X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=789667e0b2d49296053fa319b45ff933ebf0b319;hb=0125a426aecc7065538a13f48236dc1e8d268044;hp=433af79e0be514b600ff4043963115c8f3aa1755;hpb=9b2d0f1f47d3a073c91f354775bea6a274812709;p=jalview.git

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 433af79..789667e 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -34,7 +34,31 @@ public class AnnotationColourGradient extends ResidueColourScheme
     GraphLine annotationThreshold;
 
     float r1, g1, b1, rr, gg, bb, dr, dg, db;
-    float range;
+    float range = 0;
+
+    ColourSchemeI colourScheme;
+
+    /**
+     * Creates a new AnnotationColourGradient object.
+     */
+    public AnnotationColourGradient(AlignmentAnnotation annotation,
+                                    ColourSchemeI originalColour,
+                                    int aboveThreshold)
+    {
+      if(originalColour instanceof AnnotationColourGradient)
+      {
+        colourScheme = ((AnnotationColourGradient)originalColour).colourScheme;
+      }
+      else
+        colourScheme = originalColour;
+
+      this.annotation = annotation;
+
+      aboveAnnotationThreshold = aboveThreshold;
+
+      if(aboveThreshold!=NO_THRESHOLD && annotation.threshold!=null)
+        annotationThreshold = annotation.threshold;
+    }
 
     /**
      * Creates a new AnnotationColourGradient object.
@@ -80,7 +104,6 @@ public class AnnotationColourGradient extends ResidueColourScheme
      */
     public Color findColour(String n)
     {
-      System.out.println("AnnotationColourGradient findColour(string)");
         return Color.red;
     }
 
@@ -94,36 +117,42 @@ public class AnnotationColourGradient extends ResidueColourScheme
      */
     public Color findColour(String n, int j)
     {
+        currentColour = Color.white;
+
         if ((threshold == 0) || aboveThreshold(n, j))
         {
-          if( j+1>annotation.annotations.length || annotation.annotations[j]==null)
-            currentColour = Color.white;
-          else
+          if( j<annotation.annotations.length
+              && annotation.annotations[j]!=null
+              && !jalview.util.Comparison.isGap(n.charAt(0)))
           {
             if(  aboveAnnotationThreshold==NO_THRESHOLD
                || (annotationThreshold!=null && aboveAnnotationThreshold==ABOVE_THRESHOLD && annotation.annotations[j].value>=annotationThreshold.value)
                || (annotationThreshold!=null && aboveAnnotationThreshold==BELOW_THRESHOLD && annotation.annotations[j].value<=annotationThreshold.value))
             {
+              if(colourScheme!=null)
+              {
+                currentColour = colourScheme.findColour(n, j);
+              }
+              else if(range!=0)
+              {
                 dr = rr *
-                     ((annotation.annotations[j].value-annotation.graphMin) / range )
-                     +r1;
+                    ( (annotation.annotations[j].value - annotation.graphMin) /
+                     range)
+                    + r1;
                 dg = gg *
-                     ((annotation.annotations[j].value-annotation.graphMin)  / range )
-                     +g1;
+                    ( (annotation.annotations[j].value - annotation.graphMin) /
+                     range)
+                    + g1;
                 db = bb *
-                     ((annotation.annotations[j].value-annotation.graphMin) / range )
-                     +b1;
+                    ( (annotation.annotations[j].value - annotation.graphMin) /
+                     range)
+                    + b1;
 
-                 currentColour = new Color( (int) dr, (int) dg, (int) db);
+                currentColour = new Color( (int) dr, (int) dg, (int) db);
+              }
             }
-            else
-              currentColour = Color.white;
           }
         }
-        else
-        {
-            return Color.white;
-        }
 
         if(conservationColouring)
          applyConservation(j);