void DFA::changeAllStatesName(int start) {
int newStates[countOfStates];
int k = 0, oldState, index;
for (int i = 0; i < countOfStates; i++) {
newStates[i] = start;
if (isFinalState(states[i]))
finalStates[k++] = start;
start++;
}
for (int i = 0; i < countOfStates; i++) { // Презаписваме таблицата с новите състояния
for (int j = 0; j < countOfAlphabet; j++) {
if (transitionFunction(states[i], alphabet[j]) != -2
&& transitionFunction(states[i], alphabet[j]) != -1) {
oldState = table[states[i]][alphabet[j]]; //трябва да вземем индекса на oldState и да вземем новото име така newStates[индекс на oldState]
for (int z = 0; z < countOfStates; z++)
if (states[z] == oldState)
index = z;
table[newStates[i]][alphabet[j]] = newStates[index];
table[states[i]].erase(alphabet[j]); // Изтриваме старите състояния
}
}
}
for (int i = 0; i < countOfStates; i++) {
if (startState == states[i])
startState = newStates[i];
states[i] = newStates[i];
}
}
void transitionFunctionTime(){
unsigned int stateCount = 100;
unsigned int symbolCount = 5;
unsigned int wordLength = 200;
std::vector<int> w_entries(wordLength);
Word w(w_entries);
TransitionFunction transitionFunction(stateCount, symbolCount);
for(unsigned int i = 0; i < symbolCount; i++){
for(unsigned int j = 0; j < stateCount; j++){
transitionFunction.addTransition(j, i, 0);
}
}
const int wordCount = 1000;
double time;
clk::startClock();
int count = 1;
int iter = 0;
while(iter++ < count)
for(int i = 0; i < wordCount-1; i++){
for(int j = i; j < wordCount; j++){
compute(w, &transitionFunction);
}
}
time = clk::stopClock();
std::cout << "Word Count: " << wordCount << " Time: " << time << std::endl;
}
int DFA::extendedTransitionFunction(int from, const char* word) {
for (int i = 0; i < (int) strlen(word); i++)
from = transitionFunction(from, word[i]);
return from;
}
void
mspManager::addHit_(char *genSeq, char *estSeq,
int genLen, int estLen,
int genPos, int estPos,
mss_t &MSS) {
char *genBeg = 0L;
char *estBeg = 0L;
char *genEnd = 0L;
char *genTmp = 0L;
char *estTmp = 0L;
int right_sum = 0;
int middle_sum = 0;
int left_sum = 0;
int sum = 0;
int score = 0;
#ifdef DEBUG_EXTENSION
fprintf(stderr, "mspManager::addHit()-- extending hit from GEN %d to %d and EST %d to %d (length = %d)\n",
genPos-W, genPos, estPos-W, estPos, W);
#endif
#ifdef DEBUG_EXTENSION
{
char L[41], M[41], R[41];
int x;
if (genPos-MSS.seedLength > 20) genTmp = genSeq + 1 + genPos - MSS.seedLength - 20;
else genTmp = genSeq + 1;
x=0;
while (genTmp < genSeq + 1 + genPos - MSS.seedLength)
L[x++] = *genTmp++;
L[x] = 0;
x=0;
while (genTmp < genSeq + 1 + genPos)
M[x++] = *genTmp++;
M[x] = 0;
x=0;
while (genTmp < genSeq + 1 + genPos + 20)
R[x++] = *genTmp++;
R[x] = 0;
fprintf(stderr, "GEN=%8d %s:%s:%s\n", genPos, L, M, R);
if (estPos-MSS.seedLength > 20) estTmp = estSeq + 1 + estPos - MSS.seedLength - 20;
else estTmp = estSeq + 1;
x=0;
while (estTmp < estSeq + 1 + estPos - MSS.seedLength)
L[x++] = *estTmp++;
L[x] = 0;
x=0;
while (estTmp < estSeq + 1 + estPos)
M[x++] = *estTmp++;
M[x] = 0;
x=0;
while (estTmp < estSeq + 1 + estPos + 20)
R[x++] = *estTmp++;
R[x] = 0;
fprintf(stderr, "EST=%8d %s:%s:%s\n", estPos, L, M, R);
}
#endif
// We use diagonals directly -- original version offset the array of
// diagonal positions by the constant value included below.
// Extend to the right
//
left_sum = 0;
sum = 0;
genTmp = genSeq + 1 + genPos;
estTmp = estSeq + 1 + estPos;
genEnd = genTmp;
while ((*genTmp) &&
(*estTmp) &&
(estTmp <= estSeq + estLen) &&
(genTmp <= genSeq + genLen) &&
(sum >= left_sum - _wordExtAllow)) {
sum += _match;
if (*estTmp != *genTmp)
sum -= (transitionFunction(*estTmp, *genTmp) ? _imatchdiff : _vmatchdiff);
estTmp++;
genTmp++;
if (sum > left_sum) {
left_sum = sum;
genEnd = genTmp;
}
}
#ifdef TEST_SEEDS_IN_EXTENSION
// Check the bases that the seed supposedly matched
//
middle_sum = 0;
sum = 0;
genTmp = genSeq + 1 + genPos - 1;
estTmp = estSeq + 1 + estPos - 1;
for (int x=0; x<MSS.seedLength; x++) {
middle_sum += _match;
if (*genTmp != *estTmp)
middle_sum -= (transitionFunction(*estTmp, *genTmp) ? _imatchdiff : _vmatchdiff);
//fprintf(stderr, "%c %c\n", *genTmp, *estTmp);
estTmp--;
genTmp--;
}
if (middle_sum != (MSS.matchesLegth/2))) {
fprintf(stderr, "mspManager::addHit()-- ERROR: i didn't find an exact match for the seed you supplied!\n");
fprintf(stderr, "mspManager::addHit()-- ERROR: GEN=%40.40s\n", genTmp);
fprintf(stderr, "mspManager::addHit()-- ERROR: EST=%40.40s\n", estTmp);
exit(1);
}
#endif
// Calculate the score of the seed match
//
middle_sum = 0;
sum = 0;
genTmp = genSeq + 1 + genPos - 1;
estTmp = estSeq + 1 + estPos - 1;
for (int x=0; x<MSS.seedLength; x++) {
if (*genTmp == *estTmp) middle_sum += _match;
estTmp--;
genTmp--;
}
// Extend to the left
//
right_sum = 0;
sum = 0;
genTmp = genSeq + 1 + genPos - MSS.seedLength;
estTmp = estSeq + 1 + estPos - MSS.seedLength;
genBeg = genTmp;
estBeg = estTmp;
while ((estTmp > estSeq + 1) &&
(genTmp > genSeq + 1) &&
(sum >= right_sum - _wordExtAllow)) {
estTmp--;
genTmp--;
sum += _match;
if (*estTmp != *genTmp)
sum -= (transitionFunction(*estTmp, *genTmp) ? _imatchdiff : _vmatchdiff);
if (sum > right_sum) {
right_sum = sum;
estBeg = estTmp;
genBeg = genTmp;
}
}
score = middle_sum + left_sum + right_sum;
#ifdef DEBUG_MSPS
printf("TESTMSP: p1 = %7d p2 = %7d l = %7d sc = %7d (%d-%d-%d) ",
(int)(genBeg - (genSeq + 1)), (int)(estBeg - (estSeq + 1)), (int)(genEnd - genBeg),
score, left_sum, middle_sum, right_sum);
printf("g: ");
for (s=genBeg; s<genEnd; s++) printf("%c", *s);
printf(" c: ");
for (s=estBeg; s<estBeg+(int)(genEnd-genBeg); s++) printf("%c", *s);
printf(" S: %7d W: %7d cutoff: %d", MSS.seedLength, (int)(MSS.matchedLength/2), _minMSPScore);
printf("\n");
#endif
// If this hit is significant, save it
//
if (score >= _minMSPScore)
addMSP((int)(genEnd - genBeg),
(int)(genBeg - (genSeq + 1)),
(int)(estBeg - (estSeq + 1)),
score);
#ifdef DEBUG_EXTENSION
fprintf(stderr, "mspManager::addHit()-- added from GEN %d to %d and EST %d to ? (length = %d) with score %d (needed %d) l,m,r sums %d %d %d\n",
(int)(genBeg - (genSeq + 1)), (int)(genEnd - (genSeq + 1)) + W,
(int)(estBeg - (estSeq + 1)),
MSS.seedLength,
score, _minMSPScore, left_sum, middle_sum, right_sum);
#endif
// Remember the highest point that this diagonal has been extended
// to. We use this to short circuit useless mer extensions (if
// we've already extended through it).
//
_diagExt[estLen + genPos - estPos - 1] = (int)(genEnd - genSeq - 1 + MSS.seedLength);
}
