JAL-1136 give pre-existing custom settings a special name when job parameter settings...

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

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 5402d75..666834e 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -17,11 +17,15 @@
  */
 package jalview.schemes;
 
-import java.util.*;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
 
-import java.awt.*;
-
-import jalview.analysis.*;
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.Map;
 
 /**
  * DOCUMENT ME!
@@ -31,7 +35,7 @@ import jalview.analysis.*;
  */
 public class ResidueColourScheme implements ColourSchemeI
 {
-
+  final int[] symbolIndex;
   boolean conservationColouring = false;
 
   Color[] colors = null;
@@ -54,23 +58,32 @@ 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;
   }
 
   /**
@@ -79,16 +92,17 @@ public class ResidueColourScheme implements ColourSchemeI
   public Color findColour(char c)
   {
     return colors == null ? Color.white
-            : colors[ResidueProperties.aaIndex[c]];
+            : colors[symbolIndex[c]];
   }
 
-  public Color findColour(char c, int j)
+  @Override
+  public Color findColour(char c, int j, SequenceI seq)
   {
     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
     {
@@ -102,7 +116,6 @@ public class ResidueColourScheme implements ColourSchemeI
 
     return currentColour;
   }
-
   /**
    * Get the percentage threshold for this colour scheme
    * 
@@ -278,4 +291,10 @@ public class ResidueColourScheme implements ColourSchemeI
     return currentColour;
   }
 
+  @Override
+  public void alignmentChanged(AnnotatedCollectionI alignment,
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
+  {
+  }
+
 }