--- /dev/null
+/*
+ * 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;
+
+public interface MatrixI
+{
+ /**
+ * Answers the number of columns
+ *
+ * @return
+ */
+ int width();
+
+ /**
+ * Answers the number of rows
+ *
+ * @return
+ */
+ int height();
+
+ /**
+ * Answers the value at row i, column j
+ *
+ * @param i
+ * @param j
+ * @return
+ */
+ double getValue(int i, int j);
+
+ /**
+ * Sets the value at row i, colum j
+ *
+ * @param i
+ * @param j
+ * @param d
+ */
+ void setValue(int i, int j, double d);
+
+ /**
+ * Answers a copy of the values in the i'th row
+ *
+ * @return
+ */
+ double[] getRow(int i);
+
+ MatrixI copy();
+
+ MatrixI transpose();
+
+ MatrixI preMultiply(MatrixI m);
+
+ MatrixI postMultiply(MatrixI m);
+
+ double[] getD();
+
+ double[] getE();
+
+ void print(PrintStream ps, String format);
+
+ void printD(PrintStream ps, String format);
+
+ void printE(PrintStream ps, String format);
+
+ void tqli() throws Exception;
+
+ void tred();
+
+ /**
+ * Reverses the range of the matrix values, so that the smallest values become
+ * the largest, and the largest become the smallest. This operation supports
+ * using a distance measure as a similarity measure, or vice versa.
+ * <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 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
+ * operation <em>is</em> reversible.
+ *
+ * @param maxToZero
+ */
+ void reverseRange(boolean maxToZero);
+
+ /**
+ * Multiply all entries by the given value
+ *
+ * @param d
+ */
+ void multiply(double d);
+}