Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

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

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index a84ea52..764bb12 100755 (executable)
--- 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
@@ -461,7 +461,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
     {
       range = ann.graphMax == ann.threshold.value ? 1f
               : (value - ann.threshold.value)
-              / (ann.graphMax - ann.threshold.value);
+                      / (ann.graphMax - ann.threshold.value);
     }
     else if (thresholdIsMinMax && ann.threshold != null
             && aboveAnnotationThreshold == BELOW_THRESHOLD
@@ -545,4 +545,14 @@ public class AnnotationColourGradient extends FollowerColourScheme
   {
     return false;
   }
+
+  public boolean isPositionToTransparency()
+  {
+    return positionToTransparency;
+  }
+
+  public void setPositionToTransparency(boolean positionToTransparency)
+  {
+    this.positionToTransparency = positionToTransparency;
+  }
 }