Parallel_Aligner/msa.h at main · SebPorras/Parallel_Aligner · GitHub

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//msa.h

#ifndef MSA_H
#define MSA_H

#include <string>
#include <vector>
#include <map>
#include <memory>
#include <list>
#include <cmath>
#include <limits.h>
#include <iomanip>
#include <ios>
#include <iostream>
#include <float.h>
#include <fstream>
#include <chrono>
#include <immintrin.h>
#include <omp.h>
#include <mpi.h>

using namespace std;

//export out blosum matrix
extern int blosum[20][20];

const int MAX_SEQ_LEN = 200;
const int FILENAME = 1; //for accessing argv
const int NUM_LETTERS = 20; //20 amino acids
const int ROW_LEN = 24; //ascii value of 'Y' - 'A'
const int MATRIX_SIZE = 600; // substition matrix 24 * 24 + 24
const int ASCII_OFFSET = -65; //offsets 'A' to have index of 0

//error codes
const int CLI_ERROR = 1;
const int FILE_ERROR = 2;

const int GAP = -3; //penalty for adding a gap

//A representation of a sequence
struct Sequence {
    string seq; //actual sequence
    string id; //sequence name
    int index; //where the sequence is in the matrix
};

float mean_difference(vector<Sequence>& c1, vector<Sequence>& c2,
        const int numPoints, vector<float>& distanceMatrix);
vector<Sequence> read_fasta_file(string fileName);
void UPGMA(vector<vector<Sequence>>& clusters,
        vector<float>& distanceMatrix, vector<int>& subMatrix);
void print_seqs(vector<vector<Sequence>> clusters);
vector<int> make_sub_matrix(void);
void find_closest_clusters(int numClusters, vector<vector<Sequence>> &clusters,
                           int numSeqs, vector<float>& distanceMatrix,
                           vector<Sequence>& cToMerge1, int* idxC1,
                           vector<Sequence>& cToMerge2, int* idxC2);
vector<Sequence> merge_clusters(vector<Sequence>& cToMerge1,
                                vector<Sequence>& cToMerge2);

float seq_to_seq_distance(int seq1Index, int seq2Index, vector<float>& distanceMatrix,
 int chunkCount, int numSeqs);


#endif