Package org.biojava.nbio.structure.align.fatcat.calc

Class FCAlignHelper

java.lang.Object

org.biojava.nbio.structure.align.fatcat.calc.FCAlignHelper

public class FCAlignHelper
extends Object

Constructor Summary

Constructors

Constructor	Description
FCAlignHelper(double[][] sij0, int M0, int N0, double g0, double h0)	do an alignment given the provided matrix sij0

Method Summary

Modifier and Type	Method	Description
int	getAlignPos(int[][] alignList)	record the aligned pairs in alignList[][0], alignList[][1]; return the number of aligned pairs

Methods inherited from class java.lang.Object

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

Constructor Details

FCAlignHelper

public FCAlignHelper(double[][] sij0,
 int M0,
 int N0,
 double g0,
 double h0)

do an alignment given the provided matrix sij0

Parameters:

sij0 - - the matrix to perform the calculations on.

M0 -

N0 -

g0 -

h0 -

Method Details

getAlignPos

public int getAlignPos(int[][] alignList)

record the aligned pairs in alignList[][0], alignList[][1]; return the number of aligned pairs

Parameters:

alignList -

Returns:

the number of aligned pairs