import jalview.util.MessageManager;
import java.io.PrintStream;
+import java.util.Arrays;
/**
* A class to model rectangular matrices of double values and operations on them
public class Matrix implements MatrixI
{
/*
- * the cell values in row-major order
+ * maximum number of iterations for tqli
*/
- private double[][] value;
+ private static final int MAX_ITER = 45;
+ // fudge - add 15 iterations, just in case
/*
* the number of rows
*/
- protected int rows;
+ final protected int rows;
/*
* the number of columns
*/
- protected int cols;
+ final protected int cols;
+
+ /*
+ * the cell values in row-major order
+ */
+ private double[][] value;
protected double[] d; // Diagonal
protected double[] e; // off diagonal
/**
- * maximum number of iterations for tqli
+ * Constructor given number of rows and columns
*
+ * @param colCount
+ * @param rowCount
*/
- private static final int maxIter = 45; // fudge - add 15 iterations, just in
- // case
-
- /**
- * Default constructor
- */
- public Matrix()
+ protected Matrix(int rowCount, int colCount)
{
-
+ rows = rowCount;
+ cols = colCount;
}
-
+
/**
* Creates a new Matrix object containing a copy of the supplied array values.
* For example
}
}
- /**
- * Returns a new matrix which is the transpose of this one
- *
- * @return
- */
@Override
public 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)
- */
@Override
public MatrixI preMultiply(MatrixI in)
{
return out;
}
- /**
- * 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)
- */
@Override
public MatrixI postMultiply(MatrixI in)
{
return in.preMultiply(this);
}
- /**
- * Answers a new matrix with a copy of the values in this one
- *
- * @return
- */
@Override
public MatrixI copy()
{
System.arraycopy(value[i], 0, newmat[i], 0, value[i].length);
}
- return new Matrix(newmat);
+ Matrix m = new Matrix(newmat);
+ if (this.d != null)
+ {
+ m.d = Arrays.copyOf(this.d, this.d.length);
+ }
+ if (this.e != null)
+ {
+ m.e = Arrays.copyOf(this.e, this.e.length);
+ }
+
+ return m;
}
/**
{
iter++;
- if (iter == maxIter)
+ if (iter == MAX_ITER)
{
throw new Exception(MessageManager.formatMessage(
- "exception.matrix_too_many_iteration", new String[] {
- "tqli", Integer.valueOf(maxIter).toString() }));
+ "exception.matrix_too_many_iteration", new String[]
+ { "tqli", Integer.valueOf(MAX_ITER).toString() }));
}
else
{
{
f = getValue(k - 1, i);
setValue(k - 1, i, (s * getValue(k - 1, i - 1)) + (c * f));
- setValue(k - 1, i - 1, (c * getValue(k - 1, i - 1)) - (s * f));
+ setValue(k - 1, i - 1,
+ (c * getValue(k - 1, i - 1)) - (s * f));
}
}
{
iter++;
- if (iter == maxIter)
+ if (iter == MAX_ITER)
{
throw new Exception(MessageManager.formatMessage(
- "exception.matrix_too_many_iteration", new String[] {
- "tqli2", Integer.valueOf(maxIter).toString() }));
+ "exception.matrix_too_many_iteration", new String[]
+ { "tqli2", Integer.valueOf(MAX_ITER).toString() }));
}
else
{
*
* @param ps
* DOCUMENT ME!
- * @param format TODO
+ * @param format
+ * TODO
*/
@Override
public void printE(PrintStream ps, String format)
{
return e;
}
-
+
@Override
- public int height() {
+ public int height()
+ {
return rows;
}
}
}
}
+
+ @Override
+ public void setD(double[] v)
+ {
+ d = v;
+ }
+
+ @Override
+ public void setE(double[] v)
+ {
+ e = v;
+ }
+
+ public double getTotal()
+ {
+ double d = 0d;
+ for (int i = 0; i < this.height(); i++)
+ {
+ for (int j = 0; j < this.width(); j++)
+ {
+ d += value[i][j];
+ }
+ }
+ return d;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public boolean equals(MatrixI m2, double delta)
+ {
+ if (m2 == null || this.height() != m2.height()
+ || this.width() != m2.width())
+ {
+ return false;
+ }
+ for (int i = 0; i < this.height(); i++)
+ {
+ for (int j = 0; j < this.width(); j++)
+ {
+ double diff = this.getValue(i, j) - m2.getValue(i, j);
+ if (Math.abs(diff) > delta)
+ {
+ return false;
+ }
+ }
+ }
+ return true;
+ }
}