JAL-1114 - refactor methods handling Vectors and Hashtables to Lists and Maps, and...

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

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index e7c7935..4c7b49d 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 2.7)
- * 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.
  * 
@@ -17,7 +17,9 @@
  */
 package jalview.schemes;
 
-import java.awt.*;
+import jalview.datamodel.AnnotatedCollectionI;
+
+import java.awt.Color;
 
 /**
  * ColourSchemeProperty Binds names to hardwired colourschemes and tries to deal
@@ -81,6 +83,9 @@ 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 +150,11 @@ public class ColourSchemeProperty
     {
       ret = NUCLEOTIDE;
     }
+    else if (name.equalsIgnoreCase("T-Coffee scores"))
+    {
+      ret = TCOFFEE;
+    }
+
     else if (name.equalsIgnoreCase("User Defined"))
     {
       ret = USER_DEFINED;
@@ -334,26 +344,9 @@ public class ColourSchemeProperty
 
     return ret;
   }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param al
-   *          DOCUMENT ME!
-   * @param name
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al,
-          String name)
-  {
-    return getColour(al.getSequences(), al.getWidth(), name);
-  }
-
   /**
    * retrieve or create colourscheme associated with name
-   * 
+   *
    * @param seqs
    *          sequences to colour
    * @param width
@@ -363,7 +356,7 @@ public class ColourSchemeProperty
    *          string to parse as colour for new coloursheme
    * @return Valid Colourscheme
    */
-  public static ColourSchemeI getColour(java.util.Vector seqs, int width,
+  public static ColourSchemeI getColour(AnnotatedCollectionI alignment,
           String name)
   {
     int colindex = getColourIndexFromName(name);
@@ -396,30 +389,30 @@ public class ColourSchemeProperty
         }
       }
     }
-    return getColour(seqs, width, getColourIndexFromName(name));
+    return getColour(alignment, getColourIndexFromName(name));
   }
 
   /**
-   * 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)
+  public static ColourSchemeI getColour(jalview.datamodel.AnnotatedCollectionI coll, 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)
     {
     case CLUSTAL:
-      cs = new ClustalxColourScheme(seqs, width);
+      cs = new ClustalxColourScheme(coll, null);
 
       break;