Coverage Report
File FeatureRendererSettings.java
Coverage histogram
0% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| FeatureRendererSettings | 33 | 29 | 10 |
Contributing tests
This file is covered by 17 tests.
.
Source view
| 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.viewmodel.seqfeatures; | |
| 22 | ||
| 23 | import jalview.api.FeatureColourI; | |
| 24 | import jalview.datamodel.features.FeatureMatcherSetI; | |
| 25 | import jalview.schemes.FeatureColour; | |
| 26 | ||
| 27 | import java.util.Arrays; | |
| 28 | import java.util.HashMap; | |
| 29 | import java.util.Iterator; | |
| 30 | import java.util.Map; | |
| 31 | import java.util.concurrent.ConcurrentHashMap; | |
| 32 | ||
| 33 | public class FeatureRendererSettings implements Cloneable | |
| 34 | { | |
| 35 | String[] renderOrder; | |
| 36 | ||
| 37 | /* | |
| 38 | * map of {groupName, isDisplayed} | |
| 39 | */ | |
| 40 | Map<String, Boolean> featureGroups; | |
| 41 | ||
| 42 | /* | |
| 43 | * map of {featureType, colourScheme} | |
| 44 | */ | |
| 45 | Map<String, FeatureColourI> featureColours; | |
| 46 | ||
| 47 | /* | |
| 48 | * map of {featureType, filters} | |
| 49 | */ | |
| 50 | Map<String, FeatureMatcherSetI> featureFilters; | |
| 51 | ||
| 52 | float transparency; | |
| 53 | ||
| 54 | Map<String, Float> featureOrder; | |
| 55 | ||
| 56 | 36 |  public FeatureRendererSettings(String[] renderOrder, |
| 57 | Map<String, Boolean> featureGroups, | |
| 58 | Map<String, FeatureColourI> featureColours, float transparency, | |
| 59 | Map<String, Float> featureOrder) | |
| 60 | { | |
| 61 | 36 | super(); |
| 62 | 36 | this.renderOrder = Arrays.copyOf(renderOrder, renderOrder.length); |
| 63 | 36 | this.featureGroups = new ConcurrentHashMap<String, Boolean>( |
| 64 | featureGroups); | |
| 65 | 36 | this.featureColours = new ConcurrentHashMap<String, FeatureColourI>( |
| 66 | featureColours); | |
| 67 | 36 | this.transparency = transparency; |
| 68 | 36 | this.featureOrder = new ConcurrentHashMap<String, Float>(featureOrder); |
| 69 | } | |
| 70 | ||
| 71 | /** | |
| 72 | * create an independent instance of the feature renderer settings | |
| 73 | * | |
| 74 | * @param fr | |
| 75 | */ | |
| 76 | 15 | public FeatureRendererSettings( |
| 77 | jalview.viewmodel.seqfeatures.FeatureRendererModel fr) | |
| 78 | { | |
| 79 | 15 | renderOrder = null; |
| 80 | 15 | featureGroups = new ConcurrentHashMap<String, Boolean>(); |
| 81 | 15 | featureColours = new ConcurrentHashMap<String, FeatureColourI>(); |
| 82 | 15 | featureFilters = new HashMap<>(); |
| 83 | 15 | featureOrder = new ConcurrentHashMap<String, Float>(); |
| 84 | ||
| 85 | 15 | if (fr.renderOrder != null) |
| 86 | { | |
| 87 | 9 | this.renderOrder = new String[fr.renderOrder.length]; |
| 88 | 9 | System.arraycopy(fr.renderOrder, 0, renderOrder, 0, |
| 89 | fr.renderOrder.length); | |
| 90 | } | |
| 91 | 15 | if (fr.featureGroups != null) |
| 92 | { | |
| 93 | 15 | this.featureGroups = new ConcurrentHashMap<String, Boolean>( |
| 94 | fr.featureGroups); | |
| 95 | } | |
| 96 | 15 | if (fr.featureColours != null) |
| 97 | { | |
| 98 | 15 | this.featureColours = new ConcurrentHashMap<String, FeatureColourI>( |
| 99 | fr.featureColours); | |
| 100 | } | |
| 101 | 15 | Iterator<String> en = fr.featureColours.keySet().iterator(); |
| 102 | 27 | while (en.hasNext()) |
| 103 | { | |
| 104 | 12 | String next = en.next(); |
| 105 | 12 | FeatureColourI val = featureColours.get(next); |
| 106 | // if (val instanceof GraduatedColor) | |
| 107 | 12 | if (val.isGraduatedColour() || val.isColourByLabel()) // why this test? |
| 108 | { | |
| 109 | 4 | featureColours.put(next, new FeatureColour((FeatureColour) val)); |
| 110 | } | |
| 111 | } | |
| 112 | ||
| 113 | 15 | if (fr.featureFilters != null) |
| 114 | { | |
| 115 | 15 | this.featureFilters.putAll(fr.featureFilters); |
| 116 | } | |
| 117 | ||
| 118 | 15 | this.transparency = fr.transparency; |
| 119 | 15 | if (fr.featureOrder != null) |
| 120 | { | |
| 121 | 9 | this.featureOrder = new ConcurrentHashMap<String, Float>( |
| 122 | fr.featureOrder); | |
| 123 | } | |
| 124 | } | |
| 125 | } |