X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAnnotation.java;h=e3588b039fe9ac90d09e1e87d54d85b769954491;hb=47168f025aefdaa044802bd5f8f510ffe43a4808;hp=c9a623b8456a0363c73907765f8486c217d6eac6;hpb=c3583f7ab67ddb450f61af4d36af839ddf485a09;p=jalview.git

diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index c9a623b..e3588b0 100755
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -1,19 +1,22 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * 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 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 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 
  * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
@@ -44,7 +47,7 @@ public class Annotation
 
   /** Score for the position - used in histograms, line graphs and for shading */
   public float value;
-
+  
   /** Colour for position */
   public Color colour;
 
@@ -66,6 +69,7 @@ public class Annotation
     description = desc;
     secondaryStructure = ss;
     value = val;
+    
   }
 
   /**
@@ -109,6 +113,7 @@ public class Annotation
     secondaryStructure = that.secondaryStructure;
     value = that.value;
     colour = that.colour;
+
   }
 
   /**
@@ -119,9 +124,18 @@ public class Annotation
    */
   public Annotation(float val)
   {
-    this(null, null, ' ', val);
+    this(null, null, ' ', val,null);
   }
 
+  /**
+   * human readable representation of an annotation row element.
+   *
+   * Format is 'display Char','secondary Structure
+   * Char',"description",score,[colourstring]
+   *
+   * fields may be missing if they are null, whitespace, or equivalent to
+   * Float.NaN
+   */
   @Override
   public String toString()
   {