X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=57a2dd90e3b226dc97cdd3f62223ff3ffee66cd8;hb=373a0f23b37fdd3c40d3ebb4a3c9120f5773bb45;hp=385e080a1eb07c901200cb8b04ea21d3050a3bfa;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 385e080..57a2dd9 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -88,7 +88,7 @@ public class ColourSchemeProperty
   public static final int COVARIATION = 14;
 
   public static final int TCOFFEE = 15;
-  
+
   public static final int RNAHELIX = 16;
 
   public static final int RNAINTERACTION = 17;
@@ -352,11 +352,11 @@ public class ColourSchemeProperty
       ret = "T-Coffee Scores";
 
       break;
-      
+
     case RNAINTERACTION:
-        ret = "RNA Interaction type";
+      ret = "RNA Interaction type";
 
-        break;
+      break;
     case RNAHELIX:
       ret = "RNA Helices";
 
@@ -513,13 +513,13 @@ public class ColourSchemeProperty
     case TCOFFEE:
       cs = new TCoffeeColourScheme(coll);
       break;
-    
+
     case RNAHELIX:
       cs = new RNAHelicesColour(coll);
       break;
-      
-      // case COVARIATION:
-      // cs = new CovariationColourScheme(annotation);
+
+    // case COVARIATION:
+    // cs = new CovariationColourScheme(annotation);
     // break;
 
     case USER_DEFINED:
@@ -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);
+    }
+  }
+
 }