int RateGamma::computePatternRates(DoubleVector &pattern_rates, IntVector &pattern_cat) {
//cout << "Computing Gamma site rates by empirical Bayes..." << endl;
phylo_tree->computePatternLhCat(WSL_RATECAT);
int npattern = phylo_tree->aln->getNPattern();
pattern_rates.resize(npattern);
pattern_cat.resize(npattern);
double *lh_cat = phylo_tree->_pattern_lh_cat;
for (int i = 0; i < npattern; i++) {
double sum_rate = 0.0, sum_lh = 0.0;
int best = 0;
for (int c = 0; c < ncategory; c++) {
sum_rate += rates[c] * lh_cat[c];
sum_lh += lh_cat[c];
if (lh_cat[c] > lh_cat[best] || (lh_cat[c] == lh_cat[best] && random_double()<0.5)) // break tie at random
best = c;
}
pattern_rates[i] = sum_rate / sum_lh;
pattern_cat[i] = best;
lh_cat += ncategory;
}
return ncategory;
// pattern_rates.clear();
// pattern_rates.insert(pattern_rates.begin(), ptn_rates, ptn_rates + npattern);
// pattern_cat.resize(npattern, 0);
// for (int i = 0; i < npattern; i++)
// for (int j = 1; j < ncategory; j++)
// if (fabs(rates[j] - ptn_rates[i]) < fabs(rates[pattern_cat[i]] - ptn_rates[i]))
// pattern_cat[i] = j;
// delete [] ptn_rates;
}
void ZFunction::calculateAndWriteToVector(
String string, IntVector &stringFunction) {
stringFunction.resize(string.size());
stringFunction[0] = 0;
int mostRightBound = -1, mostRightBoundBegin = -1;
for (int currentPosition = 1; currentPosition < (int)string.size();
currentPosition++) {
if (currentPosition < mostRightBound) {
stringFunction[currentPosition] =
std::min(stringFunction[currentPosition - mostRightBoundBegin],
mostRightBound - currentPosition);
} else {
stringFunction[currentPosition] = 0;
}
while (currentPosition + stringFunction[currentPosition]
< (int)string.size()
&& string[currentPosition + stringFunction[currentPosition]]
== string[stringFunction[currentPosition]]) {
stringFunction[currentPosition]++;
}
if (currentPosition + stringFunction[currentPosition]
> mostRightBound) {
mostRightBound = currentPosition
+ stringFunction[currentPosition];
mostRightBoundBegin = currentPosition;
}
}
}
void Ioss::ParallelUtils::global_count(const IntVector &local_counts, IntVector &global_counts) const
{
// Vector 'local_counts' contains the number of objects
// local to this processor. On exit, global_counts
// contains the total number of objects on all processors.
// Assumes that ordering is the same on all processors
global_counts.resize(local_counts.size());
#ifdef HAVE_MPI
if (local_counts.size() > 0 && parallel_size() > 1) {
if (Ioss::SerializeIO::isEnabled() && Ioss::SerializeIO::inBarrier()) {
std::ostringstream errmsg;
errmsg << "Attempting mpi while in barrier owned by " << Ioss::SerializeIO::getOwner();
IOSS_ERROR(errmsg);
}
const int success = MPI_Allreduce((void*)&local_counts[0], &global_counts[0],
static_cast<int>(local_counts.size()),
MPI_INT, MPI_SUM, communicator_);
if (success != MPI_SUCCESS) {
std::ostringstream errmsg;
errmsg << "Ioss::ParallelUtils::global_count - MPI_Allreduce failed";
IOSS_ERROR(errmsg);
}
} else {
// Serial run, just copy local to global...
std::copy(local_counts.begin(), local_counts.end(), global_counts.begin());
}
#else
std::copy(local_counts.begin(), local_counts.end(), global_counts.begin());
#endif
}
int RateGammaInvar::computePatternRates(DoubleVector &pattern_rates, IntVector &pattern_cat) {
//cout << "Computing Gamma site rates by empirical Bayes..." << endl;
phylo_tree->computePatternLhCat(WSL_RATECAT);
int npattern = phylo_tree->aln->getNPattern();
pattern_rates.resize(npattern);
pattern_cat.resize(npattern);
double *lh_cat = phylo_tree->_pattern_lh_cat;
for (int i = 0; i < npattern; i++) {
double sum_rate = 0.0, sum_lh = phylo_tree->ptn_invar[i];
int best = 0;
double best_lh = phylo_tree->ptn_invar[i];
for (int c = 0; c < ncategory; c++) {
sum_rate += rates[c] * lh_cat[c];
sum_lh += lh_cat[c];
if (lh_cat[c] > best_lh || (lh_cat[c] == best_lh && random_double()<0.5)) { // break tie at random
best = c+1;
best_lh = lh_cat[c];
}
}
pattern_rates[i] = sum_rate / sum_lh;
pattern_cat[i] = best;
lh_cat += ncategory;
}
return ncategory+1;
}
void initializeRandomly(int totalNodes)
{
int targetCount = std::parallel_uniform_random<int>(0, totalNodes);
targets.resize(targetCount);
std::parallel_launch({targetCount}, initializeTargetsRandomly, targets,
totalNodes);
}
void readIntVector( ContainerNode &node,
const string &array_name,
IntVector &v) throw(Error)
{
ContainerNode array_node = node.readArray(array_name);
v.resize(0);
while (array_node.hasUnread()) {
v.push_back((int)array_node.readNumber());
}
}
void testResize(IntVector& test)
{
cout << "Resize to 5 " << endl;
test.resize(5);
testValues(test);
cout << "Resize to 10 " << endl;
test.resize(10);
testValues(test);
cout << "Resize to 16 " << endl;
test.resize(16);
testValues(test);
cout << "Resize to 5, fill 1 " << endl;
test.resize(5, 1);
testValues(test);
cout << "Resize to 10, fill 1 " << endl;
test.resize(10, 1);
testValues(test);
cout << "Resize to 17, fill 1 " << endl;
test.resize(17, 1);
testValues(test);
}
void PrefixFunction::calculateAndWriteToVector(
String string, IntVector &stringFunction) {
stringFunction.resize(string.size());
stringFunction[0] = 0;
for (int currentPosition = 1; currentPosition < (int)string.size();
currentPosition++) {
int currentSuffixLength = stringFunction[currentPosition - 1];
while (currentSuffixLength > 0 && string[currentPosition]
!= string[currentSuffixLength]) {
currentSuffixLength = stringFunction[currentSuffixLength - 1];
}
stringFunction[currentPosition] = currentSuffixLength
+ (string[currentPosition] == string[currentSuffixLength]);
}
}
// function to populate long prefix suffix vector
void PopulateLPS(const string& pattern, IntVector& lps) {
// lps vector should hold values for each character in pattern
lps.resize(pattern.size() + 1);
// first character don't have any lps
lps[0] = 0;
// iterator for going over pattern
int pIter = 1;
// len of the lps
int pLen = 0;
while(pIter < pattern.size()) {
// got a match, update lps
if( pattern[pIter] == pattern[pLen] ) {
lps[pIter] = pLen + 1;
pIter++;
pLen++;
}
else {
if(pLen == 0) {
// no match, move to the next character
lps[pIter ] = 0;
pIter++;
}
else {
// tricky, lps is used inside lps :)
// no match, go back to previous lps and check from there
// pIter is not incremented, since we need to check for same character again
pLen = lps[pLen-1];
}
}
}
}
void PalindromeFunction::calculateAndWriteToVector(
String string, IntVector &stringFunction) {
stringFunction.resize(string.size() * 2 + 1);
String specialString;
specialString.push_back(specialSymbol);
for (int currentPosition = 0; currentPosition < (int)string.size();
currentPosition++) {
specialString.push_back(string[currentPosition]);
specialString.push_back(specialSymbol);
}
int mostRightBound = -1, mostRightBoundBegin = -1;
for (int currentPosition = 0; currentPosition < (int)specialString.size();
currentPosition++) {
if (currentPosition < mostRightBound) {
stringFunction[currentPosition] =
std::min(stringFunction[2 * mostRightBoundBegin
- currentPosition], mostRightBound - currentPosition);
} else {
stringFunction[currentPosition] = 0;
}
while (currentPosition + stringFunction[currentPosition]
< (int)specialString.size()
&& currentPosition - stringFunction[currentPosition] >= 0
&& specialString[currentPosition
+ stringFunction[currentPosition]]
== specialString[currentPosition
- stringFunction[currentPosition]]) {
stringFunction[currentPosition]++;
}
if (currentPosition + stringFunction[currentPosition]
> mostRightBound) {
mostRightBound = currentPosition
+ stringFunction[currentPosition];
mostRightBoundBegin = currentPosition;
}
}
}
