From 7fef0501bb64f11080bdb93ee0824416d84784cc Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Sat, 5 Sep 2015 10:24:36 +0100
Subject: [PATCH 1/1] JAL-1233 tidy up and use same RNA helix colours in
 colour by annotation and RNA helix colouring

---
 src/jalview/schemes/RNAHelicesColour.java |   35 ++++++++---------------------
 1 file changed, 9 insertions(+), 26 deletions(-)

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index 5518f8f..74cc803 100644
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -40,16 +40,12 @@ import java.util.Map;
 public class RNAHelicesColour extends ResidueColourScheme
 {
 
-  /**
-   * Stores random colors generated for the number of helices
-   */
-  public Hashtable helixcolorhash = new Hashtable();
 
   /**
    * Maps sequence positions to the RNA helix they belong to. Key: position,
-   * Value: helix
+   * Value: helix TODO: Revise or drop in favour of annotation position numbers
    */
-  public Hashtable positionsToHelix = new Hashtable();
+  public Hashtable<Integer, String> positionsToHelix = new Hashtable<Integer, String>();
 
   /**
    * Number of helices in the RNA secondary structure
@@ -82,7 +78,6 @@ public class RNAHelicesColour extends ResidueColourScheme
   public RNAHelicesColour(RNAHelicesColour rnaHelicesColour)
   {
     super(ResidueProperties.nucleotideIndex);
-    helixcolorhash = rnaHelicesColour.helixcolorhash;
     annotation = rnaHelicesColour.annotation;
     refresh();
   }
@@ -123,7 +118,7 @@ public class RNAHelicesColour extends ResidueColourScheme
       annotation.getRNAStruc();
       lastrefresh = annotation._rnasecstr.hashCode();
       numHelix = 0;
-      positionsToHelix = new Hashtable();
+      positionsToHelix = new Hashtable<Integer, String>();
 
       // Figure out number of helices
       // Length of rnasecstr is the number of pairs of positions that base pair
@@ -150,16 +145,7 @@ public class RNAHelicesColour extends ResidueColourScheme
         }
 
       }
-
-      // Generate random colors and store
-      for (int j = 0; j <= numHelix; j++)
-      {
-        if (!helixcolorhash.containsKey(Integer.toString(j)))
-        {
-          helixcolorhash.put(Integer.toString(j),
-                  jalview.util.ColorUtils.generateRandomColor(Color.white));
-        }
-      }
+      ColourSchemeProperty.initRnaHelicesShading(numHelix);
     }
   }
 
@@ -186,7 +172,7 @@ public class RNAHelicesColour extends ResidueColourScheme
    * @param c
    *          Character in sequence
    * @param j
-   *          Threshold
+   *          position in sequence - used to locate helix
    * 
    * @return Color in RGB
    */
@@ -196,15 +182,12 @@ public class RNAHelicesColour extends ResidueColourScheme
     refresh();
     Color currentColour = Color.white;
     String currentHelix = null;
-    currentHelix = (String) positionsToHelix.get(j);
-
+    currentHelix = positionsToHelix.get(j);
     if (currentHelix != null)
     {
-      currentColour = (Color) helixcolorhash.get(currentHelix);
+      currentColour = ColourSchemeProperty.rnaHelices[Integer
+              .parseInt(currentHelix)];
     }
-
-    // System.out.println(c + " " + j + " helix " + currentHelix + " " +
-    // currentColour);
     return currentColour;
   }
 
@@ -214,4 +197,4 @@ public class RNAHelicesColour extends ResidueColourScheme
   {
     return new RNAHelicesColour(this);
   }
-}
+}
\ No newline at end of file
-- 
1.7.10.2