2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
5 * This program is free software; you can redistribute it and/or
\r
6 * modify it under the terms of the GNU General Public License
\r
7 * as published by the Free Software Foundation; either version 2
\r
8 * of the License, or (at your option) any later version.
\r
10 * This program is distributed in the hope that it will be useful,
\r
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
13 * GNU General Public License for more details.
\r
15 * You should have received a copy of the GNU General Public License
\r
16 * along with this program; if not, write to the Free Software
\r
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
20 package jalview.appletgui;
\r
23 import java.awt.event.*;
\r
25 import jalview.datamodel.*;
\r
27 public class AlignmentPanel extends Panel implements AdjustmentListener
\r
31 OverviewPanel overviewPanel;
\r
34 IdwidthAdjuster idwidthAdjuster;
\r
35 public AlignFrame alignFrame;
\r
36 ScalePanel scalePanel;
\r
37 AnnotationPanel annotationPanel;
\r
38 AnnotationLabels alabels;
\r
40 // this value is set false when selection area being dragged
\r
41 boolean fastPaint = true;
\r
45 public AlignmentPanel(AlignFrame af, final AlignViewport av)
\r
53 e.printStackTrace();
\r
59 seqPanel = new SeqPanel(av, this);
\r
60 idPanel = new IdPanel(av, this);
\r
61 scalePanel = new ScalePanel(av, this);
\r
62 idwidthAdjuster = new IdwidthAdjuster(this);
\r
63 annotationPanel = new AnnotationPanel(this);
\r
65 sequenceHolderPanel.add(annotationPanel, BorderLayout.SOUTH);
\r
67 alabels = new AnnotationLabels(this);
\r
69 setAnnotationVisible(av.showAnnotation);
\r
71 idPanelHolder.add(idPanel, BorderLayout.CENTER);
\r
72 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
\r
73 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
\r
74 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
\r
75 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
\r
78 setScrollValues(0, 0);
\r
80 hscroll.addAdjustmentListener(this);
\r
81 vscroll.addAdjustmentListener(this);
\r
83 addComponentListener(new ComponentAdapter()
\r
85 public void componentResized(ComponentEvent evt)
\r
87 setScrollValues(av.getStartRes(), av.getStartSeq());
\r
92 Dimension d = calculateIdWidth();
\r
93 idPanel.idCanvas.setSize(d);
\r
95 hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
\r
97 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
\r
98 annotationSpaceFillerHolder.setSize(d.width,
\r
99 annotationPanel.getSize().height);
\r
100 alabels.setSize(d.width, annotationPanel.getSize().height);
\r
102 final AlignmentPanel ap = this;
\r
103 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
\r
105 public void propertyChange(java.beans.PropertyChangeEvent evt)
\r
107 if (evt.getPropertyName().equals("alignment"))
\r
109 PaintRefresher.Refresh(ap,
\r
110 av.getSequenceSetId(),
\r
113 alignmentChanged();
\r
121 public void alignmentChanged()
\r
123 av.alignmentChanged(this);
\r
125 if (overviewPanel != null)
\r
126 overviewPanel.updateOverviewImage();
\r
128 alignFrame.updateEditMenuBar();
\r
133 public void fontChanged()
\r
135 // set idCanvas bufferedImage to null
\r
136 // to prevent drawing old image
\r
137 idPanel.idCanvas.image = null;
\r
138 FontMetrics fm = getFontMetrics(av.getFont());
\r
140 scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
\r
141 idwidthAdjuster.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
\r
143 annotationPanel.image = null;
\r
144 int ap = annotationPanel.adjustPanelHeight();
\r
145 annotationPanel.repaint();
\r
146 Dimension d = calculateIdWidth();
\r
147 d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
\r
148 alabels.setSize(d.width+4, ap );
\r
149 idPanel.idCanvas.setSize(d);
\r
150 hscrollFillerPanel.setSize(d);
\r
155 if(overviewPanel!=null)
\r
156 overviewPanel.updateOverviewImage();
\r
159 public void setIdWidth(int w, int h)
\r
161 idPanel.idCanvas.setSize(w, h);
\r
162 idPanelHolder.setSize(w, idPanelHolder.getSize().height);
\r
163 alabels.setSize(w, alabels.getSize().height);
\r
167 Dimension calculateIdWidth()
\r
169 if (av.nullFrame == null)
\r
171 av.nullFrame = new Frame();
\r
172 av.nullFrame.addNotify();
\r
175 Graphics g = av.nullFrame.getGraphics();
\r
177 FontMetrics fm = g.getFontMetrics(av.font);
\r
178 AlignmentI al = av.getAlignment();
\r
183 while (i < al.getHeight() && al.getSequenceAt(i) != null)
\r
185 SequenceI s = al.getSequenceAt(i);
\r
186 id = s.getDisplayId(av.getShowJVSuffix());
\r
188 if (fm.stringWidth(id) > idWidth)
\r
190 idWidth = fm.stringWidth(id);
\r
195 // Also check annotation label widths
\r
197 if (al.getAlignmentAnnotation() != null)
\r
199 fm = g.getFontMetrics(av.nullFrame.getFont());
\r
200 while (i < al.getAlignmentAnnotation().length)
\r
202 String label = al.getAlignmentAnnotation()[i].label;
\r
203 if (fm.stringWidth(label) > idWidth)
\r
205 idWidth = fm.stringWidth(label);
\r
211 return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
\r
214 public void highlightSearchResults(SearchResults results)
\r
216 seqPanel.seqCanvas.highlightSearchResults(results);
\r
218 // do we need to scroll the panel?
\r
219 if (results != null)
\r
221 SequenceI seq = results.getResultSequence(0);
\r
222 int seqIndex = av.alignment.findIndex(seq);
\r
223 int start = seq.findIndex(results.getResultStart(0)) - 1;
\r
224 int end = seq.findIndex(results.getResultEnd(0)) - 1;
\r
226 if(!av.wrapAlignment)
\r
228 if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||
\r
229 ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
\r
231 if (start > av.alignment.getWidth() - hextent)
\r
233 start = av.alignment.getWidth() - hextent;
\r
237 if (seqIndex > av.alignment.getHeight() - vextent)
\r
239 seqIndex = av.alignment.getHeight() - vextent;
\r
243 setScrollValues(start, seqIndex);
\r
248 scrollToWrappedVisible(start);
\r
255 void scrollToWrappedVisible(int res)
\r
257 int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
\r
258 if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
\r
260 vscroll.setValue(res / cwidth);
\r
261 av.startRes = vscroll.getValue() * cwidth;
\r
266 public OverviewPanel getOverviewPanel()
\r
268 return overviewPanel;
\r
271 public void setOverviewPanel(OverviewPanel op)
\r
273 overviewPanel = op;
\r
276 public void setAnnotationVisible(boolean b)
\r
278 if (!av.wrapAlignment)
\r
280 annotationSpaceFillerHolder.setVisible(b);
\r
281 annotationPanel.setVisible(b);
\r
287 public void setWrapAlignment(boolean wrap)
\r
290 scalePanelHolder.setVisible(!wrap);
\r
293 hscroll.setVisible(!wrap);
\r
294 idwidthAdjuster.setVisible(!wrap);
\r
298 annotationPanel.setVisible(false);
\r
299 annotationSpaceFillerHolder.setVisible(false);
\r
301 else if (av.showAnnotation)
\r
303 annotationPanel.setVisible(true);
\r
304 annotationSpaceFillerHolder.setVisible(true);
\r
308 idSpaceFillerPanel1.setVisible(!wrap);
\r
310 fontChanged();//This is so that the scalePanel is resized correctly
\r
321 // return value is true if the scroll is valid
\r
322 public boolean scrollUp(boolean up)
\r
326 if (vscroll.getValue() < 1)
\r
330 setScrollValues(hscroll.getValue(), vscroll.getValue()-1);
\r
334 if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())
\r
338 setScrollValues(hscroll.getValue(), vscroll.getValue()+1);
\r
345 public boolean scrollRight(boolean right)
\r
349 if (hscroll.getValue() < 1)
\r
353 setScrollValues(hscroll.getValue()-1, vscroll.getValue());
\r
357 if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
\r
361 setScrollValues(hscroll.getValue()+1, vscroll.getValue());
\r
368 public void setScrollValues(int x, int y)
\r
370 int width = av.alignment.getWidth();
\r
371 int height = av.alignment.getHeight();
\r
373 if(av.hasHiddenColumns)
\r
374 width = av.getColumnSelection().findColumnPosition(width);
\r
377 av.setEndRes( (x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) -1);
\r
379 hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
\r
380 vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
\r
382 if (hextent > width)
\r
387 if (vextent > height)
\r
392 if ( (hextent + x) > width)
\r
394 x = width - hextent;
\r
397 if ( (vextent + y) > height)
\r
399 y = height - vextent;
\r
414 int endSeq = y + vextent;
\r
415 if (endSeq > av.alignment.getHeight())
\r
417 endSeq = av.alignment.getHeight();
\r
420 av.setEndSeq(endSeq);
\r
421 hscroll.setValues(x, hextent, 0, width);
\r
422 vscroll.setValues(y, vextent, 0, height);
\r
424 if(overviewPanel!=null)
\r
425 overviewPanel.setBoxPosition();
\r
429 public void adjustmentValueChanged(AdjustmentEvent evt)
\r
431 int oldX = av.getStartRes();
\r
432 int oldY = av.getStartSeq();
\r
435 if (evt==null || evt.getSource() == hscroll)
\r
437 int x = hscroll.getValue();
\r
439 av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() -
\r
444 if (evt==null || evt.getSource() == vscroll)
\r
446 int offy = vscroll.getValue();
\r
447 if (av.getWrapAlignment())
\r
449 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
\r
450 seqCanvas.getSize().width);
\r
451 av.setStartRes(vscroll.getValue() * rowSize);
\r
452 av.setEndRes( (vscroll.getValue() + 1) * rowSize);
\r
456 av.setStartSeq(offy);
\r
457 av.setEndSeq(offy +
\r
458 seqPanel.seqCanvas.getSize().height / av.getCharHeight());
\r
462 if (overviewPanel != null)
\r
464 overviewPanel.setBoxPosition();
\r
467 int scrollX = av.startRes - oldX;
\r
468 int scrollY = av.startSeq - oldY;
\r
470 if (av.getWrapAlignment() || !fastPaint || av.MAC)
\r
476 // Make sure we're not trying to draw a panel
\r
477 // larger than the visible window
\r
478 if(scrollX>av.endRes-av.startRes)
\r
480 scrollX = av.endRes - av.startRes;
\r
482 else if(scrollX<av.startRes-av.endRes)
\r
483 scrollX = av.startRes - av.endRes;
\r
485 idPanel.idCanvas.fastPaint(scrollY);
\r
486 seqPanel.seqCanvas.fastPaint(scrollX,
\r
489 scalePanel.repaint();
\r
490 if (av.getShowAnnotation())
\r
492 annotationPanel.fastPaint(av.getStartRes() - oldX);
\r
498 public void update(Graphics g)
\r
503 public void paint(Graphics g)
\r
506 Dimension d = idPanel.idCanvas.getSize();
\r
507 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
\r
508 annotationSpaceFillerHolder.setSize(d.width,
\r
509 annotationPanel.getSize().height);
\r
511 alabels.setSize(d.width, annotationPanel.getSize().height);
\r
513 if (av.getWrapAlignment())
\r
515 int maxwidth = av.alignment.getWidth();
\r
517 if (av.hasHiddenColumns)
\r
518 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
\r
520 int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth
\r
521 (seqPanel.seqCanvas.getSize().width);
\r
525 int max = maxwidth / canvasWidth;
\r
526 vscroll.setMaximum(max);
\r
527 vscroll.setUnitIncrement(1);
\r
528 vscroll.setVisibleAmount(1);
\r
533 setScrollValues(av.getStartRes(), av.getStartSeq());
\r
538 seqPanel.seqCanvas.repaint();
\r
539 scalePanel.repaint();
\r
540 annotationPanel.repaint();
\r
541 idPanel.idCanvas.repaint();
\r
543 if (getBounds() == g.getClipBounds())
\r
545 if (overviewPanel != null)
\r
546 overviewPanel.updateOverviewImage();
\r
551 protected Panel sequenceHolderPanel = new Panel();
\r
552 protected Scrollbar vscroll = new Scrollbar();
\r
553 protected Scrollbar hscroll = new Scrollbar();
\r
554 protected Panel seqPanelHolder = new Panel();
\r
555 BorderLayout borderLayout1 = new BorderLayout();
\r
556 BorderLayout borderLayout3 = new BorderLayout();
\r
557 protected Panel scalePanelHolder = new Panel();
\r
558 protected Panel idPanelHolder = new Panel();
\r
559 BorderLayout borderLayout5 = new BorderLayout();
\r
560 protected Panel idSpaceFillerPanel1 = new Panel();
\r
561 public Panel annotationSpaceFillerHolder = new Panel();
\r
562 BorderLayout borderLayout6 = new BorderLayout();
\r
563 BorderLayout borderLayout7 = new BorderLayout();
\r
564 Panel hscrollHolder = new Panel();
\r
565 BorderLayout borderLayout10 = new BorderLayout();
\r
566 protected Panel hscrollFillerPanel = new Panel();
\r
567 BorderLayout borderLayout11 = new BorderLayout();
\r
568 BorderLayout borderLayout4 = new BorderLayout();
\r
569 BorderLayout borderLayout2 = new BorderLayout();
\r
571 private void jbInit() throws Exception {
\r
572 // idPanelHolder.setPreferredSize(new Dimension(70, 10));
\r
573 this.setLayout(borderLayout7);
\r
575 // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
\r
576 sequenceHolderPanel.setLayout(borderLayout3);
\r
577 seqPanelHolder.setLayout(borderLayout1);
\r
578 scalePanelHolder.setBackground(Color.white);
\r
580 // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
\r
581 scalePanelHolder.setLayout(borderLayout6);
\r
582 idPanelHolder.setLayout(borderLayout5);
\r
583 idSpaceFillerPanel1.setBackground(Color.white);
\r
585 // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
\r
586 idSpaceFillerPanel1.setLayout(borderLayout11);
\r
587 annotationSpaceFillerHolder.setBackground(Color.white);
\r
589 // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
\r
590 annotationSpaceFillerHolder.setLayout(borderLayout4);
\r
591 hscroll.setOrientation(Scrollbar.HORIZONTAL);
\r
592 hscrollHolder.setLayout(borderLayout10);
\r
593 hscrollFillerPanel.setBackground(Color.white);
\r
595 // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
\r
596 hscrollHolder.setBackground(Color.white);
\r
598 // annotationScroller.setPreferredSize(new Dimension(10, 80));
\r
599 // this.setPreferredSize(new Dimension(220, 166));
\r
600 seqPanelHolder.setBackground(Color.white);
\r
601 idPanelHolder.setBackground(Color.white);
\r
602 sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
\r
603 sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
\r
604 seqPanelHolder.add(vscroll, BorderLayout.EAST);
\r
606 // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
\r
607 this.add(idPanelHolder, BorderLayout.WEST);
\r
608 idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
\r
609 idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
\r
610 this.add(hscrollHolder, BorderLayout.SOUTH);
\r
611 hscrollHolder.add(hscroll, BorderLayout.CENTER);
\r
612 hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
\r
613 this.add(sequenceHolderPanel, BorderLayout.CENTER);
\r