[자바 정리노트] DNA 염기 서열 분석 예제

/**
 * Created by Gney on 2017-07-13.
 */
public class Practice {
    public static void main(String[] args) {
        String dna = "GATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCA"
                + "CCACGCCCGGCTAATTTTTATTTATTTATTTAAAGACAGAGTCTCACTCT"
                + "GTCACTCAGGCTAGAGTGCAGTGGCACCATCTCAGCTCACTGCAGCCTTG"
                + "ACCTCCCTGGGCTCCGGTGATTTCACCCTCCCAAGTAGCTAGGACTACAG"
                + "GCACATGCCACGACACCCAGCTAATTTTTTATTTTCTGTGAAGTCAAGGT"
                + "CTTGCTACGTTGCCCATGCTGGTATCAAACCCCTGGGCTCAATCAATCCT"
                + "TCCACCTCAGCCTCCCCAAGTATTGGGGTTACAGGCATGAGCTACCACAC"
                + "TCAGCCCTAGCCTACTTGAAACGTGTTCAGAGCATTTAAGTTACCCTACA"
                + "GTTGGGCAAAGTCATCTAACACAAAGCCCTTTTTATAGTAATAAAATGTT"
                + "GTATATCTCATGTGATTTATTGAATATTGTTACTGAAAGTGAGAAACAGC"
                + "ATGGTTGCATGAAAGGAGGCACAGTCGAGCCAGGCACAGCCTGGGCGCAG"
                + "AGCGAGACTCAAAAAAAGAAAAGGCCAGGCGCACTGGCTCACGCCTGTAA"
                + "TCCCAGCATTTCGGGAGGCTGAGGCGGGTGGATCACCTGAGGTCAGGAGT"
                + "TCAAGACCAGCCTAGCCAACATGGTGAAACCCCGTCTCTACTAAAATACA"
                + "AAAATTAACCGGGCGTGATGGCAGGTGCCTGTAATCCCAGCTACTTGGGA"
                + "GGCTGAGGCAGGAGAATCGCTTGAACCAGGAGGCGGAGGTTGCAGGGAGC"
                + "CAAGATGGCGCCACTGCACTCCAGCCTGGGCGATAGAGTGAGACTCCGTC"
                + "TCAGAAAAAAAAGAAAAGAAACGAGGCACAGTCGCATGCACATGTAGTCC"
                + "CAGTTACTTGAGAGGCTAAGGCAGGAGGATCTCTTGAGCCCAAGAGTTTG"
                + "AGTCCAGCCTGAACAACATAGCAAGACATCATCTCTAAAATTTAAAAAAG"
                + "GGCCGGGCACAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGTGGA"
                + "GGTGGGTAGATCACCTGACGTCAGGAGTTGGAAACCAGCCTGGCTAACAT";

        char[] charArray = dna.toCharArray();
        char[] current = new char[4];
        int cnt1=0;
        int cnt2=0;
        int cnt3=0;

        for (int i = 0; i < charArray.length - 3; i++) {
            for (int j = 0; j < current.length; j++) {
                current[j] = charArray[i + j];
            }

            String stringFromCharArr = new String(current);

            switch(stringFromCharArr) {
                case "TAGG":
                    cnt1++;
                    break;
                case "CCAG":
                    cnt2++;
                    break;
                case "AGCC":
                    cnt3++;
                    break;
            }

        }

        System.out.println("TAGG: " + cnt1);
        System.out.println("CCAG: " + cnt2);
        System.out.println("AGCC: " + cnt3);


    }
}