int main(){
int res;
char *a = calloc(16, sizeof(char));
sprintf(a, "%s", "AAATTTTTTTGCAAGA");
char *b = calloc(11, sizeof(char));
sprintf(b, "%s", "ATTGGCAAAG");
int lena = 15;
int lenb = 10;
int *m = calloc(lena * lenb, sizeof(int));
int *horizGap_m = calloc(lena * lenb, sizeof(int));
int *vertGap_m = calloc(lena * lenb, sizeof(int));
int *trBack = calloc(lena + lenb, sizeof(int));
res = needlemanWunsch(a, b,
1, 0, 0,
3, 0,
0, 0,
lena, lenb,
m, horizGap_m, vertGap_m, trBack,
1, "log.txt", 0, "seq1", "seq2", 0, 0);
return 0;
}
int alignAll(int nI, int nLenI, int *pnBest, int *pnBestJ, int *anRestrict, int nK, t_Data *ptSeqData, t_Data *ptRefData, t_Align* atAlign, t_Params *ptParams, int* anChi)
{
int j = 0, nCompare = 0, nBest = BIG_INT, nBestJ = -1;
int nNLen = ptSeqData->nMaxLen, nKLen = ptRefData->nMaxLen;
for(j = 0; j < nK; j++){
int nDist = 0;
if(anChi[j] == FALSE && (strcmp(ptRefData->aszID[j],ptSeqData->aszID[nI]) != 0 && ptRefData->anFreq[j] > ptParams->nSkew*ptSeqData->anFreq[nI])){
needlemanWunsch(&atAlign[j], &ptSeqData->acSequences[nI*nNLen], &ptRefData->acSequences[j*nKLen], nLenI, ptRefData->anLen[j]);
nDist = atAlign[j].nDiff;
if(nDist < nBest){
nBest = nDist;
nBestJ = j;
}
nCompare++;
anRestrict[j] = FALSE;
}
else{
anRestrict[j] = TRUE;
}
}
(*pnBest) = nBest;
(*pnBestJ) = nBestJ;
return nCompare;
}
int main() {
unsigned int k, i; // loop variables
unsigned int max;
init(); // Should init count as part of the time?
for (k=0; k<NUM_READS; k++) { // Loop through each read
best_fits[k] = needlemanWunsch(reads[k], ref_genome);
// Print the results
printf("READ #%d - Best fit at index %d\n", k, best_fits[k]);
}
return 0;
}
int main(int argc, char* argv[]){
int a = 0, i = 0, j = 0, nN = 0, nM = 0;
t_Params tParams;
t_Data tData;
double *adDists = NULL;
int numtasks, rank, rc;
int offset, nA, nA0, nSize, nCount, nStart, nFinish, nTag = 1;
int nPackets = 0, nPacketSize = 0, nPacketCurr = 0;
MPI_Status status;
fflush(stdout);
rc = MPI_Init(&argc,&argv);
if (rc != MPI_SUCCESS) {
printf ("Error starting MPI program. Terminating.\n");
MPI_Abort(MPI_COMM_WORLD, rc);
}
MPI_Comm_size(MPI_COMM_WORLD,&numtasks);
MPI_Comm_rank(MPI_COMM_WORLD,&rank);
/*get command line params*/
getCommandLineParams(&tParams, argc, argv);
fflush(stdout);
if(rank == 0){ /*head node reads data*/
//printf("%d read data\n",rank); fflush(stdout);
initLookUp(&tParams);
readData(&tData, &tParams);
MPI_Bcast(adLookUp, N_BASES*N_BASES, MPI_DOUBLE, 0, MPI_COMM_WORLD);
//printf("%d broadcast data\n",rank); fflush(stdout);
/*sends it out to other nodes*/
broadcastData(&tData);
/*do my bit*/
nN = tData.nSeq; nM = tData.nMaxLen;
/*allocate memory for whole dist matrix*/
nSize = (nN*(nN - 1))/2;
nA = (int) (floor(nSize / numtasks));
nA0 = nA + (nSize % numtasks);
adDists = (double *) malloc(nA*sizeof(double));
if(!adDists)
goto memoryError;
printf("%d\n",nN);
/*output identifiers here*/
if(tParams.bIdent == TRUE){
for(i = 0; i < tData.nSeq; i++){
printf("%s\n", tData.aszID[i]);
}
}
nCount = 0;
for(i = 0; i < nN; i++){
for(j = 0; j < i; j++){
double dDist = needlemanWunsch(&tData.acSequences[i*nM], &tData.acSequences[j*nM],tData.anLen[i], tData.anLen[j], tData.nMaxLen);
printf("%.8e\n",dDist);
nCount++;
if(nCount == nA0){
goto finish;
}
}
fflush(stdout);
}
finish:
nPackets = ((nA - 1)/MAX_PACKET_SIZE) + 1;
for (i = 1; i < numtasks; i++){
nPacketCurr = 0;
for(j = 0; j < nPackets; j++){
if(j < nPackets - 1){
nPacketSize = MAX_PACKET_SIZE;
}
else{
nPacketSize = nA % MAX_PACKET_SIZE;
}
MPI_Recv((void *) (&adDists[nPacketCurr]), nPacketSize,
MPI_DOUBLE, i, nTag, MPI_COMM_WORLD, &status);
nPacketCurr += nPacketSize;
}
for(j = 0; j < nA; j++){
printf("%.8e\n",adDists[j]);
}
}
}
else{
/* receive data*/
adLookUp = (double *) malloc(N_BASES*N_BASES*sizeof(double));
if(!adLookUp)
goto memoryError;
MPI_Bcast(adLookUp, N_BASES*N_BASES, MPI_DOUBLE, 0, MPI_COMM_WORLD);
receiveData(&tData);
nN = tData.nSeq; nM = tData.nMaxLen;
nSize = (nN*(nN - 1))/2;
nA = (int) floor(nSize / numtasks);
nA0 = nA + (nSize % numtasks);
adDists = (double *) malloc(nA*sizeof(double));
if(!adDists)
goto memoryError;
nCount = 0; nStart = nA0 + (rank - 1)*nA; nFinish = nA0 + rank*nA;
for(i = 0; i < nN; i++){
for(j = 0; j < i; j++){
if(nCount >= nStart){
double dDist = needlemanWunsch(&tData.acSequences[i*nM], &tData.acSequences[j*nM],tData.anLen[i], tData.anLen[j], tData.nMaxLen);
adDists[nCount - nStart] = dDist;
}
nCount++;
if(nCount == nFinish){
goto finish2;
}
}
}
finish2:
nPackets = ((nA - 1)/MAX_PACKET_SIZE) + 1;
nPacketCurr = 0;
for(j = 0; j < nPackets; j++){
if(j < nPackets - 1){
nPacketSize = MAX_PACKET_SIZE;
}
else{
nPacketSize = nA % MAX_PACKET_SIZE;
}
//printf("Send %d %d %d\n",rank, nPacketCurr, nPacketSize);
MPI_Send((void *) (&adDists[nPacketCurr]), nPacketSize,
MPI_DOUBLE, 0, nTag, MPI_COMM_WORLD);
nPacketCurr += nPacketSize;
}
if(nPacketCurr != nA){
printf("Message error\n");
}
}
/*free allocated memory*/
free(adDists);
free(tData.acSequences);
free(tData.anLen);
// Wait for everyone to stop
MPI_Barrier(MPI_COMM_WORLD);
// Always use MPI_Finalize as the last instruction of the program
MPI_Finalize();
exit(EXIT_SUCCESS);
memoryError:
fprintf(stderr, "Failed allocating memory in main\n");
fflush(stderr);
exit(EXIT_FAILURE);
}