formatting

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

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 4c7b49d..608d8ed 100755 (executable)
--- 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;
@@ -22,7 +22,7 @@ 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
@@ -83,9 +83,8 @@ 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')
@@ -150,7 +149,7 @@ public class ColourSchemeProperty
     {
       ret = NUCLEOTIDE;
     }
-    else if (name.equalsIgnoreCase("T-Coffee scores"))
+    else if (name.equalsIgnoreCase("T-Coffee Scores"))
     {
       ret = TCOFFEE;
     }
@@ -236,6 +235,10 @@ public class ColourSchemeProperty
     {
       index = PURINEPYRIMIDINE;
     }
+    else if (cs instanceof TCoffeeColourScheme)
+    {
+      index = TCOFFEE;
+    }
     /*
      * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
      */
@@ -326,6 +329,10 @@ public class ColourSchemeProperty
 
       break;
 
+    case TCOFFEE:
+      ret = "T-Coffee Scores";
+
+      break;
     /*
      * case COVARIATION: ret = "Covariation";
      * 
@@ -344,9 +351,10 @@ public class ColourSchemeProperty
 
     return ret;
   }
+
   /**
    * retrieve or create colourscheme associated with name
-   *
+   * 
    * @param seqs
    *          sequences to colour
    * @param width
@@ -393,20 +401,24 @@ public class ColourSchemeProperty
   }
 
   /**
-   * Construct an instance of ColourSchemeI corresponding to the given colourscheme index
+   * 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
+   * @return null or an instance of the colourscheme configured to colour given
+   *         sequence set
    */
-  public static ColourSchemeI getColour(jalview.datamodel.AnnotatedCollectionI coll, 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
+    // 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)
@@ -470,10 +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];