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.schemes;
23 import jalview.api.AlignViewportI;
24 import jalview.datamodel.AnnotatedCollectionI;
25 import jalview.datamodel.SequenceI;
26 import jalview.util.Comparison;
28 import java.awt.Color;
31 * A base class for colour schemes which define a graduated colour range based
34 * <li>a minimum colour</li>
35 * <li>a maximum colour</li>
36 * <li>a score assigned to each residue</li>
39 public class ScoreColourScheme extends ResidueColourScheme
45 public double[] scores;
51 * a lookup where the index is a character e.g. 'R' or 'r', and the
52 * value is its position in the colour table lookup
54 * per residue, indices matching colors lookup
56 public ScoreColourScheme(int symbolIndex[], double[] scores)
62 // Make colours in constructor
63 // Why wasn't this done earlier?
64 int iSize = scores.length;
65 colors = new Color[scores.length];
66 for (int i = 0; i < iSize; i++)
69 * scale score between min and max to the range 0.0 - 1.0
71 float score = (float) (scores[i] - (float) min) / (float) (max - min);
82 colors[i] = makeColour(score);
87 * Inspects score values and saves the minimum and maximum
91 void setMinMax(double[] vals)
93 double dMin = Double.MAX_VALUE;
94 double dMax = -Double.MAX_VALUE;
96 for (int i = 0; i < vals.length - 1; i++)
98 dMin = Math.min(dMin, vals[i]);
99 dMax = Math.max(dMax, vals[i]);
102 this.min = vals.length == 0 ? 0d : dMin;
103 this.max = vals.length == 0 ? 0d : dMax;
107 public Color findColour(char c, int j, SequenceI seq)
109 if (Comparison.isGap(c))
113 return super.findColour(c);
122 * @return DOCUMENT ME!
124 public Color makeColour(float c)
126 return new Color(c, (float) 0.0, (float) 1.0 - c);
130 public String getSchemeName()
136 * Returns a new instance of this colour scheme with which the given data may
140 public ColourSchemeI getInstance(AlignViewportI view,
141 AnnotatedCollectionI coll)
143 return new ScoreColourScheme(symbolIndex, scores);