X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=a390a15a23dbf0e6273c57fcc9ed5b33d4c5eea9;hb=2acaf6533dd61f649b4394082e0e600b7bc0f62d;hp=af306895bfa68210f6852eeae50973909ff7db8d;hpb=2a7635954a40451d363a03e71393bf558413ef1e;p=jalview.git

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index af30689..a390a15 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
@@ -76,8 +77,8 @@ public class AnnotationColourGradient extends FollowerColourScheme
   private IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
 
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI sg,
-          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI sg)
   {
     AnnotationColourGradient acg = new AnnotationColourGradient(annotation,
             getColourScheme(), aboveAnnotationThreshold);
@@ -319,9 +320,9 @@ public class AnnotationColourGradient extends FollowerColourScheme
     if (annotationThreshold != null)
     {
       if ((aboveAnnotationThreshold == ABOVE_THRESHOLD
-              && aj.value < annotationThreshold.value)
+              && aj.value <= annotationThreshold.value)
               || (aboveAnnotationThreshold == BELOW_THRESHOLD
-                      && aj.value > annotationThreshold.value))
+                      && aj.value >= annotationThreshold.value))
       {
         return Color.white;
       }
@@ -416,7 +417,7 @@ 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