jalviewX
File ScoreColourScheme.java
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Classes
| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| ScoreColourScheme | 37 | 19 | 9 | 6 |
Contributing tests
This file is covered by 17 tests.
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| 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.datamodel.AnnotatedCollectionI; | |
| 24 | import jalview.datamodel.SequenceCollectionI; | |
| 25 | import jalview.datamodel.SequenceI; | |
| 26 | import jalview.util.Comparison; | |
| 27 | ||
| 28 | import java.awt.Color; | |
| 29 | import java.util.Map; | |
| 30 | ||
| 31 | /** | |
| 32 | * DOCUMENT ME! | |
| 33 | * | |
| 34 | * @author $author$ | |
| 35 | * @version $Revision$ | |
| 36 | */ | |
| 37 | public class ScoreColourScheme extends ResidueColourScheme | |
| 38 | { | |
| 39 | public double min; | |
| 40 | ||
| 41 | public double max; | |
| 42 | ||
| 43 | public double[] scores; | |
| 44 | ||
| 45 | /** | |
| 46 | * Creates a new ScoreColourScheme object. | |
| 47 | * | |
| 48 | * @param scores | |
| 49 | * DOCUMENT ME! | |
| 50 | * @param min | |
| 51 | * DOCUMENT ME! | |
| 52 | * @param max | |
| 53 | * DOCUMENT ME! | |
| 54 | */ | |
| 55 | 67 |  public ScoreColourScheme(int symbolIndex[], double[] scores, double min, |
| 56 | double max) | |
| 57 | { | |
| 58 | 67 | super(symbolIndex); |
| 59 | ||
| 60 | 67 | this.scores = scores; |
| 61 | 67 | this.min = min; |
| 62 | 67 | this.max = max; |
| 63 | ||
| 64 | // Make colours in constructor | |
| 65 | // Why wasn't this done earlier? | |
| 66 | 67 | int iSize = scores.length; |
| 67 | 67 | colors = new Color[scores.length]; |
| 68 | 1613 | for (int i = 0; i < iSize; i++) |
| 69 | { | |
| 70 | /* | |
| 71 | * scale score between min and max to the range 0.0 - 1.0 | |
| 72 | */ | |
| 73 | 1546 | float score = (float) (scores[i] - (float) min) / (float) (max - min); |
| 74 | ||
| 75 | 1546 | if (score > 1.0f) |
| 76 | { | |
| 77 | 0 | score = 1.0f; |
| 78 | } | |
| 79 | ||
| 80 | 1546 | if (score < 0.0f) |
| 81 | { | |
| 82 | 104 | score = 0.0f; |
| 83 | } | |
| 84 | 1546 | colors[i] = makeColour(score); |
| 85 | } | |
| 86 | } | |
| 87 | ||
| 88 | 17764 | @Override |
| 89 | public Color findColour(char c, int j, SequenceI seq) | |
| 90 | { | |
| 91 | 17764 | if (Comparison.isGap(c)) |
| 92 | { | |
| 93 | 5598 | return Color.white; |
| 94 | } | |
| 95 | 12166 | return super.findColour(c); |
| 96 | } | |
| 97 | ||
| 98 | /** | |
| 99 | * DOCUMENT ME! | |
| 100 | * | |
| 101 | * @param c | |
| 102 | * DOCUMENT ME! | |
| 103 | * | |
| 104 | * @return DOCUMENT ME! | |
| 105 | */ | |
| 106 | 0 | public Color makeColour(float c) |
| 107 | { | |
| 108 | 0 | return new Color(c, (float) 0.0, (float) 1.0 - c); |
| 109 | } | |
| 110 | ||
| 111 | 1 | @Override |
| 112 | public String getSchemeName() | |
| 113 | { | |
| 114 | 1 | return "Score"; |
| 115 | } | |
| 116 | ||
| 117 | /** | |
| 118 | * Returns a new instance of this colour scheme with which the given data may | |
| 119 | * be coloured | |
| 120 | */ | |
| 121 | 0 | @Override |
| 122 | public ColourSchemeI getInstance(AnnotatedCollectionI coll, | |
| 123 | Map<SequenceI, SequenceCollectionI> hrs) | |
| 124 | { | |
| 125 | 0 | return new ScoreColourScheme(symbolIndex, scores, min, max); |
| 126 | } | |
| 127 | } |