X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=47dbde222727b8ab304257cd5b2c79b7b25c7910;hb=59d682209891099d46b960509907c79e3fb276fe;hp=45dd6d1aac11790c76f0a8e66e52843a1887f2c9;hpb=323a457c9d0643be2406b6661246e8e988c0d0f6;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 45dd6d1..47dbde2 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,13 +1,13 @@
 /*
- * 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 2.8)
+ * 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 
@@ -17,10 +17,12 @@
  */
 package jalview.schemes;
 
-import java.awt.*;
+import jalview.datamodel.AnnotatedCollectionI;
+
+import java.awt.Color;
 
 /**
- * ColourSchemeProperty Binds names to hardwired colourschemes and tries to deal
+ * ColourSchemeProperty binds names to hardwired colourschemes and tries to deal
  * intelligently with mapping unknown names to user defined colourschemes (that
  * exist or can be created from the string representation of the colourscheme
  * name - either a hex RGB triplet or a named colour under java.awt.color ). The
@@ -82,6 +84,8 @@ public class ColourSchemeProperty
 
   public static final int COVARIATION = 14;
 
+  public static final int TCOFFEE = 15;
+
   /**
    * index of first colourscheme (includes 'None')
    */
@@ -145,6 +149,11 @@ public class ColourSchemeProperty
     {
       ret = NUCLEOTIDE;
     }
+    else if (name.equalsIgnoreCase("T-Coffee Scores"))
+    {
+      ret = TCOFFEE;
+    }
+
     else if (name.equalsIgnoreCase("User Defined"))
     {
       ret = USER_DEFINED;
@@ -226,6 +235,10 @@ public class ColourSchemeProperty
     {
       index = PURINEPYRIMIDINE;
     }
+    else if (cs instanceof TCoffeeColourScheme)
+    {
+      index = TCOFFEE;
+    }
     /*
      * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
      */
@@ -316,6 +329,10 @@ public class ColourSchemeProperty
 
       break;
 
+    case TCOFFEE:
+      ret = "T-Coffee Scores";
+
+      break;
     /*
      * case COVARIATION: ret = "Covariation";
      * 
@@ -336,22 +353,6 @@ public class ColourSchemeProperty
   }
 
   /**
-   * 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
@@ -363,7 +364,7 @@ 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 +397,34 @@ 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;
 
@@ -477,10 +482,12 @@ public class ColourSchemeProperty
 
       break;
 
-    // case COVARIATION:
-    // cs = new CovariationColourScheme(annotation);
+    case TCOFFEE:
+      cs = new TCoffeeColourScheme(coll);
+      // case COVARIATION:
+      // cs = new CovariationColourScheme(annotation);
 
-    // break;
+      // break;
 
     case USER_DEFINED:
       Color[] col = new Color[24];