BWT算法在生物信息学中的应用（二）-算法实现

上一节中，介绍了BWT算法的基本原理，本节主要使用C++来完成BWT算法。主要思路基于上一节中的思想。
编码部分：
1.循环移位
2.排序
3.取最后一列

解码部分：
1.CalculatePreSum方法，用来获得在L列的每个字符是前面有几个同样的字符。
2.CalculateFirstIndex方法，用来标识在F列中，每一个字符的第一个字符出现的起始位置。
3.GetLastSeq方法，根据PreSum和FirstIndex，得到在L列中读取的顺序。
4.倒序赋值到pOutOriginalArray中。

class DataCompress{public:    DataCompress();    ~DataCompress();    bool BWTEncodeing(char* pOutFirstArray, char* pOutLastArray, int* pOutLastIndexSeq, const string &strInput);    bool BTWDecoding(char* pInFirstArray, char* pInLastArray, char* pOutOriginalArray);private:    string cyclicShift(const string &strInput, int n);    void calculatePreSum(int *pOutPreSum, const char *pInLastArray, int len);    void calculateFirstIndex(char *pInFirstArray, int *pOutFirstIndex, int len);    void getLastSeq(char* pInLastArray, int *pInCheckPreSum, int *pInPreSumIndex, int *pInOutLastIndexSeq, int len);};

DataCompress::DataCompress(){}DataCompress::~DataCompress(){}bool DataCompress::BWTEncodeing(char* pOutFirstArray, char* pOutLastArray, int* pOutLastIndexSeq, const string &strInput){    const int len = strInput.size();    string *strArray = new string[len];    //1. Circule shift    for (int i = 0; i < len; i++)    {        strArray[i] = cyclicShift(strInput,i);    }    //2. sort    sort(strArray, strArray + len);    //3. set LastArray    for (int i = 0; i < len; i++)    {        pOutFirstArray[i] = strArray[i][0];        pOutLastArray[i] = strArray[i][len - 1];    }    if (NULL != strArray)    {        delete[] strArray;        strArray = NULL;    }    return true;}bool DataCompress::BTWDecoding(char* pInFirstArray, char* pInLastArray, char* pOutOriginalArray){    //1. get preSum    int len = strlen(pInLastArray);    int *pCheckPreSum = new int[len];    memset(pCheckPreSum, 0, sizeof(int) * len);    calculatePreSum(pCheckPreSum, pInLastArray, len);    //2. Get preSum Index    int *pPreSumIndex = new int[4];    memset(pPreSumIndex, 0, sizeof(int) * 4);    calculateFirstIndex(pInFirstArray, pPreSumIndex, len);    //3. Get Last Seq    int* pLastIndexSeq = new int[len];    memset(pLastIndexSeq, 0, sizeof(int)*(len));    getLastSeq(pInLastArray, pCheckPreSum, pPreSumIndex, pLastIndexSeq, len);    //4. set out array    for (int i = 0; i < len; i++)    {        pOutOriginalArray[i] = pInLastArray[pLastIndexSeq[len - i - 1]];    }    if (NULL != pCheckPreSum)    {        delete[] pCheckPreSum;        pCheckPreSum = NULL;    }    if (NULL != pPreSumIndex)    {        delete[] pPreSumIndex;        pPreSumIndex = NULL;    }    if (NULL != pLastIndexSeq)    {        delete[] pLastIndexSeq;        pLastIndexSeq = NULL;    }    return true;}string DataCompress::cyclicShift(const string &strInput, int n){    int len = strInput.length();    if (n >= len)    {        n = n % len;    }    string firstStrPart = strInput.substr(0, n);    string secondStrPart = strInput.substr(n);    string resultStr = secondStrPart.append(firstStrPart);    return resultStr;}void DataCompress::calculatePreSum(int *pOutPreSum, const char *pInLastArray, int len){    int preA = 0;    int preC = 0;    int preG = 0;    int preT = 0;    for (int i = 0; i < len; i++)    {        switch (pInLastArray[i])        {        case 'A':            pOutPreSum[i] = preA;            preA++;            break;        case 'C':            pOutPreSum[i] = preC;            preC++;            break;        case 'G':            pOutPreSum[i] = preG;            preG++;            break;        case 'T':            pOutPreSum[i] = preT;            preT++;            break;        default:            break;        }    }}void DataCompress::calculateFirstIndex(char *pInFirstArray, int *pOutFirstIndex, int len){    for (int i = 0; i < len; i++)    {        switch (pInFirstArray[i])        {        case 'A':            pOutFirstIndex[1]++;            pOutFirstIndex[2]++;            pOutFirstIndex[3]++;            break;        case 'C':            pOutFirstIndex[2]++;            pOutFirstIndex[3]++;            break;        case 'G':            pOutFirstIndex[3]++;            break;        case 'T':            break;        default:            break;        }    }    return;}void DataCompress::getLastSeq(char* pInLastArray, int *pInCheckPreSum, int *pInPreSumIndex,     int *pInOutLastIndexSeq, int len){    for (int i = 0; i < len; i++)    {        switch (pInLastArray[pInOutLastIndexSeq[i]])        {        case 'A':            pInOutLastIndexSeq[i + 1] = pInPreSumIndex[0] + pInCheckPreSum[pInOutLastIndexSeq[i]] + 1;            break;        case 'C':            pInOutLastIndexSeq[i + 1] = pInPreSumIndex[1] + pInCheckPreSum[pInOutLastIndexSeq[i]] + 1;            break;        case 'G':            pInOutLastIndexSeq[i + 1] = pInPreSumIndex[2] + pInCheckPreSum[pInOutLastIndexSeq[i]] + 1;            break;        case 'T':            pInOutLastIndexSeq[i + 1] = pInPreSumIndex[3] + pInCheckPreSum[pInOutLastIndexSeq[i]] + 1;            break;        default:            break;        }    }    return;}