From: Jim Procter <jprocter@dundee.ac.uk>
Date: Mon, 3 Nov 2014 09:58:29 +0000 (+0000)
Subject: javadoc
X-Git-Tag: Jalview_2_9~155^2~15^2~8
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b58a042bc832f861d32ccbc8b1dbea74aab9541d;p=jalview.git

javadoc
---

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 78f64ac..936ba42 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -45,17 +45,24 @@ public class AlignmentAnnotation
    */
   public boolean autoCalculated = false;
 
+  /**
+   * unique ID for this annotation, used to match up the same annotation row
+   * shown in multiple views and alignments
+   */
   public String annotationId;
 
+  /**
+   * the sequence this annotation is associated with (or null)
+   */
   public SequenceI sequenceRef;
 
-  /** DOCUMENT ME!! */
+  /** label shown in dropdown menus and in the annotation label area */
   public String label;
 
-  /** DOCUMENT ME!! */
+  /** longer description text shown as a tooltip */
   public String description;
 
-  /** DOCUMENT ME!! */
+  /** Array of annotations placed in the current coordinate system */
   public Annotation[] annotations;
 
   public ArrayList<SimpleBP> bps = null;
@@ -105,6 +112,9 @@ public class AlignmentAnnotation
     // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
   }
 
+  /**
+   * map of positions in the associated annotation
+   */
   public java.util.Hashtable<Integer, Annotation> sequenceMapping;
 
   /** DOCUMENT ME!! */