Sequence Alignment problem using Pthreads - c++

Question

I am trying to implement Sequence alignment problem (Needleman-Wunsch algorithm) using p-Threads. I am confused how to map the concept of multi threading in this particular serial problem. The code of serial computation of sequence alignment is enclosed below.(Just Matrix calculation part)
#include<iostream>
#include<string.h>
#include<string>
#include<algorithm>
using namespace std;
class Matrix
{
private:
int x;
int y;
int** mat;
string gene1;
string gene2;
int match_penalty;
int mismatch_penalty;
int gap_penalty;
int minimum_penalty;
public:
Matrix(int gene1Len, int gene2Len)
{
x = gene2Len + 1; //gene2 length
y = gene1Len + 1; //gene 1 length;
mat = new int* [x];
for (int i = 0; i < x; i++)
mat[i] = new int[y];
for (int i = 0; i < x; ++i) {
for (int j = 0; j < y; ++j) {
mat[i][j] = 0;
}
}
//Default Penalties
match_penalty = 1;
mismatch_penalty = 3;
gap_penalty = 2;
minimum_penalty=0;
}
void Print_Matrix()
{
cout<<"\n";
for (int i = 0; i < x; i++)
{
for (int j = 0; j < y; j++)
{
cout << mat[i][j] << "\t";
}
cout << "\n";
}
}
void setGenes(string gene1, string gene2)
{
this->gene1 = gene1;
this->gene2 = gene2;
}
void setPenalty(int mismatch, int gp,int match)
{
mismatch_penalty = mismatch;
gap_penalty = gp;
match_penalty=match;
}
void setMatrix()
{
//1st row and 1st Column values
for (int i = 0; i < x; i++)
{
mat[i][0] = i * gap_penalty;
}
for (int i = 0; i < y; i++)
{
mat[0][i] = i * gap_penalty;
}
// Other matrix values
for (int i = 1; i < x; i++)
{
for (int j = 1; j < y; j++)
{
if (gene1[j - 1] == gene2[i - 1]) //Similar gene values (A==A ||T==T)
{
mat[i][j] = mat[i - 1][j - 1]+match_penalty;
}
else
{
mat[i][j] = max({ mat[i - 1][j - 1] + mismatch_penalty , mat[i - 1][j] + gap_penalty, mat[i][j - 1] + gap_penalty });
}
}
}
}
};
int main()
{
string gene1 = "ACCA";
string gene2 = "CCA";
int matchPenalty;
int misMatchPenalty ;
int gapPenalty ;
cout<<"Enter the value of Match Penalty" << endl;
cin >> matchPenalty;
cout<<"Enter the value of misMatchPenalty Penalty" << endl;
cin >> misMatchPenalty;
cout<<"Enter the value of gapPenalty Penalty" << endl;
cin >> gapPenalty;
Matrix dp(gene1.length(), gene2.length());
dp.setGenes(gene1, gene2);
dp.setPenalty(misMatchPenalty, gapPenalty,matchPenalty);
dp.setMatrix();
dp.Print_Matrix();
}
How can I implement the above problem in P-threads? So far, I have used two threads to calculate matrix values of 1st column and 1st row simultaneously.But I have no idea how to compute all values of matrix in parallel. Kindly see my source code:
#include<string>
#include<algorithm>
#include<iostream>
#include<string.h>
#include<pthread.h>
using namespace std;
//Global variables --shared by all threads
int matchPenalty;
int misMatchPenalty;
int gapPenalty;
struct gene_struct {
string gene1;
string gene2;
int rowSize;
int colSize;
int **mat;
};
void* set_matrix_row(void *args)
{
struct gene_struct *shared_block = (struct gene_struct *) args;
for (int i = 0; i < shared_block->rowSize; i++)
{
shared_block->mat[i][0] = i * gapPenalty;
}
return NULL;
}
void *set_matrix_column(void *args)
{
struct gene_struct *shared_block = (struct gene_struct *) args;
for (int i = 0; i < shared_block->colSize; i++)
{
shared_block->mat[0][i] = i * gapPenalty;
}
return NULL;
}
void set_Matrix_Diagnol(struct gene_struct shared_block)
{
//How Should I calculate rest of the matrix values using Pthreads?
}
void Print_Matrix(struct gene_struct shared_block)
{
cout<<"\n";
for (int i = 0; i < shared_block.rowSize; i++)
{
for (int j = 0; j < shared_block.colSize; j++)
{
cout << shared_block.mat[i][j] << "\t";
}
cout << "\n";
}
}
int main()
{
pthread_t ptid1, ptid2;
string gene1, gene2;
struct gene_struct shared_block;
cout << "Enter First Gene : ";
cin >> gene1;
cout << "Enter Second Gene : ";
cin >> gene2;
cout<<"Enter the value of Match Penalty" << endl;
cin >> matchPenalty;
cout<<"Enter the value of misMatchPenalty Penalty" << endl;
cin >> misMatchPenalty;
cout<<"Enter the value of gapPenalty Penalty" << endl;
cin >> gapPenalty;
shared_block.gene1 = gene1;
shared_block.gene2 = gene2;
shared_block.rowSize = gene2.length()+1;
shared_block.colSize = gene1.length()+1;
shared_block.mat = new int* [shared_block.rowSize]; //col = gene2+1
for (int i = 0; i < shared_block.rowSize; i++)
{
shared_block.mat[i] = new int[shared_block.colSize];
}
pthread_create(&ptid1, NULL, &set_matrix_row, (void *)&shared_block);
pthread_create(&ptid2, NULL ,&set_matrix_column, (void *)&shared_block);
pthread_join(ptid1,NULL);
pthread_join(ptid2,NULL);
Print_Matrix(shared_block);
}