From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Wed, 22 May 2013 16:45:42 +0000 (+0100)
Subject: javadoc and formatting
X-Git-Tag: Jalview_2_9~249^2~17
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c3583f7ab67ddb450f61af4d36af839ddf485a09;p=jalview.git

javadoc and formatting
---

diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index b7a83a5..c9a623b 100755
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -17,31 +17,35 @@
  */
 package jalview.datamodel;
 
-import java.awt.*;
+import java.awt.Color;
 
 /**
- * DOCUMENT ME!
+ * Holds all annotation values for a position in an AlignmentAnnotation row
  * 
  * @author $author$
  * @version $Revision$
  */
 public class Annotation
 {
-  /** DOCUMENT ME!! */
+  /** Character label - also shown below histogram */
   public String displayCharacter = "";
 
-  /** DOCUMENT ME!! */
-  public String description = ""; // currently used as mouse over
+  /**
+   * Text label for position: shown in mouse over and displayed on secondary
+   * structure glyphs
+   */
+  public String description = "";
 
-  /** DOCUMENT ME!! */
-  public char secondaryStructure = ' '; // recognises H, E and S(?)
+  /**
+   * Secondary structure symbol: Protein symbols are H, E and S(?), RNA are
+   * WUSS/Vienna plus extended pseudoknot symbols
+   */
+  public char secondaryStructure = ' ';
 
-  /** DOCUMENT ME!! */
+  /** Score for the position - used in histograms, line graphs and for shading */
   public float value;
 
-  // add visual cues here
-
-  /** DOCUMENT ME!! */
+  /** Colour for position */
   public Color colour;
 
   /**