*/
package jalview.analysis;
+import java.util.Locale;
+
import jalview.api.AlignViewportI;
import jalview.api.FinderI;
import jalview.datamodel.AlignmentI;
idMatches = new ArrayList<>();
String searchString = matchCase ? theSearchString
- : theSearchString.toUpperCase();
+ : theSearchString.toUpperCase(Locale.ROOT);
Regex searchPattern = new Regex(searchString);
searchPattern.setIgnoreCase(!matchCase);
* 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