X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=f467cb8c108777d95ace28bd4ca5fdebabc08e12;hb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;hp=e6128c9a6dcf541ce256e17b5e056044016956e8;hpb=1889827c44c51f6353fe8619e5d44b421158af23;p=jalview.git

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index e6128c9..f467cb8 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -54,13 +54,16 @@ public class AnnotationColourGradient extends FollowerColourScheme
   private boolean seqAssociated = false;
 
   IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
+
   @Override
   public ColourSchemeI applyTo(AnnotatedCollectionI sg,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
-    AnnotationColourGradient acg = new AnnotationColourGradient(annotation, colourScheme, aboveAnnotationThreshold);
+    AnnotationColourGradient acg = new AnnotationColourGradient(annotation,
+            colourScheme, aboveAnnotationThreshold);
     acg.thresholdIsMinMax = thresholdIsMinMax;
-    acg.annotationThreshold = (annotationThreshold==null) ? null : new GraphLine(annotationThreshold);
+    acg.annotationThreshold = (annotationThreshold == null) ? null
+            : new GraphLine(annotationThreshold);
     acg.r1 = r1;
     acg.g1 = g1;
     acg.b1 = b1;
@@ -72,9 +75,10 @@ public class AnnotationColourGradient extends FollowerColourScheme
     acg.db = db;
     acg.predefinedColours = predefinedColours;
     acg.seqAssociated = seqAssociated;
-    
+
     return acg;
   }
+
   /**
    * Creates a new AnnotationColourGradient object.
    */
@@ -141,7 +145,8 @@ public class AnnotationColourGradient extends FollowerColourScheme
         seqannot = new IdentityHashMap<SequenceI, AlignmentAnnotation>();
       }
       // resolve the context containing all the annotation for the sequence
-      AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment : alignment.getContext();
+      AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
+              : alignment.getContext();
       for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation
               .getCalcId()))
       {
@@ -222,7 +227,8 @@ public class AnnotationColourGradient extends FollowerColourScheme
     }
     if ((threshold == 0) || aboveThreshold(c, j))
     {
-      if (annotation.annotations!=null && j < annotation.annotations.length
+      if (annotation.annotations != null
+              && j < annotation.annotations.length
               && annotation.annotations[j] != null
               && !jalview.util.Comparison.isGap(c))
       {
@@ -268,7 +274,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
           {
             currentColour = colourScheme.findColour(c, j, seq);
           }
-          else 
+          else
           {
             dr = rr * range + r1;
             dg = gg * range + g1;