JAL-1705 align CDS and peptide products to transcripts

[jalview.git] / src / jalview / schemes / FeatureColourScheme.java

diff --git a/src/jalview/schemes/FeatureColourScheme.java b/src/jalview/schemes/FeatureColourScheme.java
deleted file mode 100644 (file)
index 308495c..0000000
--- a/src/jalview/schemes/FeatureColourScheme.java
+++ /dev/null
@@ -1,109 +0,0 @@
-package jalview.schemes;
-
-import jalview.api.FeatureColourI;
-import jalview.api.FeatureSettingsI;
-
-import java.awt.Color;
-
-/**
- * Pre-set configurations for feature settings
- * 
- * @author gmcarstairs
- *
- */
-public enum FeatureColourScheme implements FeatureSettingsI
-{
-  /**
-   * Show sequence variants in red, on top of exons coloured by label
-   */
-  EnsemblVariants
-  {
-
-    @Override
-    public boolean isFeatureDisplayed(String type)
-    {
-      // TODO accept SO sub-types of these features
-      // if (SequenceOntologyFactory.getInstance().isA(SequenceOntologyI.EXON...
-      return (EXON.equals(type) || SEQUENCE_VARIANT.equals(type));
-    }
-
-    @Override
-    public boolean isGroupDisplayed(String group)
-    {
-      return true;
-    }
-
-    @Override
-    public FeatureColourI getFeatureColour(String type)
-    {
-      if (EXON.equals(type))
-      {
-        return new FeatureColourAdapter()
-        {
-          @Override
-          public boolean isColourByLabel()
-          {
-            return true;
-          }
-        };
-      }
-      if (SEQUENCE_VARIANT.equals(type))
-      {
-        return new FeatureColourAdapter()
-        {
-
-          @Override
-          public Color getColour()
-          {
-            return Color.RED;
-          }
-        };
-      }
-      return null;
-    }
-
-    @Override
-    public float getTransparency()
-    {
-      return 1f;
-    }
-
-    /**
-     * order to render sequence_variant after exon after the rest
-     */
-    @Override
-    public int compare(String feature1, String feature2)
-    {
-      if (SEQUENCE_VARIANT.equals(feature1))
-      {
-        return +1;
-      }
-      if (SEQUENCE_VARIANT.equals(feature2))
-      {
-        return -1;
-      }
-      if (EXON.equals(feature1))
-      {
-        return +1;
-      }
-      if (EXON.equals(feature2))
-      {
-        return -1;
-      }
-      return 0;
-    }
-
-    @Override
-    public boolean optimiseOrder()
-    {
-      return false;
-    };
-
-  };
-
-  // SequenceOntologyI.SEQUENCE_VARIANT
-  private static final String SEQUENCE_VARIANT = "sequence_variant";
-
-  // SequenceOntologyI.EXON
-  private static final String EXON = "exon";
-}