Merge branch 'JAL-1139_proguard' into Release_2_8_Branch

[jalview.git] / src / jalview / schemes / ResidueColourScheme.java

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 90833c9..3f18595 100755 (executable)
--- 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 
@@ -20,10 +20,12 @@ package jalview.schemes;
 import jalview.analysis.AAFrequency;
 import jalview.analysis.Conservation;
 import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
 import java.util.Hashtable;
+import java.util.Map;
 
 /**
  * DOCUMENT ME!
@@ -33,6 +35,7 @@ import java.util.Hashtable;
  */
 public class ResidueColourScheme implements ColourSchemeI
 {
+  final int[] symbolIndex;
 
   boolean conservationColouring = false;
 
@@ -57,22 +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;
   }
 
   /**
@@ -80,8 +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
@@ -89,9 +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
     {
@@ -105,7 +123,6 @@ public class ResidueColourScheme implements ColourSchemeI
 
     return currentColour;
   }
-  @Override public void alignmentChanged(AnnotatedCollectionI alignment) {};
 
   /**
    * Get the percentage threshold for this colour scheme
@@ -282,4 +299,10 @@ public class ResidueColourScheme implements ColourSchemeI
     return currentColour;
   }
 
+  @Override
+  public void alignmentChanged(AnnotatedCollectionI alignment,
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
+  {
+  }
+
 }