void test_permute_tensor(dim_t order, dim_t nA, dim_t permutation[]){
FLA_Obj A, P;
initTensor(order, nA, &A);
FLA_Random_tensor(A);
initTensor(order, nA, &P);
FLA_Obj_print_matlab("A", A);
FLA_Permute(A, permutation, &P);
FLA_Obj_print_matlab("P", P);
}
int main (int argc, char ** argv) {
long seqNum, i, k = 0;
char * * sequences = NULL;
long * seqLen = NULL;
char * * * algnseq = NULL;
long * aSeqLen = NULL;
int alignmentsNo=0;
MOA_rec * msaAlgn = NULL;
int stype = 0;
long currentScore, currentCell = 0;
long prevScore, prevCell = 0;
Mode = Sequential;
processArguments(argc, argv, &seqNum, &sequences, &seqLen, &stype);
prevNow = NULL;
prevNow = (struct tm *) mmalloc (sizeof(struct tm));
currNow = getTime();
prevNow->tm_hour = currNow->tm_hour;
prevNow->tm_isdst = currNow->tm_isdst;
prevNow->tm_mday = currNow->tm_mday;
prevNow->tm_min = currNow->tm_min;
prevNow->tm_mon = currNow->tm_mon;
prevNow->tm_sec = currNow->tm_sec;
prevNow->tm_wday = currNow->tm_wday;
prevNow->tm_yday = currNow->tm_yday;
prevNow->tm_year = currNow->tm_year;
/* A. Crteate MOA Alignment Tensor */
/*msaAlgn = (MOA_rec *) mmalloc(sizeof(MOA_rec));*/
createMOAStruct (&msaAlgn);
createMOA(seqLen /* shape*/, seqNum /* dimension*/, msaAlgn /* MOA structure*/,0,0);
if (pdebug == 1)
mprintf(outputfilename, "MOA dimn %d, elm ub %d\n", 2, msaAlgn->dimn, msaAlgn->elements_ub);
/* B. Fill the Tensor */
if (AlignmentType == Global)
initTensor (msaAlgn, stype);
fillTensor (sequences, msaAlgn, stype);
if (pdebug == 1)
printMOA(msaAlgn);
/* C. trace back */
aSeqLen = (long *) mmalloc (sizeof(long));
aSeqLen[0] = 0;
prevCell = -1;
algnseq = (char * * *) mmalloc(sizeof(char * *));
algnseq[0] = (char * *) mmalloc (seqNum * sizeof(char *));
if (AlignmentType == Global) { /* if Global Alignment */
/*PrintPrevChains(msaAlgn);
// Get Max Cell on Last Border as Current Cell */
alignmentsNo = 0;
currentScore = getMaxOnLastBorder (msaAlgn, ¤tCell);
traceBack (seqNum, sequences, seqLen, msaAlgn, stype, &algnseq, &aSeqLen, &alignmentsNo, ¤tCell, ¤tScore, 0);
}
else { /* if Local Alignment */
alignmentsNo = -1;
for (k = 0;k<maxAlignmentsNumber;k++) {
if (k == 0)
currentScore = MOA_max(msaAlgn, 0, 0, ¤tCell);
else {
currentScore = MOA_max(msaAlgn, 1, currentScore, ¤tCell);
}
if ((prevCell != currentCell) && (currentScore > 0)){
alignmentsNo ++;
algnseq = (char * * *) realloc (algnseq, (alignmentsNo + 1) * sizeof(char * *));
if (algnseq == NULL) {
mprintf(outputfilename, "Could not reallocate memory for Aligned Sequence Set %d!\n", 1, alignmentsNo + 1);
return -1;
}
algnseq[alignmentsNo] = (char * *) mmalloc (seqNum * sizeof(char *));
aSeqLen = (long *) realloc (aSeqLen, (alignmentsNo + 1) * sizeof(long));
if (aSeqLen == NULL) {
mprintf(outputfilename, "Could not reallocate memory for Aligned Sequence Length %d!\n", 1, alignmentsNo + 1);
return -1;
}
traceBack_loc (seqNum, sequences, seqLen, msaAlgn, stype, &algnseq, &aSeqLen, &alignmentsNo, ¤tCell, ¤tScore, 0);
}
prevCell = currentCell;
prevScore = currentScore;
}
}
/* D. Print the resulting Alignemnts */
PrintASeq (seqNum, sequences, seqLen, &algnseq, aSeqLen, alignmentsNo+1) ;
/* Free all Memory Allocations & Exit. */
deleteMOA (msaAlgn);
if (sequences != NULL) {
for (i=0;i<seqNum;i++) {
if (sequences[i] != NULL)
free(sequences[i]);
}
free(sequences);
}
if (algnseq != NULL) {
for (k=0;k<=alignmentsNo;k++) {
if (algnseq[k] != NULL) {
for (i=0;i<seqNum;i++) {
if (algnseq[k][i] != NULL)
free(algnseq[k][i]);
}
free(algnseq[k]);
}
}
free(algnseq);
}
if (seqLen != NULL)
free(seqLen);
if (aSeqLen != NULL)
free(aSeqLen);
if (prevNow != NULL)
free(prevNow);
return 0;
}
