X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fmath%2FMatrixI.java;h=d72890a040145f88bfcc9818a88c8789e1c30937;hb=bc18effe68ba80213a6d03ca7e6175adc6be71d6;hp=94b933349d2352474331b8d0961a394909ae5e49;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git

diff --git a/src/jalview/math/MatrixI.java b/src/jalview/math/MatrixI.java
index 94b9333..d72890a 100644
--- a/src/jalview/math/MatrixI.java
+++ b/src/jalview/math/MatrixI.java
@@ -1,7 +1,31 @@
+/*
+ * 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;
 
+/**
+ * An interface that describes a rectangular matrix of double values and
+ * operations on it
+ */
 public interface MatrixI
 {
   /**
@@ -42,19 +66,60 @@ public interface MatrixI
    * @return
    */
   double[] getRow(int i);
-  
+
+  /**
+   * Answers a new matrix with a copy of the values in this one
+   * 
+   * @return
+   */
   MatrixI copy();
 
+  /**
+   * Returns a new matrix which is the transpose of this one
+   * 
+   * @return
+   */
   MatrixI transpose();
 
+  /**
+   * Returns a new matrix which is the result of premultiplying this matrix by
+   * the supplied argument. If this of size AxB (A rows and B columns), and the
+   * argument is CxA (C rows and A columns), the result is of size CxB.
+   * 
+   * @param in
+   * 
+   * @return
+   * @throws IllegalArgumentException
+   *           if the number of columns in the pre-multiplier is not equal to
+   *           the number of rows in the multiplicand (this)
+   */
   MatrixI preMultiply(MatrixI m);
 
+  /**
+   * Returns a new matrix which is the result of postmultiplying this matrix by
+   * the supplied argument. If this of size AxB (A rows and B columns), and the
+   * argument is BxC (B rows and C columns), the result is of size AxC.
+   * <p>
+   * This method simply returns the result of in.preMultiply(this)
+   * 
+   * @param in
+   * 
+   * @return
+   * @throws IllegalArgumentException
+   *           if the number of rows in the post-multiplier is not equal to the
+   *           number of columns in the multiplicand (this)
+   * @see #preMultiply(Matrix)
+   */
   MatrixI postMultiply(MatrixI m);
 
   double[] getD();
 
   double[] getE();
 
+  void setD(double[] v);
+
+  void setE(double[] v);
+
   void print(PrintStream ps, String format);
 
   void printD(PrintStream ps, String format);