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.Color;
33 import java.awt.Graphics;
34 import java.awt.image.BufferedImage;
36 public class OverviewRenderer
38 private FeatureColourFinder finder;
40 private jalview.api.SequenceRenderer sr;
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 public OverviewRenderer(jalview.api.SequenceRenderer seqRenderer,
52 FeatureRenderer fr, OverviewDimensions od)
53 // FeatureColourFinder colfinder, OverviewDimensions od)
56 finder = new FeatureColourFinder(fr); // colfinder;
58 pixelsPerCol = od.getPixelsPerCol();
59 pixelsPerSeq = od.getPixelsPerSeq();
60 miniMe = new BufferedImage(od.getWidth(), od.getHeight(),
61 BufferedImage.TYPE_INT_RGB);
65 * Draw alignment rows and columns onto an image
68 * Iterator over rows to be drawn
70 * Iterator over columns to be drawn
71 * @return image containing the drawing
73 public BufferedImage draw(AlignmentRowsCollectionI rows,
74 AlignmentColsCollectionI cols)
76 int rgbcolor = Color.white.getRGB();
79 for (int alignmentRow : rows)
81 // get details of this alignment row
82 boolean hidden = rows.isHidden(alignmentRow);
83 SequenceI seq = rows.getSequence(alignmentRow);
85 // calculate where this row extends to in pixels
86 int endRow = Math.min(Math.round((seqIndex + 1) * pixelsPerSeq) - 1,
87 miniMe.getHeight() - 1);
91 for (int alignmentCol : cols)
93 // calculate where this column extends to in pixels
94 int endCol = Math.min(
95 Math.round((colIndex + 1) * pixelsPerCol) - 1,
96 miniMe.getWidth() - 1);
98 // don't do expensive colour determination if we're not going to use it
99 // NB this is important to avoid performance issues in the overview
101 if (pixelCol <= endCol)
103 // determine the colour based on the sequence and column position
104 rgbcolor = getColumnColourFromSequence(seq,
105 hidden || cols.isHidden(alignmentCol), alignmentCol,
108 // fill in the appropriate number of pixels
109 for (int row = pixelRow; row <= endRow; ++row)
111 for (int col = pixelCol; col <= endCol; ++col)
113 miniMe.setRGB(col, row, rgbcolor);
117 pixelCol = endCol + 1;
121 pixelRow = endRow + 1;
128 * Find the colour of a sequence at a specified column position
130 private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq,
131 boolean isHidden, int lastcol, FeatureColourFinder fcfinder)
133 Color color = Color.white;
135 if ((seq != null) && (seq.getLength() > lastcol))
137 color = sr.getResidueColour(seq, lastcol, fcfinder);
142 color = color.darker().darker();
145 return color.getRGB();
149 * Draw the alignment annotation in the overview panel
152 * the graphics object to draw on
154 * alignment annotation information
156 * alignment character width value
158 * y-position for the annotation graph
160 * the collection of columns used in the overview panel
162 public void drawGraph(Graphics g, AlignmentAnnotation anno, int charWidth,
163 int y, AlignmentColsCollectionI cols)
165 Annotation[] annotations = anno.annotations;
166 g.setColor(Color.white);
167 g.fillRect(0, 0, miniMe.getWidth(), y);
172 for (int alignmentCol : cols)
174 if (alignmentCol >= annotations.length)
176 break; // no more annotations to draw here
180 int endCol = Math.min(
181 Math.round((colIndex + 1) * pixelsPerCol) - 1,
182 miniMe.getWidth() - 1);
184 if (annotations[alignmentCol] != null)
186 if (annotations[alignmentCol].colour == null)
188 g.setColor(Color.black);
192 g.setColor(annotations[alignmentCol].colour);
195 height = (int) ((annotations[alignmentCol].value / anno.graphMax) * y);
201 g.fillRect(pixelCol, y - height, endCol - pixelCol + 1, height);
203 pixelCol = endCol + 1;