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.AlignmentI;
27 import jalview.datamodel.Annotation;
28 import jalview.datamodel.SequenceGroup;
29 import jalview.datamodel.SequenceI;
30 import jalview.renderer.seqfeatures.FeatureColourFinder;
31 import jalview.renderer.seqfeatures.FeatureRenderer;
32 import jalview.viewmodel.OverviewDimensions;
34 import java.awt.Color;
35 import java.awt.Graphics;
36 import java.awt.image.BufferedImage;
38 public class OverviewRenderer
40 private FeatureColourFinder finder;
43 private BufferedImage miniMe;
45 // raw number of pixels to allocate to each column
46 private float pixelsPerCol;
48 // raw number of pixels to allocate to each row
49 private float pixelsPerSeq;
51 // flag to indicate whether to halt drawing
52 private volatile boolean redraw = false;
54 // reference to alignment, needed to get sequence groups
55 private AlignmentI al;
57 private ResidueShaderI shader;
59 private ResidueColourFinder resColFinder;
61 public OverviewRenderer(FeatureRenderer fr, OverviewDimensions od,
63 ResidueShaderI resshader)
65 finder = new FeatureColourFinder(fr);
66 resColFinder = new OverviewResColourFinder();
71 pixelsPerCol = od.getPixelsPerCol();
72 pixelsPerSeq = od.getPixelsPerSeq();
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();
93 for (int alignmentRow : rows)
100 // get details of this alignment row
101 boolean hidden = rows.isHidden(alignmentRow);
102 SequenceI seq = rows.getSequence(alignmentRow);
103 // rate limiting step when rendering overview for lots of groups
104 SequenceGroup[] allGroups = al.findAllGroups(seq);
106 // calculate where this row extends to in pixels
107 int endRow = Math.min(Math.round((seqIndex + 1) * pixelsPerSeq) - 1,
108 miniMe.getHeight() - 1);
112 for (int alignmentCol : cols)
119 // calculate where this column extends to in pixels
120 int endCol = Math.min(
121 Math.round((colIndex + 1) * pixelsPerCol) - 1,
122 miniMe.getWidth() - 1);
124 // don't do expensive colour determination if we're not going to use it
125 // NB this is important to avoid performance issues in the overview
127 if (pixelCol <= endCol)
129 // determine the colour based on the sequence and column position
130 rgbcolor = getColumnColourFromSequence(allGroups, seq,
131 hidden || cols.isHidden(alignmentCol), alignmentCol,
134 // fill in the appropriate number of pixels
135 for (int row = pixelRow; row <= endRow; ++row)
137 for (int col = pixelCol; col <= endCol; ++col)
139 miniMe.setRGB(col, row, rgbcolor);
143 pixelCol = endCol + 1;
147 pixelRow = endRow + 1;
154 * Find the colour of a sequence at a specified column position
156 private int getColumnColourFromSequence(SequenceGroup[] allGroups,
157 jalview.datamodel.SequenceI seq,
158 boolean isHidden, int lastcol, FeatureColourFinder fcfinder)
160 Color color = Color.white;
162 if ((seq != null) && (seq.getLength() > lastcol))
164 color = resColFinder.getResidueColour(shader, allGroups, seq, lastcol,
170 color = color.darker().darker();
173 return color.getRGB();
177 * Draw the alignment annotation in the overview panel
180 * the graphics object to draw on
182 * alignment annotation information
184 * alignment character width value
186 * y-position for the annotation graph
188 * the collection of columns used in the overview panel
190 public void drawGraph(Graphics g, AlignmentAnnotation anno, int charWidth,
191 int y, AlignmentColsCollectionI cols)
193 Annotation[] annotations = anno.annotations;
194 g.setColor(Color.white);
195 g.fillRect(0, 0, miniMe.getWidth(), y);
200 for (int alignmentCol : cols)
206 if (alignmentCol >= annotations.length)
208 break; // no more annotations to draw here
212 int endCol = Math.min(
213 Math.round((colIndex + 1) * pixelsPerCol) - 1,
214 miniMe.getWidth() - 1);
216 if (annotations[alignmentCol] != null)
218 if (annotations[alignmentCol].colour == null)
220 g.setColor(Color.black);
224 g.setColor(annotations[alignmentCol].colour);
227 height = (int) ((annotations[alignmentCol].value / anno.graphMax) * y);
233 g.fillRect(pixelCol, y - height, endCol - pixelCol + 1, height);
235 pixelCol = endCol + 1;
241 public void setRedraw(boolean b)