Smith Waterman Java 将字符串转换为字符

Question

我正在尝试在我的 java 代码中实现 Smith-waterman。如果输入只是一个字符一个字符，我成功地实现了这一点。

这是我的代码

public class Smith {

char[] mSeqA;
char[] mSeqB;
int[][] mD;
int mScore;
String mAlignmentSeqA = "";
String mAlignmentSeqB = "";

void init(char[] seqA, char[] seqB) {
    mSeqA = seqA;
    mSeqB = seqB;
    mD = new int[mSeqA.length + 1][mSeqB.length + 1];
    for (int i = 0; i <= mSeqA.length; i++) {
        mD[i][0] = 0;
    }
    for (int j = 0; j <= mSeqB.length; j++) {
        mD[0][j] = 0;
    }
}

void process() {
    for (int i = 1; i <= mSeqA.length; i++) {
        for (int j = 1; j <= mSeqB.length; j++) {
            int scoreDiag = mD[i - 1][j - 1] + weight(i, j);
            int scoreLeft = mD[i][j - 1] - 1;
            int scoreUp = mD[i - 1][j] - 1;
            mD[i][j] = Math.max(Math.max(Math.max(scoreDiag, scoreLeft), scoreUp), 0);
        }
    }
}

void backtrack() {
    int i = 1;
    int j = 1;
    int max = mD[i][j];

    for (int k = 1; k <= mSeqA.length; k++) {
        for (int l = 1; l <= mSeqB.length; l++) {
            if (mD[k][l] > max) {
                i = k;
                j = l;
                max = mD[k][l];
            }
        }
    }

    mScore = mD[i][j];

    int k = mSeqA.length;
    int l = mSeqB.length;

    while (k > i) {
        mAlignmentSeqB += "-";
        mAlignmentSeqA += mSeqA[k - 1];
        k--;
    }
    while (l > j) {
        mAlignmentSeqA += "-";
        mAlignmentSeqB += mSeqB[l - 1];
        l--;
    }

    while (mD[i][j] != 0) {
        if (mD[i][j] == mD[i - 1][j - 1] + weight(i, j)) {
            mAlignmentSeqA += mSeqA[i - 1];
            mAlignmentSeqB += mSeqB[j - 1];
            i--;
            j--;
            continue;
        } else if (mD[i][j] == mD[i][j - 1] - 1) {
            mAlignmentSeqA += "-";
            mAlignmentSeqB += mSeqB[j - 1];
            j--;
            continue;
        } else {
            mAlignmentSeqA += mSeqA[i - 1];
            mAlignmentSeqB += "-";
            i--;
            continue;
        }
    }

    while (i > 0) {
        mAlignmentSeqB += "-";
        mAlignmentSeqA += mSeqA[i - 1];
        i--;
    }
    while (j > 0) {
        mAlignmentSeqA += "-";
        mAlignmentSeqB += mSeqB[j - 1];
        j--;
    }

    mAlignmentSeqA = new StringBuffer(mAlignmentSeqA).reverse().toString();
    mAlignmentSeqB = new StringBuffer(mAlignmentSeqB).reverse().toString();
}

private int weight(int i, int j) {
    if (mSeqA[i - 1] == mSeqB[j - 1]) {
        return 2;
    } else {
        return -1;
    }
}

void printMatrix() {
    System.out.print("D =       ");
    for (int i = 0; i < mSeqB.length; i++) {
        System.out.print(String.format("%4c ", mSeqB[i]));
    }
    System.out.println();
    for (int i = 0; i < mSeqA.length + 1; i++) {
        if (i > 0) {
            System.out.print(String.format("%4c ", mSeqA[i - 1]));
        } else {
            System.out.print("     ");
        }
        for (int j = 0; j < mSeqB.length + 1; j++) {
            System.out.print(String.format("%4d ", mD[i][j]));
        }
        System.out.println();
    }
    System.out.println();
}

void printScoreAndAlignments() {
    System.out.println("Score: " + mScore);
    System.out.println("Sequence A: " + mAlignmentSeqA);
    System.out.println("Sequence B: " + mAlignmentSeqB);
    System.out.println();
}

public static void main(String[] args) {

    char[] seqB = {'A', 'C', 'G', 'A'};
    char[] seqA = {'T', 'C', 'C', 'G'};

    Smith sw = new Smith();
    sw.init(seqA, seqB);
    sw.process();
    sw.backtrack();

    sw.printMatrix();
    sw.printScoreAndAlignments();
}

}

如果我有像字符串“164164617044”和“1461646144”这样的输入，我该如何处理 m 代码 求帮助，谢谢...

Answer 1

您可以通过使用内置的字符串函数toCharArray() 将输入字符串简单地转换为字符数组来做到这一点。

让程序的其余部分保持原样，并将输入的字符串转换成这样的字符数组。

public static void main(String[] args) {

    String s1 = "164164617044";
    String s2 = "1461646144";
    char[] seqB = s1.toCharArray();
    char[] seqA = s2.toCharArray();

    Smith sw = new Smith();
    sw.init(seqA, seqB);
    sw.process();
    sw.backtrack();

    sw.printMatrix();
    sw.printScoreAndAlignments();
}

上面的Strings会自动转换成char数组。