From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 2 Nov 2016 14:53:03 +0000 (+0000)
Subject: JAL-345 javadoc and note about JAL-2300
X-Git-Tag: Release_2_10_1~10^2~6^2~1^2~9
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b9f1ae59bc2a4b45a07f7d9ac08e75b78724cff7;p=jalview.git

JAL-345 javadoc and note about JAL-2300
---

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 8cdf446..2ba1612 100755
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -56,7 +56,10 @@ public class SearchResults implements SearchResultsI
     int end;
 
     /**
-     * Constructor
+     * create a Match on a range of sequence. Match always holds region in
+     * forwards order, even if given in reverse order (such as from a mapping to
+     * a reverse strand); this avoids trouble for routines that highlight search
+     * results etc
      * 
      * @param seq
      *          a sequence
@@ -81,6 +84,9 @@ public class SearchResults implements SearchResultsI
       }
       else
       {
+        // TODO: JBP could mark match as being specified in reverse direction
+        // for use
+        // by caller ? e.g. visualizing reverse strand highlight
         this.start = end;
         this.end = start;
       }