JAL-2371 CollectionColourScheme wraps ColourSchemeI

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

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 9c0b953..49260a4 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -276,12 +276,13 @@ public class ClustalxColourScheme extends ResidueColourScheme
   }
 
   @Override
-  public Color findColour(char c, int j, SequenceI seq)
+  protected Color findColour(char c, int j, SequenceI seq)
   {
     Color currentColour;
 
+    // TODO why the test for includeGaps here?
     if (cons2.length <= j
-            || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
+    /*|| (includeGaps && threshold != 0 && !aboveThreshold(c, j))*/)
     {
       return Color.white;
     }
@@ -315,11 +316,6 @@ public class ClustalxColourScheme extends ResidueColourScheme
       }
     }
 
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
-
     return currentColour;
   }