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 implements Cloneable
  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   public FeatureRendererSettings(String[] renderOrder,
  68           Map<String, Boolean> featureGroups,
  69           Map<String, FeatureColourI> featureColours, float transparency,
  70           Map<String, Float> featureOrder)
  71   {
  72     super();
  73     this.renderOrder = Arrays.copyOf(renderOrder, renderOrder.length);
  74     this.featureGroups = new ConcurrentHashMap<>(
  75             featureGroups);
  76     this.featureColours = new ConcurrentHashMap<>(
  77             featureColours);
  78     this.transparency = transparency;
  79     this.featureOrder = new ConcurrentHashMap<>(featureOrder);
  80   }
  81
  82   /**
  83    * create an independent instance of the feature renderer settings
  84    *
  85    * @param fr
  86    */
  87   public FeatureRendererSettings(
  88           jalview.viewmodel.seqfeatures.FeatureRendererModel fr)
  89   {
  90     renderOrder = null;
  91     featureGroups = new ConcurrentHashMap<>();
  92     featureColours = new ConcurrentHashMap<>();
  93     featureFilters = new HashMap<>();
  94     featureOrder = new ConcurrentHashMap<>();
  95
  96     if (fr.renderOrder != null)
  97     {
  98       this.renderOrder = new String[fr.renderOrder.length];
  99       System.arraycopy(fr.renderOrder, 0, renderOrder, 0,
 100               fr.renderOrder.length);
 101     }
 102     if (fr.featureGroups != null)
 103     {
 104       this.featureGroups = new ConcurrentHashMap<>(
 105               fr.featureGroups);
 106     }
 107     if (fr.featureColours != null)
 108     {
 109       this.featureColours = new ConcurrentHashMap<>(
 110               fr.featureColours);
 111     }
 112     Iterator<String> en = fr.featureColours.keySet().iterator();
 113     while (en.hasNext())
 114     {
 115       String next = en.next();
 116       FeatureColourI val = featureColours.get(next);
 117       // if (val instanceof GraduatedColor)
 118       if (val.isGraduatedColour() || val.isColourByLabel()) // why this test?
 119       {
 120         featureColours.put(next, new FeatureColour((FeatureColour) val));
 121       }
 122     }
 123
 124     if (fr.featureFilters != null)
 125     {
 126       this.featureFilters.putAll(fr.featureFilters);
 127     }
 128
 129     this.transparency = fr.transparency;
 130     if (fr.featureOrder != null)
 131     {
 132       this.featureOrder = new ConcurrentHashMap<>(
 133               fr.featureOrder);
 134     }
 135   }
 136 }