com.wcohen.ss
Class AffineGap.MatrixTrio

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

Enclosing class:

AffineGap

protected class AffineGap.MatrixTrio
extends MemoMatrix

Nested Class Summary

protected class	AffineGap.MatrixTrio.InsertSMatrix
protected class	AffineGap.MatrixTrio.InsertTMatrix

Field Summary

protected AffineGap.MatrixTrio.InsertSMatrix	is
protected AffineGap.MatrixTrio.InsertTMatrix	it
protected MemoMatrix	m

Fields inherited from class com.wcohen.ss.MemoMatrix

cellFormat, printNegativeValues, s, t

Constructor Summary

AffineGap.MatrixTrio(StringWrapper s, StringWrapper t)

Method Summary

double

compute(int i, int j) Compute a new element of the matrix.

Methods inherited from class com.wcohen.ss.MemoMatrix

max3, max4, sAt, tAt, toString

Methods inherited from class java.lang.Object

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

Field Detail

m

protected MemoMatrix m

is

protected AffineGap.MatrixTrio.InsertSMatrix is

it

protected AffineGap.MatrixTrio.InsertTMatrix it

Constructor Detail

AffineGap.MatrixTrio

public AffineGap.MatrixTrio(StringWrapper s,
                            StringWrapper t)

Method Detail

compute

public double compute(int i,
                      int j)

Description copied from class: MemoMatrix

Compute a new element of the matrix. This should be defined in terms of calls to get(i,j).