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.
21 package jalview.renderer;
23 import jalview.api.AlignmentColsCollectionI;
24 import jalview.api.AlignmentRowsCollectionI;
25 import jalview.api.RendererListenerI;
26 import jalview.datamodel.AlignmentAnnotation;
27 import jalview.datamodel.Annotation;
28 import jalview.datamodel.SequenceI;
29 import jalview.renderer.seqfeatures.FeatureColourFinder;
30 import jalview.renderer.seqfeatures.FeatureRenderer;
31 import jalview.viewmodel.OverviewDimensions;
33 import java.awt.Color;
34 import java.awt.Graphics;
35 import java.awt.image.BufferedImage;
36 import java.beans.PropertyChangeSupport;
38 public class OverviewRenderer
40 public static final String UPDATE = "OverviewUpdate";
42 protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
45 private FeatureColourFinder finder;
47 private jalview.api.SequenceRenderer sr;
50 private BufferedImage miniMe;
52 // raw number of pixels to allocate to each column
53 private float pixelsPerCol;
55 // raw number of pixels to allocate to each row
56 private float pixelsPerSeq;
58 // height in pixels of graph
59 private int graphHeight;
61 // flag to indicate whether to halt drawing
62 private volatile boolean redraw = false;
64 public OverviewRenderer(jalview.api.SequenceRenderer seqRenderer,
65 FeatureRenderer fr, OverviewDimensions od)
68 finder = new FeatureColourFinder(fr);
70 pixelsPerCol = od.getPixelsPerCol();
71 pixelsPerSeq = od.getPixelsPerSeq();
72 graphHeight = od.getGraphHeight();
73 miniMe = new BufferedImage(od.getWidth(), od.getHeight(),
74 BufferedImage.TYPE_INT_RGB);
78 * Draw alignment rows and columns onto an image
81 * Iterator over rows to be drawn
83 * Iterator over columns to be drawn
84 * @return image containing the drawing
86 public BufferedImage draw(AlignmentRowsCollectionI rows,
87 AlignmentColsCollectionI cols)
89 int rgbcolor = Color.white.getRGB();
92 int alignmentHeight = miniMe.getHeight() - graphHeight;
94 changeSupport.firePropertyChange(UPDATE, -1, 0);
96 for (int alignmentRow : rows)
103 // get details of this alignment row
104 boolean hidden = rows.isHidden(alignmentRow);
105 SequenceI seq = rows.getSequence(alignmentRow);
107 // calculate where this row extends to in pixels
108 int endRow = Math.min(Math.round((seqIndex + 1) * pixelsPerSeq) - 1,
109 miniMe.getHeight() - 1);
113 for (int alignmentCol : cols)
120 // calculate where this column extends to in pixels
121 int endCol = Math.min(
122 Math.round((colIndex + 1) * pixelsPerCol) - 1,
123 miniMe.getWidth() - 1);
125 // don't do expensive colour determination if we're not going to use it
126 // NB this is important to avoid performance issues in the overview
128 if (pixelCol <= endCol)
130 // determine the colour based on the sequence and column position
131 rgbcolor = getColumnColourFromSequence(seq,
132 hidden || cols.isHidden(alignmentCol), alignmentCol,
135 // fill in the appropriate number of pixels
136 for (int row = pixelRow; row <= endRow; ++row)
138 for (int col = pixelCol; col <= endCol; ++col)
140 miniMe.setRGB(col, row, rgbcolor);
144 pixelCol = endCol + 1;
149 if (pixelRow != endRow + 1)
151 changeSupport.firePropertyChange(UPDATE,
152 Math.round(100 * (float) pixelRow / alignmentHeight),
154 100 * ((float) (endRow + 1) / alignmentHeight)));
155 pixelRow = endRow + 1;
160 // final update to progress bar if present
163 changeSupport.firePropertyChange(UPDATE,
164 Math.round(100 * (float) (pixelRow - 1) / alignmentHeight),
169 changeSupport.firePropertyChange(UPDATE,
170 Math.round(100 * alignmentHeight / miniMe.getHeight() - 1),
171 Math.round(100 * alignmentHeight / miniMe.getHeight()));
177 * Find the colour of a sequence at a specified column position
179 private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq,
180 boolean isHidden, int lastcol, FeatureColourFinder fcfinder)
182 Color color = Color.white;
184 if ((seq != null) && (seq.getLength() > lastcol))
186 color = sr.getResidueColour(seq, lastcol, fcfinder);
191 color = color.darker().darker();
194 return color.getRGB();
198 * Draw the alignment annotation in the overview panel
201 * the graphics object to draw on
203 * alignment annotation information
205 * alignment character width value
207 * y-position for the annotation graph
209 * the collection of columns used in the overview panel
211 public void drawGraph(Graphics g, AlignmentAnnotation anno, int charWidth,
212 int y, AlignmentColsCollectionI cols)
214 Annotation[] annotations = anno.annotations;
215 g.setColor(Color.white);
216 g.fillRect(0, 0, miniMe.getWidth(), y);
221 for (int alignmentCol : cols)
225 changeSupport.firePropertyChange(UPDATE, 99, 0);
229 if (alignmentCol >= annotations.length)
231 break; // no more annotations to draw here
235 int endCol = Math.min(
236 Math.round((colIndex + 1) * pixelsPerCol) - 1,
237 miniMe.getWidth() - 1);
239 if (annotations[alignmentCol] != null)
241 if (annotations[alignmentCol].colour == null)
243 g.setColor(Color.black);
247 g.setColor(annotations[alignmentCol].colour);
250 height = (int) ((annotations[alignmentCol].value / anno.graphMax) * y);
256 g.fillRect(pixelCol, y - height, endCol - pixelCol + 1, height);
258 pixelCol = endCol + 1;
262 changeSupport.firePropertyChange(UPDATE, 99, 100);
265 public void setRedraw(boolean b)
273 public void addPropertyChangeListener(RendererListenerI listener)
275 changeSupport.addPropertyChangeListener(listener);
278 public void removePropertyChangeListener(RendererListenerI listener)
280 changeSupport.removePropertyChangeListener(listener);