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.datamodel.AlignmentAnnotation;
26 import jalview.datamodel.Annotation;
27 import jalview.datamodel.SequenceI;
28 import jalview.renderer.seqfeatures.FeatureColourFinder;
29 import jalview.renderer.seqfeatures.FeatureRenderer;
30 import jalview.viewmodel.OverviewDimensions;
32 import java.awt.AlphaComposite;
33 import java.awt.Color;
34 import java.awt.Graphics;
35 import java.awt.Graphics2D;
36 import java.awt.image.BufferedImage;
38 public class OverviewRenderer
40 private FeatureColourFinder finder;
42 private jalview.api.SequenceRenderer sr;
45 private BufferedImage miniMe;
47 // raw number of pixels to allocate to each column
48 private float pixelsPerCol;
50 // raw number of pixels to allocate to each row
51 private float pixelsPerSeq;
53 // flag to indicate whether to halt drawing
54 private volatile boolean redraw = false;
56 public OverviewRenderer(jalview.api.SequenceRenderer seqRenderer,
57 FeatureRenderer fr, OverviewDimensions od)
60 finder = new FeatureColourFinder(fr);
62 pixelsPerCol = od.getPixelsPerCol();
63 pixelsPerSeq = od.getPixelsPerSeq();
64 miniMe = new BufferedImage(od.getWidth(), od.getHeight(),
65 BufferedImage.TYPE_INT_RGB);
69 * Draw alignment rows and columns onto an image
72 * Iterator over rows to be drawn
74 * Iterator over columns to be drawn
75 * @return image containing the drawing
77 public BufferedImage draw(AlignmentRowsCollectionI rows,
78 AlignmentColsCollectionI cols)
80 int rgbcolor = Color.white.getRGB();
84 BufferedImage hiddenImage = buildHiddenImage(rows, cols,
85 miniMe.getWidth(), miniMe.getHeight());
87 for (int alignmentRow : rows)
94 // get details of this alignment row
95 SequenceI seq = rows.getSequence(alignmentRow);
97 // calculate where this row extends to in pixels
98 int endRow = Math.min(Math.round((seqIndex + 1) * pixelsPerSeq) - 1,
99 miniMe.getHeight() - 1);
103 for (int alignmentCol : cols)
110 // calculate where this column extends to in pixels
111 int endCol = Math.min(
112 Math.round((colIndex + 1) * pixelsPerCol) - 1,
113 miniMe.getWidth() - 1);
115 // don't do expensive colour determination if we're not going to use it
116 // NB this is important to avoid performance issues in the overview
118 if (pixelCol <= endCol)
120 rgbcolor = getColumnColourFromSequence(seq,
124 // fill in the appropriate number of pixels
125 for (int row = pixelRow; row <= endRow; ++row)
127 for (int col = pixelCol; col <= endCol; ++col)
129 miniMe.setRGB(col, row, rgbcolor);
133 pixelCol = endCol + 1;
137 pixelRow = endRow + 1;
141 return applyMask(hiddenImage, miniMe);
145 * Find the colour of a sequence at a specified column position
147 private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq,
148 int lastcol, FeatureColourFinder fcfinder)
150 Color color = Color.white;
152 if ((seq != null) && (seq.getLength() > lastcol))
154 color = sr.getResidueColour(seq, lastcol, fcfinder);
157 return color.getRGB();
160 private BufferedImage applyMask(BufferedImage mask, BufferedImage image)
162 Graphics2D g = (Graphics2D) image.getGraphics();
164 AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.5f));
165 g.drawImage(mask, 0, 0, image.getWidth(), image.getHeight(), null);
170 * Build a masking image of hidden columns and rows to be applied on top
171 * of the main overview image.
173 private BufferedImage buildHiddenImage(AlignmentRowsCollectionI rows,
174 AlignmentColsCollectionI cols, int width, int height)
177 BufferedImage hiddenImage = new BufferedImage(width, height,
178 BufferedImage.TYPE_INT_ARGB);
183 Color hidden = Color.DARK_GRAY;
185 Graphics2D g2d = (Graphics2D) hiddenImage.getGraphics();
187 // set background to transparent
188 g2d.setComposite(AlphaComposite.Clear);
189 g2d.fillRect(0, 0, width, height);
191 // set next colour to opaque
192 g2d.setComposite(AlphaComposite.Src);
194 for (int alignmentCol : cols)
201 // calculate where this column extends to in pixels
202 int endCol = Math.min(Math.round((colIndex + 1) * pixelsPerCol) - 1,
203 hiddenImage.getWidth() - 1);
205 if (pixelCol <= endCol)
207 // determine the colour based on the sequence and column position
208 if (cols.isHidden(alignmentCol))
210 g2d.setColor(hidden);
211 g2d.fillRect(pixelCol, 0, endCol - pixelCol + 1, height);
214 pixelCol = endCol + 1;
222 for (int alignmentRow : rows)
229 // calculate where this row extends to in pixels
230 int endRow = Math.min(Math.round((seqIndex + 1) * pixelsPerSeq) - 1,
231 miniMe.getHeight() - 1);
233 // get details of this alignment row
234 if (rows.isHidden(alignmentRow))
236 g2d.fillRect(0, pixelRow, width, endRow - pixelRow + 1);
238 pixelRow = endRow + 1;
246 * Draw the alignment annotation in the overview panel
249 * the graphics object to draw on
251 * alignment annotation information
253 * alignment character width value
255 * y-position for the annotation graph
257 * the collection of columns used in the overview panel
259 public void drawGraph(Graphics g, AlignmentAnnotation anno, int charWidth,
260 int y, AlignmentColsCollectionI cols)
262 Annotation[] annotations = anno.annotations;
263 g.setColor(Color.white);
264 g.fillRect(0, 0, miniMe.getWidth(), y);
269 for (int alignmentCol : cols)
275 if (alignmentCol >= annotations.length)
277 break; // no more annotations to draw here
281 int endCol = Math.min(
282 Math.round((colIndex + 1) * pixelsPerCol) - 1,
283 miniMe.getWidth() - 1);
285 if (annotations[alignmentCol] != null)
287 if (annotations[alignmentCol].colour == null)
289 g.setColor(Color.black);
293 g.setColor(annotations[alignmentCol].colour);
296 height = (int) ((annotations[alignmentCol].value / anno.graphMax) * y);
302 g.fillRect(pixelCol, y - height, endCol - pixelCol + 1, height);
304 pixelCol = endCol + 1;
310 public void setRedraw(boolean b)