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.renderer.OverviewRenderer;
26 import jalview.renderer.OverviewResColourFinder;
27 import jalview.viewmodel.OverviewDimensions;
29 import java.awt.Color;
30 import java.awt.Dimension;
31 import java.awt.Graphics;
32 import java.awt.image.BufferedImage;
34 import javax.swing.JComponent;
36 public class OverviewCanvas extends JComponent
38 private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
40 // This is set true if the alignment view changes whilst
41 // the overview is being calculated
42 private volatile boolean restart = false;
44 private volatile boolean updaterunning = false;
46 private boolean dispose = false;
48 private BufferedImage miniMe;
50 private BufferedImage lastMiniMe = null;
52 private jalview.renderer.seqfeatures.FeatureRenderer fr;
54 private OverviewDimensions od;
56 private OverviewRenderer or = null;
58 private AlignViewportI av;
60 private OverviewResColourFinder cf;
62 private ProgressPanel progressPanel;
64 public OverviewCanvas(OverviewDimensions overviewDims,
65 AlignViewportI alignvp, ProgressPanel pp)
71 fr = new jalview.renderer.seqfeatures.FeatureRenderer(av);
73 boolean useLegacy = Cache.getDefault(Preferences.USE_LEGACY_GAP, false);
74 Color gapCol = Cache.getDefaultColour(Preferences.GAP_COLOUR,
75 jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
76 Color hiddenCol = Cache.getDefaultColour(Preferences.HIDDEN_COLOUR,
77 jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
78 cf = new OverviewResColourFinder(useLegacy, gapCol, hiddenCol);
80 setSize(od.getWidth(), od.getHeight());
84 * Update the overview dimensions object used by the canvas (e.g. if we change
85 * from showing hidden columns to hiding them or vice versa)
89 public void resetOviewDims(OverviewDimensions overviewDims)
95 * Signals to drawing code that the associated alignment viewport has changed
96 * and a redraw will be required
98 public boolean restartDraw()
112 updaterunning = true;
119 * Draw the overview sequences
121 * @param showSequenceFeatures
122 * true if sequence features are to be shown
123 * @param showAnnotation
124 * true if the annotation is to be shown
125 * @param transferRenderer
126 * the renderer to transfer feature colouring from
128 public void draw(boolean showSequenceFeatures, boolean showAnnotation,
129 FeatureRenderer transferRenderer)
133 if (showSequenceFeatures)
135 fr.transferSettings(transferRenderer);
138 setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
140 or = new OverviewRenderer(fr, od, av.getAlignment(),
141 av.getResidueShading(), cf);
143 or.addPropertyChangeListener(progressPanel);
145 miniMe = or.draw(od.getRows(av.getAlignment()),
146 od.getColumns(av.getAlignment()));
148 Graphics mg = miniMe.getGraphics();
152 mg.translate(0, od.getSequencesHeight());
153 or.drawGraph(mg, av.getAlignmentConservationAnnotation(),
154 od.getGraphHeight(), od.getColumns(av.getAlignment()));
155 mg.translate(0, -od.getSequencesHeight());
158 or.removePropertyChangeListener(progressPanel);
165 draw(showSequenceFeatures, showAnnotation, transferRenderer);
170 updaterunning = false;
176 public void paintComponent(Graphics g)
178 super.paintComponent(g);
182 if (lastMiniMe == null)
184 g.setColor(Color.white);
185 g.fillRect(0, 0, getWidth(), getHeight());
189 g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
191 g.setColor(TRANS_GREY);
192 g.fillRect(0, 0, getWidth(), getHeight());
194 else if (lastMiniMe != null)
197 if ((getWidth() > 0) && (getHeight() > 0)
198 && ((getWidth() != od.getWidth())
199 || (getHeight() != od.getHeight())))
201 // if there is annotation, scale the alignment and annotation
203 if (od.getGraphHeight() > 0)
205 BufferedImage topImage = lastMiniMe.getSubimage(0, 0,
206 od.getWidth(), od.getSequencesHeight());
207 BufferedImage bottomImage = lastMiniMe.getSubimage(0,
208 od.getSequencesHeight(), od.getWidth(),
209 od.getGraphHeight());
211 // must be done at this point as we rely on using old width/height
212 // above, and new width/height below
213 od.setWidth(getWidth());
214 od.setHeight(getHeight());
216 // stick the images back together so lastMiniMe is consistent in the
217 // event of a repaint - BUT probably not thread safe
218 lastMiniMe = new BufferedImage(od.getWidth(), od.getHeight(),
219 BufferedImage.TYPE_INT_RGB);
220 Graphics lg = lastMiniMe.getGraphics();
221 lg.drawImage(topImage, 0, 0, od.getWidth(),
222 od.getSequencesHeight(), null);
223 lg.drawImage(bottomImage, 0, od.getSequencesHeight(),
224 od.getWidth(), od.getGraphHeight(), this);
229 od.setWidth(getWidth());
230 od.setHeight(getHeight());
233 // make sure the box is in the right place
234 od.setBoxPosition(av.getAlignment().getHiddenSequences(),
235 av.getAlignment().getHiddenColumns());
237 // fall back to normal behaviour
238 g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
242 g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
246 g.setColor(Color.red);
251 public void dispose()