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();
270 if (av.isShowSequenceFeatures())
272 fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
275 if (getSize().width > 0 && getSize().height > 0)
277 width = getSize().width;
278 sequencesHeight = getSize().height - graphHeight;
281 setSize(new Dimension(width, sequencesHeight + graphHeight));
283 int fullsizeWidth = alwidth * av.getCharWidth();
284 int fullsizeHeight = alheight * av.getCharHeight();
286 scalew = (float) width / (float) fullsizeWidth;
287 scaleh = (float) sequencesHeight / (float) fullsizeHeight;
289 miniMe = nullFrame.createImage(width, sequencesHeight + graphHeight);
290 offscreen = nullFrame.createImage(width, sequencesHeight + graphHeight);
292 Graphics mg = miniMe.getGraphics();
293 float sampleCol = (float) alwidth / (float) width;
294 float sampleRow = (float) alheight / (float) sequencesHeight;
296 int lastcol = 0, lastrow = 0;
297 int xstart = 0, ystart = 0;
298 Color color = Color.yellow;
299 int row, col, sameRow = 0, sameCol = 0;
300 jalview.datamodel.SequenceI seq;
301 boolean hiddenRow = false;
302 AlignmentI alignment = av.getAlignment();
303 for (row = 0; row <= sequencesHeight; row++)
305 if ((int) (row * sampleRow) == lastrow)
312 if (av.hasHiddenRows())
314 seq = alignment.getHiddenSequences().getHiddenSequence(lastrow);
317 int index = alignment.getHiddenSequences()
318 .findIndexWithoutHiddenSeqs(lastrow);
320 seq = alignment.getSequenceAt(index);
329 seq = alignment.getSequenceAt(lastrow);
332 for (col = 0; col < width; col++)
334 if ((int) (col * sampleCol) == lastcol
335 && (int) (row * sampleRow) == lastrow)
341 lastcol = (int) (col * sampleCol);
343 if (seq.getLength() > lastcol)
345 color = sr.getResidueBoxColour(seq, lastcol);
347 if (av.isShowSequenceFeatures())
349 color = fr.findFeatureColour(color, seq, lastcol);
354 color = Color.white; // White
358 || (av.hasHiddenColumns() && !av.getColumnSelection()
359 .isVisible(lastcol)))
361 color = color.darker().darker();
365 if (sameCol == 1 && sameRow == 1)
367 mg.drawLine(xstart, ystart, xstart, ystart);
371 mg.fillRect(xstart, ystart, sameCol, sameRow);
377 lastrow = (int) (row * sampleRow);
382 if (av.getAlignmentConservationAnnotation() != null)
384 for (col = 0; col < width; col++)
386 lastcol = (int) (col * sampleCol);
388 mg.translate(col, sequencesHeight);
389 ap.annotationPanel.renderer.drawGraph(mg,
390 av.getAlignmentConservationAnnotation(),
391 av.getAlignmentConservationAnnotation().annotations,
392 (int) (sampleCol) + 1, graphHeight,
393 (int) (col * sampleCol), (int) (col * sampleCol) + 1);
394 mg.translate(-col, -sequencesHeight);
407 updateOverviewImage();
411 public void setBoxPosition()
413 int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth();
414 int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment()
415 .getHiddenSequences().getSize())
416 * av.getCharHeight();
418 int startRes = av.getStartRes();
419 int endRes = av.getEndRes();
421 if (av.hasHiddenColumns())
423 startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
424 endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
427 int startSeq = av.startSeq;
428 int endSeq = av.endSeq;
430 if (av.hasHiddenRows())
432 startSeq = av.getAlignment().getHiddenSequences()
433 .adjustForHiddenSeqs(startSeq);
435 endSeq = av.getAlignment().getHiddenSequences()
436 .adjustForHiddenSeqs(endSeq);
440 scalew = (float) width / (float) fullsizeWidth;
441 scaleh = (float) sequencesHeight / (float) fullsizeHeight;
443 boxX = (int) (startRes * av.getCharWidth() * scalew);
444 boxY = (int) (startSeq * av.getCharHeight() * scaleh);
446 if (av.hasHiddenColumns())
448 boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
452 boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
455 boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);
461 public void update(Graphics g)
467 public void paint(Graphics g)
469 Graphics og = offscreen.getGraphics();
472 og.drawImage(miniMe, 0, 0, this);
473 og.setColor(Color.red);
474 og.drawRect(boxX, boxY, boxWidth, boxHeight);
475 og.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
476 g.drawImage(offscreen, 0, 0, this);