chromosome.java

代码是一个分类器的实现,其中使用了部分weka的源代码。可以将项目导入eclipse运行

package com.lqy.GEP;
import java.util.*;
import weka.core.*;
import java.io.*;

public class Chromosome implements java.io.Serializable,java.lang.Comparable<Chromosome>{
	private double fitness=0;
	private int headLength=5;
	private boolean constructed=false;
	private String[] functionSet=new String[]{"+2","*2","exp"};
	private String[] terminalSet=new String[]{"k1","k2","k3"};
	private String[] gtype=new String[this.getTotalLength()];
	private TreeThread[] ptype=new TreeThread[this.getHeadLength()];//染色体中参数部分存放的是常数池的下标
	private double[] cp=new double[10];//常数池，存放[1，10]随机实数
	private String id;//染色体的唯一标识
	public Evator eva;
	public double SIPDT=Double.NEGATIVE_INFINITY;
	//private EVATOR eva;
//	private int tailLength;
//	private int parameterLength;
	
	//非终结符的子节点
	private TreeThread[] parameterAssign=new TreeThread[this.getHeadLength()+this.getTailLength()];
	//终结符的参数，是染色体中下标
	public Chromosome(){
		//this.randomInit();
		
	}
	public String[] getFunctionSet(){
		return this.functionSet;
	}
	public String[] getTerminalSet(){
		return this.terminalSet;
	}
	
	public double[] getCP(){
		return this.cp;
	}
	public void setCP(double[] argD){
		this.cp=argD;
	}
	
	public void setID(String argI){
		this.id=argI.trim();
	}
	public String getID(){
		return this.id;
	}
	public void updateFitness(double argF){
		this.fitness=argF;
		
	}
	public double getFitness(){
		return this.fitness;
	}
	public void updateSIPDT(EuclideanMeasure argE){
		Instances tempI=argE.getInstances();
		this.SIPDT=this.eva.getValue(this.getTerminalValues(argE,tempI.firstInstance(),tempI.firstInstance()));
		
	}
	public void randomInit(){
		Random tempR=new Random();
	    this.setGeneByIndex(0, this.functionSet[tempR.nextInt(this.functionSet.length)]);
	    //树根必须是操作符
		for(int i=1;i<this.getHeadLength();i++)
			this.setGeneByIndex(i, 
					tempR.nextDouble()>0.5?this.functionSet[tempR.nextInt(this.functionSet.length)]:
						this.terminalSet[tempR.nextInt(this.terminalSet.length)]);
		//初始化头部
		for(int i=this.headLength;i<this.headLength+this.getTailLength();i++)
			this.setGeneByIndex(i, this.terminalSet[tempR.nextInt(this.terminalSet.length)]);
		//初始化尾部
		for(int i=0;i<this.cp.length;i++)
			this.cp[i]=9*Math.random();
		//初始化参数池，0-10之间的实数
		for(int i=this.getHeadLength()+this.getTailLength();i<this.getTotalLength();i++)
			this.setGeneByIndex(i,String.valueOf((tempR.nextInt(this.cp.length))));
		//初始化参数
		this.construct();
		System.out.print("cd");
		//创建树结构
	}
	public void construct(){
		/*
		int tempArity=Integer.MIN_VALUE;
    	SymbolFactory tempSF=new SymbolFactory();
    	for(int i=0;i<this.functionSet.length;i++){
    		int tempI=tempSF.creatSymbol(this.functionSet[i]).getArity();
    		if(tempI>tempArity)
    			tempArity=tempI;
    	}
    	this.tailLength=this.headLength*(tempArity-1)+1;		
		
    	int tempPS=Integer.MIN_VALUE;
    	//SymbolFactory tempSF=new SymbolFactory();
    	for(int i=0;i<this.terminalSet.length;i++){
    		int tempI=tempSF.creatSymbol(this.terminalSet[i]).getParameterSize();
    		if(tempI>tempPS)
    			tempPS=tempI;
    	}
    	this.parameterLength=tempPS*this.getTailLength();
		*/
		if(this.constructed) return;
		else{
		    //System.out.println("now constructing");
		    this.constructPType();
		    this.constructParameterAssign();
		    this.constructed=true;
		}
	}
	public int getPTC(int argP,int argC){
		return this.ptype[argP].getChild(argC);
		
	}
	public TreeThread getPT(int argI){
		return this.ptype[argI];
	}
	public int getPAC(int argP,int argC){
		return this.parameterAssign[argP].getChild(argC);
	}
	public TreeThread getPA(int argI){
		return this.parameterAssign[argI];
		
	}
	private void constructPType(){//已经解决终止树构造的问题
		try{
		int tempM=1;
		SymbolFactory tempSF=SymbolFactory.getInstance();
		for(int i=0;i<this.headLength;i++){
			Symbol tempS=tempSF.creatSymbol(this.getGeneByIndex(i));
			this.ptype[i]=new TreeThread();
			if(!tempS.isTerminal()){
				for(int j=tempM;j<=tempM-1+tempS.getArity();j++)
					this.ptype[i].addChild(j);
				tempM=tempM+tempS.getArity();			
			}
		}
		for(int i=0;i<this.headLength;i++){
			TreeThread tempT=this.getPT(i);
			boolean tempB=false;
			for(int j=0;j<tempT.getNumberOfChildren();j++)
				if(tempT.getChild(j)<=i){
					tempB=true;
					break;
				}
			if(tempB){
				for(int j=i;j<this.getHeadLength();j++)
					this.ptype[j].clear();
				break;
			}
		}
		}catch(Exception e){System.err.println(e);}
		
	}
	private void constructParameterAssign(){
		try{
	
		int tempM=this.getHeadLength()+this.getTailLength();
		//令tempM指向第一个参数
		SymbolFactory tempSF=SymbolFactory.getInstance();
		for(int i=0;i<this.getHeadLength()+this.getTailLength();i++){
			Symbol tempS=tempSF.creatSymbol(this.getGeneByIndex(i));
			this.parameterAssign[i]=new TreeThread();
			if(tempS.isTerminal()){
				for(int j=tempM;j<tempM+tempS.getParameterSize();j++)
					this.parameterAssign[i].addChild(j);
				tempM=tempM+tempS.getParameterSize();
			}
		}
		for(int i=this.headLength-1;i>=0;i--){
			if(this.ptype[i].getNumberOfChildren()>0){
				int tempF=this.ptype[i].getChild(this.ptype[i].getNumberOfChildren()-1);
				for(int j=tempF+1;j<this.parameterAssign.length;j++)
					this.parameterAssign[j].clear();
				break;
			}
		}
		}catch(Exception e){System.out.println(e);}
	}
	public String getGeneByIndex(int argI){//如果在参数位置，返回在cp中的下标
		if((argI<0)||(argI>this.gtype.length))
			return "";
		return this.gtype[argI];
	}
	public double getParameterByIndex(int argI){
		return this.cp[Integer.parseInt(this.getGeneByIndex(argI))];
	}
	public void setGeneByIndex(int argI,String argS){
		this.gtype[argI]=argS;
	}
    public int getHeadLength(){
    	return this.headLength;
    }
    public int getTailLength(){
    	//return this.tailLength;
    	/*
    	if(this.tailLength!=0)
    		return this.tailLength;
    	*/
    	int tempArity=Integer.MIN_VALUE;
    	SymbolFactory tempSF=SymbolFactory.getInstance();
    	for(int i=0;i<this.functionSet.length;i++){
    		int tempI=tempSF.creatSymbol(this.functionSet[i]).getArity();
    		if(tempI>tempArity)
    			tempArity=tempI;
    	}
    	return this.headLength*(tempArity-1)+1;		
    }
    public int getParameterLength(){
    	//return this.parameterLength;
    	/*
    	if(this.parameterLength!=0)
    		return this.parameterLength;
    	*/
    	
    	int tempPS=Integer.MIN_VALUE;
    	SymbolFactory tempSF=SymbolFactory.getInstance();
    	for(int i=0;i<this.terminalSet.length;i++){
    		int tempI=tempSF.creatSymbol(this.terminalSet[i]).getParameterSize();
    		if(tempI>tempPS)
    			tempPS=tempI;
    	}
    	return tempPS*this.getTailLength();
    	
    }
    public int getTotalLength(){
    	return this.headLength+this.getTailLength()+this.getParameterLength();
    }
    
    private double doEvaluation(EuclideanMeasure argE,Instance argA,Instance argB,int argI){
    //递归
    	//System.out.println("henhen");
    	SymbolFactory tempSF=SymbolFactory.getInstance();
    	Symbol tempS=tempSF.creatSymbol(this.getGeneByIndex(argI));
    	if(tempS.isTerminal()){
    		double[] tempD=new double[tempS.getParameterSize()];
    		for(int i=0;i<tempS.getParameterSize();i++){
    			tempD[i]=this.getParameterByIndex(this.getPAC(argI, i));
    	//		System.out.print(tempD[i]+" ");
    		}
    		tempS.setParameters(tempD);
    		return tempS.getValue(argE, argA, argB);
    	}
    	else{
    		double[] tempD=new double[tempS.getArity()];
    		for(int i=0;i<tempS.getArity();i++)