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.schemes.FeatureColour;
  25
  26 import java.util.Arrays;
  27 import java.util.Iterator;
  28 import java.util.Map;
  29 import java.util.concurrent.ConcurrentHashMap;
  30
  31 public class FeatureRendererSettings implements Cloneable
  32 {
  33   String[] renderOrder;
  34
  35   Map<String, Boolean> featureGroups;
  36
  37   Map<String, FeatureColourI> featureColours;
  38
  39   float transparency;
  40
  41   Map<String, Float> featureOrder;
  42
  43   public FeatureRendererSettings(String[] renderOrder,
  44           Map<String, Boolean> featureGroups,
  45           Map<String, FeatureColourI> featureColours, float transparency,
  46           Map<String, Float> featureOrder)
  47   {
  48     super();
  49     this.renderOrder = Arrays.copyOf(renderOrder, renderOrder.length);
  50     this.featureGroups = new ConcurrentHashMap<String, Boolean>(
  51             featureGroups);
  52     this.featureColours = new ConcurrentHashMap<String, FeatureColourI>(
  53             featureColours);
  54     this.transparency = transparency;
  55     this.featureOrder = new ConcurrentHashMap<String, Float>(featureOrder);
  56   }
  57
  58   /**
  59    * create an independent instance of the feature renderer settings
  60    *
  61    * @param fr
  62    */
  63   public FeatureRendererSettings(
  64           jalview.viewmodel.seqfeatures.FeatureRendererModel fr)
  65   {
  66     renderOrder = null;
  67     featureGroups = new ConcurrentHashMap<String, Boolean>();
  68     featureColours = new ConcurrentHashMap<String, FeatureColourI>();
  69     featureOrder = new ConcurrentHashMap<String, Float>();
  70     if (fr.renderOrder != null)
  71     {
  72       this.renderOrder = new String[fr.renderOrder.length];
  73       System.arraycopy(fr.renderOrder, 0, renderOrder, 0,
  74               fr.renderOrder.length);
  75     }
  76     if (fr.featureGroups != null)
  77     {
  78       this.featureGroups = new ConcurrentHashMap<String, Boolean>(
  79               fr.featureGroups);
  80     }
  81     if (fr.featureColours != null)
  82     {
  83       this.featureColours = new ConcurrentHashMap<String, FeatureColourI>(
  84               fr.featureColours);
  85     }
  86     Iterator<String> en = fr.featureColours.keySet().iterator();
  87     while (en.hasNext())
  88     {
  89       String next = en.next();
  90       FeatureColourI val = featureColours.get(next);
  91       if (!val.isSimpleColour())
  92       {
  93         featureColours.put(next, new FeatureColour((FeatureColour) val));
  94       }
  95     }
  96     this.transparency = fr.transparency;
  97     if (fr.featureOrder != null)
  98     {
  99       this.featureOrder = new ConcurrentHashMap<String, Float>(
 100               fr.featureOrder);
 101     }
 102   }
 103 }