src/jalview/viewmodel/seqfeatures/FeatureRendererSettings.java

   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 /**
  34  * A data bean that holds
  35  * <ul>
  36  * <li>feature types and their render order</li>
  37  * <li>feature groups and their visibility</li>
  38  * <li>colour for each feature type</li>
  39  * <li>filters (if any) for each feature type</li>
  40  * <li>feature colour transparency</li>
  41  * </ul>
  42  * Note that feature type visibility settings are not held here.
  43  */
  44 public class FeatureRendererSettings
  45 {
  46   String[] renderOrder;
  47
  48   /*
  49    * map of {groupName, isDisplayed}
  50    */
  51   Map<String, Boolean> featureGroups;
  52
  53   /*
  54    * map of {featureType, colourScheme}
  55    */
  56   Map<String, FeatureColourI> featureColours;
  57
  58   /*
  59    * map of {featureType, filters}
  60    */
  61   Map<String, FeatureMatcherSetI> featureFilters;
  62
  63   float transparency;
  64
  65   Map<String, Float> featureOrder;
  66
  67   /**
  68    * Constructor
  69    *
  70    * @param renderOrder
  71    * @param featureGroups
  72    * @param featureColours
  73    * @param transparency
  74    * @param featureOrder
  75    * @param filters
  76    */
  77   public FeatureRendererSettings(String[] renderOrder,
  78           Map<String, Boolean> featureGroups,
  79           Map<String, FeatureColourI> featureColours, float transparency,
  80           Map<String, Float> featureOrder,
  81           Map<String, FeatureMatcherSetI> filters)
  82   {
  83     super();
  84     this.renderOrder = Arrays.copyOf(renderOrder, renderOrder.length);
  85     this.featureGroups = new ConcurrentHashMap<>(
  86             featureGroups);
  87     this.featureColours = new ConcurrentHashMap<>(
  88             featureColours);
  89     this.transparency = transparency;
  90     this.featureOrder = new ConcurrentHashMap<>(featureOrder);
  91     featureFilters = filters;
  92   }
  93
  94   /**
  95    * create an independent instance of the feature renderer settings
  96    *
  97    * @param fr
  98    */
  99   public FeatureRendererSettings(
 100           jalview.viewmodel.seqfeatures.FeatureRendererModel fr)
 101   {
 102     renderOrder = null;
 103     featureGroups = new ConcurrentHashMap<>();
 104     featureColours = new ConcurrentHashMap<>();
 105     featureFilters = new HashMap<>();
 106     featureOrder = new ConcurrentHashMap<>();
 107
 108     if (fr.renderOrder != null)
 109     {
 110       this.renderOrder = new String[fr.renderOrder.length];
 111       System.arraycopy(fr.renderOrder, 0, renderOrder, 0,
 112               fr.renderOrder.length);
 113     }
 114     if (fr.featureGroups != null)
 115     {
 116       this.featureGroups = new ConcurrentHashMap<>(
 117               fr.featureGroups);
 118     }
 119     if (fr.featureColours != null)
 120     {
 121       this.featureColours = new ConcurrentHashMap<>(
 122               fr.featureColours);
 123     }
 124     Iterator<String> en = fr.featureColours.keySet().iterator();
 125     while (en.hasNext())
 126     {
 127       String next = en.next();
 128       FeatureColourI val = featureColours.get(next);
 129       // if (val instanceof GraduatedColor)
 130       if (val.isGraduatedColour() || val.isColourByLabel()) // why this test?
 131       {
 132         featureColours.put(next, new FeatureColour((FeatureColour) val));
 133       }
 134     }
 135
 136     if (fr.featureFilters != null)
 137     {
 138       this.featureFilters.putAll(fr.featureFilters);
 139     }
 140
 141     this.transparency = fr.transparency;
 142     if (fr.featureOrder != null)
 143     {
 144       this.featureOrder = new ConcurrentHashMap<>(
 145               fr.featureOrder);
 146     }
 147   }
 148 }