From 3b5139b9b736abd652bcd00228a0e85fd8f85615 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Wed, 30 May 2012 19:28:07 +0100
Subject: [PATCH] JAL-1109 JAL-1065 resolve t-coffee score scheme by name

---
 src/jalview/schemes/ColourSchemeProperty.java |   56 +++++++++++++++----------
 1 file changed, 33 insertions(+), 23 deletions(-)

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 4c7b49d..1e2db76 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,18 +1,18 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 
+ * 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 
+ *
+ * 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/>.
  */
 package jalview.schemes;
@@ -22,14 +22,14 @@ 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
  * values of the colourscheme constants is important for callers of
  * getColourName(int i), since it can be used to enumerate the set of built in
  * colours. The FIRST_COLOUR and LAST_COLOUR symbols are provided for this.
- * 
+ *
  * @author $author$
  * @version $Revision$
  */
@@ -83,9 +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')
@@ -96,10 +96,10 @@ public class ColourSchemeProperty
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param name
    *          DOCUMENT ME!
-   * 
+   *
    * @return DOCUMENT ME!
    */
   public static int getColourIndexFromName(String name)
@@ -150,7 +150,7 @@ public class ColourSchemeProperty
     {
       ret = NUCLEOTIDE;
     }
-    else if (name.equalsIgnoreCase("T-Coffee scores"))
+    else if (name.equalsIgnoreCase("T-Coffee Scores"))
     {
       ret = TCOFFEE;
     }
@@ -177,10 +177,10 @@ public class ColourSchemeProperty
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param cs
    *          DOCUMENT ME!
-   * 
+   *
    * @return DOCUMENT ME!
    */
   public static String getColourName(ColourSchemeI cs)
@@ -236,6 +236,10 @@ public class ColourSchemeProperty
     {
       index = PURINEPYRIMIDINE;
     }
+    else if (cs instanceof TCoffeeColourScheme)
+    {
+      index = TCOFFEE;
+    }
     /*
      * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
      */
@@ -255,10 +259,10 @@ public class ColourSchemeProperty
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param index
    *          DOCUMENT ME!
-   * 
+   *
    * @return DOCUMENT ME!
    */
   public static String getColourName(int index)
@@ -326,9 +330,13 @@ public class ColourSchemeProperty
 
       break;
 
+    case TCOFFEE:
+      ret = "T-Coffee Scores";
+
+      break;
     /*
      * case COVARIATION: ret = "Covariation";
-     * 
+     *
      * break;
      */
     case USER_DEFINED:
@@ -394,14 +402,14 @@ public class ColourSchemeProperty
 
   /**
    * Construct an instance of ColourSchemeI corresponding to the given colourscheme index
-   * 
+   *
    * @param seqs
    *          sequences to be coloured by colourscheme
    * @param width
    *          geometry of alignment
    * @param index
-   *          colourscheme number 
-   * 
+   *          colourscheme number
+   *
    * @return null or an instance of the colourscheme configured to colour given sequence set
    */
   public static ColourSchemeI getColour(jalview.datamodel.AnnotatedCollectionI coll, int index)
@@ -470,6 +478,8 @@ public class ColourSchemeProperty
 
       break;
 
+    case TCOFFEE:
+      cs = new TCoffeeColourScheme(coll);
     // case COVARIATION:
     // cs = new CovariationColourScheme(annotation);
 
-- 
1.7.10.2