X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAnnotation.java;h=348c9a4b4bc9a8c3e418ceeb83a752d7de4188e3;hb=5d5387084823fabaff0069493688221c43dd93e7;hp=ca5f9e04a50f8aafe7000b2ec1dabec22f849af2;hpb=8d4cbc619c910e1948c583f53ec6fc11ea007274;p=jalview.git

diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index ca5f9e0..348c9a4 100755
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, 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 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.
- *
+ * 
  * 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
@@ -22,7 +22,7 @@ import java.awt.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
@@ -43,15 +43,19 @@ public class Annotation
   // add visual cues here
 
   /** DOCUMENT ME!! */
-  public Color colour = Color.black;
+  public Color colour;
 
   /**
    * Creates a new Annotation object.
-   *
-   * @param displayChar DOCUMENT ME!
-   * @param desc DOCUMENT ME!
-   * @param ss DOCUMENT ME!
-   * @param val DOCUMENT ME!
+   * 
+   * @param displayChar
+   *                DOCUMENT ME!
+   * @param desc
+   *                DOCUMENT ME!
+   * @param ss
+   *                DOCUMENT ME!
+   * @param val
+   *                DOCUMENT ME!
    */
   public Annotation(String displayChar, String desc, char ss, float val)
   {
@@ -63,35 +67,55 @@ public class Annotation
 
   /**
    * Creates a new Annotation object.
-   *
-   * @param displayChar DOCUMENT ME!
-   * @param desc DOCUMENT ME!
-   * @param ss DOCUMENT ME!
-   * @param val DOCUMENT ME!
-   * @param colour DOCUMENT ME!
+   * 
+   * @param displayChar
+   *                DOCUMENT ME!
+   * @param desc
+   *                DOCUMENT ME!
+   * @param ss
+   *                DOCUMENT ME!
+   * @param val
+   *                DOCUMENT ME!
+   * @param colour
+   *                DOCUMENT ME!
    */
   public Annotation(String displayChar, String desc, char ss, float val,
-                    Color colour)
+          Color colour)
   {
     this(displayChar, desc, ss, val);
     this.colour = colour;
   }
+
   /**
-   * Copy constructor
-   * New annotation takes on the same (or duplicated) attributes as the given template
-   * @param that template annotation
+   * Copy constructor New annotation takes on the same (or duplicated)
+   * attributes as the given template
+   * 
+   * @param that
+   *                template annotation
    */
-  public Annotation(Annotation that) {
-    if (that==null || this==that)
+  public Annotation(Annotation that)
+  {
+    if (that == null || this == that)
     {
       return;
     }
-    if (that.displayCharacter!=null)
+    if (that.displayCharacter != null)
       displayCharacter = new String(that.displayCharacter);
-    if (that.description!=null)
+    if (that.description != null)
       description = new String(that.description);
     secondaryStructure = that.secondaryStructure;
     value = that.value;
     colour = that.colour;
   }
+
+  /**
+   * Value only annotation.
+   * 
+   * @param val
+   *                value at this annotation position
+   */
+  public Annotation(float val)
+  {
+    this(null, null, ' ', val);
+  }
 }