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File FeatureColourFinder.java
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Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| FeatureColourFinder | 39 | 28 | 14 |
Contributing tests
This file is covered by 22 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.renderer.seqfeatures; | |
| 22 | ||
| 23 | import jalview.api.AlignViewportI; | |
| 24 | import jalview.api.FeatureRenderer; | |
| 25 | import jalview.api.FeaturesDisplayedI; | |
| 26 | import jalview.datamodel.SequenceI; | |
| 27 | import jalview.viewmodel.seqfeatures.FeatureRendererModel; | |
| 28 | ||
| 29 | import java.awt.Color; | |
| 30 | import java.awt.Graphics; | |
| 31 | import java.awt.image.BufferedImage; | |
| 32 | ||
| 33 | /** | |
| 34 | * A helper class to find feature colour using an associated FeatureRenderer | |
| 35 | * | |
| 36 | * @author gmcarstairs | |
| 37 | * | |
| 38 | */ | |
| 39 | public class FeatureColourFinder | |
| 40 | { | |
| 41 | /* | |
| 42 | * the class we delegate feature finding to | |
| 43 | */ | |
| 44 | private FeatureRenderer featureRenderer; | |
| 45 | ||
| 46 | /* | |
| 47 | * a 1-pixel image on which features can be drawn, for the case where | |
| 48 | * transparency allows 'see-through' of multiple feature colours | |
| 49 | */ | |
| 50 | private BufferedImage offscreenImage; | |
| 51 | ||
| 52 | /** | |
| 53 | * Constructor | |
| 54 | * | |
| 55 | * @param fr | |
| 56 | */ | |
| 57 | 19 |  public FeatureColourFinder(FeatureRenderer fr) |
| 58 | { | |
| 59 | 19 | featureRenderer = fr; |
| 60 | 19 | offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB); |
| 61 | } | |
| 62 | ||
| 63 | /** | |
| 64 | * Answers the feature colour to show for the given sequence and column | |
| 65 | * position. This delegates to the FeatureRenderer to find the colour, which | |
| 66 | * will depend on feature location, visibility, ordering, colour scheme, and | |
| 67 | * whether or not transparency is applied. For feature rendering with | |
| 68 | * transparency, this class provides a dummy 'offscreen' graphics context | |
| 69 | * where multiple feature colours can be overlaid and the combined colour read | |
| 70 | * back. | |
| 71 | * <p> | |
| 72 | * This method is not thread-safe when transparency is applied, since a shared | |
| 73 | * BufferedImage would be used by all threads to hold the composite colour at | |
| 74 | * a position. Each thread should use a separate instance of this class. | |
| 75 | * | |
| 76 | * @param defaultColour | |
| 77 | * @param seq | |
| 78 | * @param column | |
| 79 | * alignment column position (0..) | |
| 80 | * @return | |
| 81 | */ | |
| 82 | 3048 | public Color findFeatureColour(Color defaultColour, SequenceI seq, |
| 83 | int column) | |
| 84 | { | |
| 85 | 3048 | if (noFeaturesDisplayed()) |
| 86 | { | |
| 87 | 3018 | return defaultColour; |
| 88 | } | |
| 89 | ||
| 90 | 30 | Graphics g = null; |
| 91 | ||
| 92 | /* | |
| 93 | * if transparency applies, provide a notional 1x1 graphics context | |
| 94 | * that has been primed with the default colour | |
| 95 | */ | |
| 96 | 30 | if (featureRenderer.getTransparency() != 1f) |
| 97 | { | |
| 98 | 4 | g = offscreenImage.getGraphics(); |
| 99 | 4 | if (defaultColour != null) |
| 100 | { | |
| 101 | 4 | offscreenImage.setRGB(0, 0, defaultColour.getRGB()); |
| 102 | } | |
| 103 | } | |
| 104 | ||
| 105 | 30 | Color c = featureRenderer.findFeatureColour(seq, column + 1, g); |
| 106 | 30 | if (c == null) |
| 107 | { | |
| 108 | 8 | return defaultColour; |
| 109 | } | |
| 110 | ||
| 111 | 22 | if (g != null) |
| 112 | { | |
| 113 | 4 | c = new Color(offscreenImage.getRGB(0, 0)); |
| 114 | } | |
| 115 | 22 | return c; |
| 116 | } | |
| 117 | ||
| 118 | /** | |
| 119 | * Answers true if feature display is turned off, or there are no features | |
| 120 | * configured to be visible | |
| 121 | * | |
| 122 | * @return | |
| 123 | */ | |
| 124 | 3055 | boolean noFeaturesDisplayed() |
| 125 | { | |
| 126 | 3055 | if (featureRenderer == null) |
| 127 | { | |
| 128 | 1 | return true; |
| 129 | } | |
| 130 | 3054 | AlignViewportI av = featureRenderer.getViewport(); |
| 131 | 3054 | if (av.isShowComplementFeatures()) |
| 132 | { | |
| 133 | 0 | return false; |
| 134 | } | |
| 135 | 3054 | if (!av.isShowSequenceFeatures()) |
| 136 | { | |
| 137 | 3013 | return true; |
| 138 | } | |
| 139 | ||
| 140 | 41 | if (!((FeatureRendererModel) featureRenderer).hasRenderOrder()) |
| 141 | { | |
| 142 | 6 | return true; |
| 143 | } | |
| 144 | ||
| 145 | 35 | FeaturesDisplayedI displayed = featureRenderer.getFeaturesDisplayed(); |
| 146 | 35 | if (displayed == null || displayed.getVisibleFeatureCount() == 0) |
| 147 | { | |
| 148 | 2 | return true; |
| 149 | } | |
| 150 | ||
| 151 | 33 | return false; |
| 152 | } | |
| 153 | } |