JAL-1683 replace year/version strings with tokens in source

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

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index ef77e4d..121d6ca 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.
  * 
@@ -53,33 +53,6 @@ public class AnnotationColourGradient extends FollowerColourScheme
   private boolean predefinedColours = false;
 
   private boolean seqAssociated = false;
-  Color rnaHelices[] = null;
-  private void initRnaHelicesShading(int n)
-  {
-    int j = 0;
-    if (rnaHelices==null) 
-    {
-      rnaHelices = new Color[n + 1];
-    }
-    else
-    if (rnaHelices != null && rnaHelices.length <= n)
-    {
-      Color[] t = new Color[n + 1];
-      System.arraycopy(rnaHelices, 0, t, 0, rnaHelices.length);
-      j = rnaHelices.length;
-      rnaHelices = t;
-    }
-    else
-    {
-      return;
-    }
-    // Generate random colors and store
-    for (; j <= n; j++)
-    {
-      rnaHelices[j] = jalview.util.ColorUtils
-              .generateRandomColor(Color.white);
-    }
-  }
   /**
    * false if the scheme was constructed without a minColour and maxColour used
    * to decide if existing colours should be taken from annotation elements when
@@ -171,7 +144,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
     aamin = annotation.graphMin;
     if (annotation.isRNA())
     {
-      initRnaHelicesShading(1 + (int) aamax);
+      ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
     }
   }
 
@@ -220,7 +193,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
       }
       if (rna)
       {
-        initRnaHelicesShading(1 + (int) aamax);
+        ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
       }
     }
   }
@@ -285,7 +258,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
   public Color findColour(char c, int j, SequenceI seq)
   {
     Color currentColour = Color.white;
-    AlignmentAnnotation annotation = (seqAssociated ? seqannot.get(seq)
+    AlignmentAnnotation annotation = (seqAssociated && seqannot!=null ? seqannot.get(seq)
             : this.annotation);
     if (annotation == null)
     {
@@ -313,7 +286,8 @@ public class AnnotationColourGradient extends FollowerColourScheme
                 || (annotationThreshold != null && (aboveAnnotationThreshold == ABOVE_THRESHOLD ? aj.value >= annotationThreshold.value
                         : aj.value <= annotationThreshold.value)))
         {
-          if (predefinedColours && aj.colour != null)
+          if (predefinedColours && aj.colour != null
+                  && !aj.colour.equals(Color.black))
           {
             currentColour = aj.colour;
           }
@@ -331,7 +305,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
               {
                 if (annotation.isRNA())
                 {
-                  currentColour = rnaHelices[(int) aj.value];
+                  currentColour = ColourSchemeProperty.rnaHelices[(int) aj.value];
                 }
                 else
                 {