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   /*
  36    * map of {groupName, isDisplayed}
  37    */
  38   Map<String, Boolean> featureGroups;
  39
  40   /*
  41    * map of {featureType, colourScheme}
  42    */
  43   Map<String, FeatureColourI> featureColours;
  44
  45   float transparency;
  46
  47   Map<String, Float> featureOrder;
  48
  49   public FeatureRendererSettings(String[] renderOrder,
  50           Map<String, Boolean> featureGroups,
  51           Map<String, FeatureColourI> featureColours, float transparency,
  52           Map<String, Float> featureOrder)
  53   {
  54     super();
  55     this.renderOrder = Arrays.copyOf(renderOrder, renderOrder.length);
  56     this.featureGroups = new ConcurrentHashMap<String, Boolean>(
  57             featureGroups);
  58     this.featureColours = new ConcurrentHashMap<String, FeatureColourI>(
  59             featureColours);
  60     this.transparency = transparency;
  61     this.featureOrder = new ConcurrentHashMap<String, Float>(featureOrder);
  62   }
  63
  64   /**
  65    * create an independent instance of the feature renderer settings
  66    *
  67    * @param fr
  68    */
  69   public FeatureRendererSettings(
  70           jalview.viewmodel.seqfeatures.FeatureRendererModel fr)
  71   {
  72     renderOrder = null;
  73     featureGroups = new ConcurrentHashMap<String, Boolean>();
  74     featureColours = new ConcurrentHashMap<String, FeatureColourI>();
  75     featureOrder = new ConcurrentHashMap<String, Float>();
  76     if (fr.renderOrder != null)
  77     {
  78       this.renderOrder = new String[fr.renderOrder.length];
  79       System.arraycopy(fr.renderOrder, 0, renderOrder, 0,
  80               fr.renderOrder.length);
  81     }
  82     if (fr.featureGroups != null)
  83     {
  84       this.featureGroups = new ConcurrentHashMap<String, Boolean>(
  85               fr.featureGroups);
  86     }
  87     if (fr.featureColours != null)
  88     {
  89       this.featureColours = new ConcurrentHashMap<String, FeatureColourI>(
  90               fr.featureColours);
  91     }
  92     Iterator<String> en = fr.featureColours.keySet().iterator();
  93     while (en.hasNext())
  94     {
  95       String next = en.next();
  96       FeatureColourI val = featureColours.get(next);
  97       // if (val instanceof GraduatedColor)
  98       if (val.isGraduatedColour() || val.isColourByLabel()) // why this test?
  99       {
 100         featureColours.put(next, new FeatureColour((FeatureColour) val));
 101       }
 102     }
 103     this.transparency = fr.transparency;
 104     if (fr.featureOrder != null)
 105     {
 106       this.featureOrder = new ConcurrentHashMap<String, Float>(
 107               fr.featureOrder);
 108     }
 109   }
 110 }