From cc0bde4edc7375f46e29c1814238bb765a6882de Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 18 May 2006 09:22:26 +0000
Subject: [PATCH] added future method comment

---
 src/jalview/io/JnetAnnotationMaker.java |    2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index 9a397d7..17b4d68 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -22,6 +22,8 @@ public class JnetAnnotationMaker
   {
     int i = 0;
     SequenceI[] preds = prediction.getSeqsAsArray();
+    // in the future we could search for the query
+    // sequence in the alignment before calling this function.
     SequenceI seqRef = al.getSequenceAt(FirstSeq);
     int width = preds[0].getSequence().length();
     int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();
-- 
1.7.10.2