main.c

#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>
#include <string.h>      
#include "pairwise.h"





/*

    our main needs to take in the options
        -number of sequences
        -file name
        
*/
main(int argc, char *argv[])                                                                                                                                                                                                                                                     {
    /* 
    
        first we need to get the first variable, 
        our number of sequences and convert it 
        to an int.
    
    */
    string num_str = *(argv + 1);
    int num_seq = atoi(num_str);
    int num_comparisons = num_pairwise_comp(num_seq);
    
    /*
    
        We then need to find out the string to 
        the file we will be working with.
    
    */
    string file_name = *(argv + 2);
    // Normally, I would use string *all_seqs but it keeps giving me 
    // the following warning:
    // `warning: passing argument 3 of 'read_alignment' from incompatible pointer type`
    char *all_seqs[num_seq];
    int aln_length = read_alignment(file_name, num_seq, all_seqs);
    // Normally, I would define how many comparisons we will do
    //float pairwise_comparisons[num_comparisons];
    float *pairwise_comparisons = malloc(num_comparisons * sizeof(float));
    //calculate_hamming_dists(pairwise_comparisons, num_comparisons, all_seqs, aln_length, num_seq);
    calculate_p_dists(pairwise_comparisons, num_comparisons, all_seqs, aln_length, num_seq);

    int i;


    
    float maximum = 0.00;
    float minimum = 1.00;
    float average = 0.00;
    
    maximum = get_max_dist(pairwise_comparisons, num_comparisons);
    minimum = get_min_dist(pairwise_comparisons, num_comparisons);
    average = get_avg_dist(pairwise_comparisons, num_comparisons);

    //printf("Hamming distance (similarity)\n");
    //printf("\tMax: %f \n\tMin: %f \n\tAvg: %f \n", maximum, minimum, average);
    printf("p-distance\n");
    printf("\tMin: %f \n\tMax: %f \n\tAvg: %f \n", minimum, maximum, average);

    free(pairwise_comparisons);


    return 0;
}