void
ProgramOptions::validate() const
{
SetString missing;
for (OptionGroupMap::const_iterator it = groups.begin();
it != groups.end();
++it){
findMissingOptions(it->second, missing);
}
Size sz = missing.size();
if (sz > 0 )
{
String buffer;
std::stringstream ss(buffer);
Size index = 0;
for (SetString::const_iterator it = missing.begin(); it != missing.end(); ++it){
ss << *it;
if (index + 1 < sz)
ss << ",";
++index;
}
THROW_MSG(CoreText::instance().missingOption(ss.str()));
}
}
void LinkInfo::addUserMod ( const ParameterList* params, int num, SetString& uniqLabels )
{
string sNum = gen_itoa ( num );
string label = params->getStringValue ( "mod_" + sNum + "_label", "" );
if ( !label.empty () ) {
string comp = params->getStringValue ( "mod_" + sNum + "_composition", "" );
if ( !comp.empty () ) {
string aaMod = params->getStringValue ( "aa_modified_" + sNum, "" );
pair <SetStringIterator, bool> flag = uniqLabels.insert ( label+aaMod );
if ( !flag.second ) {
ErrorHandler::genError ()->error ( "Mod Labels need to be unique.\n" );
}
if ( aaMod == "Protein N-term" )
userMod.push_back ( new Usermod ( label, comp, 'n', "n" ) );
else if ( aaMod == "Protein C-term" )
userMod.push_back ( new Usermod ( label, comp, 'c', "c" ) );
else
userMod.push_back ( new Usermod ( label, comp, 'e', aaMod ) );
userLabels.push_back ( label );
userFormulae.push_back ( comp );
userAAs.push_back ( aaMod );
}
else
ErrorHandler::genError ()->error ( "No elemental composition specified for Mod " + sNum + " Label.\n" );
}
}
void SQLiteModifications::insert ()
{
StringVector namesList;
StringVector specificityList;
StringVector elementalFormulaStrList;
StringVector typeList;
Usermod::getAllUsermodInfo ( namesList, specificityList, elementalFormulaStrList, typeList );
MapStringToInt modTypes;
int modTypeIdx = 0;
v1 [3] = "";
v1 [4] = "1";
v1 [5] = "0";
SetString ss;
for ( int i = 0 ; i < namesList.size () ; i++ ) {
PairSetStringIteratorBool flag = ss.insert ( namesList [i] );
if ( flag.second ) {
v1 [0] = namesList [i];
v1 [1] = "formula";
v1 [2] = elementalFormulaStrList [i];
insertTable ( tableName, n1, v1 );
}
}
}
void
ProgramOptions::findMissingOptions(const OptionGroup& group, SetString& missing) const
{
for (OptionMap::const_iterator it = group.getOptions().begin();
it != group.getOptions().end();
++it)
{
if (it->second.isMandatory() && !isOptionDefined (it->first)){
missing.insert(it->second.getName());
}
}
for (OptionGroupMap::const_iterator git = group.getGroups().begin();
git != group.getGroups().end();
++git)
{
findMissingOptions(git->second, missing);
}
}
