X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=5461ec0ff1b5a3c26045e7e6d5c6baa64aa158f1;hb=595a9e25db7f4f24c17de84656d7d5391a3d104d;hp=5e48fc48c1fd3c89cc7ffc7c95ccd7d1529052b4;hpb=62babeb3c6572d8f11e64292febf1e6a382f1fca;p=jalview.git

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 5e48fc4..5461ec0 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);
@@ -166,8 +167,8 @@ public class AnnotationColourGradient extends FollowerColourScheme
     if (annotation.isRNA())
     {
       // reset colour palette
-      ColourSchemeProperty.resetRnaHelicesShading();
-      ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
+      ColourSchemes.resetRnaHelicesShading();
+      ColourSchemes.initRnaHelicesShading(1 + (int) aamax);
     }
   }
 
@@ -217,7 +218,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
       }
       if (rna)
       {
-        ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
+        ColourSchemes.initRnaHelicesShading(1 + (int) aamax);
       }
     }
   }
@@ -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;
       }
@@ -354,7 +355,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
         {
           if (ann.isRNA())
           {
-            result = ColourSchemeProperty.rnaHelices[(int) aj.value];
+            result = ColourSchemes.getInstance().rnaHelices[(int) aj.value];
           }
           else
           {
@@ -414,14 +415,17 @@ public class AnnotationColourGradient extends FollowerColourScheme
             && aboveAnnotationThreshold == ABOVE_THRESHOLD
             && value >= ann.threshold.value)
     {
-      range = (value - ann.threshold.value)
+      range = ann.graphMax == ann.threshold.value ? 1f
+              : (value - ann.threshold.value)
               / (ann.graphMax - ann.threshold.value);
     }
     else if (thresholdIsMinMax && ann.threshold != null
             && aboveAnnotationThreshold == BELOW_THRESHOLD
             && value <= ann.threshold.value)
     {
-      range = (value - ann.graphMin) / (ann.threshold.value - ann.graphMin);
+      range = ann.graphMin == ann.threshold.value ? 0f
+              : (value - ann.graphMin)
+                      / (ann.threshold.value - ann.graphMin);
     }
     else
     {