X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;fp=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=85266840c3b454a9bef1616941b10eed3f1f98d3;hb=b207001ceedbf3b9d343ce1941226575da7974d2;hp=a84ea52aa5d5a0452ea5d231e63c84fec054b1ca;hpb=327b70fcc535cee0098b53ebf928f453481be9d1;p=jalview.git

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index a84ea52..8526684 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -40,12 +40,12 @@ public class AnnotationColourGradient extends FollowerColourScheme
   /**
    * map positional scores to transparency rather than colour
    */
-  boolean positionToTransparency = true;
+  boolean positionToTransparency = false;
 
   /**
    * compute shade based on annotation row score
    */
-  boolean perLineScore = true;
+  boolean perLineScore = false;
 
   public static final int NO_THRESHOLD = -1;
 
@@ -245,7 +245,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
       }
       if (plcount > 0 && plcount == ancount)
       {
-        perLineScore = plcount == ancount;
+        perLineScore = plmax!=plmin;
         aamax=plmax;
       }
       else
@@ -545,4 +545,14 @@ public class AnnotationColourGradient extends FollowerColourScheme
   {
     return false;
   }
+
+  public boolean isPositionToTransparency()
+  {
+    return positionToTransparency;
+  }
+
+  public void setPositionToTransparency(boolean positionToTransparency)
+  {
+    this.positionToTransparency = positionToTransparency;
+  }
 }