std::string LLUriTemplate::expandJoin(const std::string& delim, const std::string& var_list, const LLSD& vars)
{
std::ostringstream query;
typedef boost::tokenizer<boost::char_separator<char> > tokenizer;
boost::char_separator<char> sep(",");
tokenizer var_names(var_list, sep);
tokenizer::const_iterator it = var_names.begin();
// First var does not need a delimiter
if (it != var_names.end())
{
const std::string& name = *it;
if (vars.has(name))
{
// URL encode the value before appending the name=value pair.
query << name << "=" << escapeURL(vars[name].asString());
}
}
for (++it; it != var_names.end(); ++it)
{
const std::string& name = *it;
if (vars.has(name))
{
// URL encode the value before appending the name=value pair.
query << delim << name << "=" << escapeURL(vars[name].asString());
}
}
return query.str();
}
SideValueSampler::SideValueSampler(const InputParameters & parameters)
: SideVectorPostprocessor(parameters), SamplerBase(parameters, this, _communicator)
{
std::vector<std::string> var_names(_coupled_moose_vars.size());
_values.resize(_coupled_moose_vars.size());
for (unsigned int i = 0; i < _coupled_moose_vars.size(); i++)
var_names[i] = _coupled_moose_vars[i]->name();
// Initialize the datastructions in SamplerBase
SamplerBase::setupVariables(var_names);
}
PointSamplerBase::PointSamplerBase(const InputParameters & parameters) :
GeneralVectorPostprocessor(parameters),
CoupleableMooseVariableDependencyIntermediateInterface(parameters, false),
SamplerBase(parameters, this, _communicator),
_mesh(_subproblem.mesh()),
_point_vec(1) // Only going to evaluate one point at a time for now
{
std::vector<std::string> var_names(_coupled_moose_vars.size());
for (unsigned int i=0; i<_coupled_moose_vars.size(); i++)
var_names[i] = _coupled_moose_vars[i]->name();
// Initialize the datastructions in SamplerBase
SamplerBase::setupVariables(var_names);
}
bool ModificationDefinitionsSet::isCompatible(const AASequence & peptide) const
{
set<String> var_names(getVariableModificationNames()), fixed_names(getFixedModificationNames());
// no modifications present and needed
if (fixed_names.empty() && !peptide.isModified())
{
return true;
}
// check whether the fixed modifications are fulfilled
if (!fixed_names.empty())
{
for (set<String>::const_iterator it1 = fixed_names.begin(); it1 != fixed_names.end(); ++it1)
{
String origin = ModificationsDB::getInstance()->getModification(*it1).getOrigin();
// only single 1lc amino acids are allowed
if (origin.size() != 1)
{
continue;
}
for (AASequence::ConstIterator it2 = peptide.begin(); it2 != peptide.end(); ++it2)
{
if (origin == it2->getOneLetterCode())
{
// check whether the residue is modified (has to be)
if (!it2->isModified())
{
return false;
}
// check whether the modification is the same
if (ModificationsDB::getInstance()->getModification(*it1).getId() != it2->getModification())
{
return false;
}
}
}
}
}
// check wether other modifications than the variable are present
for (AASequence::ConstIterator it = peptide.begin(); it != peptide.end(); ++it)
{
if (it->isModified())
{
String mod = ModificationsDB::getInstance()->getModification(it->getOneLetterCode(), it->getModification(), ResidueModification::ANYWHERE).getFullId();
if (var_names.find(mod) == var_names.end() &&
fixed_names.find(mod) == fixed_names.end())
{
return false;
}
}
}
if (peptide.hasNTerminalModification())
{
String mod = ModificationsDB::getInstance()->getTerminalModification(peptide.getNTerminalModification(), ResidueModification::N_TERM).getFullId();
if (var_names.find(mod) == var_names.end() &&
fixed_names.find(mod) == fixed_names.end())
{
return false;
}
}
if (peptide.hasCTerminalModification())
{
String mod = ModificationsDB::getInstance()->getTerminalModification(peptide.getCTerminalModification(), ResidueModification::C_TERM).getFullId();
if (var_names.find(mod) == var_names.end() &&
fixed_names.find(mod) == fixed_names.end())
{
return false;
}
}
return true;
}
