+/*
+ * 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.math;
import java.io.PrintStream;
* @return
*/
double[] getRow(int i);
-
+
MatrixI copy();
MatrixI transpose();
* <p>
* If parameter <code>maxToZero</code> is true, then the maximum value becomes
* zero, i.e. all values are subtracted from the maximum. This is consistent
- * with converting a similarity score to a distance score - the most similar
- * (identity) corresponds to zero distance. However note that the operation is
- * not reversible (unless the original minimum value is zero). For example a
- * range of 10-40 would become 30-0, which would reverse a second time to
- * 0-30. Also note that a similarity measure (such as BLOSUM) may give
- * different identity scores for different sequences, so they cannot all
- * convert to zero distance.
+ * with converting an identity similarity score to a distance score - the most
+ * similar (identity) corresponds to zero distance. However note that the
+ * operation is not reversible (unless the original minimum value is zero).
+ * For example a range of 10-40 would become 30-0, which would reverse a
+ * second time to 0-30. Also note that a general similarity measure (such as
+ * BLOSUM) may give different 'identity' scores for different sequences, so
+ * they cannot all convert to zero distance.
* <p>
* If parameter <code>maxToZero</code> is false, then the values are reflected
* about the average of {min, max} (effectively swapping min and max). This
* @param maxToZero
*/
void reverseRange(boolean maxToZero);
+
+ /**
+ * Multiply all entries by the given value
+ *
+ * @param d
+ */
+ void multiply(double d);
}