org.biojava.bio.structure.align.fatcat.calc
Class FCAlignHelper

java.lang.Object
  org.biojava.bio.structure.align.fatcat.calc.FCAlignHelper

public class FCAlignHelper
extends java.lang.Object

Constructor Summary

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

Method Summary

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 Detail

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 Detail

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