X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAnnotation.java;h=6b22cade9cd4f262abe1b727795b1b49c45771b4;hb=eadc77c31ca5a013b5bd4dad1038fe62681c2942;hp=a73ea7a491e47ac40b170c61a7517ab375c5bfb7;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index a73ea7a..6b22cad 100755
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 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.datamodel;
 
@@ -35,7 +34,7 @@ public class Annotation
   public String description = ""; // currently used as mouse over
 
   /** DOCUMENT ME!! */
-  public char secondaryStructure = ' '; // recognises H and E
+  public char secondaryStructure = ' '; // recognises H, E and S(?)
 
   /** DOCUMENT ME!! */
   public float value;
@@ -49,13 +48,13 @@ public class Annotation
    * Creates a new Annotation object.
    * 
    * @param displayChar
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param desc
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param ss
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param val
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public Annotation(String displayChar, String desc, char ss, float val)
   {
@@ -69,15 +68,15 @@ public class Annotation
    * Creates a new Annotation object.
    * 
    * @param displayChar
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param desc
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param ss
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param val
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param colour
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public Annotation(String displayChar, String desc, char ss, float val,
           Color colour)
@@ -91,7 +90,7 @@ public class Annotation
    * attributes as the given template
    * 
    * @param that
-   *                template annotation
+   *          template annotation
    */
   public Annotation(Annotation that)
   {
@@ -112,7 +111,7 @@ public class Annotation
    * Value only annotation.
    * 
    * @param val
-   *                value at this annotation position
+   *          value at this annotation position
    */
   public Annotation(float val)
   {