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.renderer.AnnotationRenderer;
24 import jalview.viewmodel.OverviewDimensions;
26 import java.awt.Color;
27 import java.awt.Dimension;
28 import java.awt.Graphics;
29 import java.awt.event.ComponentAdapter;
30 import java.awt.event.ComponentEvent;
31 import java.awt.event.MouseAdapter;
32 import java.awt.event.MouseEvent;
33 import java.awt.event.MouseMotionAdapter;
34 import java.awt.image.BufferedImage;
36 import javax.swing.JPanel;
39 * Panel displaying an overview of the full alignment, with an interactive box
40 * representing the viewport onto the alignment.
45 public class OverviewPanel extends JPanel implements Runnable
47 private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
49 private final AnnotationRenderer renderer = new AnnotationRenderer();
51 private OverviewDimensions od;
53 private BufferedImage miniMe;
55 private BufferedImage lastMiniMe = null;
57 private AlignViewport av;
59 private AlignmentPanel ap;
62 private boolean resizing = false;
64 // This is set true if the user resizes whilst
65 // the overview is being calculated
66 private boolean resizeAgain = false;
68 // Can set different properties in this seqCanvas than
69 // main visible SeqCanvas
70 private SequenceRenderer sr;
72 private jalview.renderer.seqfeatures.FeatureRenderer fr;
75 * Creates a new OverviewPanel object.
78 * The alignment panel which is shown in the overview panel
80 public OverviewPanel(AlignmentPanel alPanel)
86 sr = new SequenceRenderer(av);
87 sr.renderGaps = false;
88 sr.forOverview = true;
89 fr = new FeatureRenderer(alPanel);
91 boolean showAnnotation = false;
92 // TODO: in applet this was getSequenceConsensusHash()
93 // check if it makes any functional difference: hconsensus or conservation
94 if (av.getAlignmentConservationAnnotation() == null)
96 showAnnotation = true;
98 od = new OverviewDimensions(av, showAnnotation);
100 addComponentListener(new ComponentAdapter()
103 public void componentResized(ComponentEvent evt)
105 if ((getWidth() != od.getWidth())
106 || (getHeight() != (od.getHeight())))
108 updateOverviewImage();
113 addMouseMotionListener(new MouseMotionAdapter()
116 public void mouseDragged(MouseEvent evt)
118 if (!av.getWrapAlignment())
120 // TODO: feature: jv2.5 detect shift drag and update selection from
122 od.updateViewportFromMouse(evt.getX(), evt.getY());
123 ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
128 addMouseListener(new MouseAdapter()
131 public void mousePressed(MouseEvent evt)
133 if (!av.getWrapAlignment())
135 od.updateViewportFromMouse(evt.getX(), evt.getY());
136 ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
141 updateOverviewImage();
145 * Updates the overview image when the related alignment panel is updated
147 public void updateOverviewImage()
157 if ((getWidth() > 0) && (getHeight() > 0))
159 od.setWidth(getWidth()); // width = getWidth();
160 od.setHeight(getHeight()); // sequencesHeight = getHeight() - graphHeight;
163 setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
165 Thread thread = new Thread(this);
175 if (av.isShowSequenceFeatures())
177 fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer());
180 // why do we need to set preferred size again? was set in
181 // updateOverviewImage
182 setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
184 miniMe = new BufferedImage(od.getWidth(), od.getHeight(),
185 BufferedImage.TYPE_INT_RGB);
187 Graphics mg = miniMe.getGraphics();
188 mg.setColor(Color.orange);
189 mg.fillRect(0, 0, od.getWidth(), miniMe.getHeight());
191 // calculate sampleCol and sampleRow
192 // alignment width is max number of residues/bases
193 // alignment height is number of sequences
194 int alwidth = av.getAlignment().getWidth();
195 int alheight = av.getAlignment().getAbsoluteHeight();
197 // sampleCol or sampleRow is the width/height allocated to each residue
198 // in particular, sometimes we may need more than one row/col of the
199 // BufferedImage allocated
200 // sampleCol is how much of a residue to assign to each pixel
201 // sampleRow is how many sequences to assign to each pixel
202 float sampleCol = alwidth / (float) od.getWidth();
203 float sampleRow = alheight / (float) od.getSequencesHeight();
205 buildImage(sampleRow, sampleCol);
207 if (av.getAlignmentConservationAnnotation() != null)
209 renderer.updateFromAlignViewport(av);
210 for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
212 mg.translate(col, od.getSequencesHeight());
213 renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
214 av.getAlignmentConservationAnnotation().annotations,
215 (int) (sampleCol) + 1, od.getGraphHeight(),
216 (int) (col * sampleCol), (int) (col * sampleCol) + 1);
217 mg.translate(-col, -od.getSequencesHeight());
228 updateOverviewImage();
238 private void buildImage(float sampleRow, float sampleCol)
242 int color = Color.white.getRGB();
244 jalview.datamodel.SequenceI seq = null;
246 final boolean hasHiddenCols = av.hasHiddenColumns();
247 boolean hiddenRow = false;
248 // get hidden row and hidden column map once at beginning.
249 // clone featureRenderer settings to avoid race conditions... if state is
250 // updated just need to refresh again
251 for (int row = 0; row < od.getSequencesHeight() && !resizeAgain; row++)
253 boolean doCopy = true;
254 int currentrow = (int) (row * sampleRow);
255 if (currentrow != lastrow)
259 lastrow = currentrow;
261 // get the sequence which would be at alignment index 'lastrow' if no
262 // columns were hidden, and determine whether it is hidden or not
263 hiddenRow = av.getAlignment().isHidden(lastrow);
264 seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);
269 System.out.println(lastrow + " null");
273 for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
277 color = miniMe.getRGB(col, row - 1);
279 else if ((int) (col * sampleCol) != lastcol
280 || (int) (row * sampleRow) != lastrow)
282 lastcol = (int) (col * sampleCol);
283 color = getColumnColourFromSequence(seq, hiddenRow, hasHiddenCols,
286 // else if ((int) (col * sampleCol) == lastcol && (int) (row *
287 // sampleRow) == lastrow))
288 // we just use the color we already have , so don't need to set it
290 miniMe.setRGB(col, row, color);
296 * Find the colour of a sequence at a specified column position
298 private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq,
299 boolean hiddenRow, boolean hasHiddenCols, int lastcol)
303 if (seq.getLength() > lastcol)
305 color = sr.getResidueBoxColour(seq, lastcol).getRGB();
307 if (av.isShowSequenceFeatures())
309 color = fr.findFeatureColour(color, seq, lastcol);
314 color = Color.white.getRGB(); // White
318 || (hasHiddenCols && !av.getColumnSelection()
319 .isVisible(lastcol)))
321 color = new Color(color).darker().darker().getRGB();
328 * Update the overview panel box when the associated alignment panel is
332 public void setBoxPosition()
340 public void paintComponent(Graphics g)
342 if (resizing || resizeAgain)
344 if (lastMiniMe == null)
346 g.setColor(Color.white);
347 g.fillRect(0, 0, getWidth(), getHeight());
351 g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
353 g.setColor(TRANS_GREY);
354 g.fillRect(0, 0, getWidth(), getHeight());
356 else if (lastMiniMe != null)
358 g.drawImage(lastMiniMe, 0, 0, this);
359 if (lastMiniMe != miniMe)
361 g.setColor(TRANS_GREY);
362 g.fillRect(0, 0, getWidth(), getHeight());
365 // TODO: render selected regions
366 g.setColor(Color.red);