X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fmath%2FMatrixI.java;fp=src%2Fjalview%2Fmath%2FMatrixI.java;h=7faac734ebebe9b0ef8a368dd4b0852005eebd17;hb=ce59cf0845b1420b9382d91e4df1de78c00885d1;hp=e98007e5b084cf243c3d5919599a2a4ff7d13984;hpb=8b4b6dc36c3f57292ce9d8484ce5005eaec77262;p=jalview.git

diff --git a/src/jalview/math/MatrixI.java b/src/jalview/math/MatrixI.java
index e98007e..7faac73 100644
--- a/src/jalview/math/MatrixI.java
+++ b/src/jalview/math/MatrixI.java
@@ -61,6 +61,13 @@ public interface MatrixI
   void setValue(int i, int j, double d);
 
   /**
+  * Returns the matrix as a double[][] array
+  *
+  * @return
+  */
+  double[][] asArray();
+
+  /**
    * Answers a copy of the values in the i'th row
    * 
    * @return
@@ -68,6 +75,13 @@ public interface MatrixI
   double[] getRow(int i);
 
   /**
+   * Answers a copy of the values in the i'th column
+   * 
+   * @return
+   */
+  double[] getColumn(int i);
+
+  /**
    * Answers a new matrix with a copy of the values in this one
    * 
    * @return
@@ -161,6 +175,13 @@ public interface MatrixI
   void multiply(double d);
 
   /**
+  * Add d to all entries of this matrix
+  *
+  * @param d ~ value to add
+  */
+  void add(double d);
+
+  /**
    * Answers true if the two matrices have the same dimensions, and
    * corresponding values all differ by no more than delta (which should be a
    * positive value), else false
@@ -170,4 +191,127 @@ public interface MatrixI
    * @return
    */
   boolean equals(MatrixI m2, double delta);
+
+  /**
+   * Returns a copy in which  every value in the matrix is its absolute
+   */
+  MatrixI absolute();
+
+  /**
+   * Returns the mean of each row
+   */
+  double[] meanRow();
+
+  /**
+   * Returns the mean of each column
+   */
+  double[] meanCol();
+
+  /**
+  * Returns a flattened matrix containing the sum of each column
+  *
+  * @return
+  */
+  double[] sumCol();
+
+  /**
+  * returns the mean value of the complete matrix
+  */
+  double mean();
+
+  /**
+  * fills up a diagonal matrix with its transposed copy
+  * !other side should be filled with either 0 or Double.NaN
+  */
+  void fillDiagonal();
+
+  /**
+  * counts the number of Double.NaN in the matrix
+  *
+  * @return
+  */
+  int countNaN();
+
+  /**
+  * performs an element-wise addition of this matrix by another matrix
+  * !matrices have to be the same size
+  * @param m ~ other matrix
+  * 
+  * @return
+  * @throws IllegalArgumentException
+  *           if this and m do not have the same dimensions
+  */
+  MatrixI add(MatrixI m);
+
+  /**
+  * performs an element-wise subtraction of this matrix by another matrix
+  * !matrices have to be the same size
+  * @param m ~ other matrix
+  * 
+  * @return
+  * @throws IllegalArgumentException
+  *           if this and m do not have the same dimensions
+  */
+  MatrixI subtract(MatrixI m);
+ 
+  /**
+  * performs an element-wise multiplication of this matrix by another matrix ~ this * m
+  * !matrices have to be the same size
+  * @param m ~ other matrix
+  *
+  * @return
+  * @throws IllegalArgumentException
+  *	if this and m do not have the same dimensions
+  */
+  MatrixI elementwiseMultiply(MatrixI m);
+
+  /**
+  * performs an element-wise division of this matrix by another matrix ~ this / m
+  * !matrices have to be the same size
+  * @param m ~ other matrix
+  *
+  * @return
+  * @throws IllegalArgumentException
+  *	if this and m do not have the same dimensions
+  */
+  MatrixI elementwiseDivide(MatrixI m);
+
+  /**
+  * calculates the root-mean-square for two matrices
+  * @param m ~ other matrix
+  *  
+  * @return
+  */
+  double rmsd(MatrixI m);
+
+  /**
+  * calculates the Frobenius norm of this matrix
+  *
+  * @return
+  */
+  double norm();
+  
+  /**
+  * returns the sum of all values in this matrix
+  *
+  * @return
+  */
+  double sum();
+
+  /**
+  * returns the sum-product of this matrix with vector v
+  * @param v ~ vector
+  *
+  * @return
+  * @throws IllegalArgumentException
+  *	if this.cols and v do not have the same length
+  */
+  double[] sumProduct(double[] v);
+
+  /**
+  * mirrors the columns of this matrix
+  *
+  * @return
+  */
+  MatrixI mirrorCol();
 }