📄 pso.cpp
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// pso.cpp : Defines the entry point for the console application.
//
//pso 根据 ga-3自适应改进2 修改。
//2005 4.28
//2005 10.29
#include <stdio.h>
#include "stdafx.h"
#include "iomanip.h"
ofstream outfile("pso_output.txt"); //输出文件
ofstream outfilezz("pso_outputzz.txt");
//输入参数
int popsize; //种群大小
int chromosize; //染色体片断长度
int M; //重复代数
int EG; //PSO进化代数
int Numofpso; //pso进化的周期数；
int GLs; //GA进化的周期数
int GEG; //GA一个周期进化的代数
//中间参数
int chromo_length; //染色体的总长度
int cycle; //当前周期
int gen; //当前代数
int best_cycle; //最佳周期
int best_gen; //最佳个体生成代
int min_sequence_length=65535;//sequence中最短的长度
int max_sequence_length=0;//sequence中最长的长度
double sumfitness;//种群适应度的总和
double avefitness;//种群适应度的平均值
double maxfitness;//种群最大适应度
double minfitness = 50000;//种群最小适应度
//!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!add for pso
float maxv; //最大速度
float minv; //最小速度
int minx ; //最小变量值
int maxx ; //最大变量值
float w ;//= 1 ;
float c1 = 1.8f ;
float c2 = 1.8f ;
float c3 = 1.8f;
//float gbestfit; //最大的适应值
//指针定义
int *gbestp; //最佳位置
//!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!add for pso
//数据输入
char sequence[19][70]={
"ccuagugacaauagcggagaggaaacacccguucccaucccgaacacggaaguuaag",
"ccuaguggugauagcggaggggaaacacccguucccaucccgaacacggaaguuaag",
"uuugguggcgauagcgaagaggucacacccguucccauaccgaacacggaaguuaag",
"uuugguggcgauagcgaagaggucacacccguucucaugccgaacacggaaguuaag",
"ucugguggcgauagcgaagaggucacacccguucccauaccgaacacggaaguuaag",
"uguugugaugauggcauugaggucacaccuguucccauaccgaacacagaaguuaag",
"ugccuggcggccguagcgcgguggucccaccugaccccaugccgaacucagaagugaaa",
"ugucuggcggccauagcgcaguggucccaccugaucccaugccgaacucagaagugaaa",
"ugcuuggcgaccauagcguuauggacccaccugaucccuugccgaacucaguagugaaa",
"guuucgguggucauagcgugagggaaacgcccgguuacauuccgaacccggaagcuaag",
"uccagugucuaugacuuagagguaacacuccuucccauuccgaacaggcagguuaag",
"uguucuuugacgaguaguagcauuggaacaccugaucccaucccgaacucagaggugaaa",
"uggccugguggucauugcgggcucgaaacacccgaucccaucccgaacucggccgugaaa",
"uccuggugucuauggcgguauggaaccacucugaccccaucccgaacucaguugugaaa",
"uauucugguguccuaggcguagaggaaccacaccaauccaucccgaacuuggugguuaaa",
"uauucuggugcuccuaggcguagaggaaccaaaccaauccaucccgaacuuggugguuaaa",
"aauccccgcccuuagcggcguggaacacccguucccauuccgaacacggaagugaaa",
"uuaaggcggccauagcggugggguuacucccguacccaucccgaacacggaagauaag",
"guucacauccgccaggacgcggcgauuacacccgguauccagcccgaacccggaagcgaaa"};
const int sequence_number=19;
int sequence_length[19]={57,57,57,57,57,57,59,59,59,59,57,60,60,59,60,61,57,58,61};
class RandomNumber impor; //产生随机数需要的类
struct individual //个体定义
{
int *chromosome; //染色体
double fitness; //个体适应度
//!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!add for pso
int *lbestp; //个体局部最优位置
double lbestfit; //个体局部最佳适应度
double *speed; //个体速度
//!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!add for pso
};
struct individual *oldpop; //当前代种群
struct individual *newpop; //新一代种群
struct individual *midpop;//中间种群，保存父子两代种群，然后选择
struct individual *temper; //临时种群
struct individual *optimal_indivi; //最佳个体
struct individual *oldpopz1; //用于原方法
struct individual *oldpopz2; //用于改进方法
struct individual *pz; //当前代种群平均
struct individual *oldpopz3; //用于原方法
struct individual *oldpopz4; //用于改进方法
void inputdata() //遗传算法参数输入
{
cout<<"请输入种群大小和染色体片断长度.(10 6)\n";
cin>>popsize>>chromosize;
cout<<"请输入GA进化周期数和进化代数(20 2000)\n";
cin>>GLs>>GEG;
cout<<"请输入PSO进化周期数,PSO进化代数(1000 1000)\n";
cin>>Numofpso>>EG;
}
void initreport() //初始参数输出
{
outfile<<" 微粒群算法参数\n";
outfile<<"--------------------------------------------------------------\n";
outfile<<" 种群大小(popsize) ="<<popsize<<endl;
outfile<<" 染色体片断长度(chromosize) ="<<chromosize<<endl;
outfile<<" GA进化周期数(GLs) ="<<GLs<<endl;
outfile<<" GA进化代数(GEG) ="<<GEG<<endl;
outfile<<" PSO进化周期数(Numofpso) ="<<Numofpso<<endl;
outfile<<" PSO进化代数(EG) ="<<EG<<endl;
outfile<<" PSO最大速度为(vmax) ="<<maxv<<endl;
outfile<<"---------------------------------------------------------------\n";
outfilezz<<" 微粒群算法参数\n";
outfilezz<<"--------------------------------------------------------------\n";
outfilezz<<" 种群大小(popsize) ="<<popsize<<endl;
outfilezz<<" 染色体片断长度(chromosize) ="<<chromosize<<endl;
outfilezz<<" GA进化周期数(GLs) ="<<GLs<<endl;
outfilezz<<" GA进化代数(GEG) ="<<GEG<<endl;
outfilezz<<" PSO进化周期数(Numofpso) ="<<Numofpso<<endl;
outfilezz<<" PSO进化代数(EG) ="<<EG<<endl;
outfilezz<<" PSO最大速度为(vmax) ="<<maxv<<endl;
outfilezz<<"---------------------------------------------------------------\n";
}
void initmalloc() //为全局数据变量分配空间
{
if((oldpop=new struct individual[popsize])==NULL)
cout<<"can't allocate more memory.\n";
if((oldpopz3=new struct individual[popsize])==NULL)
cout<<"can't allocate more memory.\n";
if((oldpopz4=new struct individual[popsize])==NULL)
cout<<"can't allocate more memory.\n";
if((newpop=new struct individual[popsize])==NULL)
cout<<"can't allocate more memory.\n";
if((midpop=new struct individual[popsize])==NULL)
cout<<"can't allocate more memory.\n";
if((optimal_indivi=new struct individual)==NULL)
cout<<"can't allocate more memory.\n";
if((oldpopz1=new struct individual)==NULL)
cout<<"can't allocate more memory.\n";
if((oldpopz2=new struct individual)==NULL)
cout<<"can't allocate more memory.\n";
if((pz=new struct individual)==NULL)
cout<<"can't allocate more memory.\n";
if((temper= new struct individual)==NULL)
cout<<"can't allocate more memory.\n";
if((temper->chromosome=new int[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
for(int j=0;j<popsize;j++)
{
if((oldpop[j].chromosome=new int[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((oldpop[j].speed=new double[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((oldpop[j].lbestp=new int[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((oldpopz3[j].chromosome=new int[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((oldpopz3[j].speed=new double[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((oldpopz3[j].lbestp=new int[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((oldpopz4[j].chromosome=new int[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((oldpopz4[j].speed=new double[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((oldpopz4[j].lbestp=new int[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((newpop[j].chromosome=new int[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((newpop[j].speed=new double[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((newpop[j].lbestp=new int[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((midpop[j].chromosome=new int[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((midpop[j].speed=new double[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((midpop[j].lbestp=new int[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
}
if((optimal_indivi->chromosome=new int[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((optimal_indivi->speed=new double[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((optimal_indivi->lbestp=new int[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((oldpopz1->chromosome=new int[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((oldpopz1->speed=new double[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((oldpopz1->lbestp=new int[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((oldpopz2->chromosome=new int[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((oldpopz2->speed=new double[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((oldpopz2->lbestp=new int[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((pz->chromosome=new int[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((pz->speed=new double[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
if((pz->lbestp=new int[chromo_length])==NULL)
cout<<"can't allocate more memory.\n";
}
RandomNumber::RandomNumber (unsigned long s) //类函数定义
{
if (s == 0)
randSeed = time(0);
else
randSeed = s;
}
unsigned short RandomNumber::Random (unsigned long n) //类函数定义
{
randSeed = multiplier * randSeed + adder;
return (unsigned short)((randSeed >> 16) % n);
}
float randomperc() //随机产生一个0到1之间的小数
{
unsigned a;
float count;
a=impor.Random(10000);
count=(float)a/10000;
return count;
}
int rnd(int low,int high) //随机产生一个low到high之间的整数
{
int i;
i=(int)(randomperc()*(high-low+1)+low);
if(i>high)
i=high;
return i;
}
void fitness(struct individual *critter) //计算适应度函数
{
int *array;
int temp;
int h=0;
double sum=0.0;
char *alignment[sequence_number]; //定义alignment序列
if((array=new int[chromosize])==NULL)
cout<<"can't allocate more memory.\n";
for(int w=0;w<sequence_number;w++)
{
if((alignment[w]=new char[chromosize+min_sequence_length])==NULL)
cout<<"can't allocate more memory.\n";
}
for(int i=0;i<sequence_number;i++)
{
for(int j=0;j<chromosize-(sequence_length[i]-min_sequence_length);j++)
array[j]=critter->chromosome[j+h]; //将染色体片断的值放入临时数组array中
h+=chromosize-(sequence_length[i]-min_sequence_length);
for(int m=chromosize-(sequence_length[i]-min_sequence_length);m>1;m--) //冒泡排序 使得array数组中的值从小到大排列
for(int n=0;n<m-1;n++)
if(array[n]>array[n+1])
{
temp=array[n+1];
array[n+1]=array[n];
array[n]=temp;
}
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