2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
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.*;
23 import jalview.datamodel.*;
25 public class AlignmentPanel extends Panel implements AdjustmentListener
28 public AlignViewport av;
30 OverviewPanel overviewPanel;
36 IdwidthAdjuster idwidthAdjuster;
38 public AlignFrame alignFrame;
40 ScalePanel scalePanel;
42 AnnotationPanel annotationPanel;
44 AnnotationLabels alabels;
46 // this value is set false when selection area being dragged
47 boolean fastPaint = true;
49 public AlignmentPanel(AlignFrame af, final AlignViewport av)
61 seqPanel = new SeqPanel(av, this);
62 idPanel = new IdPanel(av, this);
63 scalePanel = new ScalePanel(av, this);
64 idwidthAdjuster = new IdwidthAdjuster(this);
65 annotationPanel = new AnnotationPanel(this);
67 sequenceHolderPanel.add(annotationPanel, BorderLayout.SOUTH);
69 alabels = new AnnotationLabels(this);
71 setAnnotationVisible(av.showAnnotation);
73 idPanelHolder.add(idPanel, BorderLayout.CENTER);
74 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
75 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
76 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
77 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
80 setScrollValues(0, 0);
82 hscroll.addAdjustmentListener(this);
83 vscroll.addAdjustmentListener(this);
85 addComponentListener(new ComponentAdapter()
87 public void componentResized(ComponentEvent evt)
89 setScrollValues(av.getStartRes(), av.getStartSeq());
94 Dimension d = calculateIdWidth();
95 idPanel.idCanvas.setSize(d);
97 hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
99 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
100 annotationSpaceFillerHolder.setSize(d.width,
101 annotationPanel.getSize().height);
102 alabels.setSize(d.width, annotationPanel.getSize().height);
104 final AlignmentPanel ap = this;
105 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
107 public void propertyChange(java.beans.PropertyChangeEvent evt)
109 if (evt.getPropertyName().equals("alignment"))
111 PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
119 public SequenceRenderer getSequenceRenderer()
121 return seqPanel.seqCanvas.sr;
124 public FeatureRenderer getFeatureRenderer()
126 return seqPanel.seqCanvas.fr;
129 public void alignmentChanged()
131 av.alignmentChanged(this);
133 if (overviewPanel != null)
135 overviewPanel.updateOverviewImage();
138 alignFrame.updateEditMenuBar();
143 public void fontChanged()
145 // set idCanvas bufferedImage to null
146 // to prevent drawing old image
147 idPanel.idCanvas.image = null;
148 FontMetrics fm = getFontMetrics(av.getFont());
150 scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
151 idwidthAdjuster.setSize(new Dimension(10, av.charHeight
153 av.updateSequenceIdColours();
154 annotationPanel.image = null;
155 int ap = annotationPanel.adjustPanelHeight();
156 annotationPanel.repaint();
157 Dimension d = calculateIdWidth();
158 d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
159 alabels.setSize(d.width + 4, ap);
160 idPanel.idCanvas.setSize(d);
161 hscrollFillerPanel.setSize(d);
166 if (overviewPanel != null)
168 overviewPanel.updateOverviewImage();
172 public void setIdWidth(int w, int h)
174 idPanel.idCanvas.setSize(w, h);
175 idPanelHolder.setSize(w, idPanelHolder.getSize().height);
176 alabels.setSize(w, alabels.getSize().height);
180 Dimension calculateIdWidth()
182 if (av.nullFrame == null)
184 av.nullFrame = new Frame();
185 av.nullFrame.addNotify();
188 Graphics g = av.nullFrame.getGraphics();
190 FontMetrics fm = g.getFontMetrics(av.font);
191 AlignmentI al = av.getAlignment();
196 while (i < al.getHeight() && al.getSequenceAt(i) != null)
198 SequenceI s = al.getSequenceAt(i);
199 id = s.getDisplayId(av.getShowJVSuffix());
201 if (fm.stringWidth(id) > idWidth)
203 idWidth = fm.stringWidth(id);
208 // Also check annotation label widths
210 if (al.getAlignmentAnnotation() != null)
212 fm = g.getFontMetrics(av.nullFrame.getFont());
213 while (i < al.getAlignmentAnnotation().length)
215 String label = al.getAlignmentAnnotation()[i].label;
216 if (fm.stringWidth(label) > idWidth)
218 idWidth = fm.stringWidth(label);
224 return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
227 public void highlightSearchResults(SearchResults results)
229 seqPanel.seqCanvas.highlightSearchResults(results);
233 * scroll the view to show the position of the highlighted region in results
238 public void scrollToPosition(SearchResults results)
240 // do we need to scroll the panel?
241 if (results != null && results.getSize() > 0)
243 int seqIndex = av.alignment.findIndex(results);
248 SequenceI seq = av.alignment.getSequenceAt(seqIndex);
249 int[] r = results.getResults(seq, seq.getStart(), seq.getEnd());
260 if (end == seq.getEnd())
264 if (!av.wrapAlignment)
266 if ((av.getStartRes() > end)
267 || (av.getEndRes() < start)
268 || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
270 if (start > av.alignment.getWidth() - hextent)
272 start = av.alignment.getWidth() - hextent;
278 if (seqIndex > av.alignment.getHeight() - vextent)
280 seqIndex = av.alignment.getHeight() - vextent;
286 setScrollValues(start, seqIndex);
291 scrollToWrappedVisible(start);
298 void scrollToWrappedVisible(int res)
300 int cwidth = seqPanel.seqCanvas
301 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
302 if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
304 vscroll.setValue(res / cwidth);
305 av.startRes = vscroll.getValue() * cwidth;
309 public OverviewPanel getOverviewPanel()
311 return overviewPanel;
314 public void setOverviewPanel(OverviewPanel op)
319 public void setAnnotationVisible(boolean b)
321 if (!av.wrapAlignment)
323 annotationSpaceFillerHolder.setVisible(b);
324 annotationPanel.setVisible(b);
330 public void setWrapAlignment(boolean wrap)
334 scalePanelHolder.setVisible(!wrap);
336 hscroll.setVisible(!wrap);
337 idwidthAdjuster.setVisible(!wrap);
341 annotationPanel.setVisible(false);
342 annotationSpaceFillerHolder.setVisible(false);
344 else if (av.showAnnotation)
346 annotationPanel.setVisible(true);
347 annotationSpaceFillerHolder.setVisible(true);
350 idSpaceFillerPanel1.setVisible(!wrap);
352 fontChanged(); // This is so that the scalePanel is resized correctly
363 // return value is true if the scroll is valid
364 public boolean scrollUp(boolean up)
368 if (vscroll.getValue() < 1)
372 setScrollValues(hscroll.getValue(), vscroll.getValue() - 1);
376 if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())
380 setScrollValues(hscroll.getValue(), vscroll.getValue() + 1);
387 public boolean scrollRight(boolean right)
391 if (hscroll.getValue() < 1)
395 setScrollValues(hscroll.getValue() - 1, vscroll.getValue());
399 if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
403 setScrollValues(hscroll.getValue() + 1, vscroll.getValue());
410 public void setScrollValues(int x, int y)
412 int width = av.alignment.getWidth();
413 int height = av.alignment.getHeight();
415 if (av.hasHiddenColumns)
417 width = av.getColumnSelection().findColumnPosition(width);
422 .setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
424 hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
425 vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
432 if (vextent > height)
437 if ((hextent + x) > width)
442 if ((vextent + y) > height)
444 y = height - vextent;
459 int endSeq = y + vextent;
460 if (endSeq > av.alignment.getHeight())
462 endSeq = av.alignment.getHeight();
465 av.setEndSeq(endSeq);
466 hscroll.setValues(x, hextent, 0, width);
467 vscroll.setValues(y, vextent, 0, height);
469 if (overviewPanel != null)
471 overviewPanel.setBoxPosition();
476 public void adjustmentValueChanged(AdjustmentEvent evt)
478 int oldX = av.getStartRes();
479 int oldY = av.getStartSeq();
481 if (evt == null || evt.getSource() == hscroll)
483 int x = hscroll.getValue();
485 av.setEndRes(x + seqPanel.seqCanvas.getSize().width
486 / av.getCharWidth() - 1);
489 if (evt == null || evt.getSource() == vscroll)
491 int offy = vscroll.getValue();
492 if (av.getWrapAlignment())
494 int rowSize = seqPanel.seqCanvas
495 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
496 av.setStartRes(vscroll.getValue() * rowSize);
497 av.setEndRes((vscroll.getValue() + 1) * rowSize);
501 av.setStartSeq(offy);
502 av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
503 / av.getCharHeight());
507 if (overviewPanel != null)
509 overviewPanel.setBoxPosition();
512 int scrollX = av.startRes - oldX;
513 int scrollY = av.startSeq - oldY;
515 if (av.getWrapAlignment() || !fastPaint || av.MAC)
521 // Make sure we're not trying to draw a panel
522 // larger than the visible window
523 if (scrollX > av.endRes - av.startRes)
525 scrollX = av.endRes - av.startRes;
527 else if (scrollX < av.startRes - av.endRes)
529 scrollX = av.startRes - av.endRes;
532 idPanel.idCanvas.fastPaint(scrollY);
533 seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
535 scalePanel.repaint();
536 if (av.getShowAnnotation())
538 annotationPanel.fastPaint(av.getStartRes() - oldX);
544 public void paintAlignment(boolean updateOverview)
550 jalview.structure.StructureSelectionManager
551 .getStructureSelectionManager().sequenceColoursChanged(this);
553 if (overviewPanel != null)
555 overviewPanel.updateOverviewImage();
560 public void update(Graphics g)
565 public void paint(Graphics g)
568 Dimension d = idPanel.idCanvas.getSize();
569 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
570 annotationSpaceFillerHolder.setSize(d.width,
571 annotationPanel.getSize().height);
573 alabels.setSize(d.width, annotationPanel.getSize().height);
575 if (av.getWrapAlignment())
577 int maxwidth = av.alignment.getWidth();
579 if (av.hasHiddenColumns)
581 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
584 int canvasWidth = seqPanel.seqCanvas
585 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
589 int max = maxwidth / canvasWidth;
590 vscroll.setMaximum(max);
591 vscroll.setUnitIncrement(1);
592 vscroll.setVisibleAmount(1);
597 setScrollValues(av.getStartRes(), av.getStartSeq());
602 seqPanel.seqCanvas.repaint();
603 scalePanel.repaint();
604 annotationPanel.repaint();
605 idPanel.idCanvas.repaint();
608 protected Panel sequenceHolderPanel = new Panel();
610 protected Scrollbar vscroll = new Scrollbar();
612 protected Scrollbar hscroll = new Scrollbar();
614 protected Panel seqPanelHolder = new Panel();
616 BorderLayout borderLayout1 = new BorderLayout();
618 BorderLayout borderLayout3 = new BorderLayout();
620 protected Panel scalePanelHolder = new Panel();
622 protected Panel idPanelHolder = new Panel();
624 BorderLayout borderLayout5 = new BorderLayout();
626 protected Panel idSpaceFillerPanel1 = new Panel();
628 public Panel annotationSpaceFillerHolder = new Panel();
630 BorderLayout borderLayout6 = new BorderLayout();
632 BorderLayout borderLayout7 = new BorderLayout();
634 Panel hscrollHolder = new Panel();
636 BorderLayout borderLayout10 = new BorderLayout();
638 protected Panel hscrollFillerPanel = new Panel();
640 BorderLayout borderLayout11 = new BorderLayout();
642 BorderLayout borderLayout4 = new BorderLayout();
644 BorderLayout borderLayout2 = new BorderLayout();
646 private void jbInit() throws Exception
648 // idPanelHolder.setPreferredSize(new Dimension(70, 10));
649 this.setLayout(borderLayout7);
651 // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
652 sequenceHolderPanel.setLayout(borderLayout3);
653 seqPanelHolder.setLayout(borderLayout1);
654 scalePanelHolder.setBackground(Color.white);
656 // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
657 scalePanelHolder.setLayout(borderLayout6);
658 idPanelHolder.setLayout(borderLayout5);
659 idSpaceFillerPanel1.setBackground(Color.white);
661 // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
662 idSpaceFillerPanel1.setLayout(borderLayout11);
663 annotationSpaceFillerHolder.setBackground(Color.white);
665 // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
666 annotationSpaceFillerHolder.setLayout(borderLayout4);
667 hscroll.setOrientation(Scrollbar.HORIZONTAL);
668 hscrollHolder.setLayout(borderLayout10);
669 hscrollFillerPanel.setBackground(Color.white);
671 // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
672 hscrollHolder.setBackground(Color.white);
674 // annotationScroller.setPreferredSize(new Dimension(10, 80));
675 // this.setPreferredSize(new Dimension(220, 166));
676 seqPanelHolder.setBackground(Color.white);
677 idPanelHolder.setBackground(Color.white);
678 sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
679 sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
680 seqPanelHolder.add(vscroll, BorderLayout.EAST);
682 // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
683 this.add(idPanelHolder, BorderLayout.WEST);
684 idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
685 idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
686 this.add(hscrollHolder, BorderLayout.SOUTH);
687 hscrollHolder.add(hscroll, BorderLayout.CENTER);
688 hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
689 this.add(sequenceHolderPanel, BorderLayout.CENTER);