X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=3f18595a3d804fa29576e4c642c24d4ce0b93f98;hb=f6b39bebb91c2b69c1e5c572e7aa116e5ab19864;hp=bbba8654713a29ee46aa9174b58b69311ed9d7e0;hpb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index bbba865..3f18595 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -35,6 +35,7 @@ import java.util.Map;
  */
 public class ResidueColourScheme implements ColourSchemeI
 {
+  final int[] symbolIndex;
 
   boolean conservationColouring = false;
 
@@ -59,22 +60,37 @@ public class ResidueColourScheme implements ColourSchemeI
   /**
    * Creates a new ResidueColourScheme object.
    * 
+   * @param final int[] index table into colors (ResidueProperties.naIndex or
+   *        ResidueProperties.aaIndex)
    * @param colors
-   *          DOCUMENT ME!
+   *          colours for symbols in sequences
    * @param threshold
-   *          DOCUMENT ME!
+   *          threshold for conservation shading
    */
-  public ResidueColourScheme(Color[] colours, int threshold)
+  public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours,
+          int threshold)
   {
+    symbolIndex = aaOrnaIndex;
     this.colors = colours;
     this.threshold = threshold;
   }
 
   /**
-   * Creates a new ResidueColourScheme object.
+   * Creates a new ResidueColourScheme object with a lookup table for indexing
+   * the colour map
+   */
+  public ResidueColourScheme(int[] aaOrNaIndex)
+  {
+    symbolIndex = aaOrNaIndex;
+  }
+
+  /**
+   * Creates a new ResidueColourScheme object - default constructor for
+   * non-sequence dependent colourschemes
    */
   public ResidueColourScheme()
   {
+    symbolIndex = null;
   }
 
   /**
@@ -82,8 +98,7 @@ public class ResidueColourScheme implements ColourSchemeI
    */
   public Color findColour(char c)
   {
-    return colors == null ? Color.white
-            : colors[ResidueProperties.aaIndex[c]];
+    return colors == null ? Color.white : colors[symbolIndex[c]];
   }
 
   @Override
@@ -91,9 +106,10 @@ public class ResidueColourScheme implements ColourSchemeI
   {
     Color currentColour;
 
-    if ((threshold == 0) || aboveThreshold(c, j))
+    if (colors != null && symbolIndex != null && (threshold == 0)
+            || aboveThreshold(c, j))
     {
-      currentColour = colors[ResidueProperties.aaIndex[c]];
+      currentColour = colors[symbolIndex[c]];
     }
     else
     {
@@ -107,6 +123,7 @@ public class ResidueColourScheme implements ColourSchemeI
 
     return currentColour;
   }
+
   /**
    * Get the percentage threshold for this colour scheme
    *