShowSequenceLogo();
778 boolean showConsHist = av.isShowConsensusHistogram();
780 boolean sortg = true;
782 // remove old automatic annotation
783 // add any new annotation
785 Vector gr = av.alignment.getGroups(); // OrderedBy(av.alignment.getSequencesArray());
786 // intersect alignment annotation with alignment groups
788 AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation();
789 Hashtable oldrfs = new Hashtable();
792 for (int an = 0; an < aan.length; an++)
794 if (aan[an].autoCalculated && aan[an].groupRef != null)
796 oldrfs.put(aan[an].groupRef, aan[an].groupRef);
797 av.alignment.deleteAnnotation(aan[an]);
805 for (int g = 0; g < gr.size(); g++)
808 sg = (SequenceGroup) gr.elementAt(g);
809 if (applyGlobalSettings || !oldrfs.containsKey(sg))
811 // set defaults for this group's conservation/consensus
812 sg.setshowSequenceLogo(showprf);
813 sg.setShowConsensusHistogram(showConsHist);
818 av.alignment.addAnnotation(sg.getConservationRow(), 0);
823 av.alignment.addAnnotation(sg.getConsensus(), 0);
825 // refresh the annotation rows
828 sg.recalcConservation();
833 adjustAnnotationHeight();
837 * automatically adjust annotation panel height for new annotation whilst
838 * ensuring the alignment is still visible.
840 public void adjustAnnotationHeight()
842 // TODO: display vertical annotation scrollbar if necessary
843 // this is called after loading new annotation onto alignment
844 if (alignFrame.getSize().height == 0)
846 System.out.println("NEEDS FIXING");
849 validateAnnotationDimensions(true);
850 apvscroll.addNotify();
857 * calculate the annotation dimensions and refresh slider values accordingly.
858 * need to do repaints/notifys afterwards.
860 protected void validateAnnotationDimensions(boolean adjustPanelHeight) {
861 int height = annotationPanel.calcPanelHeight();
862 if (hscroll.isVisible())
864 height += hscroll.getPreferredSize().height;
866 int mheight = height;
867 // sets initial preferred height
868 if ((height+40) > getSize().height / 2)
870 height = getSize().height / 2;
872 if (!adjustPanelHeight)
874 // maintain same window layout whilst updating sliders
875 height=seqPanelHolder.getSize().height;
877 Dimension d=seqPanelHolder.getSize(),e=idPanel.getSize();
878 annotationPanel.setSize(new Dimension(d.width,height));
879 alabels.setSize(e.width,height);
880 annotationSpaceFillerHolder.setSize(new Dimension(e.width, height));
881 annotationPanelHolder.setSize(new Dimension(d.width, height));
882 seqPanelHolder.setSize(d.width,d.height-height);
883 int s=apvscroll.getValue();
884 if (s>mheight-height)
888 apvscroll.setValues(apvscroll.getValue(), height, 0, mheight);
889 annotationPanel.setScrollOffset(apvscroll.getValue());
890 alabels.setScrollOffset(apvscroll.getValue());