/**
* This method simply writes a discrete character data object into a file in Nexus format.
*
* \param[in] data The discrete character data object which is written out.
*/
void NexusWriter::writeNexusBlock(const AbstractHomologousDiscreteCharacterData &data)
{
// write initial lines of the character block
outStream << std::endl;
outStream << "Begin data;" << std::endl;
outStream << "Dimensions ntax=" << data.getNumberOfIncludedTaxa() << " nchar=" << data.getNumberOfIncludedCharacters() << ";" << std::endl;
outStream << "Format datatype=" << data.getDataType() << " ";
if ( data.getDataType() == "Standard" )
{
outStream << "symbols=\"" << data.getTaxonData(0).getCharacter(0).getStateLabels() << "\" ";
}
outStream << "missing=? gap=-;" << std::endl;
outStream << "Matrix" << std::endl;
// get the taxon vector
std::vector<Taxon> taxa = data.getTaxa();
// sort the taxa (by name)
std::sort(taxa.begin(), taxa.end());
for (std::vector<Taxon>::const_iterator it = taxa.begin(); it != taxa.end(); ++it)
{
if ( !data.isTaxonExcluded( it->getName() ) )
{
outStream << it->getName() << " ";
const AbstractDiscreteTaxonData &taxon = data.getTaxonData( it->getName() );
size_t nChars = taxon.getNumberOfCharacters();
size_t count = 0;
for (size_t i = 0; i < nChars; ++i)
{
if ( !data.isCharacterExcluded( i ) )
{
const CharacterState &c = taxon.getCharacter( i );
outStream << c.getStringValue();
++count;
}
}
outStream << std::endl;
}
}
outStream << ";" << std::endl;
outStream << "End;" << std::endl;
outStream << std::endl;
}
/**
* 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();
}