/** Execute function */
RevPtr<RevVariable> Func_readStochasticVariableTrace::execute( void )
{
// get the information from the arguments for reading the file
const std::string& fn = static_cast<const RlString&>( args[0].getVariable()->getRevObject() ).getValue();
// get the column delimiter
const std::string& delimiter = static_cast<const RlString&>( args[1].getVariable()->getRevObject() ).getValue();
RevBayesCore::TraceReader reader;
std::vector<RevBayesCore::ModelTrace> data = reader.readStochasticVariableTrace(fn, delimiter);
WorkspaceVector<ModelTrace> *rv = new WorkspaceVector<ModelTrace>();
for (std::vector<RevBayesCore::ModelTrace>::iterator it = data.begin(); it != data.end(); ++it)
{
rv->push_back( ModelTrace( *it ) );
}
// return the vector of traces
return new RevVariable( rv );
}
/** Execute function */
RevPtr<RevVariable> Func_readCharacterDataUniversal::execute( void ) {
// get the information from the arguments for reading the file
const std::string& fn = static_cast<const RlString&>( args[0].getVariable()->getRevObject() ).getValue();
bool returnAsVector = static_cast<const RlBoolean&>( args[1].getVariable()->getRevObject() ).getValue();
// check that the file/path name has been correctly specified
RevBayesCore::RbFileManager myFileManager( fn );
if ( !myFileManager.testFile() && !myFileManager.testDirectory() )
{
std::string errorStr = "";
myFileManager.formatError(errorStr);
throw RbException("Could not find file or path with name \"" + fn + "\"");
}
// set up a vector of strings containing the name or names of the files to be read
std::vector<std::string> vectorOfFileNames;
if ( myFileManager.isDirectory() )
{
myFileManager.setStringWithNamesOfFilesInDirectory(vectorOfFileNames);
}
else
{
vectorOfFileNames.push_back( myFileManager.getFullFileName() );
}
// get the global instance of the NCL reader and clear warnings from its warnings buffer
RevBayesCore::NclReader reader = RevBayesCore::NclReader();
// the vector of matrices;
WorkspaceVector<AbstractCharacterData>* m = new WorkspaceVector<AbstractCharacterData>();
// the return value
RevObject* retVal = NULL;
// Set up a map with the file name to be read as the key and the file type as the value. Note that we may not
// read all of the files in the string called "vectorOfFileNames" because some of them may not be in a format
// that can be read.
size_t numFilesRead = 0;
for (std::vector<std::string>::iterator p = vectorOfFileNames.begin(); p != vectorOfFileNames.end(); p++)
{
bool isInterleaved = false;
std::string myFileType = "unknown";
std::string dType = "unknown";
if (reader.isNexusFile(*p) == true)
{
myFileType = "nexus";
}
else if (reader.isPhylipFile(*p, dType, isInterleaved) == true)
{
myFileType = "phylip";
}
else if (reader.isFastaFile(*p, dType) == true)
{
myFileType = "fasta";
}
int numMatricesReadForThisFile = 0;
if (myFileType != "unknown")
{
std::string suffix = "|" + dType;
if ( myFileType == "phylip" )
{
if (isInterleaved == true)
{
suffix += "|interleaved";
}
else
{
suffix += "|noninterleaved";
}
}
else if ( myFileType == "fasta" )
{
suffix += "|noninterleaved";
}
else
{
suffix += "|unknown";
}
myFileType += suffix;
// read the content of the file now
std::vector<RevBayesCore::AbstractCharacterData*> m_i = reader.readMatrices( *p, myFileType );
for (std::vector<RevBayesCore::AbstractCharacterData*>::iterator it = m_i.begin(); it != m_i.end(); it++)
{
dType = (*it)->getDataType();
// Assume success; correct below if failure
numMatricesReadForThisFile++;
if ( (*it)->isHomologyEstablished() == true )
{
if ( dType == "DNA" )
{
RevBayesCore::HomologousDiscreteCharacterData<RevBayesCore::DnaState> *coreM = static_cast<RevBayesCore::HomologousDiscreteCharacterData<RevBayesCore::DnaState> *>( *it );
AbstractHomologousDiscreteCharacterData mDNA = AbstractHomologousDiscreteCharacterData( coreM );
m->push_back( mDNA );
}
else if ( dType == "RNA" )
{
RevBayesCore::HomologousDiscreteCharacterData<RevBayesCore::RnaState> *coreM = static_cast<RevBayesCore::HomologousDiscreteCharacterData<RevBayesCore::RnaState> *>( *it );
AbstractHomologousDiscreteCharacterData mRNA = AbstractHomologousDiscreteCharacterData( coreM );
m->push_back( mRNA );
}
else if ( dType == "Protein" )
{
RevBayesCore::HomologousDiscreteCharacterData<RevBayesCore::AminoAcidState> *coreM = static_cast<RevBayesCore::HomologousDiscreteCharacterData<RevBayesCore::AminoAcidState> *>( *it );
AbstractHomologousDiscreteCharacterData mAA = AbstractHomologousDiscreteCharacterData( coreM );
m->push_back( mAA );
}
else if ( dType == "Standard" )
{
RevBayesCore::HomologousDiscreteCharacterData<RevBayesCore::StandardState> *coreM = static_cast<RevBayesCore::HomologousDiscreteCharacterData<RevBayesCore::StandardState> *>( *it );
AbstractHomologousDiscreteCharacterData mSS = AbstractHomologousDiscreteCharacterData( coreM );
m->push_back( mSS );
}
else if ( dType == "Continuous" )
{
RevBayesCore::ContinuousCharacterData *coreM = static_cast<RevBayesCore::ContinuousCharacterData *>( *it );
ContinuousCharacterData mCC = ContinuousCharacterData (coreM );
m->push_back( mCC );
}
else
{
numMatricesReadForThisFile--;
throw RbException("Unknown data type \"" + dType + "\".");
}
}
else
{
if ( dType == "DNA" )
{
RevBayesCore::NonHomologousDiscreteCharacterData<RevBayesCore::DnaState> *coreM = static_cast<RevBayesCore::NonHomologousDiscreteCharacterData<RevBayesCore::DnaState> *>( *it );
NonHomologousDiscreteCharacterData<DnaState> mDNA = NonHomologousDiscreteCharacterData<DnaState>( coreM );
m->push_back( mDNA );
}
else if ( dType == "RNA" )
{
RevBayesCore::NonHomologousDiscreteCharacterData<RevBayesCore::RnaState> *coreM = static_cast<RevBayesCore::NonHomologousDiscreteCharacterData<RevBayesCore::RnaState> *>( *it );
NonHomologousDiscreteCharacterData<RnaState> mRNA = NonHomologousDiscreteCharacterData<RnaState>( coreM );
m->push_back( mRNA );
}
else if ( dType == "Protein" )
{
RevBayesCore::NonHomologousDiscreteCharacterData<RevBayesCore::AminoAcidState> *coreM = static_cast<RevBayesCore::NonHomologousDiscreteCharacterData<RevBayesCore::AminoAcidState> *>( *it );
NonHomologousDiscreteCharacterData<AminoAcidState> mAA = NonHomologousDiscreteCharacterData<AminoAcidState>( coreM );
m->push_back( mAA );
}
else if ( dType == "Standard" )
{
// Can't have morphological (i.e., standard) data that don't have homology established
}
else if ( dType == "Continuous" )
{
// Can't have morphological (i.e., standard) data that don't have homology established
}
else
{
numMatricesReadForThisFile--;
throw RbException("Unknown data type \"" + dType + "\".");
}
}
}
}
else
{
reader.addWarning("Unknown file type");
}
if (numMatricesReadForThisFile > 0)
{
numFilesRead++;
}
}
// print summary of results of file reading to the user
if (myFileManager.isDirectory() == true)
{
std::stringstream o2;
if ( numFilesRead == 0 )
{
o2 << "Failed to read any files from directory '" << fn << "'";
}
else if ( numFilesRead == 1 )
{
if ( m->size() == 1 )
{
o2 << "Successfully read one file with one character matrix from directory '" << fn << "'";
}
else
{
o2 << "Successfully read one file with " << m->size() << " character matrices from directory '" << fn << "'";
}
}
else
{
o2 << "Successfully read " << numFilesRead << " files with " << m->size() << " character matrices from directory '" << fn << "'";
}
RBOUT(o2.str());
std::set<std::string> myWarnings = reader.getWarnings();
if ( vectorOfFileNames.size() - numFilesRead > 0 && myWarnings.size() > 0 )
{
std::stringstream o3;
if (vectorOfFileNames.size() - numFilesRead == 1)
{
o3 << "Did not read a file for the following ";
}
else
{
o3 << "Did not read " << vectorOfFileNames.size() - numFilesRead << " files for the following ";
}
if (myWarnings.size() == 1)
{
o3 << "reason:";
}
else
{
o3 << "reasons:";
}
RBOUT(o3.str());
for (std::set<std::string>::iterator it = myWarnings.begin(); it != myWarnings.end(); it++)
{
RBOUT("* "+(*it));
}
}
// set the return value
retVal = m;
}
else
{
if (m->size() == 1)
{
RBOUT("Successfully read one character matrix from file '" + fn + "'");
// set the return value
if ( returnAsVector == false )
{
retVal = (*m)[0].clone();
delete m;
}
else
{
retVal = m;
}
}
else if (m->size() > 1)
{
std::stringstream o3;
o3 << "Successfully read " << m->size() << " character matrices from file '" << fn << "'";
RBOUT(o3.str());
// set the return value
retVal = m;
}
else
{
std::set<std::string> myWarnings = reader.getWarnings();
if ( myWarnings.size() > 0 )
{
std::stringstream o3;
o3 << "Error reading file '" << fn << "'";
RBOUT(o3.str());
for (std::set<std::string>::iterator it = myWarnings.begin(); it != myWarnings.end(); it++)
{
RBOUT("Error: " + (*it));
}
}
}
}
return new RevVariable( retVal );
}