+/*
+ * 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.analysis.ScoreModelI;
public MatrixI findDistances(AlignmentView seqData,
SimilarityParamsI options)
{
- MatrixI result = findSimilarities(seqData, options);
+ MatrixI similarities = findSimilarities(seqData, options);
- /*
- * reverse the range of the scores mapping the maximum to zero
- */
- result.reverseRange(true);
+ MatrixI distances = similarityToDistance(similarities);
- return result;
+ return distances;
+ }
+
+ /**
+ * Converts a matrix of similarity scores to distance scores, by reversing the
+ * range of the scores, mapping the maximum to zero. The input matrix is not
+ * modified.
+ *
+ * @param similarities
+ */
+ public static MatrixI similarityToDistance(MatrixI similarities)
+ {
+ MatrixI distances = similarities.copy();
+
+ distances.reverseRange(true);
+
+ return distances;
}
}