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ScoreColourScheme | 36 | 19 | 9 |
1 | /* | |
2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
4 | * | |
5 | * This file is part of Jalview. | |
6 | * | |
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. | |
11 | * | |
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. | |
16 | * | |
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. | |
20 | */ | |
21 | package jalview.schemes; | |
22 | ||
23 | import jalview.api.AlignViewportI; | |
24 | import jalview.datamodel.AnnotatedCollectionI; | |
25 | import jalview.datamodel.SequenceI; | |
26 | import jalview.util.Comparison; | |
27 | ||
28 | import java.awt.Color; | |
29 | ||
30 | /** | |
31 | * DOCUMENT ME! | |
32 | * | |
33 | * @author $author$ | |
34 | * @version $Revision$ | |
35 | */ | |
36 | public class ScoreColourScheme extends ResidueColourScheme | |
37 | { | |
38 | public double min; | |
39 | ||
40 | public double max; | |
41 | ||
42 | public double[] scores; | |
43 | ||
44 | /** | |
45 | * Creates a new ScoreColourScheme object. | |
46 | * | |
47 | * @param scores | |
48 | * DOCUMENT ME! | |
49 | * @param min | |
50 | * DOCUMENT ME! | |
51 | * @param max | |
52 | * DOCUMENT ME! | |
53 | */ | |
54 | 329 | public ScoreColourScheme(int symbolIndex[], double[] scores, double min, |
55 | double max) | |
56 | { | |
57 | 329 | super(symbolIndex); |
58 | ||
59 | 329 | this.scores = scores; |
60 | 329 | this.min = min; |
61 | 329 | this.max = max; |
62 | ||
63 | // Make colours in constructor | |
64 | // Why wasn't this done earlier? | |
65 | 329 | int iSize = scores.length; |
66 | 329 | colors = new Color[scores.length]; |
67 | 8215 | for (int i = 0; i < iSize; i++) |
68 | { | |
69 | /* | |
70 | * scale score between min and max to the range 0.0 - 1.0 | |
71 | */ | |
72 | 7886 | float score = (float) (scores[i] - (float) min) / (float) (max - min); |
73 | ||
74 | 7886 | if (score > 1.0f) |
75 | { | |
76 | 0 | score = 1.0f; |
77 | } | |
78 | ||
79 | 7886 | if (score < 0.0f) |
80 | { | |
81 | 523 | score = 0.0f; |
82 | } | |
83 | 7886 | colors[i] = makeColour(score); |
84 | } | |
85 | } | |
86 | ||
87 | 42255 | @Override |
88 | public Color findColour(char c, int j, SequenceI seq) | |
89 | { | |
90 | 42255 | if (Comparison.isGap(c)) |
91 | { | |
92 | 10460 | return Color.white; |
93 | } | |
94 | 31795 | return super.findColour(c); |
95 | } | |
96 | ||
97 | /** | |
98 | * DOCUMENT ME! | |
99 | * | |
100 | * @param c | |
101 | * DOCUMENT ME! | |
102 | * | |
103 | * @return DOCUMENT ME! | |
104 | */ | |
105 | 0 | public Color makeColour(float c) |
106 | { | |
107 | 0 | return new Color(c, (float) 0.0, (float) 1.0 - c); |
108 | } | |
109 | ||
110 | 1 | @Override |
111 | public String getSchemeName() | |
112 | { | |
113 | 1 | return "Score"; |
114 | } | |
115 | ||
116 | /** | |
117 | * Returns a new instance of this colour scheme with which the given data may | |
118 | * be coloured | |
119 | */ | |
120 | 0 | @Override |
121 | public ColourSchemeI getInstance(AlignViewportI view, | |
122 | AnnotatedCollectionI coll) | |
123 | { | |
124 | 0 | return new ScoreColourScheme(symbolIndex, scores, min, max); |
125 | } | |
126 | } |