X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=764bb123af78d0d05d7ae06ad8356e571d07d802;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=f646963e85aa5517e099b1af52e0c2e97f4798b4;hpb=9f70ff4b6d193b340031997634c9e3602486bc8e;p=jalview.git

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index f646963..764bb12 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;
@@ -39,12 +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;
 
@@ -86,8 +87,8 @@ 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);
@@ -197,7 +198,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
       }
       else
       {
-        seqannot = new IdentityHashMap<SequenceI, AlignmentAnnotation>();
+        seqannot = new IdentityHashMap<>();
       }
       // resolve the context containing all the annotation for the sequence
       AnnotatedCollectionI alcontext = alignment instanceof AlignmentI
@@ -244,9 +245,13 @@ public class AnnotationColourGradient extends FollowerColourScheme
       }
       if (plcount > 0 && plcount == ancount)
       {
-        perLineScore = plcount == ancount;
+        perLineScore = plmax!=plmin;
         aamax=plmax;
       }
+      else
+      {
+        perLineScore = false;
+      }
       if (rna)
       {
         ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
@@ -359,9 +364,9 @@ 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;
       }
@@ -454,14 +459,17 @@ public class AnnotationColourGradient extends FollowerColourScheme
             && aboveAnnotationThreshold == ABOVE_THRESHOLD
             && value >= ann.threshold.value)
     {
-      range = (value - ann.threshold.value)
-              / (ann.graphMax - 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
     {
@@ -480,11 +488,12 @@ public class AnnotationColourGradient extends FollowerColourScheme
     if (perLineScore)
     {
       trans = (int) ((1f - range) * midtr);
-      range = (float) ((annotation.score - plmin) / (plmax - aamin));
+      range = (float) ((ann.score - plmin) / (plmax - aamin));
     }
-    int dr = (int) (rr * range + r1), dg = (int) (gg * range + g1), db = (int) (bb
-            * range + b1);
-    if (annotation.score == annotation.score && positionToTransparency)
+    int dr = (int) (redRange * range + redMin),
+            dg = (int) (greenRange * range + greenMin),
+            db = (int) (blueRange * range + blueMin);
+    if (ann.score == ann.score && positionToTransparency)
     {
       return new Color(Math.min(dr + trans, midtr), Math.min(dg
               + trans, midtr), Math.min(db + trans, midtr));
@@ -528,7 +537,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
   @Override
   public String getSchemeName()
   {
-    return "Annotation";
+    return ANNOTATION_COLOUR;
   }
 
   @Override
@@ -536,4 +545,14 @@ public class AnnotationColourGradient extends FollowerColourScheme
   {
     return false;
   }
+
+  public boolean isPositionToTransparency()
+  {
+    return positionToTransparency;
+  }
+
+  public void setPositionToTransparency(boolean positionToTransparency)
+  {
+    this.positionToTransparency = positionToTransparency;
+  }
 }