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.renderer.seqfeatures.FeatureColourFinder;
26 import jalview.viewmodel.OverviewDimensions;
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 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(ap);
93 od = new OverviewDimensions(av.getRanges(),
94 (av.isShowAnnotation() && av
95 .getAlignmentConservationAnnotation() != null));
97 addComponentListener(new ComponentAdapter()
100 public void componentResized(ComponentEvent evt)
102 if ((getWidth() != od.getWidth())
103 || (getHeight() != (od.getHeight())))
105 updateOverviewImage();
110 addMouseMotionListener(new MouseMotionAdapter()
113 public void mouseDragged(MouseEvent evt)
115 if (!av.getWrapAlignment())
117 od.updateViewportFromMouse(evt.getX(), evt.getY(), av
118 .getAlignment().getHiddenSequences(), av
119 .getColumnSelection(), av.getRanges());
120 ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
125 addMouseListener(new MouseAdapter()
128 public void mousePressed(MouseEvent evt)
130 if (!av.getWrapAlignment())
132 od.updateViewportFromMouse(evt.getX(), evt.getY(), av
133 .getAlignment().getHiddenSequences(), av
134 .getColumnSelection(), av.getRanges());
135 ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
140 updateOverviewImage();
144 * Updates the overview image when the related alignment panel is updated
146 public void updateOverviewImage()
156 if ((getWidth() > 0) && (getHeight() > 0))
158 od.setWidth(getWidth());
159 od.setHeight(getHeight());
162 setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
164 Thread thread = new Thread(this);
174 if (av.isShowSequenceFeatures())
176 fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer());
179 // why do we need to set preferred size again? was set in
180 // updateOverviewImage
181 setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
183 miniMe = new BufferedImage(od.getWidth(), od.getHeight(),
184 BufferedImage.TYPE_INT_RGB);
186 Graphics mg = miniMe.getGraphics();
187 mg.setColor(Color.orange);
188 mg.fillRect(0, 0, od.getWidth(), miniMe.getHeight());
190 // calculate sampleCol and sampleRow
191 // alignment width is max number of residues/bases
192 // alignment height is number of sequences
193 int alwidth = av.getAlignment().getWidth();
194 int alheight = av.getAlignment().getAbsoluteHeight();
196 // sampleCol or sampleRow is the width/height allocated to each residue
197 // in particular, sometimes we may need more than one row/col of the
198 // BufferedImage allocated
199 // sampleCol is how much of a residue to assign to each pixel
200 // sampleRow is how many sequences to assign to each pixel
201 float sampleCol = alwidth / (float) od.getWidth();
202 float sampleRow = alheight / (float) od.getSequencesHeight();
204 long start = System.currentTimeMillis();
205 buildImage(sampleRow, sampleCol);
207 // check for conservation annotation to make sure overview works for DNA too
208 if (av.isShowAnnotation()
209 && (av.getAlignmentConservationAnnotation() != null))
211 renderer.updateFromAlignViewport(av);
212 for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
214 mg.translate(col, od.getSequencesHeight());
215 renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
216 av.getAlignmentConservationAnnotation().annotations,
217 (int) (sampleCol) + 1, od.getGraphHeight(),
218 (int) (col * sampleCol), (int) (col * sampleCol) + 1);
219 mg.translate(-col, -od.getSequencesHeight());
223 System.out.println("Overview took "
224 + (System.currentTimeMillis() - start) + "ms");
232 updateOverviewImage();
243 * Build the overview panel image
245 private void buildImage(float sampleRow, float sampleCol)
249 int rgbColour = Color.white.getRGB();
251 SequenceI seq = null;
252 FeatureColourFinder finder = new FeatureColourFinder(fr);
254 final boolean hasHiddenCols = av.hasHiddenColumns();
255 boolean hiddenRow = false;
256 // get hidden row and hidden column map once at beginning.
257 // clone featureRenderer settings to avoid race conditions... if state is
258 // updated just need to refresh again
259 for (int row = 0; row < od.getSequencesHeight() && !resizeAgain; row++)
261 boolean doCopy = true;
262 int currentrow = (int) (row * sampleRow);
263 if (currentrow != lastrow)
267 lastrow = currentrow;
269 // get the sequence which would be at alignment index 'lastrow' if no
270 // rows were hidden, and determine whether it is hidden or not
271 hiddenRow = av.getAlignment().isHidden(lastrow);
272 seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);
275 for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
279 rgbColour = miniMe.getRGB(col, row - 1);
281 else if ((int) (col * sampleCol) != lastcol
282 || (int) (row * sampleRow) != lastrow)
284 lastcol = (int) (col * sampleCol);
285 rgbColour = getColumnColourFromSequence(seq, hiddenRow,
286 hasHiddenCols, lastcol, finder);
288 // else we just use the color we already have , so don't need to set it
290 miniMe.setRGB(col, row, rgbColour);
296 * Find the colour of a sequence at a specified column position
298 private int getColumnColourFromSequence(
299 jalview.datamodel.SequenceI seq,
300 boolean hiddenRow, boolean hasHiddenCols, int lastcol,
301 FeatureColourFinder finder)
303 Color color = Color.white;
305 if ((seq != null) && (seq.getLength() > lastcol))
307 color = sr.getResidueColour(seq, lastcol, finder);
311 || (hasHiddenCols && !av.getColumnSelection()
312 .isVisible(lastcol)))
314 color = color.darker().darker();
317 return color.getRGB();
321 * Update the overview panel box when the associated alignment panel is
325 public void setBoxPosition()
327 od.setBoxPosition(av.getAlignment()
328 .getHiddenSequences(), av.getColumnSelection(), av.getRanges());
334 public void paintComponent(Graphics g)
336 if (resizing || resizeAgain)
338 if (lastMiniMe == null)
340 g.setColor(Color.white);
341 g.fillRect(0, 0, getWidth(), getHeight());
345 g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
347 g.setColor(TRANS_GREY);
348 g.fillRect(0, 0, getWidth(), getHeight());
350 else if (lastMiniMe != null)
352 g.drawImage(lastMiniMe, 0, 0, this);
353 if (lastMiniMe != miniMe)
355 g.setColor(TRANS_GREY);
356 g.fillRect(0, 0, getWidth(), getHeight());
360 g.setColor(Color.red);