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 FeatureColour()
  42         {
  43           @Override
  44           public boolean isColourByLabel()
  45           {
  46             return true;
  47           }
  48         };
  49       }
  50       if (SEQUENCE_VARIANT.equals(type))
  51       {
  52         return new FeatureColour(Color.RED);
  53       }
  54       return null;
  55     }
  56
  57     @Override
  58     public float getTransparency()
  59     {
  60       return 1f;
  61     }
  62
  63     /**
  64      * Order sequence_variant above exon above the rest
  65      */
  66     @Override
  67     public int compareTo(String feature1, String feature2)
  68     {
  69       if (SEQUENCE_VARIANT.equals(feature1))
  70       {
  71         return -1;
  72       }
  73       if (SEQUENCE_VARIANT.equals(feature2))
  74       {
  75         return +1;
  76       }
  77       if (EXON.equals(feature1))
  78       {
  79         return -1;
  80       }
  81       if (EXON.equals(feature2))
  82       {
  83         return +1;
  84       }
  85       return 0;
  86     }
  87
  88     @Override
  89     public boolean optimiseOrder()
  90     {
  91       return false;
  92     };
  93
  94   };
  95
  96   // SequenceOntologyI.SEQUENCE_VARIANT
  97   private static final String SEQUENCE_VARIANT = "sequence_variant";
  98
  99   // SequenceOntologyI.EXON
 100   private static final String EXON = "exon";
 101 }