+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io;
+import java.io.IOException;
+import java.util.StringTokenizer;
+
import jalview.analysis.scoremodels.ScoreMatrix;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.datamodel.SequenceI;
-import java.io.IOException;
-import java.util.StringTokenizer;
-
/**
* A class that can parse a file containing a substitution matrix and register
* it for use in Jalview
{
continue;
}
- if (data.toUpperCase().startsWith(SCOREMATRIX))
+ // equivalent to data.startsWithIgnoreCase(SCOREMATRIX)
+ if (data.regionMatches(true, 0, SCOREMATRIX, 0, SCOREMATRIX.length()))
{
/*
* Parse name from ScoreMatrix <name>