jalviewX
File FeatureColourFinder.java
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Classes
| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| FeatureColourFinder | 38 | 23 | 13 | 1 |
Contributing tests
This file is covered by 23 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.FeatureRenderer; | |
| 24 | import jalview.api.FeaturesDisplayedI; | |
| 25 | import jalview.datamodel.SequenceI; | |
| 26 | import jalview.viewmodel.seqfeatures.FeatureRendererModel; | |
| 27 | ||
| 28 | import java.awt.Color; | |
| 29 | import java.awt.Graphics; | |
| 30 | import java.awt.image.BufferedImage; | |
| 31 | ||
| 32 | /** | |
| 33 | * A helper class to find feature colour using an associated FeatureRenderer | |
| 34 | * | |
| 35 | * @author gmcarstairs | |
| 36 | * | |
| 37 | */ | |
| 38 | public class FeatureColourFinder | |
| 39 | { | |
| 40 | /* | |
| 41 | * the class we delegate feature finding to | |
| 42 | */ | |
| 43 | private FeatureRenderer featureRenderer; | |
| 44 | ||
| 45 | /* | |
| 46 | * a 1-pixel image on which features can be drawn, for the case where | |
| 47 | * transparency allows 'see-through' of multiple feature colours | |
| 48 | */ | |
| 49 | private BufferedImage offscreenImage; | |
| 50 | ||
| 51 | /** | |
| 52 | * Constructor | |
| 53 | * | |
| 54 | * @param fr | |
| 55 | */ | |
| 56 | 18 |  public FeatureColourFinder(FeatureRenderer fr) |
| 57 | { | |
| 58 | 18 | featureRenderer = fr; |
| 59 | 18 | offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB); |
| 60 | } | |
| 61 | ||
| 62 | /** | |
| 63 | * Answers the feature colour to show for the given sequence and column | |
| 64 | * position. This delegates to the FeatureRenderer to find the colour, which | |
| 65 | * will depend on feature location, visibility, ordering, colour scheme, and | |
| 66 | * whether or not transparency is applied. For feature rendering with | |
| 67 | * transparency, this class provides a dummy 'offscreen' graphics context | |
| 68 | * where multiple feature colours can be overlaid and the combined colour read | |
| 69 | * back. | |
| 70 | * <p> | |
| 71 | * This method is not thread-safe when transparency is applied, since a shared | |
| 72 | * BufferedImage would be used by all threads to hold the composite colour at | |
| 73 | * a position. Each thread should use a separate instance of this class. | |
| 74 | * | |
| 75 | * @param defaultColour | |
| 76 | * @param seq | |
| 77 | * @param column | |
| 78 | * alignment column position (0..) | |
| 79 | * @return | |
| 80 | */ | |
| 81 | 3344 | public Color findFeatureColour(Color defaultColour, SequenceI seq, |
| 82 | int column) | |
| 83 | { | |
| 84 | 3344 | if (noFeaturesDisplayed()) |
| 85 | { | |
| 86 | 3314 | return defaultColour; |
| 87 | } | |
| 88 | ||
| 89 | 30 | Graphics g = null; |
| 90 | ||
| 91 | /* | |
| 92 | * if transparency applies, provide a notional 1x1 graphics context | |
| 93 | * that has been primed with the default colour | |
| 94 | */ | |
| 95 | 30 | if (featureRenderer.getTransparency() != 1f) |
| 96 | { | |
| 97 | 4 | g = offscreenImage.getGraphics(); |
| 98 | 4 | if (defaultColour != null) |
| 99 | { | |
| 100 | 4 | offscreenImage.setRGB(0, 0, defaultColour.getRGB()); |
| 101 | } | |
| 102 | } | |
| 103 | ||
| 104 | 30 | Color c = featureRenderer.findFeatureColour(seq, column + 1, g); |
| 105 | 30 | if (c == null) |
| 106 | { | |
| 107 | 8 | return defaultColour; |
| 108 | } | |
| 109 | ||
| 110 | 22 | if (g != null) |
| 111 | { | |
| 112 | 4 | c = new Color(offscreenImage.getRGB(0, 0)); |
| 113 | } | |
| 114 | 22 | return c; |
| 115 | } | |
| 116 | ||
| 117 | /** | |
| 118 | * Answers true if feature display is turned off, or there are no features | |
| 119 | * configured to be visible | |
| 120 | * | |
| 121 | * @return | |
| 122 | */ | |
| 123 | 3351 | boolean noFeaturesDisplayed() |
| 124 | { | |
| 125 | 3351 | if (featureRenderer == null |
| 126 | || !featureRenderer.getViewport().isShowSequenceFeatures()) | |
| 127 | { | |
| 128 | 3310 | return true; |
| 129 | } | |
| 130 | ||
| 131 | 41 | if (!((FeatureRendererModel) featureRenderer).hasRenderOrder()) |
| 132 | { | |
| 133 | 6 | return true; |
| 134 | } | |
| 135 | ||
| 136 | 35 | FeaturesDisplayedI displayed = featureRenderer.getFeaturesDisplayed(); |
| 137 | 35 | if (displayed == null || displayed.getVisibleFeatureCount() == 0) |
| 138 | { | |
| 139 | 2 | return true; |
| 140 | } | |
| 141 | ||
| 142 | 33 | return false; |
| 143 | } | |
| 144 | } |