Merge branch 'patch/JAL-3750_JAL-3741_https_patch' into releases/Release_2_11_1_Branch

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

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 5d42905..c545c7f 100644 (file)
--- 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);
   }
 
   /**