2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
3 * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
19 package jalview.appletgui;
22 import java.awt.event.*;
24 import jalview.datamodel.*;
26 public class AlignmentPanel extends Panel implements AdjustmentListener
29 public AlignViewport av;
31 OverviewPanel overviewPanel;
37 IdwidthAdjuster idwidthAdjuster;
39 public AlignFrame alignFrame;
41 ScalePanel scalePanel;
43 AnnotationPanel annotationPanel;
45 AnnotationLabels alabels;
47 // this value is set false when selection area being dragged
48 boolean fastPaint = true;
50 public AlignmentPanel(AlignFrame af, final AlignViewport av)
62 seqPanel = new SeqPanel(av, this);
63 idPanel = new IdPanel(av, this);
64 scalePanel = new ScalePanel(av, this);
65 idwidthAdjuster = new IdwidthAdjuster(this);
66 annotationPanel = new AnnotationPanel(this);
68 sequenceHolderPanel.add(annotationPanel, BorderLayout.SOUTH);
70 alabels = new AnnotationLabels(this);
72 setAnnotationVisible(av.showAnnotation);
74 idPanelHolder.add(idPanel, BorderLayout.CENTER);
75 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
76 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
77 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
78 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
81 setScrollValues(0, 0);
83 hscroll.addAdjustmentListener(this);
84 vscroll.addAdjustmentListener(this);
86 addComponentListener(new ComponentAdapter()
88 public void componentResized(ComponentEvent evt)
90 setScrollValues(av.getStartRes(), av.getStartSeq());
95 Dimension d = calculateIdWidth();
96 idPanel.idCanvas.setSize(d);
98 hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
100 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
101 annotationSpaceFillerHolder.setSize(d.width,
102 annotationPanel.getSize().height);
103 alabels.setSize(d.width, annotationPanel.getSize().height);
105 final AlignmentPanel ap = this;
106 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
108 public void propertyChange(java.beans.PropertyChangeEvent evt)
110 if (evt.getPropertyName().equals("alignment"))
112 PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
120 public SequenceRenderer getSequenceRenderer()
122 return seqPanel.seqCanvas.sr;
125 public FeatureRenderer getFeatureRenderer()
127 return seqPanel.seqCanvas.fr;
130 public void alignmentChanged()
132 av.alignmentChanged(this);
134 if (overviewPanel != null)
136 overviewPanel.updateOverviewImage();
139 alignFrame.updateEditMenuBar();
144 public void fontChanged()
146 // set idCanvas bufferedImage to null
147 // to prevent drawing old image
148 idPanel.idCanvas.image = null;
149 FontMetrics fm = getFontMetrics(av.getFont());
151 scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
152 idwidthAdjuster.setSize(new Dimension(10, av.charHeight
154 av.updateSequenceIdColours();
155 annotationPanel.image = null;
156 int ap = annotationPanel.adjustPanelHeight();
157 annotationPanel.repaint();
158 Dimension d = calculateIdWidth();
159 d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
160 alabels.setSize(d.width + 4, ap);
161 idPanel.idCanvas.setSize(d);
162 hscrollFillerPanel.setSize(d);
167 if (overviewPanel != null)
169 overviewPanel.updateOverviewImage();
173 public void setIdWidth(int w, int h)
175 idPanel.idCanvas.setSize(w, h);
176 idPanelHolder.setSize(w, idPanelHolder.getSize().height);
177 alabels.setSize(w, alabels.getSize().height);
181 Dimension calculateIdWidth()
183 if (av.nullFrame == null)
185 av.nullFrame = new Frame();
186 av.nullFrame.addNotify();
189 Graphics g = av.nullFrame.getGraphics();
191 FontMetrics fm = g.getFontMetrics(av.font);
192 AlignmentI al = av.getAlignment();
197 while (i < al.getHeight() && al.getSequenceAt(i) != null)
199 SequenceI s = al.getSequenceAt(i);
200 id = s.getDisplayId(av.getShowJVSuffix());
202 if (fm.stringWidth(id) > idWidth)
204 idWidth = fm.stringWidth(id);
209 // Also check annotation label widths
211 if (al.getAlignmentAnnotation() != null)
213 fm = g.getFontMetrics(av.nullFrame.getFont());
214 while (i < al.getAlignmentAnnotation().length)
216 String label = al.getAlignmentAnnotation()[i].label;
217 if (fm.stringWidth(label) > idWidth)
219 idWidth = fm.stringWidth(label);
225 return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
228 public void highlightSearchResults(SearchResults results)
230 seqPanel.seqCanvas.highlightSearchResults(results);
232 // do we need to scroll the panel?
235 SequenceI seq = results.getResultSequence(0);
236 int seqIndex = av.alignment.findIndex(seq);
237 int start = seq.findIndex(results.getResultStart(0)) - 1;
238 int end = seq.findIndex(results.getResultEnd(0)) - 1;
240 if (!av.wrapAlignment)
242 if ((av.getStartRes() > end)
243 || (av.getEndRes() < start)
244 || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
246 if (start > av.alignment.getWidth() - hextent)
248 start = av.alignment.getWidth() - hextent;
254 if (seqIndex > av.alignment.getHeight() - vextent)
256 seqIndex = av.alignment.getHeight() - vextent;
262 setScrollValues(start, seqIndex);
267 scrollToWrappedVisible(start);
274 void scrollToWrappedVisible(int res)
276 int cwidth = seqPanel.seqCanvas
277 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
278 if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
280 vscroll.setValue(res / cwidth);
281 av.startRes = vscroll.getValue() * cwidth;
285 public OverviewPanel getOverviewPanel()
287 return overviewPanel;
290 public void setOverviewPanel(OverviewPanel op)
295 public void setAnnotationVisible(boolean b)
297 if (!av.wrapAlignment)
299 annotationSpaceFillerHolder.setVisible(b);
300 annotationPanel.setVisible(b);
306 public void setWrapAlignment(boolean wrap)
310 scalePanelHolder.setVisible(!wrap);
312 hscroll.setVisible(!wrap);
313 idwidthAdjuster.setVisible(!wrap);
317 annotationPanel.setVisible(false);
318 annotationSpaceFillerHolder.setVisible(false);
320 else if (av.showAnnotation)
322 annotationPanel.setVisible(true);
323 annotationSpaceFillerHolder.setVisible(true);
326 idSpaceFillerPanel1.setVisible(!wrap);
328 fontChanged(); // This is so that the scalePanel is resized correctly
339 // return value is true if the scroll is valid
340 public boolean scrollUp(boolean up)
344 if (vscroll.getValue() < 1)
348 setScrollValues(hscroll.getValue(), vscroll.getValue() - 1);
352 if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())
356 setScrollValues(hscroll.getValue(), vscroll.getValue() + 1);
363 public boolean scrollRight(boolean right)
367 if (hscroll.getValue() < 1)
371 setScrollValues(hscroll.getValue() - 1, vscroll.getValue());
375 if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
379 setScrollValues(hscroll.getValue() + 1, vscroll.getValue());
386 public void setScrollValues(int x, int y)
388 int width = av.alignment.getWidth();
389 int height = av.alignment.getHeight();
391 if (av.hasHiddenColumns)
393 width = av.getColumnSelection().findColumnPosition(width);
398 .setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
400 hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
401 vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
408 if (vextent > height)
413 if ((hextent + x) > width)
418 if ((vextent + y) > height)
420 y = height - vextent;
435 int endSeq = y + vextent;
436 if (endSeq > av.alignment.getHeight())
438 endSeq = av.alignment.getHeight();
441 av.setEndSeq(endSeq);
442 hscroll.setValues(x, hextent, 0, width);
443 vscroll.setValues(y, vextent, 0, height);
445 if (overviewPanel != null)
447 overviewPanel.setBoxPosition();
452 public void adjustmentValueChanged(AdjustmentEvent evt)
454 int oldX = av.getStartRes();
455 int oldY = av.getStartSeq();
457 if (evt == null || evt.getSource() == hscroll)
459 int x = hscroll.getValue();
461 av.setEndRes(x + seqPanel.seqCanvas.getSize().width
462 / av.getCharWidth() - 1);
465 if (evt == null || evt.getSource() == vscroll)
467 int offy = vscroll.getValue();
468 if (av.getWrapAlignment())
470 int rowSize = seqPanel.seqCanvas
471 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
472 av.setStartRes(vscroll.getValue() * rowSize);
473 av.setEndRes((vscroll.getValue() + 1) * rowSize);
477 av.setStartSeq(offy);
478 av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
479 / av.getCharHeight());
483 if (overviewPanel != null)
485 overviewPanel.setBoxPosition();
488 int scrollX = av.startRes - oldX;
489 int scrollY = av.startSeq - oldY;
491 if (av.getWrapAlignment() || !fastPaint || av.MAC)
497 // Make sure we're not trying to draw a panel
498 // larger than the visible window
499 if (scrollX > av.endRes - av.startRes)
501 scrollX = av.endRes - av.startRes;
503 else if (scrollX < av.startRes - av.endRes)
505 scrollX = av.startRes - av.endRes;
508 idPanel.idCanvas.fastPaint(scrollY);
509 seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
511 scalePanel.repaint();
512 if (av.getShowAnnotation())
514 annotationPanel.fastPaint(av.getStartRes() - oldX);
520 public void paintAlignment(boolean updateOverview)
526 jalview.structure.StructureSelectionManager
527 .getStructureSelectionManager().sequenceColoursChanged(this);
529 if (overviewPanel != null)
531 overviewPanel.updateOverviewImage();
536 public void update(Graphics g)
541 public void paint(Graphics g)
544 Dimension d = idPanel.idCanvas.getSize();
545 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
546 annotationSpaceFillerHolder.setSize(d.width,
547 annotationPanel.getSize().height);
549 alabels.setSize(d.width, annotationPanel.getSize().height);
551 if (av.getWrapAlignment())
553 int maxwidth = av.alignment.getWidth();
555 if (av.hasHiddenColumns)
557 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
560 int canvasWidth = seqPanel.seqCanvas
561 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
565 int max = maxwidth / canvasWidth;
566 vscroll.setMaximum(max);
567 vscroll.setUnitIncrement(1);
568 vscroll.setVisibleAmount(1);
573 setScrollValues(av.getStartRes(), av.getStartSeq());
578 seqPanel.seqCanvas.repaint();
579 scalePanel.repaint();
580 annotationPanel.repaint();
581 idPanel.idCanvas.repaint();
584 protected Panel sequenceHolderPanel = new Panel();
586 protected Scrollbar vscroll = new Scrollbar();
588 protected Scrollbar hscroll = new Scrollbar();
590 protected Panel seqPanelHolder = new Panel();
592 BorderLayout borderLayout1 = new BorderLayout();
594 BorderLayout borderLayout3 = new BorderLayout();
596 protected Panel scalePanelHolder = new Panel();
598 protected Panel idPanelHolder = new Panel();
600 BorderLayout borderLayout5 = new BorderLayout();
602 protected Panel idSpaceFillerPanel1 = new Panel();
604 public Panel annotationSpaceFillerHolder = new Panel();
606 BorderLayout borderLayout6 = new BorderLayout();
608 BorderLayout borderLayout7 = new BorderLayout();
610 Panel hscrollHolder = new Panel();
612 BorderLayout borderLayout10 = new BorderLayout();
614 protected Panel hscrollFillerPanel = new Panel();
616 BorderLayout borderLayout11 = new BorderLayout();
618 BorderLayout borderLayout4 = new BorderLayout();
620 BorderLayout borderLayout2 = new BorderLayout();
622 private void jbInit() throws Exception
624 // idPanelHolder.setPreferredSize(new Dimension(70, 10));
625 this.setLayout(borderLayout7);
627 // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
628 sequenceHolderPanel.setLayout(borderLayout3);
629 seqPanelHolder.setLayout(borderLayout1);
630 scalePanelHolder.setBackground(Color.white);
632 // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
633 scalePanelHolder.setLayout(borderLayout6);
634 idPanelHolder.setLayout(borderLayout5);
635 idSpaceFillerPanel1.setBackground(Color.white);
637 // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
638 idSpaceFillerPanel1.setLayout(borderLayout11);
639 annotationSpaceFillerHolder.setBackground(Color.white);
641 // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
642 annotationSpaceFillerHolder.setLayout(borderLayout4);
643 hscroll.setOrientation(Scrollbar.HORIZONTAL);
644 hscrollHolder.setLayout(borderLayout10);
645 hscrollFillerPanel.setBackground(Color.white);
647 // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
648 hscrollHolder.setBackground(Color.white);
650 // annotationScroller.setPreferredSize(new Dimension(10, 80));
651 // this.setPreferredSize(new Dimension(220, 166));
652 seqPanelHolder.setBackground(Color.white);
653 idPanelHolder.setBackground(Color.white);
654 sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
655 sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
656 seqPanelHolder.add(vscroll, BorderLayout.EAST);
658 // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
659 this.add(idPanelHolder, BorderLayout.WEST);
660 idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
661 idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
662 this.add(hscrollHolder, BorderLayout.SOUTH);
663 hscrollHolder.add(hscroll, BorderLayout.CENTER);
664 hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
665 this.add(sequenceHolderPanel, BorderLayout.CENTER);