/**
* Open the file stream to a file with the name used in the constructor.
*/
void NexusWriter::openStream( void )
{
RbFileManager f = RbFileManager(fileName);
f.createDirectoryForFile();
// open the stream to the file
outStream.open( fileName.c_str(), std::fstream::out );
// write header line
outStream << "#NEXUS" << std::endl;
}
void PowerPosteriorAnalysis::summarizeStones( void )
{
// create the directory if necessary
RbFileManager f = RbFileManager(filename);
f.createDirectoryForFile();
std::ofstream outStream;
outStream.open( filename.c_str(), std::fstream::out);
outStream << "state\t" << "power\t" << "likelihood" << std::endl;
/* Append each stone */
for (size_t idx = 0; idx < powers.size(); ++idx)
{
RbFileManager fm = RbFileManager(filename);
std::string stoneFileName = fm.getFileNameWithoutExtension() + "_stone_" + idx + "." + fm.getFileExtension();
RbFileManager f = RbFileManager(fm.getFilePath(), stoneFileName);
// read the i-th stone
std::ifstream inStream;
inStream.open( f.getFullFileName().c_str(), std::fstream::in);
if (inStream.is_open())
{
bool header = true;
std::string line = "";
while ( std::getline (inStream,line) )
{
// we need to skip the header line
if ( header == true )
{
header = false;
}
else
{
outStream << line << std::endl;
}
}
inStream.close();
}
else
{
std::cerr << "Problem reading stone " << idx+1 << " from file " << stoneFileName << "." << std::endl;
}
}
}
/** open the file stream for printing */
void AbstractFileMonitor::openStream(void)
{
RbFileManager f = RbFileManager(working_file_name);
f.createDirectoryForFile();
// open the stream to the file
if ( append == true )
{
out_stream.open( working_file_name.c_str(), std::fstream::in | std::fstream::out | std::fstream::app);
}
else
{
out_stream.open( working_file_name.c_str(), std::fstream::out);
out_stream.close();
out_stream.open( working_file_name.c_str(), std::fstream::in | std::fstream::out);
}
// out_stream.close();
}
/**
* This method simply writes a character data object into a file in Fasta format.
*
* \param[in] fileName The name of the file into which the objects is to be written.
* \param[in] data The character data object which is written out.
*/
void FastaWriter::writeData(std::string const &fileName, const AbstractHomologousDiscreteCharacterData &data)
{
// the filestream object
std::fstream outStream;
RbFileManager f = RbFileManager(fileName);
f.createDirectoryForFile();
// open the stream to the file
outStream.open( fileName.c_str(), std::fstream::out );
const std::vector<Taxon> &taxa = data.getTaxa();
for (std::vector<Taxon>::const_iterator it = taxa.begin(); it != taxa.end(); ++it)
{
if ( !data.isTaxonExcluded( it->getName() ) )
{
const AbstractDiscreteTaxonData &taxon = data.getTaxonData( it->getName() );
outStream << ">" << it->getName() << std::endl;
size_t nChars = taxon.getNumberOfCharacters();
for (size_t i = 0; i < nChars; ++i)
{
if ( !data.isCharacterExcluded( i ) )
{
const CharacterState &c = taxon.getCharacter( i );
outStream << c.getStringValue();
}
}
outStream << std::endl;
}
}
// close the stream
outStream.close();
}
void PowerPosteriorAnalysis::runStone(size_t idx, size_t gen)
{
// create the directory if necessary
RbFileManager fm = RbFileManager(filename);
std::string stoneFileName = fm.getFileNameWithoutExtension() + "_stone_" + idx + "." + fm.getFileExtension();
RbFileManager f = RbFileManager(fm.getFilePath(), stoneFileName);
f.createDirectoryForFile();
std::fstream outStream;
outStream.open( f.getFullFileName().c_str(), std::fstream::out);
outStream << "state\t" << "power\t" << "likelihood" << std::endl;
// reset the counters for the move schedules
sampler->reset();
// if ( sampler->getCurrentGeneration() == 0 )
// {
// }
/* Reset the monitors */
// for (size_t i=0; i<replicates; ++i)
// {
// for (size_t j=0; i<runs[i].getMonitors().size(); i++)
// {
// runs[i].getMonitors()[j].reset( kIterations);
// }
// }
// reset the stopping rules
// for (size_t i=0; i<rules.size(); ++i)
// {
// rules[i].runStarted();
// }
size_t burnin = size_t( ceil( 0.25*gen ) );
size_t printInterval = size_t( round( fmax(1,gen/20.0) ) );
size_t digits = size_t( ceil( log10( powers.size() ) ) );
/* Run the chain */
if ( processActive )
{
std::cout << "Step ";
for (size_t d = size_t( ceil( log10( idx+1.1 ) ) ); d < digits; d++ )
{
std::cout << " ";
}
std::cout << (idx+1) << " / " << powers.size();
std::cout << "\t\t";
}
// set the power of this sampler
sampler->setLikelihoodHeat( powers[idx] );
sampler->setStoneIndex( idx );
// Monitor
sampler->startMonitors(gen);
sampler->monitor(0);
double p = powers[idx];
for (size_t k=1; k<=gen; k++)
{
if ( processActive )
{
if ( k % printInterval == 0 )
{
std::cout << "**";
std::cout.flush();
}
}
sampler->nextCycle( true );
// Monitor
sampler->monitor(k);
// sample the likelihood
if ( k > burnin && k % sampleFreq == 0 )
{
// compute the joint likelihood
double likelihood = sampler->getModelLnProbability();
outStream << k << "\t" << p << "\t" << likelihood << std::endl;
}
}
if ( processActive )
{
std::cout << std::endl;
}
outStream.close();
}