Merge branch 'releases/Release_2_11_1_4_debianpatches' into task/JAL-3521_Slimmed_dow...

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

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 5d42905..d52e42a 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;
-      }
     }
   }
 
@@ -421,7 +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
@@ -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);
   }
 
   /**