X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FFinder.java;h=c545c7f1ae05fa21883641b7a03a708190f1f9e5;hb=406c75985c3585f3c6bf8d6f4778d9fb28c7bf2c;hp=5d42905ba40dad454a23b8c1e2ec0a4219cd6cd7;hpb=4016a0a5baf92cea3f1303fdaae3804244857427;p=jalview.git

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 5d42905..c545c7f 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -164,14 +164,10 @@ public class Finder implements FinderI
     getSequence(ignoreHidden);
 
     boolean found = false;
-    while (!found || findAll)
+    while ((!found || findAll) && sequenceIndex < end)
     {
       found = findNextMatch(searchString, searchPattern, searchDescription,
               ignoreHidden);
-      if (sequenceIndex >= end)
-      {
-        break;
-      }
     }
   }
 
@@ -475,10 +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);
   }
 
   /**