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.
23 import jalview.datamodel.SequenceI;
24 import jalview.renderer.AnnotationRenderer;
25 import jalview.viewmodel.OverviewDimensions;
26 import jalview.renderer.seqfeatures.FeatureColourFinder;
28 import java.awt.Color;
29 import java.awt.Dimension;
30 import java.awt.Graphics;
31 import java.awt.event.ComponentAdapter;
32 import java.awt.event.ComponentEvent;
33 import java.awt.event.MouseAdapter;
34 import java.awt.event.MouseEvent;
35 import java.awt.event.MouseMotionAdapter;
36 import java.awt.image.BufferedImage;
38 import javax.swing.JPanel;
41 * Panel displaying an overview of the full alignment, with an interactive box
42 * representing the viewport onto the alignment.
47 public class OverviewPanel extends JPanel implements Runnable
49 private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
51 private final AnnotationRenderer renderer = new AnnotationRenderer();
53 private OverviewDimensions od;
55 private BufferedImage miniMe;
57 private BufferedImage lastMiniMe = null;
59 private AlignViewport av;
61 private AlignmentPanel ap;
64 private boolean resizing = false;
66 // This is set true if the user resizes whilst
67 // the overview is being calculated
68 private boolean resizeAgain = false;
70 // Can set different properties in this seqCanvas than
71 // main visible SeqCanvas
72 private SequenceRenderer sr;
74 private jalview.renderer.seqfeatures.FeatureRenderer fr;
77 * Creates a new OverviewPanel object.
80 * The alignment panel which is shown in the overview panel
82 public OverviewPanel(AlignmentPanel alPanel)
88 sr = new SequenceRenderer(av);
89 sr.renderGaps = false;
90 sr.forOverview = true;
91 fr = new FeatureRenderer(alPanel);
93 od = new OverviewDimensions(av.getRanges(), av.isShowAnnotation());
95 addComponentListener(new ComponentAdapter()
98 public void componentResized(ComponentEvent evt)
100 if ((getWidth() != od.getWidth())
101 || (getHeight() != (od.getHeight())))
103 updateOverviewImage();
108 addMouseMotionListener(new MouseMotionAdapter()
111 public void mouseDragged(MouseEvent evt)
113 if (!av.getWrapAlignment())
115 od.updateViewportFromMouse(evt.getX(), evt.getY(), av
116 .getAlignment().getHiddenSequences(), av
117 .getColumnSelection(), av.getRanges());
118 ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
123 addMouseListener(new MouseAdapter()
126 public void mousePressed(MouseEvent evt)
128 if (!av.getWrapAlignment())
130 od.updateViewportFromMouse(evt.getX(), evt.getY(), av
131 .getAlignment().getHiddenSequences(), av
132 .getColumnSelection(), av.getRanges());
133 ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
138 updateOverviewImage();
142 * Updates the overview image when the related alignment panel is updated
144 public void updateOverviewImage()
154 if ((getWidth() > 0) && (getHeight() > 0))
156 od.setWidth(getWidth());
157 od.setHeight(getHeight());
160 setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
162 Thread thread = new Thread(this);
172 if (av.isShowSequenceFeatures())
174 fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer());
177 // why do we need to set preferred size again? was set in
178 // updateOverviewImage
179 setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
181 miniMe = new BufferedImage(od.getWidth(), od.getHeight(),
182 BufferedImage.TYPE_INT_RGB);
184 Graphics mg = miniMe.getGraphics();
185 mg.setColor(Color.orange);
186 mg.fillRect(0, 0, od.getWidth(), miniMe.getHeight());
189 // calculate sampleCol and sampleRow
190 // alignment width is max number of residues/bases
191 // alignment height is number of sequences
192 int alwidth = av.getAlignment().getWidth();
193 int alheight = av.getAlignment().getAbsoluteHeight();
195 // sampleCol or sampleRow is the width/height allocated to each residue
196 // in particular, sometimes we may need more than one row/col of the
197 // BufferedImage allocated
198 // sampleCol is how much of a residue to assign to each pixel
199 // sampleRow is how many sequences to assign to each pixel
200 float sampleCol = alwidth / (float) od.getWidth();
201 float sampleRow = alheight / (float) od.getSequencesHeight();
203 buildImage(sampleRow, sampleCol);
205 float sampleCol = (float) alwidth / (float) width;
206 float sampleRow = (float) alheight / (float) sequencesHeight;
208 int lastcol = -1, lastrow = -1;
209 Color color = Color.white;
211 jalview.datamodel.SequenceI seq;
212 final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
214 boolean hiddenRow = false;
215 // get hidden row and hidden column map once at beginning.
216 // clone featureRenderer settings to avoid race conditions... if state is
217 // updated just need to refresh again
219 FeatureColourFinder finder = new FeatureColourFinder(fr);
221 for (row = 0; row < sequencesHeight; row++)
227 if ((int) (row * sampleRow) == lastrow)
229 // No need to recalculate the colours,
230 // Just copy from the row above
231 for (col = 0; col < width; col++)
237 miniMe.setRGB(col, row, miniMe.getRGB(col, row - 1));
242 lastrow = (int) (row * sampleRow);
247 seq = av.getAlignment().getHiddenSequences()
248 .getHiddenSequence(lastrow);
251 int index = av.getAlignment().getHiddenSequences()
252 .findIndexWithoutHiddenSeqs(lastrow);
254 seq = av.getAlignment().getSequenceAt(index);
263 seq = av.getAlignment().getSequenceAt(lastrow);
268 System.out.println(lastrow + " null");
272 for (col = 0; col < width; col++)
278 if ((int) (col * sampleCol) == lastcol
279 && (int) (row * sampleRow) == lastrow)
281 miniMe.setRGB(col, row, color.getRGB());
285 lastcol = (int) (col * sampleCol);
287 if (seq.getLength() > lastcol)
289 color = sr.getResidueColour(seq, lastcol, finder);
297 || (hasHiddenCols && !av.getColumnSelection().isVisible(
300 color = color.darker().darker();
303 miniMe.setRGB(col, row, color.getRGB());
304 >>>>>>> bug/JAL-2436featureRendererThreading
306 if (av.isShowAnnotation())
308 renderer.updateFromAlignViewport(av);
309 for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
311 mg.translate(col, od.getSequencesHeight());
312 renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
313 av.getAlignmentConservationAnnotation().annotations,
314 (int) (sampleCol) + 1, od.getGraphHeight(),
315 (int) (col * sampleCol), (int) (col * sampleCol) + 1);
316 mg.translate(-col, -od.getSequencesHeight());
327 updateOverviewImage();
338 * Build the overview panel image
340 private void buildImage(float sampleRow, float sampleCol)
344 int color = Color.white.getRGB();
346 SequenceI seq = null;
348 final boolean hasHiddenCols = av.hasHiddenColumns();
349 boolean hiddenRow = false;
350 // get hidden row and hidden column map once at beginning.
351 // clone featureRenderer settings to avoid race conditions... if state is
352 // updated just need to refresh again
353 for (int row = 0; row < od.getSequencesHeight() && !resizeAgain; row++)
355 boolean doCopy = true;
356 int currentrow = (int) (row * sampleRow);
357 if (currentrow != lastrow)
361 lastrow = currentrow;
363 // get the sequence which would be at alignment index 'lastrow' if no
364 // rows were hidden, and determine whether it is hidden or not
365 hiddenRow = av.getAlignment().isHidden(lastrow);
366 seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);
369 for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
373 color = miniMe.getRGB(col, row - 1);
375 else if ((int) (col * sampleCol) != lastcol
376 || (int) (row * sampleRow) != lastrow)
378 lastcol = (int) (col * sampleCol);
379 color = getColumnColourFromSequence(seq, hiddenRow, hasHiddenCols,
382 // else we just use the color we already have , so don't need to set it
384 miniMe.setRGB(col, row, color);
390 * Find the colour of a sequence at a specified column position
392 private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq,
393 boolean hiddenRow, boolean hasHiddenCols, int lastcol)
399 color = Color.white.getRGB();
401 else if (seq.getLength() > lastcol)
403 color = sr.getResidueBoxColour(seq, lastcol).getRGB();
405 if (av.isShowSequenceFeatures())
407 color = fr.findFeatureColour(color, seq, lastcol);
412 color = Color.white.getRGB();
416 || (hasHiddenCols && !av.getColumnSelection()
417 .isVisible(lastcol)))
419 color = new Color(color).darker().darker().getRGB();
426 * Update the overview panel box when the associated alignment panel is
430 public void setBoxPosition()
432 od.setBoxPosition(av.getAlignment()
433 .getHiddenSequences(), av.getColumnSelection(), av.getRanges());
439 public void paintComponent(Graphics g)
441 if (resizing || resizeAgain)
443 if (lastMiniMe == null)
445 g.setColor(Color.white);
446 g.fillRect(0, 0, getWidth(), getHeight());
450 g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
452 g.setColor(TRANS_GREY);
453 g.fillRect(0, 0, getWidth(), getHeight());
455 else if (lastMiniMe != null)
457 g.drawImage(lastMiniMe, 0, 0, this);
458 if (lastMiniMe != miniMe)
460 g.setColor(TRANS_GREY);
461 g.fillRect(0, 0, getWidth(), getHeight());
465 g.setColor(Color.red);