import java.util.*;

public class matchseq
{
    private String seq1 = "";           //the source sequence
    private String seq2 = "";           //the recognition sequence
    private char allele1 = ' '; 
    private char allele2 = ' ';
    private int snploc = 0;
    private int misloc = 0;
    private int len1 = 0;
    private int len2 = 0;

    public matchseq (String s1, String s2, char c1, char c2, int p1, int p2)
    {
        seq1 = s1;
        seq2 = s2;
        allele1 = c1;
        allele2 = c2;
        snploc = p1;
        misloc = p2;
        len1 = seq1.length();
        len2 = seq2.length();
    }

    //a method the check whether two nucleotides match each other
    private boolean checksnp (char ch1, char ch2)
    {
        //ch1 is snp allele, ch2 is allele in recognition sequence
        if (ch1 == 'A')
        {
            if ((ch2 == 'A') || (ch2 == 'R') || (ch2 == 'H') ||
                (ch2 == 'V') || (ch2 == 'N') || (ch2 == 'M') ||
                (ch2 == 'W') || (ch2 == 'D'))
                return true;
        }

        else if (ch1 == 'T')
        {
            if ((ch2 == 'T') || (ch2 == 'K') || (ch2 == 'H') ||
                (ch2 == 'Y') || (ch2 == 'N') || (ch2 == 'B') ||
                (ch2 == 'W') || (ch2 == 'D'))
                return true;
        }

        else if (ch1 == 'G')
        {
            if ((ch2 == 'G') || (ch2 == 'R') || (ch2 == 'K') ||
                (ch2 == 'Y') || (ch2 == 'N') || (ch2 == 'S') ||
                (ch2 == 'B') || (ch2 == 'D'))
                return true;
        }

        else if (ch1 == 'C')
        {
            if ((ch2 == 'C') || (ch2 == 'H') || (ch2 == 'V') ||
                (ch2 == 'Y') || (ch2 == 'N') || (ch2 == 'S') ||
                (ch2 == 'B') || (ch2 == 'M'))
                return true;
        }

        return false;
    }

    //a method to check whether the two sequences match each other
    private boolean checkseq (int p)
    {
        int p1 = 0;
        int p2 = 0;
        boolean mismatchIn = false;

        //move backwards and compare one by one
        for (int i=1; i<(p+1) && i<snploc; i++)
        {
            p1 = snploc - i - 1;
            p2 = p - i;
            if (seq1.charAt(p1) != seq2.charAt(p2))
                return false;
            else if (p1 == misloc - 1)
                mismatchIn = true;
        }

        //move forwards and compare one by one
        for (int i=0; i<(len1-snploc) && i<(len2-p-1); i++)
        {
            p1 = snploc + i;
            p2 = p + i + 1;
            if (seq1.charAt(p1) != seq2.charAt(p2))
                return false;
            else if (p1 == misloc - 1)
                mismatchIn = true;
        }

        //check whether mismatch contributes to the recogintion sequence
        if ((snploc != misloc) && (mismatchIn == false))
            return false;
        
        return true;
    }

    //a method to find the SNP allele in the recognisiton sequence
    //and to check whether the enzyme serves as a candidate
    public int anchorseq()
    {
        boolean allele1OK = false;
        boolean allele2OK = false;

        //source sequence not long enough?!
        if (len1 <= len2)
            return -1;

        for (int i=0; i<len2; i++)
        {
            if (checksnp(allele1, seq2.charAt(i)) && checksnp(allele2, seq2.charAt(i)))
                {} //not a good recognition sequence, do nothing
            else if (checksnp(allele1, seq2.charAt(i)))
            {
                if (checkseq(i) == true)
                    allele1OK = true;
            }
            else if (checksnp(allele2, seq2.charAt(i)))
            {
                if (checkseq(i) == true)
                    allele2OK = true;
            }
        }

        if ((allele1OK == true) && (allele2OK == true))
            return -1;
        else if (allele1OK == true)
            return 1;
        else if (allele2OK == true)
            return 2;
        else
            return -1;
    }
}