Class FCAlignHelper

    • 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