JAL-2446 merged to spike branch

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

diff --git a/src/jalview/schemes/RNAInteractionColourScheme.java b/src/jalview/schemes/RNAInteractionColourScheme.java
index 794195a..d236803 100644 (file)
--- a/src/jalview/schemes/RNAInteractionColourScheme.java
+++ b/src/jalview/schemes/RNAInteractionColourScheme.java
@@ -20,9 +20,12 @@
  */
 package jalview.schemes;
 
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
+import java.util.Map;
 
 public class RNAInteractionColourScheme extends ResidueColourScheme
 {
@@ -31,55 +34,48 @@ public class RNAInteractionColourScheme extends ResidueColourScheme
     super();
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param n
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
   @Override
   public Color findColour(char c)
   {
-    // System.out.println("called"); log.debug
+    // FIXME this is just a copy of NucleotideColourScheme
     return colors[ResidueProperties.nucleotideIndex[c]];
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param n
-   *          DOCUMENT ME!
-   * @param j
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
   @Override
   public Color findColour(char c, int j, SequenceI seq)
   {
-    Color currentColour;
-    if ((threshold == 0) || aboveThreshold(c, j))
+    // FIXME this is just a copy of NucleotideColourScheme
+    Color currentColour = Color.white;
+    try
     {
-      try
-      {
-        currentColour = colors[ResidueProperties.nucleotideIndex[c]];
-      } catch (Exception ex)
-      {
-        return Color.white;
-      }
-    }
-    else
+      currentColour = colors[ResidueProperties.nucleotideIndex[c]];
+    } catch (Exception ex)
     {
-      return Color.white;
-    }
-
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
     }
 
     return currentColour;
   }
+
+  @Override
+  public boolean isNucleotideSpecific()
+  {
+    return true;
+  }
+
+  @Override
+  public String getSchemeName()
+  {
+    return "RNA Interaction type";
+  }
+
+  /**
+   * Returns a new instance of this colour scheme with which the given data may
+   * be coloured
+   */
+  @Override
+  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+          Map<SequenceI, SequenceCollectionI> hrs)
+  {
+    return new RNAInteractionColourScheme();
+  }
 }