void RbSettings::setOption(const std::string &key, const std::string &value, bool write)
{
if ( key == "moduledir" )
{
moduleDir = value;
}
else if ( key == "printNodeIndex" )
{
printNodeIndex = value == "TRUE";
}
else if ( key == "tolerance" )
{
//std::string::size_type sz; // alias of size_t
//tolerance = std::stod (value,&sz);
tolerance = (double)atof(value.c_str());
}
else if ( key == "linewidth" )
{
//std::string::size_type sz; // alias of size_t
//lineWidth = std::stoi (value,&sz);
lineWidth = atoi(value.c_str());
}
else if ( key == "useScaling" )
{
useScaling = value == "TRUE";
}
else if ( key == "scalingDensity" )
{
size_t w = atoi(value.c_str());
if(w < 1)
throw(RbException("scalingDensity must be an integer greater than 0"));
scalingDensity = atoi(value.c_str());
}
else if ( key == "collapseSampledAncestors" )
{
collapseSampledAncestors = value == "TRUE";
}
else
{
std::cout << "Unknown user setting with key '" << key << "'." << std::endl;
}
if ( write == true )
{
writeUserSettings();
}
}
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();
}
std::vector<double> RevBayesCore::operator/(const std::vector<double>& x, const std::vector<double>& y)
{
size_t n = x.size();
if ( n != y.size() )
{
throw RbException("Can only divide vectors of same size!");
}
std::vector<double> z(n,0);
for (size_t i = 0; i < n; ++i)
{
z[i] = x[i] / y[i];
}
return z;
}
std::vector<int> RevBayesCore::operator*(const std::vector<int>& x, const std::vector<int>& y)
{
size_t n = x.size();
if ( n != y.size() )
{
throw RbException("Can only multiply vectors of same size!");
}
std::vector<int> z(n,0);
for (size_t i = 0; i < n; ++i)
{
z[i] = x[i] * y[i];
}
return z;
}
void TraceTree::constructInternalObject( void )
{
throw RbException("We do not support a constructor function for TraceTree.");
}
RevLanguage::ParserInfo RevLanguage::Parser::breakIntoLines(const std::string& cmd, std::list<std::string>& lines, bool validate) const {
bool inComment, inQuote;
// Initialize
lines.clear(); // just in case
inComment = inQuote = false;
std::stringstream buf(cmd); // a stream is convenient for reading
// Process command buffer
while (buf.good()) {
std::stringstream temp;
while (buf.good()) {
char c = char( buf.get());
if (c == EOF && inQuote == true) {
if (validate) {
throw RbException("End of line while in quote");
}
continue;
} else if (c == '"') {
/* switch quote on or off if not in comment */
if (inQuote == true)
inQuote = false;
else if (inComment == false)
inQuote = true;
} else if (c == '#' && inQuote == false) {
/* we are now in comment */
inComment = true;
} else if (c == ';' && inQuote == false && inComment == false) {
/* break line here */
break;
} else if (c == EOF && inQuote == false) {
/* break line here */
break;
} else if (c == '\n' && inQuote == false) {
/* break line here */
break;
} else if (c == '\377' && inQuote == false) {
/* break line here */
// c = '\n';
continue;
} else if (c == '\r' && inQuote == false) {
/* break line here but first swallow any extra newline in DOS line ending */
char d = char( buf.peek());
if (d == '\n')
c = char( buf.get());
break;
}
temp.put(c);
}
if (temp.str().size() > 0)
{
lines.push_back(temp.str() + "\n");
}
}
ParserInfo pi;
pi.inComment = inComment;
pi.inQuote = inQuote;
pi.lines = lines;
return pi;
}
