From 879293251d1072b24403df2f4bf3ac6a69d4a012 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Mon, 24 Nov 2014 16:07:45 +0000
Subject: [PATCH] JAL-1593 refactor rna helix colours to static singleton for
 consistent shading

---
 src/jalview/schemes/AnnotationColourGradient.java |   33 ++-------------------
 src/jalview/schemes/ColourSchemeProperty.java     |   29 ++++++++++++++++++
 2 files changed, 32 insertions(+), 30 deletions(-)

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index ef77e4d..3cada8b 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -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);
       }
     }
   }
@@ -331,7 +304,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
               {
                 if (annotation.isRNA())
                 {
-                  currentColour = rnaHelices[(int) aj.value];
+                  currentColour = ColourSchemeProperty.rnaHelices[(int) aj.value];
                 }
                 else
                 {
diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index cc303d6..57a2dd9 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -597,4 +597,33 @@ public class ColourSchemeProperty
 
     return col;
   }
+
+  public static Color rnaHelices[] = null;
+
+  public static 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);
+    }
+  }
+
 }
-- 
1.7.10.2