com.wcohen.ss
Class MemoMatrix

java.lang.Object
  com.wcohen.ss.MemoMatrix

Direct Known Subclasses:

AffineGap.MatrixTrio, AffineGap.MatrixTrio.InsertSMatrix, AffineGap.MatrixTrio.InsertTMatrix, ApproxMemoMatrix

public abstract class MemoMatrix
extends java.lang.Object

A matrix of doubles, defined recursively by the compute(i,j) method, that will not be recomputed more than necessary.

Field Summary

protected java.lang.String	cellFormat
protected boolean	printNegativeValues
protected StringWrapper	s
protected StringWrapper	t

Method Summary

protected static double	max3(double x, double y, double z) Return max of three numbers.
protected static double	max4(double w, double x, double y, double z) Return max of four numbers.
protected char	sAt(int i) Get i-th char of s, indexing s from 1..n
protected char	tAt(int i) Get i-th char of t, indexing s from 1..n
java.lang.String	toString() Print the matrix, for debugging and/or explanation.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

s

protected StringWrapper s

t

protected StringWrapper t

cellFormat

protected java.lang.String cellFormat

printNegativeValues

protected boolean printNegativeValues

Method Detail

sAt

protected final char sAt(int i)

Get i-th char of s, indexing s from 1..n

tAt

protected final char tAt(int i)

Get i-th char of t, indexing s from 1..n

toString

public java.lang.String toString()

Print the matrix, for debugging and/or explanation.

Overrides:

toString in class java.lang.Object

max3

protected static final double max3(double x,
                                   double y,
                                   double z)

Return max of three numbers.

max4

protected static final double max4(double w,
                                   double x,
                                   double y,
                                   double z)

Return max of four numbers.