Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

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

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index c545c7f..9aef9c0 100644 (file)
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -20,6 +20,8 @@
  */
 package jalview.analysis;
 
+import java.util.Locale;
+
 import jalview.api.AlignViewportI;
 import jalview.api.FinderI;
 import jalview.datamodel.AlignmentI;
@@ -29,6 +31,7 @@ import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
+import jalview.util.Platform;
 import jalview.util.MapList;
 
 import java.util.ArrayList;
@@ -148,8 +151,8 @@ public class Finder implements FinderI
     idMatches = new ArrayList<>();
 
     String searchString = matchCase ? theSearchString
-            : theSearchString.toUpperCase();
-    Regex searchPattern = new Regex(searchString);
+            : theSearchString.toUpperCase(Locale.ROOT);
+  Regex searchPattern = Platform.newRegex(searchString);
     searchPattern.setIgnoreCase(!matchCase);
 
     SequenceGroup selection = viewport.getSelectionGroup();
@@ -417,7 +420,7 @@ 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