JAL-1432 updated copyright notices

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

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 5402d75..943d2fa 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,27 +1,32 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * 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 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.schemes;
 
-import java.util.*;
-
-import java.awt.*;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
 
-import jalview.analysis.*;
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.Map;
 
 /**
  * DOCUMENT ME!
@@ -31,6 +36,7 @@ import jalview.analysis.*;
  */
 public class ResidueColourScheme implements ColourSchemeI
 {
+  final int[] symbolIndex;
 
   boolean conservationColouring = false;
 
@@ -55,22 +61,37 @@ 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;
   }
 
   /**
@@ -78,17 +99,18 @@ 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]];
   }
 
-  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
     {
@@ -278,4 +300,10 @@ public class ResidueColourScheme implements ColourSchemeI
     return currentColour;
   }
 
+  @Override
+  public void alignmentChanged(AnnotatedCollectionI alignment,
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
+  {
+  }
+
 }