Ticket #1: main.cpp

/*
 * main.cpp
 *
 *  Created on: Feb 24, 2014
 *      Author: Ismail
 */

#include <time.h>
#include <iostream>
#include <stdio.h>
#include <algorithm>
#include <fstream>
#include <string>
#include <vector>
#include <cstring>
#include <cmath>
#include <map>
#include "functions.h"
#include <stdio.h>
#include <ctype.h>
#include <sstream>
using namespace std;


int main()
{

        //cout << -DBL_MAX << endl;
        //cout << "Enter the second number: ";
        //cin >> num2;
        //outputFile << "1" << "\t\t\t" << "0.7" << "\t\t\t" << "0.8" << endl;
        //cout << "Enter the third number: ";
        //cin >> num3;
        //outputFile << num3 << endl;
        //cout << "Enter the fourth number: ";
        //cin >> num4;
        //outputFile << num4 << endl;
        //cout << "Enter the fifth number: ";
        //cin >> num5;
        //outputFile << num5 << endl;

        //cout << "Done!\n";

        //string number;
        //ostringstream strstream;

        /*
        strstream << 111;
        number = strstream.str();
        cout << number << endl;
        strstream.str("");
        strstream << 110;
        number = strstream.str();
        cout << number << endl;
        */


        //      141     142     143
        //      141     142     144
        //      141     143     144
        //      142     143     144

        //cout << "Hello World!" << endl;

        //int a = 10;
        //int b = 20;
        //double c = (double)a/b;

        string one = "AAA";
        string two = "AAA";

        if (one == two)
        {
                int wait = 0;
        }

        //int dim3;
        //for (dim3 = one.length(); dim3 >= 0; dim3--)
        //{
                //cout << dim3 << " ";
        //}

        int no_of_seqs = 3;
        functions obj;

        //obj.x1 = "GCGCCCUUAGCUC";             //obj.x1 = "GCGCCCUUAGCUC";
        //obj.x2 = "GGCCCUAGCU";                //obj.x2 = "G-GCCCU-AGCU-";
        //obj.x3 = "GCGCCCUACUC";               //obj.x3 = "GCGCCCU-A-CUC";
        //obj.x1 = "GGGAAAUUAAUGUGAA";  //obj.x1 = "GGGAAAUUAAUGUGAA"   "UGGGAAAUUAAUGUGAA";
        //obj.x2 = "GGGAAUAAUGUGAA";    //obj.x2 = "GGGA-AU-AAUGUGAA"   "UGG-AAAUUAAUG-GAA";
        //obj.x3 = "GGGAAUUAAUGUGAA";   //obj.x3 = "GGGA-AUUAAUGUGAA"   "UGG-AAAUUAAUGUGAA";
        //obj.x1 = "GCGC";//obj.x1 = "GCGC";
        //obj.x2 = "GCC";       //obj.x3 = "GC.C";
        //obj.x3 = "GC";        //obj.x2 = "GC..";
        //obj.x1 = "ACCCGGCCAUAGUGGCCGGGCAACACCCGGUCUCGUUUCGAACCCGGAAGUUAAGCCGGCCACGUCAGAACGGCCGUGAGGUCCGAGAGGCCUCGCAGCCGUUCUGAGCUGGGAU";
        //obj.x2 = "ACCCGGCCAUAGCGGCCGGGCAACACCCGGACUCAUGUCGAACCCGGAAGUUAAGCCGGCCGCGUUGGGGGAUGCUGUGGGGUCCGCGAGGCCCCGCAGCGCCCCCAAGCCGGGAU";
        //obj.x3 = "ACCCGGCAAUAGGCGCCGGUGCUACGCCCGGUCUCUUCAGAACCCGGAAGCUAAGGCCGGCGCCGCGGACGGGAGUACUGGGGUCCGCGAGGCCCCGGGAAACCGCCGUGCUGGGA";

        //obj.x1 = "ACCCGGUCACAGUGAGCGGGCAACACCCGGACUCAUUUCGAACCCGGAAGUUAAGCCGCUCACGUUAGUGGGGCCGUGGAUACCGUGAGGAUCCGCAGCCCCACUAAGCUGGGAU";
        //obj.x2 = "ACCCGGCCACAGUGAGCGGGCAACACCCGGACUCAUUUCGAACCCGGAAGUUAAGCCGCUCACGUUGGUGGGGCCGUGGAUACCGUGAGGAUCCGCAGCCCCACUAAGCUGGGAU";
        //obj.x3 = "ACCCGGUCAUAGUGAGCGGGUAACACCCGGACUCGUUUCGAACCCGGAAGUUAAGCCGCUCACGUCAGAGGGGCCGUGGGAUCCGAGAGGGCCCGCAGCCUCUCUGAGCUGGGAU";

        //obj.x1 = "GUAGCGGCCACAGCGGUGGGGUUCCUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCCACCAGCGUUCCGGGGAUACUGGAGUGCGCGACCCUCUGGGAAACCGGGUUCGCCGCUAC";
        //obj.x2 = "AGUGGUGGCCAUAUCGGCGGGGUUCCUCCCCGUACCCAUCCUGAACACGGAAGAUAAGCCCGCCAGCGUCCGGCAAUACUGGAGUGCGCGAGCCUCUGGGAAAUCCGGUUCGCCGCCAC";
        //obj.x3 = "GGCGGCCACAGCGGUGGGGUUGCCUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCCACCAGCGUUCCAGGGAUACUGGAGUGCGCGAGCCUCUGGGAAAUCCGGUUCGCCGCCA";

        //obj.x1 = "UAAGGCGGCCAUAGCGGUGGGGUUACUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCCGCCUGCGUUCCGGUCAGUACUGGAGUGCGCGAGCCUCUGGGAAAUCCGGUUCGCCGCCUACU";
        //obj.x2 = "GCGGCCAGGGCGGAGGGGAAACACCCGUACCCAUUCCGAACACGGAAGUGAAGCCCUCCAGCGAACCAGCUAGUACUAGAGUGGGAGACCCUCUGGGAGCGCUGGUUCGCCGCC";
        //obj.x3 = "UUGGCGACCAUAGCGGCGAGUGACCUCCCGUACCCAUCCCGAACACGGAAGAUAAGCUCGCCUGCGUUUCGGUCAGUACUGGAUUGGGCGACCCUCUGGGAAAUCUGAUUCGCCGCCACC";

        //obj.x1 = "GCGGCCACAGCGGCGGGGCGACUCCCGUACCCAUCCCGAACACGGCAGAUAAGCCCGCCAGCGUUCCAGCGAGUACUGGAGUGUGCGAACCUCUGGGAAAACUG";
        //obj.x2 = "GGGCGGCCAGAGCGGUGAGGUUCCACCCGUACCCAUCCCGAACACGGAAGUUAAGCUCGCCUGCGUUCUGGUCAGUACUGGAGUGAGCGAUCCUCUGGGAAAUCCAGUUCGCCGCCCCU";
        //obj.x3 = "GGCGGCCAGAGCGGUGAGGUUCCACCCGUACCCAUCCCGAACACGGAAGUUAAGCUCACCUGCGUUCUGGUCAGUACUGGAGUGAGCGAUCCUCUGGGAAAUCCAGUUCGCCGCCC";


        //obj.x1 = "AAUU";      //"A-AUU"
        //obj.x2 = "AUAU";      //"AUAU-"
        //obj.x3 = "AAU";       //"A--U-"

        for (int count = 1; count < pow(2, no_of_seqs); count++)
        {
                obj.states.push_back(obj.dec_2_bin((long)count));
                //cout << obj.states[count-1] << endl;
        }

        obj.string_parser_prob("hmmparam_states_3seq.txt");             // reading state transition parameters
        obj.string_parser_prob("hmmparam_emissions_3seq.txt");  // reading state emission parameters
        obj.prob_matrix_fill();                                                                 // forming matrix of all probabilities of emission
        // cout << obj.emission_double.size() << endl;
        obj.vector_assigner();

        obj.map_fill();

        char c[] = "emissions.txt";
        obj.string_parser_emission(c);


        /*// viterbi testing
        obj.viterbi_matrix_initialisation();
        obj.viterbi_3seq();
        cout << "x1_aligned: " << obj.x1_aligned_reverse << endl;
        cout << "x2_aligned: " << obj.x2_aligned_reverse << endl;
        cout << "x3_aligned: " << obj.x3_aligned_reverse << endl;*/

        //cout << "state trans: " << obj.prev_state_to_111["111"] << endl;

        //cout << "index for '..C': " << obj.emission_indexes["..C"] << endl;
        //cout << "index for '..G': " << obj.emission_indexes["..G"] << endl;
        //cout << "index for 'AAA': " << obj.emission_indexes["AAA"] << endl;

        // Reading Sequences

        // printing sequences
        // char a[] = "3_aligned_seq.aa";
        // char a[] = "RF00005.seed.aa";
        // char a[] = "RF00100.aa";     // 45 choose 3 possible combinations
        // char a[] = "RF01689.aa";     // 144 choose 3 possible combinations
        // obj.readfasta(a);

        /*char a[] = "5s-rRNA.aa";      // 144 choose 3 possible combinations
        obj.readfasta(a);
        //cout << "length of seqs: " << obj.seqs.size() << endl;

        //char b[] = "45choose3.txt";
        char b[] = "120choose3.txt";  // testing for 487343 different combinations
        obj.string_parser(b);
        obj.standardiser();*/

        //cout << "obj.seq_combinations.size: " << obj.seq_combinations.size() << endl;

        //cout << "final combination: " << obj.seq_combinations[280839][0] << " " << obj.seq_combinations[280839][1] << " " << obj.seq_combinations[280839][2] << endl;

        //cout << "seq1: " << obj.seqs[0] << endl;
        //cout << "seq2: " << obj.seqs[1] << endl;
        //cout << "seq3: " << obj.seqs[2] << endl;

        //int seq_count;
        //cout << "size of seq_comb: " << obj.seq_combinations.size() << endl;

        //ofstream outputFile;
        //outputFile.open("measurementparameters.txt");
        cout << "combo#" << "\t\t" << "PPV" << "\t\t\t" << "Sensitivity" << endl;
        //outputFile << "combo#" << "\t\t" << "PPV" << "\t\t\t" << "Sensitivity" << endl;

        char a[] = "5s-rRNA.aa";        // 144 choose 3 possible combinations
        obj.readfasta(a);

        char b[] = "120choose3.txt";  // testing for 487343 different combinations
        obj.string_parser(b);
        obj.standardiser();

        string known1, known2, known3;

        //obj.x1_aligned_reverse = "AAA";
        //obj.x2_aligned_reverse = "AAG";
        //obj.x3_aligned_reverse = "A.A";

        //obj.x1_aligned_reverse = "ACCCGGUCACAGUGAGCGGGCAACACCCGGACUCAUUUCGAACCCGGAAGUUAAGCCGCUCACGUUAGUGGG.GCCGUGGAUACCGUGAGGAUCCGCAG.CCCCACUAAGCUGGGAU";
        //obj.x2_aligned_reverse = "ACCCGGCCACAGUGAGCGGGCAACACCCGGACUCAUUUCGAACCCGGAAGUUAAGCCGCUCACGUUGGUGGG.GCCGUGGAUACCGUGAGGAUCCGCAG.CCCCACUAAGCUGGGAU";
        //obj.x3_aligned_reverse = "ACCCGGUCAUAGUGAGCGGGUAACACCCGGACUCGUUUCGAACCCGGAAGUUAAGCCGCUCA.CGUCAGAGGGGCCGUGGGAUCCGAGAGGGCCCGCAGCCUCUCUGA.GCUGGGAU";

        //obj.x1_aligned_reverse = "ACCCGGCCAUAGUGGCCGG.GCAACACCCGGUCUCGUUUCGAACCCGGAAGUUAAGCCGGCCACGUCAGAACG....GCCGUGAGGUCCGAGAGGCCUCGCAGCCGUUCUGAGCUGGGAU";
        //obj.x2_aligned_reverse = "ACCCGGCCAUAGCGGCCGG.GCAACACCCGGACUCAUGUCGAACCCGGAAGUUAAGCCGGCCGCGUUGG...GGGAUGCUGUGGGGUCCGCGAGGCCCCGCAGCGCCCCCAAGCCGGGAU";
        //obj.x3_aligned_reverse = "ACCCGGCAAUAGGCGCCGGUGCUACGCCCGGUCUC.UUCAGAACCCGGAAGCUAAGGCCGGCGCCGCGG.ACGGGA.GUACUGGGGUCCGCGAGGCCCCGGGAAACCGCCGUGCUGGGA.";

        //obj.known1 = "ACCCGGCCAUAGU.GGCCGGGCAACACCCGGUCUCGUUUCGAACCCGGAAGUUAAGCCGGCCACGUCAG..AACG.GCCGUGAGGUCCGAGAGG.CCUCGCAGCCGUU.CUGAGCUGGGAU";
        //obj.known2 = "ACCCGGCCAUAGC.GGCCGGGCAACACCCGGACUCAUGUCGAACCCGGAAGUUAAGCCGGCCGCGUUGG..GGGAUGCUGUGGGGUCCGCGAGGCCCC.GCAGCGCCC.CCAAGCCGGGAU";
        //obj.known3 = "ACCCGGCAAUAGGCGCCGGUGCUACGCCCGGUCUCUUCA.GAACCCGGAAGCUAAGGCCGGCG.CCGCGGACGGGAGUACUGGGGUCCGCGAGGCCCCGGGAA.ACCGCCGU.GCUGGGA.";

        obj.x1_aligned_reverse = "G..CGGCCACAGCGGCGGGGCGACUCCCGUACCCAUCCCGAACACGGCAGAUAAGCCCGCCAGCGUUCCAGCGAGUACUGGAGUGUGCGAACCUCUGGGAAAACUG.............";
        obj.x2_aligned_reverse = "GGGCGGCCAGAGCGGUGAGGUUCCACCCGUACCCAUCCCGAACACGGAAGUUAAGCUCGCCUGCGUUCUGGUCAGUACUGGAGUGAGCGAUCCUCUGGGAAAUCCAGUUCGCCGCCCCU";
        obj.x3_aligned_reverse = "GG.CGGCCAGAGCGGUGAGGUUCCACCCGUACCCAUCCCGAACACGGAAGUUAAGCUCACCUGCGUUCUGGUCAGUACUGGAGUGAGCGAUCCUCUGGGAAAUCCAGUUCGCCGCCC..";

        obj.known1 = "..GCGGCCACAGCGGCGGGGCGACUCCCGUACCCAUCCCGAACACGGCAGAUAAGCCCGCCAGCG.UUCCAGCGA.GUACUGGAGUGUGCGAACCUCUGGGAA.AACU....G........";
        obj.known2 = "GGGCGGCCAGAGCGGUGAGGUUCCACCCGUACCCAUCCCGAACACGGAAGUUAAGCUCGCCUGCGUUC..UGGUCAGUACUGGAGUGAGCGAUCCUCUGGGAAAUCCAGUUCGCCGCCCCU";
        obj.known3 = ".GGCGGCCAGAGCGGUGAGGUUCCACCCGUACCCAUCCCGAACACGGAAGUUAAGCUCACCUGCGUUC..UGGUCAGUACUGGAGUGAGCGAUCCUCUGGGAAAUCCAGUUCGCCGCCC..";


        obj.alignment_scorer();
        cout << "score_known: " << obj.score_known << endl;
        cout << "score_pred: " << obj.score_pred << endl;
        int wait = 1;



        /*for (int i = 0; i < 50; i++)
        {
                int index1 = obj.seq_combinations[i][0] - 1;
                int index2 = obj.seq_combinations[i][1] - 1;
                int index3 = obj.seq_combinations[i][2] - 1;
                //cout << "index1: " << index1 << endl;
                //cout << "index2: " << index2 << endl;
                //cout << "index3: " << index3 << endl;
                obj.x1 = obj.seqs[index1];
                obj.x2 = obj.seqs[index2];
                obj.x3 = obj.seqs[index3];

                obj.x1.erase(std::remove(obj.x1.begin(), obj.x1.end(), 'X'), obj.x1.end());
                obj.x2.erase(std::remove(obj.x2.begin(), obj.x2.end(), 'X'), obj.x2.end());
                obj.x3.erase(std::remove(obj.x3.begin(), obj.x3.end(), 'X'), obj.x3.end());

                //cout << "i: " << i << endl;
                //cout << "obj.seq_combinations[i][0]: " << obj.seq_combinations[i][0] << endl;
                //cout << "obj.seq_combinations[i][1]: " << obj.seq_combinations[i][1] << endl;
                //cout << "obj.seq_combinations[i][2]: " << obj.seq_combinations[i][2] << endl;
                //cout << "x1_orig: " << obj.x1 << endl;
                //cout << "x2_orig: " << obj.x2 << endl;
                //cout << "x3_orig: " << obj.x3 << endl;

                obj.standardiser2();
                known1 = obj.x1;
                known2 = obj.x2;
                known3 = obj.x3;
                //cout << "after processing: " << endl;
                //cout << "known1: " << known1 << endl;
                //cout << "known2: " << known2 << endl;
                //cout << "known3: " << known3 << endl;

                obj.standardiser3();
                //cout << "x1: " << obj.x1 << endl;
                //cout << "x2: " << obj.x2 << endl;
                //cout << "x3: " << obj.x3 << endl;

                obj.viterbi_matrix_initialisation();
                obj.viterbi_3seq();

                //cout << "x1: " << obj.x1 << endl;
                //cout << "x2: " << obj.x2 << endl;
                //cout << "x3: " << obj.x3 << endl;
                //cout << "x1_aligned: " << obj.x1_aligned_reverse << endl;
                //cout << "x2_aligned: " << obj.x2_aligned_reverse << endl;
                //cout << "x3_aligned: " << obj.x3_aligned_reverse << endl;

                obj.sensitivity_and_ppv_calculator(known1, known2, known3);

                obj.x1_aligned.clear();
                obj.x2_aligned.clear();
                obj.x3_aligned.clear();
                obj.x1_aligned_reverse.clear();
                obj.x2_aligned_reverse.clear();
                obj.x3_aligned_reverse.clear();

                cout << i+1 << "\t\t\t" << obj.ppv << "\t\t\t" << obj.sensitivity << endl;
                //outputFile << i+1 << "\t\t\t" << obj.ppv << "\t\t\t" << obj.sensitivity << endl;
        }

        //outputFile.close();
        cout << "Done!" << endl;*/


        //for (seq_count = 0; seq_count < obj.seq_combinations.size(); seq_count++)
        //{
        //      cout << "index: " << seq_count << endl; // << " " << obj.seq_combinations[seq_count][0] << " "<< obj.seq_combinations[seq_count][1] << " " << obj.seq_combinations[seq_count][2] << endl;
        //}

        /*
        obj.standardiser();
        //obj.emission_prob_calc();
         *
         *
         */

        /*
        string onefourtyone = "AUACUGAAGUUUGGUGGGGAAUCAGUGUGAAAUUCAUUGGCUCUACCUGGAACCGUAAAGUCGGAGCGCCACCCAGUAUAGUCCGUUGUUGAAUGAAGGCCAGGGAAAGUCUAGUUCUACUAAUAAUAA";
        string onefourtytwo = "GUACUGUUAUUAAGGUGGGAAAUGAUGUGAAAUUCAUCAGCUGUGCUCGCAACGGUAAAUUAGUUAAAGUCCGAAGGCCACUCAGUAUAGUCCGGUGUUAGAAAGUAAUCGAGAAGAAUUACAAUCUUACAAUGAAAAA";
        string onefourtythree = "UUCCUAAAAGCAUAGUGGGAAAGAGACGUGUAAUUCGUCCACAUUACUUGAUACGGUGAUAGUCCGAAUGCCACCUAGGAAUAGAUAGAGCAAGGAGACUCAAUGAAUAAAGUAACU";
        string onefourtyfour = "AGGCUGAAAUGCAUGGUGGGAAAUCAGUGUGAAAUUCAUUGGCUGUUCCUGCAACCGUAAAGUCGGAGCGCCACCCAGCUUAGUCCGCUGAUGAAUGAUGGCCAGGAAAAGUCUAAUUCUAUAAUGAAAAA";
        */

        //cout << onefourtyone << endl;
        //cout << onefourtytwo << endl;
        //cout << onefourtythree << endl;

        //obj.x1 = onefourtyone;
        //obj.x2 = onefourtytwo;
        //obj.x3 = onefourtythree;

        //obj.x1 = onefourtyone;
        //obj.x2 = onefourtytwo;
        //obj.x3 = onefourtythree;

        // rRNA seqs:
        //obj.x1 = "ACCCGGCCAUAGUGGCCGGGCAACACCCGGUCUCGUUUCGAACCCGGAAGUUAAGCCGGCCACGUCAGAACGGCCGUGAGGUCCGAGAGGCCUCGCAGCCGUUCUGAGCUGGGAU";
        //obj.x2 = "ACCCGGCCAUAGCGGCCGGGCAACACCCGGACUCAUGUCGAACCCGGAAGUUAAGCCGGCCGCGUUGGGGGAUGCUGUGGGGUCCGCGAGGCCCCGCAGCGCCCCCAAGCCGGGAU";
        //obj.x3 = "ACCCGGCAAUAGGCGCCGGUGCUACGCCCGGUCUCUUCAGAACCCGGAAGCUAAGGCCGGCGCCGCGGACGGGAGUACUGGGGUCCGCGAGGCCCCGGGAAACCGCCGUGCUGGGA";

        //obj.x1 = "ACCCGGUCACAGUGAGCGGGCAACACCCGGACUCAUUUCGAACCCGGAAGUUAAGCCGCUCACGUUAGUGGGGCCGUGGAUACCGUGAGGAUCCGCAGCCCCACUAAGCUGGGAU";
        //obj.x2 = "ACCCGGCCACAGUGAGCGGGCAACACCCGGACUCAUUUCGAACCCGGAAGUUAAGCCGCUCACGUUGGUGGGGCCGUGGAUACCGUGAGGAUCCGCAGCCCCACUAAGCUGGGAU";
        //obj.x3 = "ACCCGGUCAUAGUGAGCGGGUAACACCCGGACUCGUUUCGAACCCGGAAGUUAAGCCGCUCACGUCAGAGGGGCCGUGGGAUCCGAGAGGGCCCGCAGCCUCUCUGAGCUGGGAU";

        //obj.x1 = "GUAGCGGCCACAGCGGUGGGGUUCCUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCCACCAGCGUUCCGGGGAUACUGGAGUGCGCGACCCUCUGGGAAACCGGGUUCGCCGCUAC";
        //obj.x2 = "AGUGGUGGCCAUAUCGGCGGGGUUCCUCCCCGUACCCAUCCUGAACACGGAAGAUAAGCCCGCCAGCGUCCGGCAAUACUGGAGUGCGCGAGCCUCUGGGAAAUCCGGUUCGCCGCCAC";
        //obj.x3 = "GGCGGCCACAGCGGUGGGGUUGCCUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCCACCAGCGUUCCAGGGAUACUGGAGUGCGCGAGCCUCUGGGAAAUCCGGUUCGCCGCCA";

        //obj.x1 = "UAAGGCGGCCAUAGCGGUGGGGUUACUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCCGCCUGCGUUCCGGUCAGUACUGGAGUGCGCGAGCCUCUGGGAAAUCCGGUUCGCCGCCUACU";
        //obj.x2 = "GCGGCCAGGGCGGAGGGGAAACACCCGUACCCAUUCCGAACACGGAAGUGAAGCCCUCCAGCGAACCAGCUAGUACUAGAGUGGGAGACCCUCUGGGAGCGCUGGUUCGCCGCC";
        //obj.x3 = "UUGGCGACCAUAGCGGCGAGUGACCUCCCGUACCCAUCCCGAACACGGAAGAUAAGCUCGCCUGCGUUUCGGUCAGUACUGGAUUGGGCGACCCUCUGGGAAAUCUGAUUCGCCGCCACC";

        //obj.x1 = "GCGGCCACAGCGGCGGGGCGACUCCCGUACCCAUCCCGAACACGGCAGAUAAGCCCGCCAGCGUUCCAGCGAGUACUGGAGUGUGCGAACCUCUGGGAAAACUG";
        //obj.x2 = "GGGCGGCCAGAGCGGUGAGGUUCCACCCGUACCCAUCCCGAACACGGAAGUUAAGCUCGCCUGCGUUCUGGUCAGUACUGGAGUGAGCGAUCCUCUGGGAAAUCCAGUUCGCCGCCCCU";
        //obj.x3 = "GGCGGCCAGAGCGGUGAGGUUCCACCCGUACCCAUCCCGAACACGGAAGUUAAGCUCACCUGCGUUCUGGUCAGUACUGGAGUGAGCGAUCCUCUGGGAAAUCCAGUUCGCCGCCC";


        //obj.x1 = "AUACUGAAGUUUGGUGGGGAAUCAGUGUG";             //"AUACUGAAG.UUUGGUGGGGAAUCAGUGUG"
        //obj.x2 = "GUACUGUUAUUAAGGUGGGAAAUGAUGUG";             //"GUACUGUUAUUAAGGUGGGAAA.UGAUGUG"
        //obj.x3 = "UUCCUAAAAGCAUAGUGGGAAAGAGACGUG";    //"UUCCUAAAAGCAUAGUGGGAAAGAGACGUG"


        //obj.x1 = "GCGC";              //obj.x1 = "GCGC";
        //obj.x2 = "GCG";               //obj.x2 = "GCG-";
        //obj.x3 = "GC";                //obj.x3 = "G--C";

        //obj.x1 = "GCGC";              //obj.x1 = "GCGC";
        //obj.x2 = "GGC";               //obj.x3 = "G-GC";
        //obj.x3 = "GG";                //obj.x2 = "G-G-";

        //int sum = 0;


        /*
        // verifying emission probabilites
        cout << "total emissions in state 010: " << obj.emission_in_states_count[10] << endl;
        for ( map<string, double>::const_iterator iter =  obj.emission_prob.begin(); iter != obj.emission_prob.end(); ++iter)
        {
                if (iter->first[0] == obj.gap && iter->first[1] != obj.gap && iter->first[2] == obj.gap)
                {
                        //cout << "symbol: " << iter->first << " with count: " << iter->second << endl;
                        cout << "symbol: " << iter->first << " with prob: " << iter->second << endl;
                        sum += iter->second;
                }
        }

        cout << sum << endl;

        // verifying state transitions
        cout << obj.prev_state_to_001["10"] << endl;
        cout << obj.prev_state_to_010["10"] << endl;
        cout << obj.prev_state_to_011["10"] << endl;
        cout << obj.prev_state_to_100["10"] << endl;
        cout << obj.prev_state_to_101["10"] << endl;
        cout << obj.prev_state_to_110["10"] << endl;
        cout << obj.prev_state_to_111["10"] << endl;




        //cout << "size of emission prob. collection: " << obj.emission_prob_collection.size() << endl;
        //obj.final_probability_calc();

        //double sum = 0;


        // traversing emission probabilities calculated from entire set of data
        cout << "For state 001" << endl;
        for ( map<string, double>::const_iterator iter = obj.emission_prob.begin(); iter != obj.emission_prob.end(); ++iter)
        {
                if (iter->first[0] == obj.gap && iter->first[1] == obj.gap && iter->first[2] != obj.gap)
                {
                        cout << "emission: " << iter->first << " " << "prob: " << iter->second << endl;
                        sum += iter->second;
                }
        }


        cout << "For state 010" << endl;
        for ( map<string, double>::const_iterator iter = obj.emission_prob.begin(); iter != obj.emission_prob.end(); ++iter)
        {
                if (iter->first[0] == obj.gap && iter->first[1] != obj.gap && iter->first[2] == obj.gap)
                {
                        cout << "emission: " << iter->first << " " << "prob: " << iter->second << endl;
                        sum += iter->second;
                }
        }

        cout << "For state 011" << endl;
        for ( map<string, double>::const_iterator iter = obj.emission_prob.begin(); iter != obj.emission_prob.end(); ++iter)
        {
                if (iter->first[0] == obj.gap && iter->first[1] != obj.gap && iter->first[2] != obj.gap)
                {
                        cout << "emission: " << iter->first << " " << "prob: " << iter->second << endl;
                        sum += iter->second;
                }
        }

        cout << "For state 100" << endl;
        for ( map<string, double>::const_iterator iter = obj.emission_prob.begin(); iter != obj.emission_prob.end(); ++iter)
        {
                if (iter->first[0] != obj.gap && iter->first[1] == obj.gap && iter->first[2] == obj.gap)
                {
                        cout << "emission: " << iter->first << " " << "prob: " << iter->second << endl;
                        sum += iter->second;
                }
        }

        cout << "For state 101" << endl;
        for ( map<string, double>::const_iterator iter = obj.emission_prob.begin(); iter != obj.emission_prob.end(); ++iter)
        {
                if (iter->first[0] != obj.gap && iter->first[1] == obj.gap && iter->first[2] != obj.gap)
                {
                        cout << "emission: " << iter->first << " " << "prob: " << iter->second << endl;
                        sum += iter->second;
                }
        }

        cout << "For state 110" << endl;
        for ( map<string, double>::const_iterator iter = obj.emission_prob.begin(); iter != obj.emission_prob.end(); ++iter)
        {
                if (iter->first[0] != obj.gap && iter->first[1] != obj.gap && iter->first[2] == obj.gap)
                {
                        cout << "emission: " << iter->first << " " << "prob: " << iter->second << endl;
                        sum += iter->second;
                }
        }

        cout << "For state 111" << endl;
        for ( map<string, double>::const_iterator iter = obj.emission_prob.begin(); iter != obj.emission_prob.end(); ++iter)
        {
                if (iter->first[0] != obj.gap && iter->first[1] != obj.gap && iter->first[2] != obj.gap)
                {
                        cout << "emission: " << iter->first << " " << "prob: " << iter->second << endl;
                        sum += iter->second;
                }
        }*/


        //cout << "sum of of emission probabilities in state: " << sum;

        //for ( map<string, double>::const_iterator iter =  obj.prev_state_to_001.begin(); iter != obj.prev_state_to_001.end(); ++iter)
        //{
        //      cout << "state from: " << iter->first << " " << "prob: " << iter->second << endl;
        //}

        /*
        string number;
        stringstream strstream;
        for(int it = 0; it < obj.states.size(); ++it)
        {
                strstream.str("");
                strstream << obj.states[it];
                number = strstream.str();
                cout << "to state 001 from " << obj.states[it] << " " << "with prob: " << obj.prev_state_to_001[number] << endl;
                cout << "to state 010 from " << obj.states[it] << " " << "with prob: " << obj.prev_state_to_010[number] << endl;
                cout << "to state 011 from " << obj.states[it] << " " << "with prob: " << obj.prev_state_to_011[number] << endl;
                cout << "to state 100 from " << obj.states[it] << " " << "with prob: " << obj.prev_state_to_100[number] << endl;
                cout << "to state 101 from " << obj.states[it] << " " << "with prob: " << obj.prev_state_to_101[number] << endl;
                cout << "to state 110 from " << obj.states[it] << " " << "with prob: " << obj.prev_state_to_110[number] << endl;
                cout << "to state 111 from " << obj.states[it] << " " << "with prob: " << obj.prev_state_to_111[number] << endl;
        }
        */


        /*cout << "printing emission_double" << endl;
        for (int i = 0; i < obj.emission_double.size(); i++)
        {
                for (int j = 0; j < obj.emission_double[0].size(); j++)
                {
                        cout << obj.emission_double[i][j] << " ";
                }
                cout << endl;
        }*/


        //cout << "index of ..A: " << obj.emission_indexes["..A"] << endl;
        //cout << "index of ..C: " << obj.emission_indexes["..C"] << endl;
        //cout << "value of prob1: " << obj.emission_double[obj.emission_indexes["..A"]][0] << endl;
        //cout << "value of prob2: " << obj.emission_double[obj.emission_indexes["..C"]][0] << endl;

        //obj.viterbi_matrix_initialisation();
        //obj.viterbi_3seq();
        //obj.forward_algo_3seq();
        //obj.backward_algo_3seq();
        //obj.max_expected_accuracy();

        //cout << "x1_aligned: " << obj.x1_aligned_reverse << endl;
        //cout << "x2_aligned: " << obj.x2_aligned_reverse << endl;
        //cout << "x3_aligned: " << obj.x3_aligned_reverse << endl;

        //cout << "aligned1: " << obj.align1 << endl;
        //cout << "aligned2: " << obj.align2 << endl;
        //cout << "aligned3: " << obj.align3 << endl;

        /*cout << "x1: " << obj.x1 << endl;
        cout << "x2: " << obj.x2 << endl;
        cout << "x3: " << obj.x3 << endl;
        cout << "x1_aligned_reversed: " << obj.x1_aligned << endl;
        cout << "x2_aligned_reversed: " << obj.x2_aligned << endl;
        cout << "x3_aligned_reversed: " << obj.x3_aligned << endl;*/

        //obj.x1_aligned_reverse = "AUACUG.AAGUUUGGUGGGGAAUCAGUGUGAAAUUCAUUGGCUCUACCUGGAACCGUAA.........AGUCGGAGCGCCACCCAGUAUAGUCCGUUGUU.GAAUGAAGGCCAGGGAAAGUCUAGUUCUACUAAUAAUAA.......";
        //obj.x2_aligned_reverse = "GUACUGUUAUUAAGGUGGGAAA.UGAUGUGAAAUUCAUCAGCUGUGCUCGCAACGGUAAAUUAGUUAAAGUCCGAAGGCCACUCAGUAUAGUCCGGUGUUAGAAAGUAAUCGAGAAGAAUUACAAUCUUACAAUGAAAAA.......";
        //obj.x3_aligned_reverse = "UUCCUAAAAGCAUAGUGGGAAAGAGACGUGUAAUUCGUCCACAUUACUUGAUACGGUGAU........AGUCCGAAUGCCACCUAGGAA............UAGAUAGAGCAAGGAGA..........CUCAAUGAAUAAAGUAACU";

        //string one_known = "AUACUGAAG.UUUGGUGGGGAAUCAGUGUGAAAUUCAUUGGCUCUACCUGGAACCGU...AA.A.....GUCGGAGCGCCACCCAGUAU.AGUCCGUUGUUGAAUGAAGGCCAGGGAAAGUC..U.AGUUCUACUAAUAAUA";
        //string two_known = "GUACUGUUAUUAAGGUGGGAAA.UGAUGUGAAAUUCAUCAGCUGUGCUCGCAACGGUAAAUUAGUUAAAGUCCGAAGGCCACUCAGUAU.AGUCCGGUGUUAGAAAGUAAUCGAGAAGAAUU..ACAAUCUUAC.AAUGAAA";
        //string three_known = "UUCCUAAAAGCAUAGUGGGAAAGAGACGUGUAAUUCGUCCACAUUACUUGAUACGGU...GAUA.....GUCCGAAUGCCACCUAGGAAUAGA...........U..AGAGCAAGGAGACUCAAUGAA...UAA.AGUAACU";

        //string one_known =   "AUACUGAAG..UUUGGUGGGGAAUCAGUGUGAAAUUCAUUGGCUCUACCUGGAACCGU...AA.A.....GUCGGAGCGCCACCCAGUAUAGUCCGUUGUUGAAUGAAGGCCAGGGAAAGUCU.AGUUCUACUAAUAAUAA.";
        //string two_known =   "GUACUGUUAU.UAAGGUGGGAAA.UGAUGUGAAAUUCAUCAGCUGUGCUCGCAACGGUAAAUUAGUUAAAGUCCGAAGGCCACUCAGUAUAGUCCGGUGUUAGAAAGUAAUCGAGAAGAAUUACAAUCUUAC.AAUGAAAAA";
        //string three_known = "AGGCUGAAAUGCAUGGUGGGAAAUCAGUGUGAAAUUCAUUGGCUGUUCCUGCAACCGU...AA.A.....GUCGGAGCGCCACCCAGCUUAGUCCGCUGAUGAAUGAUGGCCAGGAAAAGUCU.AAUUCUAU.AAUGAAAAA";

        //string one_known = "AUACUGAAG..UUUGGUGGGGAAUCAGUGUGAAAUUCAUUGGCUCUACCUGGAACCGUAA.AGUCGGAGCGCCACCCAGUAU.AGUCCGUUGUUGAAUGAAGGCCAGGGAAAGUC..U.AGUUCUACUAAUAAUAA.";
        //string two_known = "UUCCUAAAAG.CAUAGUGGGAAAGAGACGUGUAAUUCGUCCACAUUACUUGAUACGGUGAUAGUCCGAAUGCCACCUAGGAAUAGA...........U..AGAGCAAGGAGACUCAAUGAA...UAA.AGUAACU..";
        //string three_known = "AGGCUGAAAUGCAUGGUGGGAAAUCAGUGUGAAAUUCAUUGGCUGUUCCUGCAACCGUAA.AGUCGGAGCGCCACCCAGCUU.AGUCCGCUGAUGAAUGAUGGCCAGGAAAAGUC..U.AAUUCUAU.AAUGAAAAA";

        //string one_known =   "GUACUGUUAU.UAAGGUGGGAAA.UGAUGUGAAAUUCAUCAGCUGUGCUCGCAACGGUAAAUUAGUUAAAGUCCGAAGGCCACUCAGUAU.AGUCCGGUGUUAGAAAGUAAUCGAGAAGAAUU..ACAAUCUUAAAUGAAAAA";
        //string two_known =   "UUCCUAAAAG.CAUAGUGGGAAAGAGACGUGUAAUUCGUCCACAUUACUUGAUACGGU...GAUA.....GUCCGAAUGCCACCUAGGAAUAGA...........U..AGAGCAAGGAGACUCAAUGAA...UAAGUAACU..";
        //string three_known = "AGGCUGAAAUGCAUGGUGGGAAAUCAGUGUGAAAUUCAUUGGCUGUUCCUGCAACCGU...AA.A.....GUCGGAGCGCCACCCAGCUU.AGUCCGCUGAUGAAUGAUGGCCAGGAAAAGUC..U.AAUUCUAAAUGAAAAA";

        // rRNA seqs:
        //string one_known =   "ACCCGGCCAUAGU.GGCCGGGCAACACCCGGUCUCGUUUCGAACCCGGAAGUUAAGCCGGCCACGUCAG..AACG.GCCGUGAGGUCCGAGAGG.CCUCGCAGCCGUU.CUGAGCUGGGAU";
        //string two_known =   "ACCCGGCCAUAGC.GGCCGGGCAACACCCGGACUCAUGUCGAACCCGGAAGUUAAGCCGGCCGCGUUGG..GGGAUGCUGUGGGGUCCGCGAGGCCCC.GCAGCGCCC.CCAAGCCGGGAU";
        //string three_known = "ACCCGGCAAUAGGCGCCGGUGCUACGCCCGGUCUCUUCA.GAACCCGGAAGCUAAGGCCGGCG.CCGCGGACGGGAGUACUGGGGUCCGCGAGGCCCCGGGAA.ACCGCCGU.GCUGGGA.";

        //string one_known =   "ACCCGGUCACAGUGAGCGGGCAACACCCGGACUCAUUUCGAACCCGGAAGUUAAGCCGCUCACGUUAGUGGG.GCCGUGGAUACCGUGAGGAUCCGCAG.CCCCACUAAGCUGGGAU";
        //string two_known =   "ACCCGGCCACAGUGAGCGGGCAACACCCGGACUCAUUUCGAACCCGGAAGUUAAGCCGCUCACGUUGGUGGG.GCCGUGGAUACCGUGAGGAUCCGCAG.CCCCACUAAGCUGGGAU";
        //string three_known = "ACCCGGUCAUAGUGAGCGGGUAACACCCGGACUCGUUUCGAACCCGGAAGUUAAGCCGCUCA.CGUCAGAGGGGCCGUGGGAUCCGAGAGGGCCCGCAGCCUCUCUGA.GCUGGGAU";

        //string one_known =   ".GUAGCGGCCACAGCGGUGGGGUUCC.UC.CCGUACCCAUCCCGAACACGGAAGAUAAGCCCACCAGCGUUCCGGGGA.UACUGGAGUGCGCGACCCUCUGGGAA.ACCGGGUUCGCCGCUAC";
        //string two_known =   "AGUGGUGGCCAUAUCGGCGGGGUUCC.UCCCCGUACCCAUCCUGAACACGGAAGAUAAGCCCGCCAGCG..UCCGGCAAUACUGGAGUGCGCGAGCCUCUGGGAAAUCCGGU.UCGCCGCCAC";
        //string three_known = "...GGCGGCCACAGCGGUGGGGUUGCCUC.CCGUACCCAUCCCGAACACGGAAGAUAAGCCCACCAGCGUUCCAGGGA.UACUGGAGUGCGCGAGCCUCUGGGAA.AUCCGGUUCGCCGCCA.";

        //string one_known =   "UAAGGCGGCCAUAGCGGUGGGGUUACUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCCGCCUGCGUUCCGGUCAGUACUGGAGUGCGCGAGCCUCUGGGAAAUCCGGUUCGCCGCCUACU";
        //string two_known =   "....GCGGCCAGGGCGGAGGGGAAACACCCGUACCCAUUCCGAACACGGAAGUGAAGCCCUCCAGCGAACCAGCUAGUACUAGAGUGGGAGACCCUCUGGGAGCGCUGGUUCGCCGCC....";
        //string three_known = ".UUGGCGACCAUAGCGGCGAGUGACCUCCCGUACCCAUCCCGAACACGGAAGAUAAGCUCGCCUGCGUUUCGGUCAGUACUGGAUUGGGCGACCCUCUGGGAAAUCUGAUUCGCCGCCACC.";

        /*string one_known =   "..GCGGCCACAGCGGCGGGGCGACUCCCGUACCCAUCCCGAACACGGCAGAUAAGCCCGCCAGCG.UUCCAGCGA.GUACUGGAGUGUGCGAACCUCUGGGAA.AACU....G........";
        string two_known =   "GGGCGGCCAGAGCGGUGAGGUUCCACCCGUACCCAUCCCGAACACGGAAGUUAAGCUCGCCUGCGUUC..UGGUCAGUACUGGAGUGAGCGAUCCUCUGGGAAAUCCAGUUCGCCGCCCCU";
        string three_known = ".GGCGGCCAGAGCGGUGAGGUUCCACCCGUACCCAUCCCGAACACGGAAGUUAAGCUCACCUGCGUUC..UGGUCAGUACUGGAGUGAGCGAUCCUCUGGGAAAUCCAGUUCGCCGCCC..";

        obj.sensitivity_and_ppv_calculator(one_known, two_known, three_known);*/
        //cout << "sensitivity: " << obj.sensitivity << endl;
        //cout << "ppv: " << obj.ppv << endl;

        //comb 1:
        //"AUACUGAAG.UUUGGUGGGGAAUCAGUGUGAAAUUCAUUGGCUCUACCUGGAACCGU...AA.A.....GUCGGAGCGCCACCCAGUAU.AGUCCGUUGUUGAAUGAAGGCCAGGGAAAGUC..U.AGUUCUACUAAUAAUA"
        //"GUACUGUUAUUAAGGUGGGAAA.UGAUGUGAAAUUCAUCAGCUGUGCUCGCAACGGUAAAUUAGUUAAAGUCCGAAGGCCACUCAGUAU.AGUCCGGUGUUAGAAAGUAAUCGAGAAGAAUU..ACAAUCUUAC.AAUGAAA"
        //"UUCCUAAAAGCAUAGUGGGAAAGAGACGUGUAAUUCGUCCACAUUACUUGAUACGGU...GAUA.....GUCCGAAUGCCACCUAGGAAUAGA...........U..AGAGCAAGGAGACUCAAUGAA...UAA.AGUAACU"

        //comb 2:
        //AUACUGAAG..UUUGGUGGGGAAUCAGUGUGAAAUUCAUUGGCUCUACCUGGAACCGU...AA.A.....GUCGGAGCGCCACCCAGUAUAGUCCGUUGUUGAAUGAAGGCCAGGGAAAGUCU.AGUUCUACUAAUAAUAA.
        //GUACUGUUAU.UAAGGUGGGAAA.UGAUGUGAAAUUCAUCAGCUGUGCUCGCAACGGUAAAUUAGUUAAAGUCCGAAGGCCACUCAGUAUAGUCCGGUGUUAGAAAGUAAUCGAGAAGAAUUACAAUCUUAC.AAUGAAAAA
        //AGGCUGAAAUGCAUGGUGGGAAAUCAGUGUGAAAUUCAUUGGCUGUUCCUGCAACCGU...AA.A.....GUCGGAGCGCCACCCAGCUUAGUCCGCUGAUGAAUGAUGGCCAGGAAAAGUCU.AAUUCUAU.AAUGAAAAA

        //comb 4:
        //GUACUGUUAU.UAAGGUGGGAAA.UGAUGUGAAAUUCAUCAGCUGUGCUCGCAACGGUAAAUUAGUUAAAGUCCGAAGGCCACUCAGUAU.AGUCCGGUGUUAGAAAGUAAUCGAGAAGAAUU..ACAAUCUUAAAUGAAAAA
        //UUCCUAAAAG.CAUAGUGGGAAAGAGACGUGUAAUUCGUCCACAUUACUUGAUACGGU...GAUA.....GUCCGAAUGCCACCUAGGAAUAGA...........U..AGAGCAAGGAGACUCAAUGAA...UAAGUAACU..
        //AGGCUGAAAUGCAUGGUGGGAAAUCAGUGUGAAAUUCAUUGGCUGUUCCUGCAACCGU...AA.A.....GUCGGAGCGCCACCCAGCUU.AGUCCGCUGAUGAAUGAUGGCCAGGAAAAGUC..U.AAUUCUAAAUGAAAAA

        return 0;
}