ATCG问题zzy bugfix1

package org.lwc.exam;

import org.apache.logging.log4j.util.Strings;

import java.io.*;
import java.math.RoundingMode;
import java.sql.SQLOutput;
import java.text.DecimalFormat;
import java.util.*;

/**
 * Title:
 *
 * @author l00563781
 * @version 1.0
 * @Description
 * @since 2020/10/19
 */
public class ACTG {

    static DecimalFormat df = new DecimalFormat( "0.00");

    static boolean isLoop = false;
    // 非特异性指数的最大值序列 默认1，长度和拒绝文库长度相同,循环模式的第一次循环中启用
    static List<Double> loopMaxNS1 = Arrays.asList(
            1.0,1.0,1.0
    );

    // 非特异性指数的最大值序列 默认1，长度和拒绝文库长度相同,循环模式的除第一次循环外启用
    static List<Double> loopMaxNS2 = Arrays.asList(
            1.0,1.0,1.0,1.0,1.0
    );

    // 循环次数
    static int loopNum = 3;

    // 每次循环的链长
    static List<Integer> loopSizeList = Arrays.asList(3,4,5);


    static boolean stopFlag = false;
    // 需要指定的数据
    static int rejNum;
    static ArrayList<Compos> totalCompos;
    static ArrayList<Result> resultArrayList;

    // 是否具有碱基倾向性
    static boolean isTendency = false;

    // 碱基倾向性
    static char tendency;

    // 输入序列的数量
    static int inputNum;

    // 输入序列
    static List<String> inputList = Arrays.asList(
           "AATCATG"
    );

    // 非特异性指数的最大值序列 默认1，长度和拒绝文库长度相同
    static List<Double> maxNS = Arrays.asList(
            1.0,1.0,1.0
    );

    // 输出序列数目： -1 遍历所有可能性； i=0，遍历完结果后立即停止程序；i=n,计算出n条结果后程序停止
    static int generateNum;

    // 输出链长,暂时认为>=3
    static int resultLength;

    static double maxCGRate;
    static double minCGRate;

    /**
     * 四种碱基组合map
     */
    static Map<Character, Character> ref = null;

    /**
     * 拒绝文库中不同碱基对增加值map
     */
    static Map<Compos,Double> rejAccuRef = null;

    // 连续字符的最长数量
    static  Map<Character,Integer> maxSequenceRef = null;

    static {
        df.setRoundingMode(RoundingMode.HALF_UP);
        generateNum = -1;
        inputNum = 1;
        resultLength = 4;
        ref = new HashMap<>();
        ref.put('A', 'T');
        ref.put('C', 'G');
        ref.put('G', 'C');
        ref.put('T', 'A');

        rejAccuRef = new HashMap<>();
        rejAccuRef.put(new Compos('A','A'),1.0);
        rejAccuRef.put(new Compos('A','T'),1.0);
        rejAccuRef.put(new Compos('A','C'),1.0);
        rejAccuRef.put(new Compos('A','G'),1.0);
        rejAccuRef.put(new Compos('T','A'),1.0);
        rejAccuRef.put(new Compos('T','T'),1.0);
        rejAccuRef.put(new Compos('T','C'),1.0);
        rejAccuRef.put(new Compos('T','G'),1.0);
        rejAccuRef.put(new Compos('C','A'),1.0);
        rejAccuRef.put(new Compos('C','T'),1.0);
        rejAccuRef.put(new Compos('C','C'),1.0);
        rejAccuRef.put(new Compos('C','G'),1.0);
        rejAccuRef.put(new Compos('G','A'),1.0);
        rejAccuRef.put(new Compos('G','T'),1.0);
        rejAccuRef.put(new Compos('G','C'),1.0);
        rejAccuRef.put(new Compos('G','G'),1.0);

        maxSequenceRef = new HashMap<>();
        maxSequenceRef.put('A',10);
        maxSequenceRef.put('T',10);
        maxSequenceRef.put('C',10);
        maxSequenceRef.put('G',10);
    }

    public static void main(String[] args) throws IOException, ClassNotFoundException {

        if(!isLoop){
            handle();
        }else {

            // 设置非特异型指数的最大值序列
            // 设置得到的序列数量为1
            // 设置本次链长
            ArrayList<Result> results = new ArrayList<>();
            String lastLastString = "";
            String lastString = inputList.get(0);
            for(int i =0;i<loopNum;i++){

                stopFlag = false;
                if(i==0){
                    maxNS = loopMaxNS1;
                }else {
                    maxNS = loopMaxNS2;
                }
                resultLength = loopSizeList.get(i);
                generateNum = 1;
                if(lastLastString.equals("")){
                    inputList = Arrays.asList(lastString);
                }else {
                    inputList = Arrays.asList(lastLastString,lastString);
                }
                Result result = handle();
                if(result == null){
                    System.err.println("循环第"+(i+1)+"次失败,请检查输入");
                    break;
                }
                results.add(result);
                lastLastString = lastString;
                lastString = result.chain;
            }

            System.out.println("LOOP RESULT:");
            for(int j = 0;j<results.size();j++){
                Result result = results.get(j);
                System.out.println("---"+result.id+"---"+result.chain+"---"+Arrays.toString(formatDoubleArray(result.degree))+"---"+formatDouble(result.cgRate)+"---"+getReverseRef(result.chain));
            }
        }
    }

    public static Result handle() throws IOException, ClassNotFoundException {

        // 初始化
        maxCGRate = 0.75;
        minCGRate = 0.25;
        tendency = 'A';
        isTendency = true;

        // 初始化拒绝文库 ArrayList<List<Compos>>
        ArrayList<List<Compos>> rejCompos = new ArrayList<>();
        for (String string : inputList) {

            List<Compos> composList = getComposList(string);
            rejCompos.add(composList);

            List<Compos> composList1 = getComposList(getReverseRef(string));
            rejCompos.add(composList1);
        }
        List<Compos> lastComposList = new ArrayList<>();
        rejCompos.add(lastComposList);


        // 初始化非特异性指数数组
        rejNum = rejCompos.size();
        double[] degree = new double[rejNum];

        // 生成全组合文库
        totalCompos = null;
        if (isTendency) {
            String base = "ATCG";
            StringBuilder newBase = new StringBuilder();
            newBase.append(tendency);
            for (int i = 0; i < 4; i++) {

                char current = base.charAt(i);
                if (current == tendency) {
                    continue;
                }
                newBase.append(current);
            }
            String baseString = newBase.toString();
            totalCompos = new ArrayList<Compos>();
            totalCompos.addAll(generateComposStartWith(baseString));
        } else {
            String base = "ATCG";
            totalCompos = new ArrayList<Compos>();
            totalCompos.addAll(generateComposStartWith(base));
        }

        resultArrayList = new ArrayList<Result>();
        String lastChain = "";
        ArrayList<List<Compos>> rejComposCopy = deepCopy(rejCompos);
        diGui(degree,lastChain,rejComposCopy);
        for(int j = 0;j<resultArrayList.size();j++){
            Result result = resultArrayList.get(j);
            System.out.println("---"+result.id+"---"+result.chain+"---"+Arrays.toString(formatDoubleArray(result.degree))+"---"+formatDouble(result.cgRate)+"---"+getReverseRef(result.chain));
        }
        return resultArrayList.get(0);
    }

    public static void diGui(double[] degree,String lastChain,ArrayList<List<Compos>> rejCompos) throws IOException, ClassNotFoundException {
        // 深度遍历，在开始设置递归路径，并且记录相关
        // 初始话场景，非追加场景，不会生成result
        if(Strings.isBlank(lastChain)){
            for(int i=0;i<totalCompos.size();i++){
                ArrayList<List<Compos>> newRejCompos = deepCopy(rejCompos);
                double[] newDegree = degree.clone();

                Compos current = totalCompos.get(i);
                String newChain = current.first+""+current.last;

                // 得到此组合的互补组合
                Compos reverseCurrent = new Compos(
                        getRef(current.last),
                        getRef(current.first)
                );

                // 最后一个拒绝文库获得互补组合
                newRejCompos.get(rejNum - 1).add(reverseCurrent);

                // 判断拒绝文库中是否有此组合
                for (int j = 0; j < rejNum; j++) {

                    // 如果有，
                    if (newRejCompos.get(j).contains(current)) {
                        // 对应ns元素+1
//                        System.out.println(current);
//                        System.out.println(newDegree[j]);
//                        System.out.println(rejAccuRef.get(current));
                        newDegree[j] += rejAccuRef.get(current);
                        // 文库移除一次此组合
                        Iterator<Compos> it = newRejCompos.get(j).iterator();
                        while (it.hasNext()) {
                            Compos compos = (Compos) it.next();
                            if (compos.equals(current)) {
                                it.remove();
                                break;
                            }
                        }
                    }
                }
                diGui(newDegree,newChain,newRejCompos);
            }
        } else {
            if(stopFlag){
                return;
            }
            // 首先对上一次的结果进行判断
            // 等于规定的链长才有可能是正确结果
            if (lastChain.length() == resultLength) {
                boolean etNumOne = false;
                // 判断非特异性数组中是否有大于1的元素
                for(int x=0;x<degree.length;x++){
                    double maxValue = maxNS.get(x);
                    if (degree[x] > maxValue) {
                        etNumOne = true;
                        break;
                    }
                }
                // 通过特异性验证
                if (!etNumOne) {
                    // 计算CG碱基数量
                    double cgRate;
                    int CGNum = 0;
                    for(int index =0; index<lastChain.length();index++){
                        char charToCG = lastChain.charAt(index);
                        if(charToCG == 'C' || charToCG == 'G'){
                            CGNum++;
                        }
                    }
                    cgRate = (CGNum+0.0)/resultLength;
                    if(cgRate>=minCGRate && cgRate<=maxCGRate){
                        // 成功情况， 保留此Result
                        Result result = new Result();
                        result.id = resultArrayList.size()+1;
                        result.chain = lastChain;
                        result.cgRate = cgRate;
                        result.degree = degree;

                        char lastChar = '0';
                        int length = 1;
                        boolean overMaxSequence = false;
                        for(int x=0; x<lastChain.length();x++){
                            if(lastChar == lastChain.charAt(x)){
                                length++;
                                if(length>maxSequenceRef.get(lastChar)){
                                    overMaxSequence = true;
                                    break;
                                }
                            }else {
                                length = 1;

                            }
                            lastChar = lastChain.charAt(x);
                        }

                        if(!overMaxSequence) {
                            System.out.println("process:  "+result.chain+"  succeed");
                            resultArrayList.add(result);
                        }
                        if(generateNum == 0){
                            // 暂时看不懂这种情况
                        }else if(generateNum == -1){
                            // 继续遍历出所有情况
                        }else {
                            // 设置停止flag
                            if(resultArrayList.size()>=generateNum){
                                stopFlag = true;
                            }
                        }
                    }
                }
            }else {
                // 这里的lastChain的长度一定没有到达resultLength
                for(int i=0;i<totalCompos.size();i++){
                    char lastChar = lastChain.charAt(lastChain.length()-1);
                    Compos current = totalCompos.get(i);
                    char currentFirstChar = current.first;
                    if (lastChar == currentFirstChar) {
                        ArrayList<List<Compos>> newRejCompos = deepCopy(rejCompos);
                        double[] newDegree = degree.clone();
                        String newChain = lastChain + current.last;
                        // 得到此组合的互补组合
                        Compos reverseCurrent = new Compos(
                                getRef(current.last),
                                getRef(current.first)
                        );
                        // 最后一个拒绝文库获得互补组合
                        newRejCompos.get(rejNum - 1).add(reverseCurrent);
                        // 判断拒绝文库中是否有此组合
                        for (int j = 0; j < rejNum; j++) {
                            // 如果有，
                            if (newRejCompos.get(j).contains(current)) {
                                // 对应ns元素+1
                                newDegree[j] += rejAccuRef.get(current);
                                // 文库移除一次此组合
                                Iterator<Compos> it = newRejCompos.get(j).iterator();
                                while (it.hasNext()) {
                                    Compos compos = (Compos) it.next();
                                    if (compos.equals(current)) {
                                        it.remove();
                                        break;
                                    }
                                }
                            }
                        }
                        System.out.println("process:  "+newChain);
                        diGui(newDegree, newChain, newRejCompos);
                    }
                }
            }
        }
    }

    public static ArrayList deepCopy(ArrayList src) throws IOException, ClassNotFoundException {
        ByteArrayOutputStream byteOut = new ByteArrayOutputStream();
        ObjectOutputStream out = new ObjectOutputStream(byteOut);
        out.writeObject(src);
        ByteArrayInputStream byteIn = new ByteArrayInputStream(byteOut.toByteArray());
        ObjectInputStream in = new ObjectInputStream(byteIn);
        ArrayList dest = (ArrayList) in.readObject();
        return dest;
    }

    public static ArrayList<Compos> generateComposStartWith(String string) {
        ArrayList<Compos> arrayList = new ArrayList<>();
        for(int i=0;i<4;i++){
            for(int j=0;j<4;j++){
                arrayList.add(new Compos(string.charAt(i),string.charAt(j)));
            }
        }
        return arrayList;
    }

    /**
     * 获得一个序列的碱基对组合
     *
     * @param input1 输入的碱基序列
     * @return List, 碱基组合的列表
     */
    public static ArrayList<Compos> getComposList(String input1) {
        ArrayList<Compos> result = new ArrayList<>();
        for (int i = 1; i < input1.length(); i++) {
            Compos newCompos = new Compos(input1.charAt(i - 1)
                    , input1.charAt(i));
            result.add(newCompos);
        }
        return result;
    }


    /**
     * 获得一个序列的反向序列
     */
    public static String getReverseRef(String input) {

        StringBuilder output = new StringBuilder();
        for (int i = input.length()-1; i > -1; i--) {

            char current = input.charAt(i);
            output.append(getRef(current));
        }
        return output.toString();
    }

    /**
     * 得到碱基的互补字符
     */
    public static char getRef(char origin) {

        if (ref.containsKey(origin)) {
            return ref.get(origin);
        } else {
            System.out.println("输入的字符错误");
            throw new RuntimeException();
        }
    }

    public static String formatDouble(double d) {
        return df.format(d);
    }

    public static String[] formatDoubleArray(double[] ds) {
        String[] strings = new String[ds.length];
        int i = 0;
        for (double d : ds) {
            strings[i++] = formatDouble(d);
        }
        return strings;
    }
}

/**
 * 两个碱基形成一个碱基组合
 */
class Compos implements Comparable<Compos>,Serializable {
    char first;
    char last;

    public Compos(char first, char last) {
        this.first = first;
        this.last = last;
    }

    @Override
    public boolean equals(Object o){
        if(o instanceof Compos){
            Compos compos = (Compos)o;
            if(compos.first == this.first && compos.last==this.last){
                return true;
            }
        }
        return false;
    }

    @Override
    public int compareTo(Compos o) {

        if (this.first == o.first
                && this.last == o.last) {
            return 0;
        } else {
            return 1;
        }
    }

    @Override
    public int hashCode(){
        return this.first*100+this.last;
    }

    @Override
    public String toString(){
        return this.first+" "+this.last;
    }
}

class Result implements Serializable{
    int id;
    String chain;
    double[] degree;
    double cgRate;
}