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