2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.viewmodel.seqfeatures;
23 import jalview.api.FeatureColourI;
24 import jalview.datamodel.features.FeatureMatcherSetI;
25 import jalview.schemes.FeatureColour;
27 import java.util.Arrays;
28 import java.util.HashMap;
29 import java.util.Iterator;
31 import java.util.concurrent.ConcurrentHashMap;
33 public class FeatureRendererSettings implements Cloneable
38 * map of {groupName, isDisplayed}
40 Map<String, Boolean> featureGroups;
43 * map of {featureType, colourScheme}
45 Map<String, FeatureColourI> featureColours;
48 * map of {featureType, filters}
50 Map<String, FeatureMatcherSetI> featureFilters;
54 Map<String, Float> featureOrder;
56 public FeatureRendererSettings(String[] renderOrder,
57 Map<String, Boolean> featureGroups,
58 Map<String, FeatureColourI> featureColours, float transparency,
59 Map<String, Float> featureOrder)
62 this.renderOrder = Arrays.copyOf(renderOrder, renderOrder.length);
63 this.featureGroups = new ConcurrentHashMap<String, Boolean>(
65 this.featureColours = new ConcurrentHashMap<String, FeatureColourI>(
67 this.transparency = transparency;
68 this.featureOrder = new ConcurrentHashMap<String, Float>(featureOrder);
72 * create an independent instance of the feature renderer settings
76 public FeatureRendererSettings(
77 jalview.viewmodel.seqfeatures.FeatureRendererModel fr)
80 featureGroups = new ConcurrentHashMap<String, Boolean>();
81 featureColours = new ConcurrentHashMap<String, FeatureColourI>();
82 featureFilters = new HashMap<>();
83 featureOrder = new ConcurrentHashMap<String, Float>();
85 if (fr.renderOrder != null)
87 this.renderOrder = new String[fr.renderOrder.length];
88 System.arraycopy(fr.renderOrder, 0, renderOrder, 0,
89 fr.renderOrder.length);
91 if (fr.featureGroups != null)
93 this.featureGroups = new ConcurrentHashMap<String, Boolean>(
96 if (fr.featureColours != null)
98 this.featureColours = new ConcurrentHashMap<String, FeatureColourI>(
101 Iterator<String> en = fr.featureColours.keySet().iterator();
104 String next = en.next();
105 FeatureColourI val = featureColours.get(next);
106 // if (val instanceof GraduatedColor)
107 if (val.isGraduatedColour() || val.isColourByLabel()) // why this test?
109 featureColours.put(next, new FeatureColour((FeatureColour) val));
113 if (fr.featureFilters != null)
115 this.featureFilters.putAll(fr.featureFilters);
118 this.transparency = fr.transparency;
119 if (fr.featureOrder != null)
121 this.featureOrder = new ConcurrentHashMap<String, Float>(