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

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

public class FCAlignHelper
extends 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