javadoc

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

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index f50ac0a..a7f2311 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -17,7 +17,7 @@
  */
 package jalview.schemes;
 
-import java.awt.*;
+import java.awt.Color;
 
 /**
  * ColourSchemeProperty Binds names to hardwired colourschemes and tries to deal
@@ -81,6 +81,9 @@ public class ColourSchemeProperty
   public static final int PURINEPYRIMIDINE = 13;
 
   public static final int COVARIATION = 14;
+  
+  public static final int TCOFFEE = 15;
+  
 
   /**
    * index of first colourscheme (includes 'None')
@@ -145,6 +148,11 @@ public class ColourSchemeProperty
     {
       ret = NUCLEOTIDE;
     }
+    else if (name.equalsIgnoreCase("T-Coffee scores"))
+    {
+      ret = TCOFFEE;
+    }
+
     else if (name.equalsIgnoreCase("User Defined"))
     {
       ret = USER_DEFINED;
@@ -375,20 +383,21 @@ public class ColourSchemeProperty
   }
 
   /**
-   * DOCUMENT ME!
+   * Construct an instance of ColourSchemeI corresponding to the given colourscheme index
    * 
    * @param seqs
-   *          DOCUMENT ME!
+   *          sequences to be coloured by colourscheme
    * @param width
-   *          DOCUMENT ME!
+   *          geometry of alignment
    * @param index
-   *          DOCUMENT ME!
+   *          colourscheme number 
    * 
-   * @return DOCUMENT ME!
+   * @return null or an instance of the colourscheme configured to colour given sequence set
    */
   public static ColourSchemeI getColour(java.util.Vector seqs, int width,
           int index)
   {
+    // TODO 3.0 2.8 refactor signature to take an alignmentI like container so colourschemes based on annotation can be initialised
     ColourSchemeI cs = null;
 
     switch (index)