X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=500047b1e554a1423a4a6cfaf04872716aa8bb8d;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=cc303d65e21308178bd79cd596701250d85897e8;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index cc303d6..500047b 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.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 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -597,4 +597,41 @@ 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);
+    }
+  }
+
+  /**
+   * delete the existing cached RNA helces colours
+   */
+  public static void resetRnaHelicesShading()
+  {
+    rnaHelices = null;
+  }
+
 }