java - 我不明白为什么我的 if 语句有效

Question

所以如果序列 1 :CAG 和序列 2 :AG，我应该得到响应

"Best alignment score :2 CAG AG"

但是我得到了

"Best alignment score :0 CAG AG"

我相信我的问题出在第二个 if 语句中，就像调试器中的情况一样。

当使用调试器时，它显示计算机没有进入 if 语句。

public static int allignment (String dnaSequence1 , String dnaSequence2 /*,int offset*/){
    int newScore = 0;
    int bestScore = 0;
    int newOffset = 0;
    int bestOffset = 0;

    for(int offset =0; offset<=(dnaSequence1.length()-dnaSequence2.length());offset++){
        //newOffset ++;
        newScore = 0;
        for(int place =0; place<dnaSequence2.length();place++ ){
            if(dnaSequence1.charAt(place) == dnaSequence2.charAt(place/*+offset*/)){

                newScore ++;
                if(newScore>bestScore){
                    bestScore = newScore;
                    bestOffset = newOffset;

                }
            }else{ continue;}
        }
        newOffset ++;
    }

    String space = " ";
    System.out.println("Best alignment score :"+bestScore);
    System.out.println(dnaSequence1);
    System.out.print( space(bestOffset) + dnaSequence2);

    int alignmentScore = dnaSequence1.compareToIgnoreCase(dnaSequence2);

    return alignmentScore;
}

public static String space (int bestOffset){
    String space = " ";
    String offsetScaces = "";

    for(int i = 0; i<bestOffset; i++){
        offsetScaces+=space;
        return offsetScaces;
    }
    return offsetScaces;
}

Answer 1

您的版本对两个字符串使用相同的索引。因此，它检查 sequence1 中索引 0 处的核苷酸('C')是否与 sequence2 中索引 0 处的核苷酸('A')匹配，然后递增索引并检查如果 sequence1 中索引 1 处的核苷酸('A')与 sequence2 中索引 1 处的核苷酸('G')匹配，则它将停止而不会找到匹配项。

012
CAG
AG

从上面的示例中可以看出，第一个字符串中的字符永远不会与第二个字符串中的字符相同(0:C/A、1:A/G、2:G/null)

我突然想到，也许您正在寻找与 dnaSequence1 中的某些内容对齐的 dnaSequence2 中最长的片段，而不仅仅是从索引 0 开始的最长片段。

此版本尝试在第一个序列中找到整个第二个序列，如果找不到，它将从第二个序列的末尾修剪 1 个核苷酸，然后重试。一旦将第二个序列修剪为空，它就会再次从整个第二个序列开始，从头开始修剪 1 个核苷酸，然后重复该过程(如果找到匹配则停止)

public static int allignment(String dnaSequence1, String dnaSequence2 /*,int offset*/) {
    int bestScore = -1;
    int bestOffset = 0;
    String bestSequence = null;

    for(String tempSequence = dnaSequence2; tempSequence.length() > 0; tempSequence = tempSequence.substring(1)) {
        for(String match = tempSequence; match.length() > 0; match = match.substring(0, match.length() - 1)) {
            int matchIndex;
            if (-1 != (matchIndex = dnaSequence1.indexOf(match))) {
                if (match.length() > bestScore) {
                    bestOffset = matchIndex;
                    bestScore = match.length() ;
                    bestSequence = match;
                    break;
                }
            }
        }
        if (null != bestSequence && bestScore > tempSequence.length()) {
            break; // don't bother checking any shorter sequences, we already have a better match
        }
    }

    if (null != bestSequence) {
        System.out.println("Best alignment score :" + bestScore);
        System.out.println(dnaSequence1);
        System.out.print(space(bestOffset) + bestSequence);
    } else {
        System.out.print(dnaSequence1+" and "+dnaSequence2+" cannot be aligned");
    }

    int alignmentScore = dnaSequence1.compareToIgnoreCase(dnaSequence2);

    return alignmentScore;
}

public static String space(int bestOffset) {
    StringBuilder builder = new StringBuilder();

    for (int i = 0; i < bestOffset; i++) {
        builder.append(" ");
    }
    return builder.toString();
}