From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 7 Oct 2015 11:51:59 +0000 (+0100)
Subject: JAL-1912 javadoc for adjustForAlignment stating current behaviour
X-Git-Tag: Release_2_10_0~365^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=837b34ffd916e7aa1cefd068b952652bad8482b5;p=jalview.git

JAL-1912 javadoc for adjustForAlignment stating current behaviour
---

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index b00f27d..830dbc7 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -957,6 +957,12 @@ public class AlignmentAnnotation
 
   }
 
+  /**
+   * When positional annotation and a sequence reference is present, clears and
+   * resizes the annotations array to the current alignment width, and adds
+   * annotation according to aligned positions of the sequenceRef given by
+   * sequenceMapping.
+   */
   public void adjustForAlignment()
   {
     if (sequenceRef == null)