/** Execute function */
RevPtr<RevVariable> Func_readBranchLengthTrees::execute( void ) {
// get the information from the arguments for reading the file
const RlString& fn = static_cast<const RlString&>( args[0].getVariable()->getRevObject() );
// get the global instance of the NCL reader and clear warnings from its warnings buffer
RevBayesCore::NclReader reader = RevBayesCore::NclReader();
ModelVector<BranchLengthTree> *trees = new ModelVector<BranchLengthTree>();
std::vector<RevBayesCore::BranchLengthTree*> tmp = *(reader.readBranchLengthTrees( fn.getValue() ));
for (std::vector<RevBayesCore::BranchLengthTree*>::iterator t = tmp.begin(); t != tmp.end(); ++t)
{
trees->push_back( BranchLengthTree(*t) );
}
return new RevVariable( trees );
}
/** Execute function */
RevPtr<Variable> Func_range::execute( void ) {
int f = static_cast<const Integer &>( args[0].getVariable()->getRevObject() ).getValue();
int l = static_cast<const Integer &>( args[1].getVariable()->getRevObject() ).getValue();
ModelVector<Integer> *range = new ModelVector<Integer>();
if (f < l) {
for ( int i = f; i <= l; i++ )
range->push_back( Integer(i) );
}
else {
for ( int i = f; i >= l; i-- )
range->push_back( Integer(i) );
}
return new Variable( range );
}
/* Map calls to member methods */
RevPtr<Variable> RlAtlas::executeMethod(std::string const &name, const std::vector<Argument> &args) {
if (name == "nAreas")
{
return new Variable(new Natural((int)this->dagNode->getValue().getNumAreas())) ;
}
else if (name == "nEpochs")
{
return new Variable(new Natural((int)this->dagNode->getValue().getNumEpochs())) ;
}
else if (name == "names")
{
ModelVector<RlString> *n = new ModelVector<RlString>();
const std::vector<std::vector<RevBayesCore::GeographicArea*> >& areas = this->dagNode->getValue().getAreas();
for (size_t i = 0; i < areas[0].size(); ++i)
{
std::string name = areas[0][i]->getName();
n->push_back( RlString( name ) );
}
return new Variable( n );
}
return ModelObject<RevBayesCore::TimeAtlas>::executeMethod( name, args );
}
/** 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 = "";
formatError(myFileManager, 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;
ModelVector<AbstractDiscreteCharacterData> *m = new ModelVector<AbstractDiscreteCharacterData>();
// 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 ( dType == "DNA" )
{
RevBayesCore::DiscreteCharacterData<RevBayesCore::DnaState> *coreM = static_cast<RevBayesCore::DiscreteCharacterData<RevBayesCore::DnaState> *>( *it );
DiscreteCharacterData<DnaState> mDNA = DiscreteCharacterData<DnaState>( coreM );
m->push_back( mDNA );
}
else if ( dType == "RNA" )
{
RevBayesCore::DiscreteCharacterData<RevBayesCore::RnaState> *coreM = static_cast<RevBayesCore::DiscreteCharacterData<RevBayesCore::RnaState> *>( *it );
DiscreteCharacterData<RnaState> mRNA = DiscreteCharacterData<RnaState>( coreM );
m->push_back( mRNA );
}
else if ( dType == "Protein" )
{
RevBayesCore::DiscreteCharacterData<RevBayesCore::AminoAcidState> *coreM = static_cast<RevBayesCore::DiscreteCharacterData<RevBayesCore::AminoAcidState> *>( *it );
DiscreteCharacterData<AminoAcidState> mAA = DiscreteCharacterData<AminoAcidState>( coreM );
m->push_back( mAA );
}
else if ( dType == "Standard" )
{
RevBayesCore::DiscreteCharacterData<RevBayesCore::StandardState> *coreM = static_cast<RevBayesCore::DiscreteCharacterData<RevBayesCore::StandardState> *>( *it );
DiscreteCharacterData<StandardState> mSS = DiscreteCharacterData<StandardState>( 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
{
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 = new AbstractDiscreteCharacterData( (*m)[0] );
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 );
}
/* Map calls to member methods */
RevPtr<RevVariable> RlAtlas::executeMethod(std::string const &name, const std::vector<Argument> &args, bool &found)
{
if (name == "nAreas")
{
found = true;
return new RevVariable(new Natural((int)this->dagNode->getValue().getNumAreas())) ;
}
else if (name == "nEpochs")
{
found = true;
return new RevVariable(new Natural((int)this->dagNode->getValue().getNumEpochs())) ;
}
else if (name == "names")
{
found = true;
ModelVector<RlString> *n = new ModelVector<RlString>();
const std::vector<std::vector<RevBayesCore::GeographicArea*> >& areas = this->dagNode->getValue().getAreas();
for (size_t i = 0; i < areas[0].size(); ++i)
{
std::string name = areas[0][i]->getName();
n->push_back( name );
}
return new RevVariable( n );
}
else if (name == "epochTimes")
{
found = true;
ModelVector<RealPos> *n = new ModelVector<RealPos>( this->dagNode->getValue().getEpochs() );
return new RevVariable( n );
}
else if (name == "getValues")
{
found = true;
// get the member with give index
std::string value = static_cast<const RlString &>( args[0].getVariable()->getRevObject() ).getValue();
std::vector<std::vector<RevBayesCore::GeographicArea*> > areas = this->dagNode->getValue().getAreas();
ModelVector<ModelVector<ModelVector<Real > > > *f = new ModelVector<ModelVector<ModelVector<Real > > >();
for (size_t i = 0; i < areas.size(); i++)
{
RevBayesCore::RbVector<RevBayesCore::RbVector<double> > v;
for (size_t j = 0; j < areas[i].size(); j++)
{
if (value == "dispersal")
v.push_back(areas[i][j]->getDispersalValues());
else if (value == "dispersal-upper")
v.push_back(areas[i][j]->getDispersalValues());
else if (value == "extinction")
v.push_back(areas[i][j]->getExtinctionValues());
else if (value == "latlon")
v.push_back(areas[i][j]->getLatlon());
else if (value == "altitude")
v.push_back( RevBayesCore::RbVector<double>(1, areas[i][j]->getAltitude()) );
else if (value == "size")
v.push_back( RevBayesCore::RbVector<double>(1, areas[i][j]->getSize()) );
}
f->push_back( ModelVector<ModelVector<Real> >(v) );
}
return new RevVariable(f);
}
return ModelObject<RevBayesCore::TimeAtlas>::executeMethod( name, args, found );
}
/* Map calls to member methods */
RevPtr<RevVariable> AbstractCharacterData::executeCharacterDataMethod(std::string const &name, const std::vector<Argument> &args, bool &found)
{
if (name == "chartype")
{
found = true;
return new RevVariable( new RlString( charDataObject->getDatatype() ) );
}
else if (name == "excludeTaxa")
{
found = true;
const RevObject& argument = args[0].getVariable()->getRevObject();
if ( argument.isType( RlString::getClassTypeSpec() ) )
{
const std::string &n = static_cast<const RlString&>( argument ).getValue();
// remember that we internally store the character indeces from 0 to n-1
// but externally represent it as 1 to n
charDataObject->excludeTaxon( n );
}
else if ( argument.isType( ModelVector<RlString>::getClassTypeSpec() ) )
{
const ModelVector<RlString>& x = static_cast<const ModelVector<RlString>&>( argument );
RevBayesCore::AbstractCharacterData &v = *charDataObject;
for ( size_t i=0; i<x.size(); i++ )
{
v.excludeTaxon( x[i] );
}
}
return NULL;
}
else if (name == "includeTaxa")
{
found = true;
const RevObject& argument = args[0].getVariable()->getRevObject();
if ( argument.isType( RlString::getClassTypeSpec() ) )
{
const std::string &n = static_cast<const RlString&>( argument ).getValue();
// remember that we internally store the character indeces from 0 to n-1
// but externally represent it as 1 to n
charDataObject->includeTaxon( n );
}
else if ( argument.isType( ModelVector<RlString>::getClassTypeSpec() ) )
{
const ModelVector<RlString>& x = static_cast<const ModelVector<RlString>&>( argument );
RevBayesCore::AbstractCharacterData &v = *charDataObject;
for ( size_t i=0; i<x.size(); i++ )
{
// remember that we internally store the character indeces from 0 to n-1
// but externally represent it as 1 to n
v.includeTaxon( x[i] );
}
}
return NULL;
}
else if (name == "isSequenceMissing")
{
found = true;
const RevObject& argument = args[0].getVariable()->getRevObject();
const std::string &n = static_cast<const RlString&>( argument ).getValue();
bool tf = charDataObject->isSequenceMissing( n );
return new RevVariable( new RlBoolean(tf) );
}
else if (name == "names")
{
found = true;
ModelVector<RlString> *n = new ModelVector<RlString>();
for (size_t i = 0; i < charDataObject->getNumberOfTaxa(); ++i)
{
n->push_back( charDataObject->getTaxonNameWithIndex( i ) );
}
return new RevVariable( n );
}
else if (name == "ntaxa")
{
found = true;
int n = (int)charDataObject->getNumberOfTaxa();
return new RevVariable( new Natural(n) );
}
else if (name == "percentageMissing")
{
found = true;
const RevObject& argument = args[0].getVariable()->getRevObject();
const std::string &n = static_cast<const RlString&>( argument ).getValue();
double p = charDataObject->getPercentageMissing( n );
return new RevVariable( new Probability(p) );
}
else if (name == "size")
{
found = true;
int n = (int)charDataObject->getNumberOfTaxa();
return new RevVariable( new Natural(n) );
}
else if (name == "removeTaxa" )
{
found = true;
const RevObject& argument = args[0].getVariable()->getRevObject();
if ( argument.isType( RlString::getClassTypeSpec() ) )
{
std::string n = std::string( static_cast<const RlString&>( argument ).getValue() );
charDataObject->excludeTaxon( n );
}
else if ( argument.isType( ModelVector<RlString>::getClassTypeSpec() ) )
{
const ModelVector<RlString>& x = static_cast<const ModelVector<RlString>&>( argument );
RevBayesCore::AbstractCharacterData &v = *charDataObject;
for ( size_t i=0; i<x.size(); i++ )
{
std::string n = std::string( static_cast<const RlString&>( x[i] ).getValue() );
v.excludeTaxon( n );
}
}
return NULL;
}
else if (name == "setTaxonName")
{
found = true;
const RevObject& current = args[0].getVariable()->getRevObject();
if ( current.isType( RlString::getClassTypeSpec() ) )
{
std::string n = std::string( static_cast<const RlString&>( current ).getValue() );
const RevObject& newName = args[1].getVariable()->getRevObject();
if ( newName.isType( RlString::getClassTypeSpec() ) )
{
std::string name = std::string( static_cast<const RlString&>( newName ).getValue() );
charDataObject->setTaxonName( n ,name );
// std::cout << "new name: "<< dagNode->getValue().getTaxonData( n ).getTaxonName() << std::endl;
}
}
return NULL;
}
else if (name == "show")
{
found = true;
charDataObject->show(std::cout);
return NULL;
}
// not found a matching method
found = false;
return NULL;
}
/* Map calls to member methods */
RevPtr<RevVariable> RlDistanceMatrix::executeMethod(std::string const &name, const std::vector<Argument> &args, bool &found)
{
if (name == "matrix")
{
found = true;
return new RevVariable(new MatrixReal((RevBayesCore::MatrixReal) (this->dagNode->getValue().getMatrix() ) ) ) ;
}
else if (name == "names")
{
found = true;
std::vector<std::string> names = this->dagNode->getValue().getNames();
ModelVector<RlString> *n = new ModelVector<RlString>();
for (size_t i = 0; i < names.size(); ++i)
{
n->push_back( names[i] );
}
return new RevVariable( n );
}
else if ( name == "size" )
{
found = true;
// return a new RevVariable with the size of this container
return RevPtr<RevVariable>( new RevVariable( new Natural( size() ), "" ) );
}
else if ( name == "getElement" )
{
if ( args.size() > 1 && args[0].getVariable()->getRevObject().isType( Natural::getClassTypeSpec() ) && args[1].getVariable()->getRevObject().isType( Natural::getClassTypeSpec() ) )
{
found = true;
// get the member with given indices
const Natural& i = static_cast<const Natural&>( args[0].getVariable()->getRevObject() );
const Natural& j = static_cast<const Natural&>( args[1].getVariable()->getRevObject() );
if ( size() < (size_t)(i.getValue()) )
{
throw RbException("Index i out of bounds in getElement");
}
if ( size() < (size_t)(j.getValue()) )
{
throw RbException("Index j out of bounds in getElement");
}
double element = static_cast< RevBayesCore::DistanceMatrix& >( this->dagNode->getValue() ).getElement(size_t(i.getValue()) - 1, size_t(j.getValue()) - 1);
return new RevVariable( new Real( element ) );
}
}
else if ( name == "setElement" )
{
if ( args.size() > 2 && args[0].getVariable()->getRevObject().isType( Natural::getClassTypeSpec() ) && args[1].getVariable()->getRevObject().isType( Natural::getClassTypeSpec() ) && args[2].getVariable()->getRevObject().isType( Real::getClassTypeSpec() ) )
{
found = true;
// get the member with given indices
const Natural& i = static_cast<const Natural&>( args[0].getVariable()->getRevObject() );
const Natural& j = static_cast<const Natural&>( args[1].getVariable()->getRevObject() );
const Real& v = static_cast<const Real&>( args[2].getVariable()->getRevObject() );
if ( size() < (size_t)(i.getValue()) )
{
throw RbException("Index i out of bounds in getElement");
}
if ( size() < (size_t)(j.getValue()) )
{
throw RbException("Index j out of bounds in getElement");
}
static_cast< RevBayesCore::DistanceMatrix& >( this->dagNode->getValue() ).getElement(size_t(i.getValue()) - 1, size_t(j.getValue()) - 1) = double(v.getValue() );
}
return NULL;
}
return ModelObject<RevBayesCore::DistanceMatrix>::executeMethod( name, args, found );
}