JAL-1503 update version in GPL header

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

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 4c7b49d..04ffbe9 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,19 +1,20 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * 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 
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.schemes;
 
@@ -22,7 +23,7 @@ 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
@@ -83,16 +84,17 @@ public class ColourSchemeProperty
   public static final int PURINEPYRIMIDINE = 13;
 
   public static final int COVARIATION = 14;
-  
+
   public static final int TCOFFEE = 15;
   
+  public static final int RNAHELIX = 16;
 
   /**
    * index of first colourscheme (includes 'None')
    */
   public static final int FIRST_COLOUR = NONE;
 
-  public static final int LAST_COLOUR = NUCLEOTIDE;
+  public static final int LAST_COLOUR = RNAHELIX;
 
   /**
    * DOCUMENT ME!
@@ -150,7 +152,7 @@ public class ColourSchemeProperty
     {
       ret = NUCLEOTIDE;
     }
-    else if (name.equalsIgnoreCase("T-Coffee scores"))
+    else if (name.equalsIgnoreCase("T-Coffee Scores"))
     {
       ret = TCOFFEE;
     }
@@ -167,6 +169,10 @@ public class ColourSchemeProperty
     {
       ret = PURINEPYRIMIDINE;
     }
+    else if (name.equalsIgnoreCase("RNA Helices"))
+    {
+      ret = RNAHELIX;
+    }
     // else if (name.equalsIgnoreCase("Covariation"))
     // {
     // ret = COVARIATION;
@@ -236,6 +242,14 @@ public class ColourSchemeProperty
     {
       index = PURINEPYRIMIDINE;
     }
+    else if (cs instanceof TCoffeeColourScheme)
+    {
+      index = TCOFFEE;
+    }
+    else if (cs instanceof RNAHelicesColour)
+    {
+      index = RNAHELIX;
+    }
     /*
      * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
      */
@@ -326,6 +340,14 @@ public class ColourSchemeProperty
 
       break;
 
+    case TCOFFEE:
+      ret = "T-Coffee Scores";
+
+      break;
+    case RNAHELIX:
+      ret = "RNA Helices";
+
+      break;
     /*
      * case COVARIATION: ret = "Covariation";
      * 
@@ -344,9 +366,10 @@ public class ColourSchemeProperty
 
     return ret;
   }
+
   /**
    * retrieve or create colourscheme associated with name
-   *
+   * 
    * @param seqs
    *          sequences to colour
    * @param width
@@ -393,20 +416,24 @@ 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 +497,18 @@ public class ColourSchemeProperty
 
       break;
 
-    // case COVARIATION:
-    // cs = new CovariationColourScheme(annotation);
+    case TCOFFEE:
+      cs = new TCoffeeColourScheme(coll);
+      break;
+    
+    case RNAHELIX:
+      cs = new RNAHelicesColour(coll);
+      break;
+      
+      // case COVARIATION:
+      // cs = new CovariationColourScheme(annotation);
 
-    // break;
+      // break;
 
     case USER_DEFINED:
       Color[] col = new Color[24];