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.api.AlignViewportI;
24 import jalview.bin.Cache;
25 import jalview.datamodel.AlignmentI;
26 import jalview.renderer.OverviewRenderer;
27 import jalview.renderer.OverviewResColourFinder;
28 import jalview.viewmodel.OverviewDimensions;
30 import java.awt.Color;
31 import java.awt.Dimension;
32 import java.awt.Graphics;
33 import java.awt.image.BufferedImage;
35 import javax.swing.JPanel;
37 @SuppressWarnings("serial")
38 public class OverviewCanvas extends JPanel
40 private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
42 // This is set true if the alignment view changes whilst
43 // the overview is being calculated
44 private volatile boolean restart = false;
46 private volatile boolean updaterunning = false;
48 private boolean disposed = false;
50 private BufferedImage lastMiniMe = null;
52 // Can set different properties in this seqCanvas than
53 // main visible SeqCanvas
54 private SequenceRenderer sr;
56 private jalview.renderer.seqfeatures.FeatureRenderer fr;
58 private OverviewDimensions od;
60 private OverviewRenderer or = null;
62 private AlignViewportI av;
64 private OverviewResColourFinder cf;
66 private ProgressPanel progressPanel;
68 private boolean showSequenceFeatures;
70 private boolean showAnnotation;
72 private jalview.api.FeatureRenderer featureRenderer;
74 private OverviewPanel panel;
76 public OverviewCanvas(OverviewPanel panel,
77 OverviewDimensions overviewDims,
78 AlignViewportI alignvp, ProgressPanel pp)
85 sr = new SequenceRenderer(av);
86 sr.renderGaps = false;
87 fr = new jalview.renderer.seqfeatures.FeatureRenderer(av);
89 boolean useLegacy = Cache.getDefault(Preferences.USE_LEGACY_GAP, false);
90 Color gapCol = Cache.getDefaultColour(Preferences.GAP_COLOUR,
91 jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
92 Color hiddenCol = Cache.getDefaultColour(Preferences.HIDDEN_COLOUR,
93 jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
94 cf = new OverviewResColourFinder(useLegacy, gapCol, hiddenCol);
96 setSize(od.getWidth(), od.getHeight());
97 setPreferredSize(getSize()); // BH 2019.07.29 added
101 * Update the overview dimensions object used by the canvas (e.g. if we change
102 * from showing hidden columns to hiding them or vice versa)
104 * @param overviewDims
106 public void resetOviewDims(OverviewDimensions overviewDims)
112 * Signals to drawing code that the associated alignment viewport has changed
113 * and a redraw will be required
115 public boolean restartDraw()
121 setRestart("restartDraw");
125 updaterunning = true;
131 private void setRestart(String why)
133 // System.out.println("OC restart true " + why);
142 * Draw the overview sequences
144 * @param showSequenceFeatures
145 * true if sequence features are to be shown
146 * @param showAnnotation
147 * true if the annotation is to be shown
148 * @param featureRenderer
149 * the renderer to transfer feature colouring from
151 public void draw(boolean showSequenceFeatures, boolean showAnnotation,
152 jalview.api.FeatureRenderer featureRenderer)
154 this.showSequenceFeatures = showSequenceFeatures;
155 this.showAnnotation = showAnnotation;
156 this.featureRenderer = featureRenderer;
158 // System.out.println("OC draw " + ++ndraw + " showseqf="
159 // + showSequenceFeatures + " showAnno=" + showAnnotation);
161 if (showSequenceFeatures)
163 fr.transferSettings(featureRenderer);
166 setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
168 AlignmentI al = av.getAlignment();
169 or = new OverviewRenderer(panel.ap, fr, od, al,
170 av.getResidueShading(), cf,
171 progressPanel != null);
172 if (progressPanel != null)
174 or.addPropertyChangeListener(progressPanel);
176 or.draw(od.getRows(al), od.getColumns(al));
179 void finalizeDraw(BufferedImage miniMe)
181 Graphics mg = miniMe.getGraphics();
184 mg.translate(0, od.getSequencesHeight());
185 or.drawGraph(mg, av.getAlignmentConservationAnnotation(),
186 od.getGraphHeight(), od.getColumns(av.getAlignment()));
187 mg.translate(0, -od.getSequencesHeight());
189 mg.dispose(); // BH 2019
190 if (progressPanel != null)
192 or.removePropertyChangeListener(progressPanel);
200 draw(showSequenceFeatures, showAnnotation, featureRenderer);
205 updaterunning = false;
212 public void paintComponent(Graphics g)
217 if (w == 0 || od.getBoxWidth() <= 0)
219 // BH 2019.07.27 removes two unnecessary paints, since boxwidth can be -1
220 // or 0 during early-stage painting
224 boolean drawMe = (lastMiniMe != null);
229 g.drawImage(lastMiniMe, 0, 0, w, h, this);
233 g.setColor(Color.white);
234 g.fillRect(0, 0, w, h);
236 g.setColor(TRANS_GREY);
237 g.fillRect(0, 0, w, h);
243 if (w != od.getWidth() || h != od.getHeight()) {
244 // if there is annotation, scale the alignment and annotation
246 if (od.getGraphHeight() <= 0 && od.getSequencesHeight() <= 0)
252 // System.out.println("OC new subimages");
253 BufferedImage topImage = lastMiniMe.getSubimage(0, 0, od.getWidth(),
254 od.getSequencesHeight());
255 BufferedImage bottomImage = lastMiniMe.getSubimage(0,
256 od.getSequencesHeight(), od.getWidth(), od.getGraphHeight());
258 // must be done at this point as we rely on using old width/height
259 // above, and new width/height below
263 // stick the images back together so lastMiniMe is consistent in the
264 // event of a repaint - BUT probably not thread safe
265 // System.out.println("OC new lastminime " + w + " " + h);
266 lastMiniMe = new BufferedImage(w, h, BufferedImage.TYPE_INT_RGB);
267 Graphics lg = lastMiniMe.getGraphics();
268 lg.drawImage(topImage, 0, 0, w, od.getSequencesHeight(), null);
269 lg.drawImage(bottomImage, 0, od.getSequencesHeight(), w,
270 od.getGraphHeight(), this);
272 // BH 2019: removed -- this is now taken care of using vpbox in
274 // // make sure the box is in the right place
275 // od.setBoxPosition(av.getAlignment().getHiddenSequences(),
276 // av.getAlignment().getHiddenColumns());
282 g.drawImage(lastMiniMe, 0, 0, w, h, this);
285 g.setColor(Color.red);
286 // System.out.println("OC paintComponent nd=" + ndraw + " nr=" + nrepaint
287 // + " np=" + ++npaint);
291 private int ndraw, npaint, nrepaint;
294 // public void repaint()
296 // System.out.println("OC repaint " + (++nrepaint));
300 public void dispose()
306 setRestart("dispose");