1 文本格式

using System;
using System.Collections.Generic;

namespace Legalsoft.Truffer
{
    public class Phylo_nj : Phylagglom
    {
        public double[] u;
        
        public override void premin(double[,] d, int[] nextp)
        {
            int ncurr = 0;
            for (int i = 0; i >= 0; i = nextp[i])
            {
                ncurr++;
            }
            for (int i = 0; i >= 0; i = nextp[i])
            {
                double sum = 0.0;
                for (int j = 0; j >= 0; j = nextp[j])
                {
                    if (i != j)
                    {
                        sum += d[i, j];
                    }
                }
                u[i] = sum / (ncurr - 2);
            }
        }

        public override double dminfn(double[,] d, int i, int j)
        {
            return d[i, j] - u[i] - u[j];
        }

        public override double dbranchfn(double[,] d, int i, int j)
        {
            return 0.5 * (d[i, j] + u[i] - u[j]);
        }

        public override double dnewfn(double[,] d, int k, int i, int j, int ni, int nj)
        {
            return 0.5 * (d[i, k] + d[j, k] - d[i, j]);
        }

        public override void drootbranchfn(double[,] d, int i, int j, int ni, int nj, ref double bi, ref double bj)
        {
            bi = d[i, j] * (nj - 1 + 1.0e-15) / (ni + nj - 2 + 2.0e-15);
            bj = d[i, j] * (ni - 1 + 1.0e-15) / (ni + nj - 2 + 2.0e-15);
        }

        public Phylo_nj(double[,] dist, int fsr = -1) : base(dist, fsr)
        {
            this.u = new double[n];
            makethetree(dist);
        }
    }
}
 

2 代码格式

using System;
using System.Collections.Generic;

namespace Legalsoft.Truffer
{
    public class Phylo_nj : Phylagglom
    {
        public double[] u;
        
        public override void premin(double[,] d, int[] nextp)
        {
            int ncurr = 0;
            for (int i = 0; i >= 0; i = nextp[i])
            {
                ncurr++;
            }
            for (int i = 0; i >= 0; i = nextp[i])
            {
                double sum = 0.0;
                for (int j = 0; j >= 0; j = nextp[j])
                {
                    if (i != j)
                    {
                        sum += d[i, j];
                    }
                }
                u[i] = sum / (ncurr - 2);
            }
        }

        public override double dminfn(double[,] d, int i, int j)
        {
            return d[i, j] - u[i] - u[j];
        }

        public override double dbranchfn(double[,] d, int i, int j)
        {
            return 0.5 * (d[i, j] + u[i] - u[j]);
        }

        public override double dnewfn(double[,] d, int k, int i, int j, int ni, int nj)
        {
            return 0.5 * (d[i, k] + d[j, k] - d[i, j]);
        }

        public override void drootbranchfn(double[,] d, int i, int j, int ni, int nj, ref double bi, ref double bj)
        {
            bi = d[i, j] * (nj - 1 + 1.0e-15) / (ni + nj - 2 + 2.0e-15);
            bj = d[i, j] * (ni - 1 + 1.0e-15) / (ni + nj - 2 + 2.0e-15);
        }

        public Phylo_nj(double[,] dist, int fsr = -1) : base(dist, fsr)
        {
            this.u = new double[n];
            makethetree(dist);
        }
    }
}