Merge branch 'releases/Release_2_11_3_Branch'

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

diff --git a/src/jalview/schemes/RNAInteractionColourScheme.java b/src/jalview/schemes/RNAInteractionColourScheme.java
index f4c831a..8610417 100644 (file)
--- a/src/jalview/schemes/RNAInteractionColourScheme.java
+++ b/src/jalview/schemes/RNAInteractionColourScheme.java
@@ -20,12 +20,11 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 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
 {
@@ -45,25 +44,12 @@ public class RNAInteractionColourScheme extends ResidueColourScheme
   public Color findColour(char c, int j, SequenceI seq)
   {
     // FIXME this is just a copy of NucleotideColourScheme
-    Color currentColour;
-    if ((threshold == 0) || aboveThreshold(c, j))
+    Color currentColour = Color.white;
+    try
     {
-      try
-      {
-        currentColour = colors[ResidueProperties.nucleotideIndex[c]];
-      } catch (Exception ex)
-      {
-        return Color.white;
-      }
-    }
-    else
-    {
-      return Color.white;
-    }
-
-    if (conservationColouring)
+      currentColour = colors[ResidueProperties.nucleotideIndex[c]];
+    } catch (Exception ex)
     {
-      currentColour = applyConservation(currentColour, j);
     }
 
     return currentColour;
@@ -86,8 +72,8 @@ public class RNAInteractionColourScheme extends ResidueColourScheme
    * be coloured
    */
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
-          Map<SequenceI, SequenceCollectionI> hrs)
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll)
   {
     return new RNAInteractionColourScheme();
   }