2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2006 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
20 package jalview.appletgui;
23 import java.awt.event.*;
25 import jalview.datamodel.*;
27 public class AlignmentPanel extends Panel implements AdjustmentListener
31 OverviewPanel overviewPanel;
34 IdwidthAdjuster idwidthAdjuster;
35 public AlignFrame alignFrame;
36 ScalePanel scalePanel;
37 AnnotationPanel annotationPanel;
38 AnnotationLabels alabels;
40 // this value is set false when selection area being dragged
41 boolean fastPaint = true;
45 public AlignmentPanel(AlignFrame af, final AlignViewport av)
59 seqPanel = new SeqPanel(av, this);
60 idPanel = new IdPanel(av, this);
61 scalePanel = new ScalePanel(av, this);
62 idwidthAdjuster = new IdwidthAdjuster(this);
63 annotationPanel = new AnnotationPanel(this);
65 sequenceHolderPanel.add(annotationPanel, BorderLayout.SOUTH);
67 alabels = new AnnotationLabels(this);
69 setAnnotationVisible(av.showAnnotation);
71 idPanelHolder.add(idPanel, BorderLayout.CENTER);
72 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
73 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
74 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
75 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
78 setScrollValues(0, 0);
80 hscroll.addAdjustmentListener(this);
81 vscroll.addAdjustmentListener(this);
83 addComponentListener(new ComponentAdapter()
85 public void componentResized(ComponentEvent evt)
87 setScrollValues(av.getStartRes(), av.getStartSeq());
92 Dimension d = calculateIdWidth();
93 idPanel.idCanvas.setSize(d);
95 hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
97 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
98 annotationSpaceFillerHolder.setSize(d.width,
99 annotationPanel.getSize().height);
100 alabels.setSize(d.width, annotationPanel.getSize().height);
105 public void fontChanged()
107 // set idCanvas bufferedImage to null
108 // to prevent drawing old image
109 idPanel.idCanvas.image = null;
110 FontMetrics fm = getFontMetrics(av.getFont());
112 scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
113 idwidthAdjuster.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
115 annotationPanel.image = null;
116 int ap = annotationPanel.adjustPanelHeight();
117 annotationPanel.repaint();
118 Dimension d = calculateIdWidth();
119 d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
120 alabels.setSize(d.width+4, ap );
121 idPanel.idCanvas.setSize(d);
122 hscrollFillerPanel.setSize(d);
127 if(overviewPanel!=null)
128 overviewPanel.updateOverviewImage();
131 public void setIdWidth(int w, int h)
133 idPanel.idCanvas.setSize(w, h);
134 idPanelHolder.setSize(w, idPanelHolder.getSize().height);
135 alabels.setSize(w, alabels.getSize().height);
139 Dimension calculateIdWidth()
141 if (av.nullFrame == null)
143 av.nullFrame = new Frame();
144 av.nullFrame.addNotify();
147 Graphics g = av.nullFrame.getGraphics();
149 FontMetrics fm = g.getFontMetrics(av.font);
150 AlignmentI al = av.getAlignment();
155 while (i < al.getHeight() && al.getSequenceAt(i) != null)
157 SequenceI s = al.getSequenceAt(i);
158 id = s.getDisplayId(av.getShowJVSuffix());
160 if (fm.stringWidth(id) > idWidth)
162 idWidth = fm.stringWidth(id);
167 // Also check annotation label widths
169 if (al.getAlignmentAnnotation() != null)
171 fm = g.getFontMetrics(av.nullFrame.getFont());
172 while (i < al.getAlignmentAnnotation().length)
174 String label = al.getAlignmentAnnotation()[i].label;
175 if (fm.stringWidth(label) > idWidth)
177 idWidth = fm.stringWidth(label);
183 return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
186 public void highlightSearchResults(SearchResults results)
188 seqPanel.seqCanvas.highlightSearchResults(results);
190 // do we need to scroll the panel?
193 SequenceI seq = results.getResultSequence(0);
194 int seqIndex = av.alignment.findIndex(seq);
195 int start = seq.findIndex(results.getResultStart(0)) - 1;
196 int end = seq.findIndex(results.getResultEnd(0)) - 1;
198 if(!av.wrapAlignment)
200 if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||
201 ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
203 if (start > av.alignment.getWidth() - hextent)
205 start = av.alignment.getWidth() - hextent;
209 if (seqIndex > av.alignment.getHeight() - vextent)
211 seqIndex = av.alignment.getHeight() - vextent;
215 setScrollValues(start, seqIndex);
220 scrollToWrappedVisible(start);
227 void scrollToWrappedVisible(int res)
229 int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
230 if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
232 vscroll.setValue(res / cwidth);
233 av.startRes = vscroll.getValue() * cwidth;
238 public OverviewPanel getOverviewPanel()
240 return overviewPanel;
243 public void setOverviewPanel(OverviewPanel op)
248 public void setAnnotationVisible(boolean b)
250 if (!av.wrapAlignment)
252 annotationSpaceFillerHolder.setVisible(b);
253 annotationPanel.setVisible(b);
259 public void setWrapAlignment(boolean wrap)
262 scalePanelHolder.setVisible(!wrap);
265 hscroll.setVisible(!wrap);
266 idwidthAdjuster.setVisible(!wrap);
270 annotationPanel.setVisible(false);
271 annotationSpaceFillerHolder.setVisible(false);
273 else if (av.showAnnotation)
275 annotationPanel.setVisible(true);
276 annotationSpaceFillerHolder.setVisible(true);
280 idSpaceFillerPanel1.setVisible(!wrap);
282 fontChanged();//This is so that the scalePanel is resized correctly
293 // return value is true if the scroll is valid
294 public boolean scrollUp(boolean up)
298 if (vscroll.getValue() < 1)
302 setScrollValues(hscroll.getValue(), vscroll.getValue()-1);
306 if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())
310 setScrollValues(hscroll.getValue(), vscroll.getValue()+1);
317 public boolean scrollRight(boolean right)
321 if (hscroll.getValue() < 1)
325 setScrollValues(hscroll.getValue()-1, vscroll.getValue());
329 if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
333 setScrollValues(hscroll.getValue()+1, vscroll.getValue());
340 public void setScrollValues(int x, int y)
342 int width = av.alignment.getWidth();
343 int height = av.alignment.getHeight();
345 if(av.hasHiddenColumns)
346 width = av.getColumnSelection().findColumnPosition(width);
351 av.setEndRes( (x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) -1);
353 hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
354 vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
361 if (vextent > height)
366 if ( (hextent + x) > width)
371 if ( (vextent + y) > height)
373 y = height - vextent;
386 int endSeq = y + vextent;
387 if (endSeq > av.alignment.getHeight())
389 endSeq = av.alignment.getHeight();
392 av.setEndSeq(endSeq);
393 hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
394 vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
396 if(overviewPanel!=null)
397 overviewPanel.setBoxPosition();
401 public void adjustmentValueChanged(AdjustmentEvent evt)
403 int oldX = av.getStartRes();
404 int oldY = av.getStartSeq();
407 if (evt==null || evt.getSource() == hscroll)
409 int x = hscroll.getValue();
411 av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() -
416 if (evt==null || evt.getSource() == vscroll)
418 int offy = vscroll.getValue();
419 if (av.getWrapAlignment())
421 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
422 seqCanvas.getSize().width);
423 av.setStartRes(vscroll.getValue() * rowSize);
424 av.setEndRes( (vscroll.getValue() + 1) * rowSize);
428 av.setStartSeq(offy);
430 seqPanel.seqCanvas.getSize().height / av.getCharHeight());
434 if (overviewPanel != null)
436 overviewPanel.setBoxPosition();
439 int scrollX = av.startRes - oldX;
440 int scrollY = av.startSeq - oldY;
442 if (av.getWrapAlignment() || !fastPaint || av.MAC)
448 // Make sure we're not trying to draw a panel
449 // larger than the visible window
450 if(scrollX>av.endRes-av.startRes)
452 scrollX = av.endRes - av.startRes;
454 else if(scrollX<av.startRes-av.endRes)
455 scrollX = av.startRes - av.endRes;
457 idPanel.idCanvas.fastPaint(scrollY);
458 seqPanel.seqCanvas.fastPaint(scrollX,
461 scalePanel.repaint();
462 if (av.getShowAnnotation())
464 annotationPanel.fastPaint(av.getStartRes() - oldX);
470 public void update(Graphics g)
475 public void paint(Graphics g)
478 Dimension d = idPanel.idCanvas.getSize();
479 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
480 annotationSpaceFillerHolder.setSize(d.width,
481 annotationPanel.getSize().height);
483 alabels.setSize(d.width, annotationPanel.getSize().height);
485 if (av.getWrapAlignment())
487 int maxwidth = av.alignment.getWidth();
489 if (av.hasHiddenColumns)
490 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
493 seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width) +
496 vscroll.setMaximum(max);
497 vscroll.setUnitIncrement(1);
498 vscroll.setVisibleAmount(1);
502 setScrollValues(av.getStartRes(), av.getStartSeq());
507 seqPanel.seqCanvas.repaint();
508 scalePanel.repaint();
509 annotationPanel.repaint();
510 idPanel.idCanvas.repaint();
512 if (getBounds() == g.getClipBounds())
514 if (overviewPanel != null)
515 overviewPanel.updateOverviewImage();
520 protected Panel sequenceHolderPanel = new Panel();
521 protected Scrollbar vscroll = new Scrollbar();
522 protected Scrollbar hscroll = new Scrollbar();
523 protected Panel seqPanelHolder = new Panel();
524 BorderLayout borderLayout1 = new BorderLayout();
525 BorderLayout borderLayout3 = new BorderLayout();
526 protected Panel scalePanelHolder = new Panel();
527 protected Panel idPanelHolder = new Panel();
528 BorderLayout borderLayout5 = new BorderLayout();
529 protected Panel idSpaceFillerPanel1 = new Panel();
530 public Panel annotationSpaceFillerHolder = new Panel();
531 BorderLayout borderLayout6 = new BorderLayout();
532 BorderLayout borderLayout7 = new BorderLayout();
533 Panel hscrollHolder = new Panel();
534 BorderLayout borderLayout10 = new BorderLayout();
535 protected Panel hscrollFillerPanel = new Panel();
536 BorderLayout borderLayout11 = new BorderLayout();
537 BorderLayout borderLayout4 = new BorderLayout();
538 BorderLayout borderLayout2 = new BorderLayout();
540 private void jbInit() throws Exception {
541 // idPanelHolder.setPreferredSize(new Dimension(70, 10));
542 this.setLayout(borderLayout7);
544 // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
545 sequenceHolderPanel.setLayout(borderLayout3);
546 seqPanelHolder.setLayout(borderLayout1);
547 scalePanelHolder.setBackground(Color.white);
549 // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
550 scalePanelHolder.setLayout(borderLayout6);
551 idPanelHolder.setLayout(borderLayout5);
552 idSpaceFillerPanel1.setBackground(Color.white);
554 // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
555 idSpaceFillerPanel1.setLayout(borderLayout11);
556 annotationSpaceFillerHolder.setBackground(Color.white);
558 // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
559 annotationSpaceFillerHolder.setLayout(borderLayout4);
560 hscroll.setOrientation(Scrollbar.HORIZONTAL);
561 hscrollHolder.setLayout(borderLayout10);
562 hscrollFillerPanel.setBackground(Color.white);
564 // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
565 hscrollHolder.setBackground(Color.white);
567 // annotationScroller.setPreferredSize(new Dimension(10, 80));
568 // this.setPreferredSize(new Dimension(220, 166));
569 seqPanelHolder.setBackground(Color.white);
570 idPanelHolder.setBackground(Color.white);
571 sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
572 sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
573 seqPanelHolder.add(vscroll, BorderLayout.EAST);
575 // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
576 this.add(idPanelHolder, BorderLayout.WEST);
577 idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
578 idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
579 this.add(hscrollHolder, BorderLayout.SOUTH);
580 hscrollHolder.add(hscroll, BorderLayout.CENTER);
581 hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
582 this.add(sequenceHolderPanel, BorderLayout.CENTER);