X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=f06c10f99a2ed021bf71a28fe37fba5654897e22;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=69d4647c798e3b45291d10ce28f97469110c208a;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 69d4647..f06c10f 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.
  * 
@@ -23,54 +23,71 @@ import java.awt.*;
  * 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 )
+ * 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 $Revision$
  */
 public class ColourSchemeProperty
 {
-  /** DOCUMENT ME!! */
-  public static final int CLUSTAL = 0;
+  /** Undefined Colourscheme Index */
+  public static final int UNDEFINED = -1;
+
+  /** for schemes defined on the fly */
+  public static final int USER_DEFINED = 0;
+
+  /** No Colourscheme Index */
+  public static final int NONE = 1;
 
   /** DOCUMENT ME!! */
-  public static final int BLOSUM = 1;
+  public static final int CLUSTAL = 2;
 
   /** DOCUMENT ME!! */
-  public static final int PID = 2;
+  public static final int BLOSUM = 3;
 
   /** DOCUMENT ME!! */
-  public static final int ZAPPO = 3;
+  public static final int PID = 4;
 
   /** DOCUMENT ME!! */
-  public static final int TAYLOR = 4;
+  public static final int ZAPPO = 5;
 
   /** DOCUMENT ME!! */
-  public static final int HYDROPHOBIC = 5;
+  public static final int TAYLOR = 6;
 
   /** DOCUMENT ME!! */
-  public static final int HELIX = 6;
+  public static final int HYDROPHOBIC = 7;
 
   /** DOCUMENT ME!! */
-  public static final int STRAND = 7;
+  public static final int HELIX = 8;
 
   /** DOCUMENT ME!! */
-  public static final int TURN = 8;
+  public static final int STRAND = 9;
 
   /** DOCUMENT ME!! */
-  public static final int BURIED = 9;
+  public static final int TURN = 10;
 
   /** DOCUMENT ME!! */
-  public static final int NUCLEOTIDE = 10;
+  public static final int BURIED = 11;
 
   /** DOCUMENT ME!! */
-  public static final int USER_DEFINED = 11;
+  public static final int NUCLEOTIDE = 12;
 
-  /** No Colourscheme Index */
-  public static final int NONE = 12;
+  /**
+   * purine/pyrimidine
+   */
+  public static final int PURINEPYRIMIDINE = 13;
 
-  /** Undefined Colourscheme Index */
-  public static final int UNDEFINED = 13;
+  public static final int COVARIATION = 14;
+
+  /**
+   * index of first colourscheme (includes 'None')
+   */
+  public static final int FIRST_COLOUR = NONE;
+
+  public static final int LAST_COLOUR = NUCLEOTIDE;
 
   /**
    * DOCUMENT ME!
@@ -136,6 +153,14 @@ public class ColourSchemeProperty
     {
       ret = NONE;
     }
+    else if (name.equalsIgnoreCase("Purine/Pyrimidine"))
+    {
+      ret = PURINEPYRIMIDINE;
+    }
+    // else if (name.equalsIgnoreCase("Covariation"))
+    // {
+    // ret = COVARIATION;
+    // }
 
     return ret;
   }
@@ -197,6 +222,13 @@ public class ColourSchemeProperty
     {
       index = NUCLEOTIDE;
     }
+    else if (cs instanceof PurinePyrimidineColourScheme)
+    {
+      index = PURINEPYRIMIDINE;
+    }
+    /*
+     * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
+     */
     else if (cs instanceof UserColourScheme)
     {
       if ((((UserColourScheme) cs).getName() != null)
@@ -279,6 +311,16 @@ public class ColourSchemeProperty
 
       break;
 
+    case PURINEPYRIMIDINE:
+      ret = "Purine/Pyrimidine";
+
+      break;
+
+    /*
+     * case COVARIATION: ret = "Covariation";
+     * 
+     * break;
+     */
     case USER_DEFINED:
       ret = "User Defined";
 
@@ -430,6 +472,16 @@ public class ColourSchemeProperty
 
       break;
 
+    case PURINEPYRIMIDINE:
+      cs = new PurinePyrimidineColourScheme();
+
+      break;
+
+    // case COVARIATION:
+    // cs = new CovariationColourScheme(annotation);
+
+    // break;
+
     case USER_DEFINED:
       Color[] col = new Color[24];
       for (int i = 0; i < 24; i++)