/** Execute function */
RevPtr<RevVariable> Func_write::execute( void )
{
// get the information from the arguments for reading the file
const std::string& fn = static_cast<const RlString&>( args[1].getVariable()->getRevObject() ).getValue();
bool append = static_cast<const RlBoolean&>( args[2].getVariable()->getRevObject() ).getValue();
const std::string& separator = static_cast<const RlString&>( args[3].getVariable()->getRevObject() ).getValue();
if ( processID == 0 )
{
if ( fn != "" )
{
RevBayesCore::RbFileManager fm = RevBayesCore::RbFileManager(fn);
fm.createDirectoryForFile();
std::ofstream outStream;
if ( append == true )
{
// open the stream to the file
outStream.open(fn.c_str(), std::fstream::out | std::fstream::app);
}
else
{
// open the stream to the file
outStream.open(fn.c_str(), std::fstream::out);
}
// print the arguments
args[0].getVariable()->getRevObject().printValue(outStream, false);
for (size_t i = 4; i < args.size(); i++)
{
outStream << separator;
args[i].getVariable()->getRevObject().printValue( outStream , false );
}
outStream.close();
}
else
{
std::ostream& o = std::cout;
// print the arguments
args[0].getVariable()->getRevObject().printValue( o, false );
for (size_t i = 4; i < args.size(); i++)
{
o << separator;
args[i].getVariable()->getRevObject().printValue( o, false );
}
o << std::endl;
}
}
return NULL;
}
std::vector<std::string> getFileList(const std::string &path)
{
std::vector<std::string> v;
RbSettings& s = RbSettings::userSettings();
const std::string& wd = s.getWorkingDirectory();
RevBayesCore::RbFileManager fm = RevBayesCore::RbFileManager(wd, path);
fm.setStringWithNamesOfFilesInDirectory( v );
return v;
}
void RbSettings::setWorkingDirectory(const std::string &wd)
{
RevBayesCore::RbFileManager fm = RevBayesCore::RbFileManager( wd );
if ( !fm.isDirectory() )
{
throw RbException("Cannot set the current directory to '" + wd + "'.");
}
workingDirectory = fm.getFullFilePath();
// save the current settings for the future.
writeUserSettings();
}
void RbSettings::setModuleDir(const std::string &md)
{
RevBayesCore::RbFileManager fm = RevBayesCore::RbFileManager(md);
if ( !fm.isDirectory() )
{
throw RbException("Cannot set the help directory to '" + md + "'.");
}
moduleDir = fm.getFullFilePath();
// save the current settings for the future.
writeUserSettings();
}
/** Initialize the help from an XML file */
void Help::initializeHelp(std::string helpDir)
{
// find the path to the directory containing the help files
RevBayesCore::RbFileManager fMngr = RevBayesCore::RbFileManager();
//pathToHelpDir = fMngr.getCurrentDirectory();
fMngr.setFilePath(this->helpDir);
if (fMngr.testDirectory() == false)
{
RBOUT("Warning: Cannot find directory containing help files. User help is unavailable. Path = " + this->helpDir);
return;
}
}
/** Format the error exception string for problems specifying the file/path name */
void Func_readCharacterDataUniversal::formatError(RevBayesCore::RbFileManager& fm, std::string& errorStr) {
bool fileNameProvided = fm.isFileNamePresent();
bool isFileNameGood = fm.testFile();
bool isDirectoryNameGood = fm.testDirectory();
if ( fileNameProvided == false && isDirectoryNameGood == false )
errorStr += "Could not read contents of directory \"" + fm.getFilePath() + "\" because the directory does not exist";
else if (fileNameProvided == true && (isFileNameGood == false || isDirectoryNameGood == false))
{
errorStr += "Could not read file named \"" + fm.getFileName() + "\" in directory named \"" + fm.getFilePath() + "\" ";
if (isFileNameGood == false && isDirectoryNameGood == true)
errorStr += "because the file does not exist";
else if (isFileNameGood == true && isDirectoryNameGood == false)
errorStr += "because the directory does not exist";
else
errorStr += "because neither the directory nor the file exist";
}
}
void RbSettings::writeUserSettings( void )
{
std::string user_dir = RevBayesCore::RbFileManager::expandUserDir("~");
// open the ini file
std::string settings_file_name = ".RevBayes.ini";
RevBayesCore::RbFileManager fm = RevBayesCore::RbFileManager(user_dir, settings_file_name);
std::ofstream writeStream;
fm.openFile( writeStream );
writeStream << "moduledir=" << moduleDir << std::endl;
writeStream << "printNodeIndex=" << (printNodeIndex ? "TRUE" : "FALSE") << std::endl;
writeStream << "tolerance=" << tolerance << std::endl;
writeStream << "linewidth=" << lineWidth << std::endl;
writeStream << "useScaling=" << useScaling << std::endl;
writeStream << "scalingDensity=" << scalingDensity << std::endl;
writeStream << "collapseSampledAncestors=" << (collapseSampledAncestors ? "TRUE" : "FALSE") << std::endl;
fm.closeFile( writeStream );
}
Module::Module(const std::string &fn)
{
// first we need to load the file
std::ifstream readStream;
RevBayesCore::RbFileManager fm = RevBayesCore::RbFileManager(fn);
fm.openFile( readStream );
/* File-processing loop */
while ( readStream.good() )
{
// Read a line
std::string line;
getline( readStream, line );
commandLines.push_back( line );
}
}
/** Initialize the help from an XML file */
void RbHelpSystem::initializeHelp(const std::string &helpDir)
{
// find the path to the directory containing the help files
RevBayesCore::RbFileManager fMngr = RevBayesCore::RbFileManager();
fMngr.setFilePath(helpDir);
if (fMngr.testDirectory() == false)
{
throw RbException("Warning: Cannot find directory containing help files. User help is unavailable. Path = " + helpDir);
}
// get a help parser instance
RbHelpParser parser = RbHelpParser();
// get the files contained in the directory
// gather all xml files in help dir, filtered by '.ext'
std::string ext = "xml";
std::vector<std::string> files;
std::vector<std::string> fileNames;
fMngr.setStringWithNamesOfFilesInDirectory( files );
for (std::vector<std::string>::iterator it = files.begin(); it != files.end(); ++it)
{
RevBayesCore::RbFileManager tmpFM = RevBayesCore::RbFileManager( *it );
if ( tmpFM.getFileExtension() == ext)
{
fileNames.push_back( *it );
}
}
for (std::vector<std::string>::iterator it = fileNames.begin(); it != fileNames.end(); ++it)
{
if ( parser.testHelpEntry( *it ) == RbHelpParser::FUNCTION )
{
RbHelpFunction h = parser.parseHelpFunction( *it );
helpForFunctions.insert( std::pair<std::string,RbHelpFunction>( h.getName() , h) );
helpFunctionNames.insert( h.getName() );
// also add all aliases
const std::vector<std::string>& aliases = h.getAliases();
for (std::vector<std::string>::const_iterator alias = aliases.begin(); alias != aliases.end(); ++alias)
{
helpForFunctions.insert( std::pair<std::string,RbHelpFunction>( *alias , h) );
}
}
if ( parser.testHelpEntry( *it ) == RbHelpParser::TYPE || parser.testHelpEntry( *it ) == RbHelpParser::DISTRIBUTION || parser.testHelpEntry( *it ) == RbHelpParser::MONITOR || parser.testHelpEntry( *it ) == RbHelpParser::MOVE )
{
RbHelpType* h = NULL;
if ( parser.testHelpEntry( *it ) == RbHelpParser::TYPE )
{
h = parser.parseHelpType( *it );
}
else if ( parser.testHelpEntry( *it ) == RbHelpParser::DISTRIBUTION )
{
h = parser.parseHelpDistribution( *it );
}
else if ( parser.testHelpEntry( *it ) == RbHelpParser::MONITOR )
{
h = parser.parseHelpMonitor( *it );
}
else if ( parser.testHelpEntry( *it ) == RbHelpParser::MOVE )
{
h = parser.parseHelpMove( *it );
}
helpForTypes.insert( std::pair<std::string,RbHelpType*>( h->getName() , h) );
helpTypeNames.insert( h->getName() );
// create a map for all methods for this type
std::map<std::string, RbHelpFunction> methodsHelp;
const std::vector<RbHelpFunction>& method = h->getMethods();
for (std::vector<RbHelpFunction>::const_iterator m = method.begin(); m != method.end(); ++m)
{
methodsHelp.insert( std::pair<std::string,RbHelpFunction>( m->getName() , *m) );
}
// add the methods to our global map
helpForMethods.insert( std::pair<std::string, std::map<std::string,RbHelpFunction> >(h->getName(),methodsHelp) );
// also add all aliases
const std::vector<std::string>& aliases = h->getAliases();
for (std::vector<std::string>::const_iterator alias = aliases.begin(); alias != aliases.end(); ++alias)
{
helpForTypes.insert( std::pair<std::string,RbHelpType*>( *alias , h->clone() ) );
helpForMethods.insert( std::pair<std::string, std::map<std::string,RbHelpFunction> >(*alias,methodsHelp) );
}
}
}
}
void RbSettings::initializeUserSettings(void)
{
moduleDir = "modules"; // the default module directory
useScaling = false; // the default useScaling
scalingDensity = 4; // the default scaling density
lineWidth = 160; // the default line width
tolerance = 10E-10; // set default value for tolerance comparing doubles
printNodeIndex = true; // print node indices of tree nodes as comments
collapseSampledAncestors = true;
std::string user_dir = RevBayesCore::RbFileManager::expandUserDir("~");
// read the ini file, override defaults if applicable
std::string settings_file_name = ".RevBayes.ini";
RevBayesCore::RbFileManager fm = RevBayesCore::RbFileManager(user_dir, settings_file_name);
// bool failed = false; //unused
if ( fm.isFile() )
{
std::ifstream readStream;
fm.openFile( readStream );
std::string readLine = "";
while ( std::getline(readStream,readLine) )
{
std::vector<std::string> tokens = std::vector<std::string>();
StringUtilities::stringSplit(readLine, "=", tokens);
if (tokens.size() > 1)
{
setOption(tokens[0], tokens[1], false);
}
}
fm.closeFile(readStream);
}
// initialize the current directory to be the directory the binary is sitting in
# ifdef RB_WIN
char buffer[MAX_DIR_PATH];
GetModuleFileName( NULL, buffer, MAX_DIR_PATH );
std::string::size_type pos = std::string( buffer ).find_last_of( "\\/" );
workingDirectory = std::string( buffer ).substr( 0, pos);
# else
char cwd[MAX_DIR_PATH+1];
if ( getcwd(cwd, MAX_DIR_PATH+1) )
{
std::string pathSeparator = "/";
std::string curdir = cwd;
if ( curdir.at( curdir.length()-1 ) == pathSeparator[0] )
{
curdir.erase( curdir.length()-1 );
}
workingDirectory = curdir;
}
else
{
workingDirectory = "";
}
# endif
// save the current settings for the future.
// writeUserSettings();
}
