src/jalview/schemes/FeatureColourScheme.java

   1 package jalview.schemes;
   2
   3 import jalview.api.FeatureColourI;
   4 import jalview.api.FeatureSettingsI;
   5
   6 import java.awt.Color;
   7
   8 /**
   9  * Pre-set configurations for feature settings
  10  *
  11  * @author gmcarstairs
  12  *
  13  */
  14 public enum FeatureColourScheme implements FeatureSettingsI
  15 {
  16   /**
  17    * Show sequence variants in red, on top of exons coloured by label
  18    */
  19   EnsemblVariants
  20   {
  21
  22     @Override
  23     public boolean isFeatureDisplayed(String type)
  24     {
  25       // TODO accept SO sub-types of these features
  26       // if (SequenceOntologyFactory.getInstance().isA(SequenceOntologyI.EXON...
  27       return (EXON.equals(type) || SEQUENCE_VARIANT.equals(type));
  28     }
  29
  30     @Override
  31     public boolean isGroupDisplayed(String group)
  32     {
  33       return true;
  34     }
  35
  36     @Override
  37     public FeatureColourI getFeatureColour(String type)
  38     {
  39       if (EXON.equals(type))
  40       {
  41         return new FeatureColourAdapter()
  42         {
  43           @Override
  44           public boolean isColourByLabel()
  45           {
  46             return true;
  47           }
  48         };
  49       }
  50       if (SEQUENCE_VARIANT.equals(type))
  51       {
  52         return new FeatureColourAdapter()
  53         {
  54
  55           @Override
  56           public Color getColour()
  57           {
  58             return Color.RED;
  59           }
  60         };
  61       }
  62       return null;
  63     }
  64
  65     @Override
  66     public float getTransparency()
  67     {
  68       return 1f;
  69     }
  70
  71     /**
  72      * Order sequence_variant above exon above the rest
  73      */
  74     @Override
  75     public int compareTo(String feature1, String feature2)
  76     {
  77       if (SEQUENCE_VARIANT.equals(feature1))
  78       {
  79         return -1;
  80       }
  81       if (SEQUENCE_VARIANT.equals(feature2))
  82       {
  83         return +1;
  84       }
  85       if (EXON.equals(feature1))
  86       {
  87         return -1;
  88       }
  89       if (EXON.equals(feature2))
  90       {
  91         return +1;
  92       }
  93       return 0;
  94     }
  95
  96     @Override
  97     public boolean optimiseOrder()
  98     {
  99       return false;
 100     };
 101
 102   };
 103
 104   // SequenceOntologyI.SEQUENCE_VARIANT
 105   private static final String SEQUENCE_VARIANT = "sequence_variant";
 106
 107   // SequenceOntologyI.EXON
 108   private static final String EXON = "exon";
 109 }