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 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   public FeatureRendererSettings(String[] renderOrder,
  57           Map<String, Boolean> featureGroups,
  58           Map<String, FeatureColourI> featureColours, float transparency,
  59           Map<String, Float> featureOrder)
  60   {
  61     super();
  62     this.renderOrder = Arrays.copyOf(renderOrder, renderOrder.length);
  63     this.featureGroups = new ConcurrentHashMap<String, Boolean>(
  64             featureGroups);
  65     this.featureColours = new ConcurrentHashMap<String, FeatureColourI>(
  66             featureColours);
  67     this.transparency = transparency;
  68     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   public FeatureRendererSettings(
  77           jalview.viewmodel.seqfeatures.FeatureRendererModel fr)
  78   {
  79     renderOrder = null;
  80     featureGroups = new ConcurrentHashMap<String, Boolean>();
  81     featureColours = new ConcurrentHashMap<String, FeatureColourI>();
  82     featureFilters = new HashMap<>();
  83     featureOrder = new ConcurrentHashMap<String, Float>();
  84
  85     if (fr.renderOrder != null)
  86     {
  87       this.renderOrder = new String[fr.renderOrder.length];
  88       System.arraycopy(fr.renderOrder, 0, renderOrder, 0,
  89               fr.renderOrder.length);
  90     }
  91     if (fr.featureGroups != null)
  92     {
  93       this.featureGroups = new ConcurrentHashMap<String, Boolean>(
  94               fr.featureGroups);
  95     }
  96     if (fr.featureColours != null)
  97     {
  98       this.featureColours = new ConcurrentHashMap<String, FeatureColourI>(
  99               fr.featureColours);
 100     }
 101     Iterator<String> en = fr.featureColours.keySet().iterator();
 102     while (en.hasNext())
 103     {
 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?
 108       {
 109         featureColours.put(next, new FeatureColour((FeatureColour) val));
 110       }
 111     }
 112
 113     if (fr.featureFilters != null)
 114     {
 115       this.featureFilters.putAll(fr.featureFilters);
 116     }
 117
 118     this.transparency = fr.transparency;
 119     if (fr.featureOrder != null)
 120     {
 121       this.featureOrder = new ConcurrentHashMap<String, Float>(
 122               fr.featureOrder);
 123     }
 124   }
 125 }