fix for JAL-3765

[jalview.git] / src / jalview / analysis / Finder.java

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 0d8665f..d52e42a 100644 (file)
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -417,7 +417,7 @@ public class Finder implements FinderI
      * update residueIndex to next position after the start of the match
      * (findIndex returns a value base 1, columnIndex is held base 0)
      */
-    residueIndex += offset + 1;
+    residueIndex = searchPattern.matchedFrom()+1;
 
     /*
      * return false if the match is entirely in a hidden region
@@ -471,10 +471,7 @@ public class Finder implements FinderI
      */
     int[] truePositions = searchedSequenceMap
             .locateInFrom(matchStartPosition, matchEndPosition);
-    for (int i = 0; i < truePositions.length - 1; i += 2)
-    {
-      searchResults.addResult(seq, truePositions[i], truePositions[i + 1]);
-    }
+    searchResults.addResult(seq, truePositions);
   }
 
   /**