优化DNA序列基因查找算法：解决大字符串处理中的停靠密码子定位问题

public class part1 {
    // 查找停靠密码子
    public int findStopCodon(String dna, int startIndex, String stopCodon) {
        int stopIndex = dna.indexOf(stopCodon, startIndex);
        if (stopIndex != -1) {
            // 检查从startIndex到stopIndex+3的长度是否为3的倍数
            if (dna.substring(startIndex, stopIndex + 3).length() % 3 == 0) {
                return stopIndex;
            }
        }
        return dna.length(); // 问题所在：如果第一个停靠密码子无效，则直接返回DNA长度
    }

    // 查找单个基因
    public String findGene(String dna, int startIndex) {
        if (startIndex != -1) {
            int taaIndex = findStopCodon(dna, startIndex, "TAA");
            int tgaIndex = findStopCodon(dna, startIndex, "TGA");
            int tagIndex = findStopCodon(dna, startIndex, "TAG");

            int temp = Math.min(taaIndex, tgaIndex);
            int minIndex = Math.min(temp, tagIndex);
            if (minIndex <= dna.length() - 3) {
                return dna.substring(startIndex, minIndex + 3);
            }
        }
        return "";
    }

    // 查找所有基因并存储
    public StorageResource allGenes(String dna) {
        StorageResource geneList = new StorageResource();
        int prevIndex = 0;
        while (prevIndex <= dna.length()) {
            int startIndex = dna.indexOf("ATG", prevIndex);
            if (startIndex == -1) {
                return geneList;
            }
            String gene = findGene(dna, startIndex);
            if (!gene.isEmpty()) {
                geneList.add(gene);
            }
            prevIndex = startIndex + gene.length() + 1;
        }
        return geneList;
    }
}