Class FCAlignHelper


  • public class FCAlignHelper
    extends java.lang.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

      All Methods Instance Methods Concrete Methods 
      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 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