void FONSEModel::updateTracesWithInitialValues(Genome & genome)
{
std::vector <std::string> groupList = parameter->getGroupList();
for (unsigned i = 0; i < genome.getGenomeSize(); i++)
{
parameter->updateSynthesisRateTrace(0, i);
parameter->updateMixtureAssignmentTrace(0, i);
}
for (unsigned i = 0; i < groupList.size(); i++)
{
parameter->updateCodonSpecificParameterTrace(0, getGrouping(i));
}
}
double FONSEModel::calculateAllPriors()
{
double priorRatio = 0.0;
unsigned size = getGroupListSize();
for (unsigned i = 0; i < size; i++)
{
std::string grouping = getGrouping(i);
priorRatio += calculateMutationPrior(grouping, false);
}
// add more priors if necessary.
return priorRatio;
}
void FONSEModel::calculateLogLikelihoodRatioPerGene(Gene& gene, unsigned geneIndex, unsigned k, double* logProbabilityRatio)
{
double likelihood = 0.0;
double likelihood_proposed = 0.0;
std::string curAA;
std::vector <unsigned> positions;
double mutation[5];
double selection[5];
//SequenceSummary *sequenceSummary = gene.getSequenceSummary(); //currently unused
// get correct index for everything
unsigned mutationCategory = parameter->getMutationCategory(k);
unsigned selectionCategory = parameter->getSelectionCategory(k);
unsigned expressionCategory = parameter->getSynthesisRateCategory(k);
double phiValue = parameter->getSynthesisRate(geneIndex, expressionCategory, false);
double phiValue_proposed = parameter->getSynthesisRate(geneIndex, expressionCategory, true);
/* TODO: This loop causes a compiler warning because i is an int, but openMP won't compile if I change i to unsigned.
Maybe worth looking into? */
#ifdef _OPENMP
//#ifndef __APPLE__
#pragma omp parallel for private(mutation, selection, positions, curAA) reduction(+:likelihood,likelihood_proposed)
#endif
for (unsigned i = 0u; i < getGroupListSize(); i++)
{
curAA = getGrouping(i);
parameter->getParameterForCategory(mutationCategory, FONSEParameter::dM, curAA, false, mutation);
parameter->getParameterForCategory(selectionCategory, FONSEParameter::dOmega, curAA, false, selection);
likelihood += calculateLogLikelihoodRatioPerAA(gene, curAA, mutation, selection, phiValue);
likelihood_proposed += calculateLogLikelihoodRatioPerAA(gene, curAA, mutation, selection, phiValue_proposed);
}
//my_print("% %\n", logLikelihood, logLikelihood_proposed);
double stdDevSynthesisRate = parameter->getStdDevSynthesisRate(selectionCategory, false);
double logPhiProbability = Parameter::densityLogNorm(phiValue, (-(stdDevSynthesisRate * stdDevSynthesisRate) / 2), stdDevSynthesisRate, true);
double logPhiProbability_proposed = Parameter::densityLogNorm(phiValue_proposed, (-(stdDevSynthesisRate * stdDevSynthesisRate) / 2), stdDevSynthesisRate, true);
double currentLogLikelihood = (likelihood + logPhiProbability);
double proposedLogLikelihood = (likelihood_proposed + logPhiProbability_proposed);
if (phiValue == 0) {
my_print("phiValue is 0\n");
}
if (phiValue_proposed == 0) {
my_print("phiValue_prop is 0\n");
}
logProbabilityRatio[0] = (proposedLogLikelihood - currentLogLikelihood) - (std::log(phiValue) - std::log(phiValue_proposed));
logProbabilityRatio[1] = currentLogLikelihood - std::log(phiValue_proposed);
if (std::isinf(logProbabilityRatio[1])) {
my_print("logProb1 inf\n");
}
logProbabilityRatio[2] = proposedLogLikelihood - std::log(phiValue);
if (std::isinf(logProbabilityRatio[2])) {
my_print("logProb2 inf\n");
}
//------------NOTE: Jeremy, Cedric changed the reverse jump to where we DON'T include it. I had my PA
//LogLikelihood go to 0 because of now missing terms. I have added the code underneath to where we calculate it---/
logProbabilityRatio[3] = currentLogLikelihood;
logProbabilityRatio[4] = proposedLogLikelihood;
}
void BrowseThread::populateModel() {
m_path_mutex.lock();
MDir thisPath = m_path;
BrowseTableModel* thisModelObserver = m_model_observer;
m_path_mutex.unlock();
// Refresh the name filters in case we loaded new SoundSource plugins.
QStringList nameFilters(SoundSourceProxy::getSupportedFileNamePatterns());
QDirIterator fileIt(thisPath.dir().absolutePath(), nameFilters,
QDir::Files | QDir::NoDotAndDotDot);
// remove all rows
// This is a blocking operation
// see signal/slot connection in BrowseTableModel
emit(clearModel(thisModelObserver));
QList< QList<QStandardItem*> > rows;
int row = 0;
// Iterate over the files
while (fileIt.hasNext()) {
// If a user quickly jumps through the folders
// the current task becomes "dirty"
m_path_mutex.lock();
MDir newPath = m_path;
m_path_mutex.unlock();
if (thisPath.dir() != newPath.dir()) {
qDebug() << "Abort populateModel()";
return populateModel();
}
QString filepath = fileIt.next();
auto pTrack = Track::newTemporary(filepath, thisPath.token());
SoundSourceProxy(pTrack).updateTrackFromSource();
QList<QStandardItem*> row_data;
QStandardItem* item = new QStandardItem("0");
item->setData("0", Qt::UserRole);
row_data.insert(COLUMN_PREVIEW, item);
item = new QStandardItem(pTrack->getFileName());
item->setToolTip(item->text());
item->setData(item->text(), Qt::UserRole);
row_data.insert(COLUMN_FILENAME, item);
item = new QStandardItem(pTrack->getArtist());
item->setToolTip(item->text());
item->setData(item->text(), Qt::UserRole);
row_data.insert(COLUMN_ARTIST, item);
item = new QStandardItem(pTrack->getTitle());
item->setToolTip(item->text());
item->setData(item->text(), Qt::UserRole);
row_data.insert(COLUMN_TITLE, item);
item = new QStandardItem(pTrack->getAlbum());
item->setToolTip(item->text());
item->setData(item->text(), Qt::UserRole);
row_data.insert(COLUMN_ALBUM, item);
item = new QStandardItem(pTrack->getAlbumArtist());
item->setToolTip(item->text());
item->setData(item->text(), Qt::UserRole);
row_data.insert(COLUMN_ALBUMARTIST, item);
item = new QStandardItem(pTrack->getTrackNumber());
item->setToolTip(item->text());
item->setData(item->text().toInt(), Qt::UserRole);
row_data.insert(COLUMN_TRACK_NUMBER, item);
const QString year(pTrack->getYear());
item = new YearItem(year);
item->setToolTip(year);
// The year column is sorted according to the numeric calendar year
item->setData(mixxx::TrackMetadata::parseCalendarYear(year), Qt::UserRole);
row_data.insert(COLUMN_YEAR, item);
item = new QStandardItem(pTrack->getGenre());
item->setToolTip(item->text());
item->setData(item->text(), Qt::UserRole);
row_data.insert(COLUMN_GENRE, item);
item = new QStandardItem(pTrack->getComposer());
item->setToolTip(item->text());
item->setData(item->text(), Qt::UserRole);
row_data.insert(COLUMN_COMPOSER, item);
item = new QStandardItem(pTrack->getGrouping());
item->setToolTip(item->text());
item->setData(item->text(), Qt::UserRole);
row_data.insert(COLUMN_GROUPING, item);
item = new QStandardItem(pTrack->getComment());
item->setToolTip(item->text());
item->setData(item->text(), Qt::UserRole);
row_data.insert(COLUMN_COMMENT, item);
QString duration = pTrack->getDurationText(mixxx::Duration::Precision::SECONDS);
item = new QStandardItem(duration);
item->setToolTip(item->text());
item->setData(item->text(), Qt::UserRole);
row_data.insert(COLUMN_DURATION, item);
item = new QStandardItem(pTrack->getBpmText());
item->setToolTip(item->text());
item->setData(pTrack->getBpm(), Qt::UserRole);
row_data.insert(COLUMN_BPM, item);
item = new QStandardItem(pTrack->getKeyText());
item->setToolTip(item->text());
item->setData(item->text(), Qt::UserRole);
row_data.insert(COLUMN_KEY, item);
item = new QStandardItem(pTrack->getType());
item->setToolTip(item->text());
item->setData(item->text(), Qt::UserRole);
row_data.insert(COLUMN_TYPE, item);
item = new QStandardItem(pTrack->getBitrateText());
item->setToolTip(item->text());
item->setData(pTrack->getBitrate(), Qt::UserRole);
row_data.insert(COLUMN_BITRATE, item);
QString location = pTrack->getLocation();
QString nativeLocation = QDir::toNativeSeparators(location);
item = new QStandardItem(nativeLocation);
item->setToolTip(nativeLocation);
item->setData(location, Qt::UserRole);
row_data.insert(COLUMN_NATIVELOCATION, item);
QDateTime modifiedTime = pTrack->getFileModifiedTime().toLocalTime();
item = new QStandardItem(modifiedTime.toString(Qt::DefaultLocaleShortDate));
item->setToolTip(item->text());
item->setData(modifiedTime, Qt::UserRole);
row_data.insert(COLUMN_FILE_MODIFIED_TIME, item);
QDateTime creationTime = pTrack->getFileCreationTime().toLocalTime();
item = new QStandardItem(creationTime.toString(Qt::DefaultLocaleShortDate));
item->setToolTip(item->text());
item->setData(creationTime, Qt::UserRole);
row_data.insert(COLUMN_FILE_CREATION_TIME, item);
const mixxx::ReplayGain replayGain(pTrack->getReplayGain());
item = new QStandardItem(
mixxx::ReplayGain::ratioToString(replayGain.getRatio()));
item->setToolTip(item->text());
item->setData(item->text(), Qt::UserRole);
row_data.insert(COLUMN_REPLAYGAIN, item);
rows.append(row_data);
++row;
// If 10 tracks have been analyzed, send it to GUI
// Will limit GUI freezing
if (row % 10 == 0) {
// this is a blocking operation
emit(rowsAppended(rows, thisModelObserver));
qDebug() << "Append " << rows.count() << " from " << filepath;
rows.clear();
}
// Sleep additionally for 10ms which prevents us from GUI freezes
msleep(20);
}
emit(rowsAppended(rows, thisModelObserver));
qDebug() << "Append last " << rows.count();
}
