//fine name: doPrimer.java, Done on 01 November 2000

import java.io.*;
import java.util.*;

public class doPrimer {

    static int InputCount = 22;      //expected number of inputs
    public static void main(String[] args) {

        String seq = "";             //source sequence
        int snploc = 0;              //position of snp in sequence
        String allele1 = "";         //first snp allele
        String allele2 = "";         //second snp allele
        int optprimersize = 0;       //optimum primer size
        int maxprimersize = 0;       //maximum primer size
        int minprimersize = 0;       //minimum primer size
        int optproductsize = 0;      //optimum product size
        int maxproductsize = 0;      //maximum product size
        int minproductsize = 0;      //minimum product size
        double maxsizedif = 0;       //maximum relative size difference of inner products
        double minsizedif = 0;       //minimum relative size difference of inner products
        double optprimerTm = 0;      //optimum primer Tm
        double maxprimerTm = 0;      //maximum primer Tm
        double minprimerTm = 0;      //minimum primer Tm
        double maxprimergc = 0;      //maximum primer GC%
        double minprimergc = 0;      //minimum primer GC%
        double maxprimercom = 0;     //maximum primer complementarity
        double maxprimer3com = 0;    //maximum primer 3' complementarity
        double saltconc = 0;         //salt (K+) concentration in mM
        double primerconc = 0;       //primer concentration in nM
        int numoutput = 0;           //number of outputs

        //work out the input values
        StringTokenizer st = new StringTokenizer(args[0]);
        int currentcount = st.countTokens();
        if (currentcount == InputCount)
        {
            seq = st.nextToken();
            snploc = Integer.valueOf(st.nextToken()).intValue();
            allele1 = st.nextToken().toUpperCase();
            allele2 = st.nextToken().toUpperCase();
            optprimersize = Integer.valueOf(st.nextToken()).intValue();
            maxprimersize = Integer.valueOf(st.nextToken()).intValue();
            minprimersize = Integer.valueOf(st.nextToken()).intValue();
            optproductsize = Integer.valueOf(st.nextToken()).intValue();
            maxproductsize = Integer.valueOf(st.nextToken()).intValue();
            minproductsize = Integer.valueOf(st.nextToken()).intValue();
            maxsizedif = Double.valueOf(st.nextToken()).doubleValue();
            minsizedif = Double.valueOf(st.nextToken()).doubleValue();
            optprimerTm = Double.valueOf(st.nextToken()).doubleValue();
            maxprimerTm = Double.valueOf(st.nextToken()).doubleValue();
            minprimerTm = Double.valueOf(st.nextToken()).doubleValue();
            maxprimergc = Double.valueOf(st.nextToken()).doubleValue();
            minprimergc = Double.valueOf(st.nextToken()).doubleValue();
            maxprimercom = Double.valueOf(st.nextToken()).doubleValue();
            maxprimer3com = Double.valueOf(st.nextToken()).doubleValue();
            saltconc = Double.valueOf(st.nextToken()).doubleValue();
            primerconc = Double.valueOf(st.nextToken()).doubleValue();
            numoutput = Integer.valueOf(st.nextToken()).intValue();

//            System.out.println("Source sequence - ");
//            if (seq.length() < 81)
//                System.out.println(seq);
//            else
//            {
//                int i = 0;
//                int p = 0;
//                p = seq.length() / 80 + 1;
//                for (i=0; i<p; i++)
//                {
//                    if (i == 0)
//                        System.out.println(seq.substring(0, 80));
//                    else if (seq.length() <= (i+1)*80+1)
//                        System.out.println(seq.substring(i*80));
//                    else if (seq.length() > (i+1)*80+1)
//                        System.out.println(seq.substring((i*80), (i+1)*80));
//                }
//            }
        }
        else
        {
            System.out.println("Only " + currentcount + " out of " + InputCount + " inputs - Abort!");
            return;
        }

        //validate the input sequence: 1) snploc should be greater than input
        //sequence length. 2) Allele 1 should be the same as the Nucleotide as
        //indicated by snploc in the sequence. 3) Allele 1 and 2 should not be
        //'N' (unknown). 4) at least (minimum product size - maximum primer
        //size) before the SNP location. 5) at least (minimum product size -
        //maximum primer size) after the SNP location. 
        if ((snploc >= seq.length()) ||
            (snploc < minproductsize - maxprimersize) ||
            (seq.length() - snploc < minproductsize - maxprimersize))
        {
            System.out.println("Input sequence too short to design primers");
            return;
        }
        else if (allele1.equalsIgnoreCase(seq.substring(snploc, (snploc+1))))
        {
            System.out.println("Allele 1 not agree with allele in input sequence");
            return;
        }
        else if ((allele1.equalsIgnoreCase("N")) || (allele2.equalsIgnoreCase("N")))
        {
            System.out.println("Undefined SNP Input!");
            return;
        }
        
        Lock1 l1 = new Lock1(); 
        Lock2 l2 = new Lock2(); 
        Lock3 l3 = new Lock3(); 
        Lock4 l4 = new Lock4(); 

        innerForward innerf = new innerForward(l1, l2, seq, snploc, allele1, allele2, optprimersize, maxprimersize, minprimersize, optprimerTm, maxprimerTm, minprimerTm, maxprimergc, minprimergc, maxprimercom, maxprimer3com, saltconc, primerconc, numoutput);
        innerReverse innerr = new innerReverse(l2, l3, seq, snploc, allele1, allele2, optprimersize, maxprimersize, minprimersize, optprimerTm, maxprimerTm, minprimerTm, maxprimergc, minprimergc, maxprimercom, maxprimer3com, saltconc, primerconc);
        outerReverse outerr = new outerReverse(l3, l4, seq, snploc, optprimersize, maxprimersize, minprimersize, optproductsize, maxproductsize, minproductsize, optprimerTm, maxprimerTm, minprimerTm, maxprimergc, minprimergc, maxprimercom, maxprimer3com, saltconc, primerconc);
        outerForward outerf = new outerForward(l1, l4, seq, snploc, allele1, allele2, optprimersize, maxprimersize, minprimersize, optproductsize, maxproductsize, minproductsize, maxsizedif, minsizedif, optprimerTm, maxprimerTm, minprimerTm, maxprimergc, minprimergc, maxprimercom, maxprimer3com, saltconc, primerconc, numoutput);

        innerf.start();
        innerr.start();
        outerr.start();
        outerf.start();

        l1.put(0);

        return;
    }
}