update author list in license for (JAL-826)

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

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index dd4eb53..f06c10f 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, 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 program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * 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.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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;
 
@@ -24,54 +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!
@@ -137,6 +153,14 @@ public class ColourSchemeProperty
     {
       ret = NONE;
     }
+    else if (name.equalsIgnoreCase("Purine/Pyrimidine"))
+    {
+      ret = PURINEPYRIMIDINE;
+    }
+    // else if (name.equalsIgnoreCase("Covariation"))
+    // {
+    // ret = COVARIATION;
+    // }
 
     return ret;
   }
@@ -198,6 +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)
@@ -280,6 +311,16 @@ public class ColourSchemeProperty
 
       break;
 
+    case PURINEPYRIMIDINE:
+      ret = "Purine/Pyrimidine";
+
+      break;
+
+    /*
+     * case COVARIATION: ret = "Covariation";
+     * 
+     * break;
+     */
     case USER_DEFINED:
       ret = "User Defined";
 
@@ -431,6 +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++)