2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import jalview.datamodel.AlignmentI;
25 import java.awt.Color;
26 import java.awt.Dimension;
27 import java.awt.Frame;
28 import java.awt.Graphics;
29 import java.awt.Image;
30 import java.awt.Panel;
31 import java.awt.event.ComponentAdapter;
32 import java.awt.event.ComponentEvent;
33 import java.awt.event.MouseEvent;
34 import java.awt.event.MouseListener;
35 import java.awt.event.MouseMotionListener;
37 public class OverviewPanel extends Panel implements Runnable,
38 MouseMotionListener, MouseListener
52 public int width, sequencesHeight;
56 int boxX = -1, boxY = -1, boxWidth = -1, boxHeight = -1;
58 boolean resizing = false;
60 // Can set different properties in this seqCanvas than
61 // main visible SeqCanvas
68 public OverviewPanel(AlignmentPanel ap)
73 nullFrame = new Frame();
74 nullFrame.addNotify();
76 sr = new SequenceRenderer(av);
77 sr.graphics = nullFrame.getGraphics();
78 sr.renderGaps = false;
79 sr.forOverview = true;
80 fr = new FeatureRenderer(av);
82 // scale the initial size of overviewpanel to shape of alignment
83 float initialScale = (float) av.getAlignment().getWidth()
84 / (float) av.getAlignment().getHeight();
86 if (av.getSequenceConsensusHash() == null)
91 if (av.getAlignment().getWidth() > av.getAlignment().getHeight())
95 sequencesHeight = (int) (400f / initialScale);
96 if (sequencesHeight < 40)
104 width = (int) (400f * initialScale);
105 sequencesHeight = 300;
112 setSize(new Dimension(width, sequencesHeight + graphHeight));
113 addComponentListener(new ComponentAdapter()
117 public void componentResized(ComponentEvent evt)
119 if (getSize().width != width
120 || getSize().height != sequencesHeight + graphHeight)
122 updateOverviewImage();
127 addMouseMotionListener(this);
129 addMouseListener(this);
131 updateOverviewImage();
136 public void mouseEntered(MouseEvent evt)
141 public void mouseExited(MouseEvent evt)
146 public void mouseClicked(MouseEvent evt)
151 public void mouseMoved(MouseEvent evt)
156 public void mousePressed(MouseEvent evt)
164 public void mouseReleased(MouseEvent evt)
172 public void mouseDragged(MouseEvent evt)
186 if (boxY > (sequencesHeight - boxHeight))
188 boxY = sequencesHeight - boxHeight + 1;
196 if (boxX > (width - boxWidth))
198 if (av.hasHiddenColumns())
200 // Try smallest possible box
201 boxWidth = (int) ((av.endRes - av.startRes + 1) * av.getCharWidth() * scalew);
203 boxX = width - boxWidth;
206 int col = (int) (boxX / scalew / av.getCharWidth());
207 int row = (int) (boxY / scaleh / av.getCharHeight());
209 if (av.hasHiddenColumns())
211 if (!av.getColumnSelection().isVisible(col))
216 col = av.getColumnSelection().findColumnPosition(col);
219 if (av.hasHiddenRows())
221 row = av.getAlignment().getHiddenSequences()
222 .findIndexWithoutHiddenSeqs(row);
225 ap.setScrollValues(col, row);
226 ap.paintAlignment(false);
232 public void updateOverviewImage()
240 if (av.isShowSequenceFeatures())
242 fr.transferSettings(ap.seqPanel.seqCanvas.fr);
247 if ((getSize().width > 0) && (getSize().height > 0))
249 width = getSize().width;
250 sequencesHeight = getSize().height - graphHeight;
252 setSize(new Dimension(width, sequencesHeight + graphHeight));
254 Thread thread = new Thread(this);
259 // This is set true if the user resizes whilst
260 // the overview is being calculated
261 boolean resizeAgain = false;
267 int alwidth = av.getAlignment().getWidth();
268 int alheight = av.getAlignment().getHeight()
269 + av.getAlignment().getHiddenSequences().getSize();
271 if (av.isShowSequenceFeatures())
273 fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
276 if (getSize().width > 0 && getSize().height > 0)
278 width = getSize().width;
279 sequencesHeight = getSize().height - graphHeight;
282 setSize(new Dimension(width, sequencesHeight + graphHeight));
284 int fullsizeWidth = alwidth * av.getCharWidth();
285 int fullsizeHeight = alheight * av.getCharHeight();
287 scalew = (float) width / (float) fullsizeWidth;
288 scaleh = (float) sequencesHeight / (float) fullsizeHeight;
290 miniMe = nullFrame.createImage(width, sequencesHeight + graphHeight);
291 offscreen = nullFrame.createImage(width, sequencesHeight + graphHeight);
293 Graphics mg = miniMe.getGraphics();
294 float sampleCol = (float) alwidth / (float) width;
295 float sampleRow = (float) alheight / (float) sequencesHeight;
297 int lastcol = 0, lastrow = 0;
298 int xstart = 0, ystart = 0;
299 Color color = Color.yellow;
300 int row, col, sameRow = 0, sameCol = 0;
301 jalview.datamodel.SequenceI seq;
302 final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
304 boolean hiddenRow = false;
305 AlignmentI alignment = av.getAlignment();
306 for (row = 0; row <= sequencesHeight; row++)
308 if ((int) (row * sampleRow) == lastrow)
317 seq = alignment.getHiddenSequences().getHiddenSequence(lastrow);
320 int index = alignment.getHiddenSequences()
321 .findIndexWithoutHiddenSeqs(lastrow);
323 seq = alignment.getSequenceAt(index);
332 seq = alignment.getSequenceAt(lastrow);
335 for (col = 0; col < width; col++)
337 if ((int) (col * sampleCol) == lastcol
338 && (int) (row * sampleRow) == lastrow)
344 lastcol = (int) (col * sampleCol);
346 if (seq.getLength() > lastcol)
348 color = sr.getResidueBoxColour(seq, lastcol);
350 if (av.isShowSequenceFeatures())
352 color = fr.findFeatureColour(color, seq, lastcol);
357 color = Color.white; // White
361 || (hasHiddenCols && !av.getColumnSelection().isVisible(
364 color = color.darker().darker();
368 if (sameCol == 1 && sameRow == 1)
370 mg.drawLine(xstart, ystart, xstart, ystart);
374 mg.fillRect(xstart, ystart, sameCol, sameRow);
380 lastrow = (int) (row * sampleRow);
385 if (av.getAlignmentConservationAnnotation() != null)
387 for (col = 0; col < width; col++)
389 lastcol = (int) (col * sampleCol);
391 mg.translate(col, sequencesHeight);
392 ap.annotationPanel.renderer.drawGraph(mg,
393 av.getAlignmentConservationAnnotation(),
394 av.getAlignmentConservationAnnotation().annotations,
395 (int) (sampleCol) + 1, graphHeight,
396 (int) (col * sampleCol), (int) (col * sampleCol) + 1);
397 mg.translate(-col, -sequencesHeight);
410 updateOverviewImage();
414 public void setBoxPosition()
416 int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth();
417 int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment()
418 .getHiddenSequences().getSize())
419 * av.getCharHeight();
421 int startRes = av.getStartRes();
422 int endRes = av.getEndRes();
424 if (av.hasHiddenColumns())
426 startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
427 endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
430 int startSeq = av.startSeq;
431 int endSeq = av.endSeq;
433 if (av.hasHiddenRows())
435 startSeq = av.getAlignment().getHiddenSequences()
436 .adjustForHiddenSeqs(startSeq);
438 endSeq = av.getAlignment().getHiddenSequences()
439 .adjustForHiddenSeqs(endSeq);
443 scalew = (float) width / (float) fullsizeWidth;
444 scaleh = (float) sequencesHeight / (float) fullsizeHeight;
446 boxX = (int) (startRes * av.getCharWidth() * scalew);
447 boxY = (int) (startSeq * av.getCharHeight() * scaleh);
449 if (av.hasHiddenColumns())
451 boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
455 boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
458 boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);
464 public void update(Graphics g)
470 public void paint(Graphics g)
472 Graphics og = offscreen.getGraphics();
475 og.drawImage(miniMe, 0, 0, this);
476 og.setColor(Color.red);
477 og.drawRect(boxX, boxY, boxWidth, boxHeight);
478 og.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
479 g.drawImage(offscreen, 0, 0, this);