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;
24 import jalview.datamodel.SequenceI;
26 import java.awt.Color;
27 import java.awt.Dimension;
28 import awt2swing.Frame;
29 import java.awt.Graphics;
30 import java.awt.Image;
31 import awt2swing.Panel;
32 import java.awt.event.ComponentAdapter;
33 import java.awt.event.ComponentEvent;
34 import java.awt.event.MouseEvent;
35 import java.awt.event.MouseListener;
36 import java.awt.event.MouseMotionListener;
38 public class OverviewPanel extends Panel implements Runnable,
39 MouseMotionListener, MouseListener
53 public int width, sequencesHeight;
57 int boxX = -1, boxY = -1, boxWidth = -1, boxHeight = -1;
59 boolean resizing = false;
61 // Can set different properties in this seqCanvas than
62 // main visible SeqCanvas
69 public OverviewPanel(AlignmentPanel ap)
74 nullFrame = new Frame();
75 nullFrame.addNotify();
77 sr = new SequenceRenderer(av);
78 sr.graphics = nullFrame.getGraphics();
79 sr.renderGaps = false;
80 sr.forOverview = true;
81 fr = new FeatureRenderer(av);
83 // scale the initial size of overviewpanel to shape of alignment
84 float initialScale = (float) av.getAlignment().getWidth()
85 / (float) av.getAlignment().getHeight();
87 if (av.getSequenceConsensusHash() == null)
92 if (av.getAlignment().getWidth() > av.getAlignment().getHeight())
96 sequencesHeight = (int) (400f / initialScale);
97 if (sequencesHeight < 40)
105 width = (int) (400f * initialScale);
106 sequencesHeight = 300;
113 setSize(new Dimension(width, sequencesHeight + graphHeight));
114 addComponentListener(new ComponentAdapter()
118 public void componentResized(ComponentEvent evt)
120 if (getSize().width != width
121 || getSize().height != sequencesHeight + graphHeight)
123 updateOverviewImage();
128 addMouseMotionListener(this);
130 addMouseListener(this);
132 updateOverviewImage();
137 public void mouseEntered(MouseEvent evt)
142 public void mouseExited(MouseEvent evt)
147 public void mouseClicked(MouseEvent evt)
152 public void mouseMoved(MouseEvent evt)
157 public void mousePressed(MouseEvent evt)
165 public void mouseReleased(MouseEvent evt)
173 public void mouseDragged(MouseEvent evt)
187 if (boxY > (sequencesHeight - boxHeight))
189 boxY = sequencesHeight - boxHeight + 1;
197 if (boxX > (width - boxWidth))
199 if (av.hasHiddenColumns())
201 // Try smallest possible box
202 boxWidth = (int) ((av.endRes - av.startRes + 1) * av.getCharWidth() * scalew);
204 boxX = width - boxWidth;
207 int col = (int) (boxX / scalew / av.getCharWidth());
208 int row = (int) (boxY / scaleh / av.getCharHeight());
210 if (av.hasHiddenColumns())
212 if (!av.getColumnSelection().isVisible(col))
217 col = av.getColumnSelection().findColumnPosition(col);
220 if (av.hasHiddenRows())
222 row = av.getAlignment().getHiddenSequences()
223 .findIndexWithoutHiddenSeqs(row);
226 ap.setScrollValues(col, row);
227 ap.paintAlignment(false);
233 public void updateOverviewImage()
241 if (av.isShowSequenceFeatures())
243 fr.transferSettings(ap.seqPanel.seqCanvas.fr);
248 if ((getSize().width > 0) && (getSize().height > 0))
250 width = getSize().width;
251 sequencesHeight = getSize().height - graphHeight;
253 setSize(new Dimension(width, sequencesHeight + graphHeight));
255 Thread thread = new Thread(this);
260 // This is set true if the user resizes whilst
261 // the overview is being calculated
262 boolean resizeAgain = false;
268 int alwidth = av.getAlignment().getWidth();
269 int alheight = av.getAlignment().getHeight();
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;
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()
362 .isVisible(lastcol)))
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 paintComponent(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);