Midi2UdpThread::~Midi2UdpThread()
{
mutex.lock();
abort = true;
mutex.unlock();
wait();
freeSeq();
}
int main(int argc, char **argv) {
const char* s= "aacaaaccggguuuguu";
initSeq("../vienna/rna_turner2004.par",s);
/*
printf("%d -- /\n",ext_mismatch_energy(0, 9)); // dlr
printf("%d -- /\n",termau_energy(0,9));
printf("%d -- %d\n",sr_energy(0,9), E_stack(0,9)); // stack
printf("%d -- %d\n",sr_energy(1,8), E_stack(1,8)); // hairpin
printf("%d -- %d\n",hl_energy(2,7), E_Hairpin(4,_bp(2,7),3,6,"CUCAGG",c_P));
*/
/*
int r =
ext_mismatch_energy(0, 9) + termau_energy(0,9) + // dlr(0,9)
sr_energy(0,9) + // stack(0,9)
sr_energy(1,8) + hl_energy(2,7); // hairpin (1,8)
printf("Result = %d (goal = -130)\n",r);
*/
printf("CPU Result = %d\n",
ext_mismatch_energy(1,16) + termau_energy(1,16)
);
printf("GPU Result = %d\n",
ext_mismatch_energy(0,17) + termau_energy(0,17) +
sr_energy(1,16)
);
freeSeq();
return 0;
}
void determineLineHighlighting(bstring a, bstring b, int ** maskPtrA, int ** maskPtrB)
{
seq alignA = initSeq(a->slen * 1.5);
seq alignB = initSeq(b->slen * 1.5);
seq seqA = stringToSeq(a);
seq seqB = stringToSeq(b);
determineAlignment(seqA, seqB, &compareChars, &alignA, &alignB);
assert(alignA.alen == alignB.alen);
int len = alignA.alen;
// Both sequences should be the same length. We'll just get the length of
// one, which should be the upper limit needed for the masks.
// Allocate memory for two integer masks.
int * maskA = malloc(len * sizeof(int));
if (maskA == NULL)
{
free(maskA);
printf("Memory allocation error.\n");
exit(-1);
}
int * maskB = malloc(len * sizeof(int));
if (maskB == NULL)
{
free(maskB);
printf("Memory allocation error.\n");
exit(-1);
}
int i; // Position along the aligned sequences.
int firstValueInBlockA = -1;
int firstPosInBlockA = -1;
int lastComparisonA = MASK_SAME;
// Positions in each mask.
int posA = 0;
int posB = 0;
for (i = 0; i < len; i++)
{
int currentComparisonA = compareStringPositions(alignA, alignB, i);
int currentComparisonB = compareStringPositions(alignB, alignA, i);
// Look ahead and back a place in the strings to see if we have an
// isolated matching character among differences.
if (currentComparisonA == MASK_SAME &&
i > 0 &&
i < len - 1 &&
compareStringPositions(alignA, alignB, i - 1) != MASK_SAME &&
compareStringPositions(alignA, alignB, i + 1) != MASK_SAME)
{
if (firstPosInBlockA > 0 && firstValueInBlockA == seqA.val[posA])
{
// Special case for when the char we are about to smooth is
// actually at the beginning of the highlighted block.
maskA[firstPosInBlockA] = MASK_SAME;
currentComparisonA = MASK_DIFFERENT;
//printf("%c|%c\n", seqA.val[posA-1], seqA.val[posA]);
}
else
{
// Pretend the matching characters are different to make the diff
// look more readable.
//printf("S");
if (currentComparisonA != MASK_GAP) currentComparisonA = MASK_DIFFERENT;
if (currentComparisonB != MASK_GAP) currentComparisonB = MASK_DIFFERENT;
}
}
else {
//printf("-");
}
// Entering region of difference.
if (currentComparisonA != lastComparisonA &&
currentComparisonA == MASK_DIFFERENT)
{
// Record position and value.
firstValueInBlockA = seqA.val[posA];
firstPosInBlockA = posA;
}
if (currentComparisonA != MASK_GAP)
{
maskA[posA] = currentComparisonA;
posA++;
}
if (currentComparisonB != MASK_GAP)
{
maskB[posB] = currentComparisonB;
posB++;
}
if (currentComparisonA != MASK_GAP)
{
lastComparisonA = currentComparisonA;
}
}
//printf("\n");
*maskPtrA = maskA;
*maskPtrB = maskB;
freeSeq(&seqA);
freeSeq(&seqB);
freeSeq(&alignA);
freeSeq(&alignB);
}
