Merge branch 'develop' into features/JAL-250_hideredundantseqs

[jalview.git] / src / jalview / math / MatrixI.java

diff --git a/src/jalview/math/MatrixI.java b/src/jalview/math/MatrixI.java
new file mode 100644 (file)
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+++ b/src/jalview/math/MatrixI.java
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+/*
+ * 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);
+}