X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=f13a90cfa84961c1103314ecb6ea341040a6c0a9;hb=41644b7b7ef2179b8568c2b528df4d10a00eb790;hp=9c0b9534ffed69e3a339ab9dc1bb39ffd9b9b7b9;hpb=f831ddf7f52d6c4a1918e87d94877b22bd322648;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 9c0b953..f13a90c 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -23,6 +23,7 @@ package jalview.schemes;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.util.List;
@@ -276,23 +277,22 @@ 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;
-
-    if (cons2.length <= j
-            || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
+    // TODO why the test for includeGaps here?
+    if (cons2.length <= j || Comparison.isGap(c)
+    /*|| (includeGaps && threshold != 0 && !aboveThreshold(c, j))*/)
     {
       return Color.white;
     }
 
     int i = ResidueProperties.aaIndex[c];
 
-    currentColour = Color.white;
+    Color colour = Color.white;
 
     if (i > 19)
     {
-      return currentColour;
+      return colour;
     }
 
     for (int k = 0; k < residueColour[i].cons.length; k++)
@@ -300,27 +300,22 @@ public class ClustalxColourScheme extends ResidueColourScheme
       if (residueColour[i].cons[k].isConserved(cons2, j, size,
               includeGaps))
       {
-        currentColour = residueColour[i].c;
+        colour = residueColour[i].c;
       }
     }
 
     if (i == 4)
     {
       /*
-       * override to colour C pink if 100% conserved
+       * override to colour C pink if >85% conserved
        */
       if (conses[27].isConserved(cons2, j, size, includeGaps))
       {
-        currentColour = ClustalColour.PINK.colour;
+        colour = ClustalColour.PINK.colour;
       }
     }
 
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
-
-    return currentColour;
+    return colour;
   }
 
   /**