Jalview 2.8 Source Header

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

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 1e2db76..47dbde2 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
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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;
@@ -29,7 +29,7 @@ import java.awt.Color;
  * 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 $Revision$
  */
@@ -86,7 +86,6 @@ public class ColourSchemeProperty
 
   public static final int TCOFFEE = 15;
 
-
   /**
    * index of first colourscheme (includes 'None')
    */
@@ -96,10 +95,10 @@ public class ColourSchemeProperty
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param name
    *          DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public static int getColourIndexFromName(String name)
@@ -177,10 +176,10 @@ public class ColourSchemeProperty
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param cs
    *          DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public static String getColourName(ColourSchemeI cs)
@@ -259,10 +258,10 @@ public class ColourSchemeProperty
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param index
    *          DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public static String getColourName(int index)
@@ -336,7 +335,7 @@ public class ColourSchemeProperty
       break;
     /*
      * case COVARIATION: ret = "Covariation";
-     *
+     * 
      * break;
      */
     case USER_DEFINED:
@@ -352,9 +351,10 @@ public class ColourSchemeProperty
 
     return ret;
   }
+
   /**
    * retrieve or create colourscheme associated with name
-   *
+   * 
    * @param seqs
    *          sequences to colour
    * @param width
@@ -401,20 +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
-   *
-   * @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)
@@ -480,10 +484,10 @@ public class ColourSchemeProperty
 
     case TCOFFEE:
       cs = new TCoffeeColourScheme(coll);
-    // case COVARIATION:
-    // cs = new CovariationColourScheme(annotation);
+      // case COVARIATION:
+      // cs = new CovariationColourScheme(annotation);
 
-    // break;
+      // break;
 
     case USER_DEFINED:
       Color[] col = new Color[24];