+/*
+ * 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.analysis.scoremodels;
+import jalview.api.AlignmentViewPanel;
import jalview.api.analysis.PairwiseScoreModelI;
+import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.datamodel.AlignmentView;
import jalview.math.Matrix;
/**
* A class to provide sequence pairwise similarity based on residue identity.
- * Instances of this class are immutable and thread-safe.
+ * Instances of this class are immutable and thread-safe, so the same object is
+ * returned from calls to getInstance().
*/
-public class PIDModel extends SimilarityScoreModel implements
- PairwiseScoreModelI
+public class PIDModel extends SimilarityScoreModel
+ implements PairwiseScoreModelI
{
private static final String NAME = "PID";
return divideBy == 0 ? 0D : 100D * total / divideBy;
}
+
+ @Override
+ public ScoreModelI getInstance(AlignmentViewPanel avp)
+ {
+ return this;
+ }
}