+/*
+ * 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.gff;
import jalview.datamodel.AlignmentI;
*/
public static boolean recognises(String[] columns)
{
- SequenceOntology so = SequenceOntology.getInstance();
+ SequenceOntologyI so = SequenceOntologyFactory.getInstance();
String type = columns[TYPE_COL];
- if (so.isProteinMatch(type)
- || (".".equals(columns[SOURCE_COL]) && so.isPolypeptide(type)))
+ if (so.isA(type, SequenceOntologyI.PROTEIN_MATCH)
+ || (".".equals(columns[SOURCE_COL]) && so.isA(type,
+ SequenceOntologyI.POLYPEPTIDE)))
{
return true;
}