added future method comment

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