+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.viewmodel;
import java.util.Vector;
seqstrings = seqstrings2;
seqs = seqs2;
nucleotide = nucleotide2;
+ score_matrix = nucleotide2 ? "PID" : "BLOSUM62";
}
private volatile PCA pca;
SequenceI[] seqs;
/**
+ * Score matrix used to calculate PC
+ */
+ String score_matrix;
+
+ /**
* use the identity matrix for calculating similarity between sequences.
*/
private boolean nucleotide = false;
public void run()
{
- pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide);
+ pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide,
+ score_matrix);
pca.setJvCalcMode(jvCalcMode);
pca.run();
jvCalcMode = state;
}
+ public String getScore_matrix()
+ {
+ return score_matrix;
+ }
+
+ public void setScore_matrix(String score_matrix)
+ {
+ this.score_matrix = score_matrix;
+ }
+
}