JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / schemes / AnnotationColourGradient.java

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index efad430..89b8f07 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -53,12 +53,14 @@ public class AnnotationColourGradient extends FollowerColourScheme
   private boolean predefinedColours = false;
 
   private boolean seqAssociated = false;
+
   /**
    * false if the scheme was constructed without a minColour and maxColour used
    * to decide if existing colours should be taken from annotation elements when
    * they exist
    */
   private boolean noGradient = false;
+
   IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
 
   @Override
@@ -114,6 +116,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
     bb = 0;
 
     noGradient = true;
+    checkLimits();
   }
 
   /**
@@ -140,10 +143,17 @@ public class AnnotationColourGradient extends FollowerColourScheme
     bb = maxColour.getBlue() - b1;
 
     noGradient = false;
+    checkLimits();
+  }
+
+  private void checkLimits()
+  {
     aamax = annotation.graphMax;
     aamin = annotation.graphMin;
     if (annotation.isRNA())
     {
+      // reset colour palette
+      ColourSchemeProperty.resetRnaHelicesShading();
       ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
     }
   }
@@ -167,7 +177,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
       // resolve the context containing all the annotation for the sequence
       AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
               : alignment.getContext();
-      boolean f = true,rna=false;
+      boolean f = true, rna = false;
       for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation
               .getCalcId()))
       {
@@ -199,6 +209,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
   }
 
   float aamin = 0f, aamax = 0f;
+
   public String getAnnotation()
   {
     return annotation.label;
@@ -258,8 +269,8 @@ public class AnnotationColourGradient extends FollowerColourScheme
   public Color findColour(char c, int j, SequenceI seq)
   {
     Color currentColour = Color.white;
-    AlignmentAnnotation annotation = (seqAssociated ? seqannot.get(seq)
-            : this.annotation);
+    AlignmentAnnotation annotation = (seqAssociated && seqannot != null ? seqannot
+            .get(seq) : this.annotation);
     if (annotation == null)
     {
       return currentColour;
@@ -388,6 +399,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
     return new Color(dr, dg, db);
 
   }
+
   public boolean isPredefinedColours()
   {
     return predefinedColours;