package OSI.SSI.ASU.OSU.PSU.MSU.pds;
//这个函数用于元基进行数字逻辑丝化变换
//思想：肽展公式，十六 十七进制元基数字，元基数字逻辑
//作者：罗瑶光
//算法参考如下（肽展公式在离散数学中根据贝叶斯进行数字逻辑变换）
//#### 元基数字  =   元基符号=   肽展公式元基数字变换 = (肽概率展开数字逻辑集合)
//#### 0  =    D  =   DD =(D, DD)         
//#### E   =    I  =   I  =(I) 
//#### F   =    U  =   I++ OR Q--  =(I, Q) 
//#### G   =    Q  =    Q  =(Q) 
//
//#### 1  =    C  =    DI  =(DI) 
//#### 3   =    E  =    IU, DU  =(IU, DU) 
//#### 4   =    H  =    (IU, DU) OR DI  =(IU, DU, DI) OR (IUDI, DUDI) 
//#### D   =    V  =   UQ  =(UQ) 
//#### 9   =    S  =   QI  =(QI) 
//
//
//#### 2   =    P  =   (IU, DU) + DI  =(IUDI, DUDI) 
//#### 5   =    HC =    ((IU, DU) OR DI) + DI  =(IUDI, DUDI, DIDI) OR (IUDIDI
//, DUDIDI)
//#### B   =    HE =    ((IU, DU) OR DI) + (IU, DU)  =(IUIU, IUDU, DUIU, DUDU
//, DIIU, DIDU) OR (IUDIIU, IUDIDU, DUDIIU, DUDIDU) 
//#### A   =    O  =   (IU, DU) + QI  =(IUQI, DUQI) 
//#### 7   =    A  =   UQQI  =(UQQI) 
//
//
//#### 8   =    M  =   ((IU, DU) OR DI) + DI + QI  =(IUDIQI, DUDIQI, DIDIQI)
//OR (IUDIDIQI, DUDIDIQI) 
//#### 6   =    X  =    UQ + ((IU, DU) OR DI) + DI  =(UQIUDI, UQDUDI, UQDIDI) 
//OR (UQIUDIDI, UQDUDIDI)
//#### C   =    T  =   UQ + ((IU, DU) OR DI) + (IU, DU)  =(UQIUIU, UQIUDU,
//UQDUIU, UQDUDU, UQDIIU, UQDIDU) OR (UQIUDIIU, UQIUDIDU, UQDUDIIU, UQDUDIDU) 


//根据结构式进行分析 全嘌呤肽展公式PDE PDS。罗瑶光20211201
//F全嘌呤 = E OR C OR S = E OR S OR C = (IU, DU) OR QI OR DI = (IUQIDI, DUQIDI)
// 排列方式为 活泼组合E + 稳定组合S + 中性组合C

//作者,著作权人： 罗瑶光，浏阳
public class PDE_PDS_DL16 {
  public String initonPDSwithBYS(String initon, double bys, StringBuilder pDEKey
      , boolean isBys) {
    if(initon.equalsIgnoreCase("D")) {
      return "D";
    }
    if(initon.equalsIgnoreCase("I")) {
      return "I";
    }
    if(initon.equalsIgnoreCase("U")) {
      if(!isBys) {
        if(Math.random()< 0.5) {
          pDEKey.append("0");
          return "I";  
        }else {
          pDEKey.append("1");
          return "Q";
        }
      }else {
        if(Math.random()< bys) {
          pDEKey.append("0");
          return "I";  
        }else {
          pDEKey.append("1");
          return "Q";
        }  
      }
    }
    if(initon.equalsIgnoreCase("Q")) {
      return "Q";
    }

    if(initon.equalsIgnoreCase("C")) {
      return "DI";
    }
    if(initon.equalsIgnoreCase("E")) {
      if(!isBys) {
        if(Math.random()< 0.5) {
          pDEKey.append("0");
          return "IU";  
        }else {
          pDEKey.append("1");
          return "DU";
        }
      }else {
        if(Math.random()< bys) {
          pDEKey.append("0");
          return "IU";  
        }else {
          pDEKey.append("1");
          return "DU";
        }
      }
    }
    //#### 4   =    H  =    (IU, DU) OR DI  =(IU, DU, DI) OR (IUDI, DUDI) 
    if(initon.equalsIgnoreCase("H")) {
      if(!isBys) {
        if(Math.random()< 0.5) {
          pDEKey.append("0");
          return "IUDI";  
        }else {
          pDEKey.append("1");
          return "DUDI";
        }
      }else {
        if(Math.random()< bys) {
          pDEKey.append("0");
          return "IUDI";  
        }else {
          pDEKey.append("1");
          return "DUDI";
        }
      }
    }

    //+- 符号见 FindOulerRing 函数 的 332行。
    //#### 5   =    HC =    ((IU, DU) OR DI) + DI  
    //=(IUDI, DUDI, DIDI) OR (IUDIDI, DUDIDI)
    if(initon.equalsIgnoreCase("-")) {  
      if(!isBys) {
        if(Math.random()< 0.5) {
          pDEKey.append("0");
          return "IUDIDI";  
        }else {
          pDEKey.append("1");
          return "DUDIDI";
        }
      }else {
        if(Math.random()< bys) {
          pDEKey.append("0");
          return "IUDIDI";  
        }else {
          pDEKey.append("1");
          return "DUDIDI";
        }
      }
    }
    //+- 符号见 FindOulerRing 函数 的 332行。
    //#### B   =    HE =    ((IU, DU) OR DI) + (IU, DU)  
    //=(IUIU, IUDU, DUIU, DUDU, DIIU, DIDU) OR (IUDIIU, IUDIDU, DUDIIU
    //, DUDIDU) 
    if(initon.equalsIgnoreCase("+")) {
      if(!isBys) {
        if(Math.random()< 0.5) {
          pDEKey.append("0");
          if(Math.random()< 0.5) {
            pDEKey.append("0");
            return "IUDIIU";  
          }else {
            pDEKey.append("1");
            return "IUDIDU";
          }  
        }else {
          pDEKey.append("1");
          if(Math.random()< 0.5) {
            pDEKey.append("0");
            return "DUDIIU";  
          }else {
            pDEKey.append("1");
            return "DUDIDU";
          }
        }
      }else {
        if(Math.random()< bys) {
          pDEKey.append("0");
          if(Math.random()< bys) {
            pDEKey.append("0");
            return "IUDIIU";  
          }else {
            pDEKey.append("1");
            return "IUDIDU";
          }  
        }else {
          pDEKey.append("1");
          if(Math.random()< bys) {
            pDEKey.append("0");
            return "DUDIIU";  
          }else {
            pDEKey.append("1");
            return "DUDIDU";
          }
        }
      }
    }
    if(initon.equalsIgnoreCase("V")) {
      return "UQ";
    }
    if(initon.equalsIgnoreCase("S")) {
      return "QI";
    }
    //#### 2   =    P  =   (IU, DU) + DI  =(IUDI, DUDI) 
    if(initon.equalsIgnoreCase("P")) {
      if(!isBys) {
        if(Math.random()< 0.5) {
          pDEKey.append("0");
          return "IUDI";  
        }else {
          pDEKey.append("1");
          return "DUDI";
        }
      }else {
        if(Math.random()< bys) {
          pDEKey.append("0");
          return "IUDI";  
        }else {
          pDEKey.append("1");
          return "DUDI";
        }
      }
    }
    //#### A   =    O  =   (IU, DU) + QI  =(IUQI, DUQI) 
    if(initon.equalsIgnoreCase("O")) {
      if(!isBys) {
        if(Math.random()< 0.5) {
          pDEKey.append("0");
          return "IUQI";  
        }else {
          pDEKey.append("1");
          return "DUQI";
        }
      }else {
        if(Math.random()< bys) {
          pDEKey.append("0");
          return "IUQI";  
        }else {
          pDEKey.append("1");
          return "DUQI";
        }
      }
    }
    if(initon.equalsIgnoreCase("A")) {
      return "UQQI";
    }
    //根据结构式进行分析 全嘌呤肽展公式PDE PDS。罗瑶光20211201
    //F全嘌呤 = E OR C OR S = E OR S OR C = (IU, DU) OR QI OR DI = (IUQIDI, DUQIDI)
    // 排列方式为 活泼组合E + 稳定组合S + 中性组合C
    if(initon.equalsIgnoreCase("F")) {
      if(!isBys) {
        if(Math.random()< 0.5) {
          pDEKey.append("0");
          return "IUQIDI";   
        }else {
          pDEKey.append("1");
          return "DUQIDI";  
        }
      }else {
        if(Math.random()< bys) {
          pDEKey.append("0");
          return "IUQIDI";    
        }else {
          pDEKey.append("1");
          return "DUQIDI";    
        }
      }
    }
    //#### 8   =    M  =   ((IU, DU) OR DI) + DI + QI  
    //=(IUDIQI, DUDIQI, DIDIQI) OR (IUDIDIQI, DUDIDIQI) 
    if(initon.equalsIgnoreCase("M")) {
      if(!isBys) {
        if(Math.random()< 0.5) {
          pDEKey.append("0");
          return "IUDIDIQI";  
        }else {
          pDEKey.append("1");
          return "DUDIDIQI";
        }
      }else {
        if(Math.random()< bys) {
          pDEKey.append("0");
          return "IUDIDIQI";  
        }else {
          pDEKey.append("1");
          return "DUDIDIQI";
        }
      }

    }
    //#### 6   =    X  =    UQ + ((IU, DU) OR DI) + DI 
    // =(UQIUDI, UQDUDI, UQDIDI) OR (UQIUDIDI, UQDUDIDI)
    if(initon.equalsIgnoreCase("X")) {
      if(!isBys) {
        if(Math.random()< 0.5) {
          pDEKey.append("0");
          return "UQIUDIDI";  
        }else {
          pDEKey.append("1");
          return "UQDUDIDI";
        }
      }else {
        if(Math.random()< bys) {
          pDEKey.append("0");
          return "UQIUDIDI";  
        }else {
          pDEKey.append("1");
          return "UQDUDIDI";
        }
      }

    }
    //#### C   =    T  =   UQ + ((IU, DU) OR DI) + (IU, DU)  
    //=(UQIUIU, UQIUDU, UQDUIU, UQDUDU, UQDIIU, UQDIDU) OR (UQIUDIIU, UQIUDIDU, UQDUDIIU, UQDUDIDU) 
    if(initon.equalsIgnoreCase("T")) {    
      if(!isBys) {
        if(Math.random()< 0.5) {
          pDEKey.append("0");
          if(Math.random()< 0.5) {
            pDEKey.append("0");
            return "UQIUDIIU";  
          }else {
            pDEKey.append("1");
            return "UQIUDIDU";
          }
        }else {
          pDEKey.append("1");
          if(Math.random()< 0.5) {
            pDEKey.append("0");
            return "UQDUDIIU";  
          }else {
            pDEKey.append("1");
            return "UQDUDIDU";
          }
        }
      }else {
        if(Math.random()< bys) {
          pDEKey.append("0");
          if(Math.random()< bys) {
            pDEKey.append("0");
            return "UQIUDIIU";  
          }else {
            pDEKey.append("1");
            return "UQIUDIDU";
          }
        }else {
          pDEKey.append("1");
          if(Math.random()< bys) {
            pDEKey.append("0");
            return "UQDUDIIU";  
          }else {
            pDEKey.append("1");
            return "UQDUDIDU";
          }
        }
      }
    }
    return initon;//出现null 的脏字符串，
  }
  //IUQ D CEVS H POA -+ MXT
  //反向排列后如下
  //TXM +- AOP H SVEC D QUI
  public String initonPDIwithBYS(String pds, double bys, StringBuilder pDEKey
      , boolean isBys) {
    pds= pds.replace("UQIUDIIU", "T");
    pds= pds.replace("UQIUDIDU", "T");
    pds= pds.replace("UQDUDIIU", "T");
    pds= pds.replace("UQDUDIDU", "T");
    pds= pds.replace("UQIUDIDI", "X");
    pds= pds.replace("UQDUDIDI", "X");
    pds= pds.replace("IUDIDIQI", "M");
    pds= pds.replace("DUDIDIQI", "M");
    pds= pds.replace("IUDIIU", "+");
    pds= pds.replace("IUDIDU", "+");
    pds= pds.replace("DUDIIU", "+");
    pds= pds.replace("DUDIDU", "+");
    pds= pds.replace("IUDIDI", "-");
    pds= pds.replace("IUQIDI", "F");//增加F PDE
    pds= pds.replace("DUQIDI", "F");
    pds= pds.replace("UQQI", "A");
    pds= pds.replace("IUQI", "O");
    pds= pds.replace("DUQI", "O");
    pds= pds.replace("IUDI", "P");
    pds= pds.replace("DUDI", "P");    
    pds= pds.replace("IUDI", "H");
    pds= pds.replace("DUDI", "H");
    pds= pds.replace("QI", "S");
    pds= pds.replace("UQ", "V");
    pds= pds.replace("IU", "E");
    pds= pds.replace("DU", "E");  
    pds= pds.replace("DI", "C");  
    pds= pds.replace("D", "D");  
    pds= pds.replace("Q", "Q");  
    pds= pds.replace("U", "U");  
    pds= pds.replace("I", "I");
    return pds;
  }

  //用于肽展公式逐级变换
  //QUI  D  SVEC  H AOP +-  TXM 
  public String initonPDEwithBYS(String pds, double pDE_KEY_rate, StringBuilder
      pDEKey, boolean isBys) {
    if(!isBys) {
      pds= pds.replace("Q", "Q");  
      pds= pds.replace("U", "D");
      pds= pds.replace("I", "I");
      pds= pds.replace("D", "D");
      pds= pds.replace("QI", "S");
      pds= pds.replace("UQ", "V");
      pds= pds.replace("IU", "E");
      pds= pds.replace("DU", "E");
      pds= pds.replace("DI", "C");
      pds= pds.replace("IUDI", "H");
      pds= pds.replace("DUDI", "H");
      pds= pds.replace("UQQI", "A");
      pds= pds.replace("IUQI", "O");
      pds= pds.replace("DUQI", "O");
      pds= pds.replace("IUDI", "P");
      pds= pds.replace("DUDI", "P");  
      pds= pds.replace("IUDIIU", "+");
      pds= pds.replace("IUDIDU", "+");
      pds= pds.replace("DUDIIU", "+");
      pds= pds.replace("DUDIDU", "+");
      pds= pds.replace("IUDIDI", "-");
      pds= pds.replace("DUDIDI", "-");
      pds= pds.replace("UQIUDIIU", "T");
      pds= pds.replace("UQIUDIDU", "T");
      pds= pds.replace("UQDUDIIU", "T");
      pds= pds.replace("UQDUDIDU", "T");
      pds= pds.replace("UQIUDIDI", "X");
      pds= pds.replace("UQDUDIDI", "X");
      pds= pds.replace("IUDIDIQI", "M");
      pds= pds.replace("DUDIDIQI", "M");
      return pds;
    }
    pds= pds.replace("Q", "Q");  
    pds= pds.replace("U", "U");
    pds= pds.replace("I", "I");
    pds= pds.replace("D", "D");
    pds= pds.replace("QI", "S");
    pds= pds.replace("UQ", "V");

    if(Math.random()<pDE_KEY_rate) {
      pds= pds.replace("IU", "E");
    }else {
      pds= pds.replace("DU", "E");
    }

    pds= pds.replace("DI", "C");

    if(Math.random()< pDE_KEY_rate) {
      pds= pds.replace("IUDI", "H");
    }else {
      pds= pds.replace("DUDI", "H");
    }

    pds= pds.replace("UQQI", "A");

    if(Math.random()<pDE_KEY_rate) {
      pds= pds.replace("IUQI", "O");
    }else {
      pds= pds.replace("DUQI", "O");
    }

    if(Math.random()< pDE_KEY_rate) {
      pds= pds.replace("IUDI", "P");
    }else {
      pds= pds.replace("DUDI", "P");  
    }

    if(Math.random()< pDE_KEY_rate) {
      if(Math.random()<pDE_KEY_rate) {
        pds= pds.replace("IUDIIU", "+");
      }else {
        pds= pds.replace("IUDIDU", "+");
      }
    }else {
      if(Math.random()< pDE_KEY_rate) {
        pds= pds.replace("DUDIIU", "+");
      }else {
        pds= pds.replace("DUDIDU", "+");
      }
    }

    if(Math.random()< pDE_KEY_rate) {
      pds= pds.replace("IUDIDI", "-");
    }else {
      pds= pds.replace("DUDIDI", "-");
    }


    if(Math.random()< pDE_KEY_rate) {
      if(Math.random()< pDE_KEY_rate) {
        pds= pds.replace("UQIUDIIU", "T");
      }else {
        pds= pds.replace("UQIUDIDU", "T");
      }
    }else {
      if(Math.random()< pDE_KEY_rate) {
        pds= pds.replace("UQDUDIIU", "T");
      }else {
        pds= pds.replace("UQDUDIDU", "T");
      }
    }

    if(Math.random()< pDE_KEY_rate) {
      pds= pds.replace("UQIUDIDI", "X");
    }else {
      pds= pds.replace("UQDUDIDI", "X");
    }

    if(Math.random()<pDE_KEY_rate) {
      pds= pds.replace("IUDIDIQI", "M");
    }else {
      pds= pds.replace("DUDIDIQI", "M");
    }

    if(Math.random()<pDE_KEY_rate) {
      pds= pds.replace("IUQIDI", "F");//增加F PDE
    }else {
      pds= pds.replace("DUQIDI", "F");
    }
    
    return pds;
  }

  //融合肽展公式，离散数学和数字逻辑 的元基变换
  //  pds= pds.replace("UQ", "V");
  //  pds= pds.replace("DI", "C");
  //  pds= pds.replace("IQ", "S");
  //  pds= pds.replace("VS", "A");
  //  pds= pds.replace("ES", "O");
  //  pds= pds.replace("EC", "P");
  //  pds= pds.replace("CS", "M");
  //  pds= pds.replace("VE", "T");
  //  pds= pds.replace("VC", "X");
  // 我的思维逻辑是先将PDS的数字逻辑和离散数学归纳识别，然后走肽展识别，最大缩短元基长度
  public String initonPDE_DCDLwithBYS(String pds, double pDE_KEY_rate
      , StringBuilder pDEKey, boolean isBys) {
    if(!isBys) {
      pds= pds.replace("UQIUDIIU", "T");//UQIUDIIU
      pds= pds.replace("UQIUDIDU", "T");
      pds= pds.replace("UQDUDIIU", "T");
      pds= pds.replace("UQDUDIDU", "T");
      pds= pds.replace("UQIUDIDI", "X");
      pds= pds.replace("UQDUDIDI", "X");
      pds= pds.replace("IUDIDIQI", "M");
      pds= pds.replace("DUDIDIQI", "M");
      pds= pds.replace("IUDIIU", "+");
      pds= pds.replace("IUDIDU", "+");
      pds= pds.replace("DUDIIU", "+");
      pds= pds.replace("DUDIDU", "+");
      pds= pds.replace("IUDIDI", "-");
      pds= pds.replace("DUDIDI", "-");
      
      pds= pds.replace("IUQIDI", "F");//增加F PDE
      pds= pds.replace("DUQIDI", "F");
      
      pds= pds.replace("IUDI", "H");
      pds= pds.replace("DUDI", "H");
      pds= pds.replace("UQQI", "A");
      pds= pds.replace("IUQI", "O");
      pds= pds.replace("DUQI", "O");
      pds= pds.replace("IUDI", "P");
      pds= pds.replace("DUDI", "P");
      pds= pds.replace("QI", "S");
      pds= pds.replace("UQ", "V");
      pds= pds.replace("IU", "E");
      pds= pds.replace("DU", "E");
      pds= pds.replace("DI", "C");
      pds= pds.replace("Q", "Q");  
      pds= pds.replace("U", "D");
      pds= pds.replace("I", "I");
      pds= pds.replace("D", "D");

      //PDE
      pds= pds.replace("VS", "A");
      pds= pds.replace("ES", "O");
      pds= pds.replace("EC", "P");
      pds= pds.replace("HE", "+");
      pds= pds.replace("HC", "-");
      pds= pds.replace("VE", "T");
      pds= pds.replace("VC", "X");
      pds= pds.replace("CS", "M");

      return pds;
    }
    if(Math.random()< pDE_KEY_rate) {
      if(Math.random()< pDE_KEY_rate) {
        pds= pds.replace("UQIUDIIU", "T");
      }else {
        pds= pds.replace("UQIUDIDU", "T");
      }
    }else {
      if(Math.random()< pDE_KEY_rate) {
        pds= pds.replace("UQDUDIIU", "T");
      }else {
        pds= pds.replace("UQDUDIDU", "T");
      }
    }
    if(Math.random()< pDE_KEY_rate) {
      pds= pds.replace("UQIUDIDI", "X");
    }else {
      pds= pds.replace("UQDUDIDI", "X");
    }
    if(Math.random()<pDE_KEY_rate) {
      pds= pds.replace("IUDIDIQI", "M");
    }else {
      pds= pds.replace("DUDIDIQI", "M");
    }
    if(Math.random()< pDE_KEY_rate) {
      if(Math.random()<pDE_KEY_rate) {
        pds= pds.replace("IUDIIU", "+");
      }else {
        pds= pds.replace("IUDIDU", "+");
      }
    }else {
      if(Math.random()< pDE_KEY_rate) {
        pds= pds.replace("DUDIIU", "+");
      }else {
        pds= pds.replace("DUDIDU", "+");
      }
    }
    if(Math.random()< pDE_KEY_rate) {
      pds= pds.replace("IUDIDI", "-");
    }else {
      pds= pds.replace("DUDIDI", "-");
    }
    
    if(Math.random()<pDE_KEY_rate) {
      pds= pds.replace("IUQIDI", "F");//增加F PDE
    }else {
      pds= pds.replace("DUQIDI", "F");
    }
    
    if(Math.random()< pDE_KEY_rate) {
      pds= pds.replace("IUDI", "H");
    }else {
      pds= pds.replace("DUDI", "H");
    }
    pds= pds.replace("UQQI", "A");
    if(Math.random()<pDE_KEY_rate) {
      pds= pds.replace("IUQI", "O");
    }else {
      pds= pds.replace("DUQI", "O");
    }
    if(Math.random()< pDE_KEY_rate) {
      pds= pds.replace("IUDI", "P");
    }else {
      pds= pds.replace("DUDI", "P");  
    }
    pds= pds.replace("QI", "S");
    pds= pds.replace("UQ", "V");
    if(Math.random()<pDE_KEY_rate) {
      pds= pds.replace("IU", "E");
    }else {
      pds= pds.replace("DU", "E");
    }
    pds= pds.replace("DI", "C");
    pds= pds.replace("D", "D");
    pds= pds.replace("Q", "Q");  
    pds= pds.replace("U", "U");
    pds= pds.replace("I", "I");
    //PDE
    pds= pds.replace("VS", "A");
    pds= pds.replace("ES", "O");
    pds= pds.replace("EC", "P");
    pds= pds.replace("HE", "+");
    pds= pds.replace("HC", "-");
    pds= pds.replace("VE", "T");
    pds= pds.replace("VC", "X");
    pds= pds.replace("CS", "M");
    return pds;
  }
}