void CommandlineInterface(vector<string> Arguments) {
bool InputArgument = false;
vector<string> ParameterFiles;
for (int i=0; i < int(Arguments.size()); i++) {
if (Arguments[i].compare("inputfilelist") == 0) {
if (int(Arguments.size()) >= i+2) {
InputArgument = true;
SetInputParametersFile(Arguments[i+1].data());
}
} if (Arguments[i].compare("parameterfile") == 0) {
if (int(Arguments.size()) >= i+2) {
ParameterFiles.push_back(Arguments[i+1].data());
i++;
}
}
}
if (!InputArgument) {
SetInputParametersFile(COMMANDLINE_INPUT_FILE);
}
LoadParameters();
for(int i=0; i < int(ParameterFiles.size()); i++) {
LoadParameterFile(ParameterFiles[i]);
}
for (int i=0; i < int(Arguments.size()); i++) {
if (Arguments[i].compare("resetparameter") == 0) {
if (int(Arguments.size()) >= i+3) {
string ParameterName = Arguments[i+1];
findandreplace(ParameterName,"_"," ");
SetParameter(ParameterName.data(),Arguments[i+2].data());
}
}
}
ClearParameterDependance("CLEAR ALL PARAMETER DEPENDANCE");
if (Initialize() != SUCCESS) {
return;
}
LoadFIGMODELParameters();
ClearParameterDependance("CLEAR ALL PARAMETER DEPENDANCE");
for (int i=0; i < int(Arguments.size()); i++) {
if (Arguments[i].compare("stringcode") == 0) {
if (int(Arguments.size()) < i+3) {
cout << "Insufficient arguments" << endl;
FErrorFile() << "Insufficient arguments" << endl;
FlushErrorFile();
} else {
CreateStringCode(Arguments[i+1],Arguments[i+2]);
i += 2;
}
} else if (Arguments[i].compare("LoadCentralSystem") == 0 || Arguments[i].compare("LoadDecentralSystem") == 0) {
if (int(Arguments.size()) < i+2) {
cout << "Insufficient arguments" << endl;
FErrorFile() << "Insufficient arguments" << endl;
FlushErrorFile();
} else {
LoadDatabaseFile(Arguments[i+1].data());
}
} else if (Arguments[i].compare("ProcessDatabase") == 0) {
ProcessDatabase();
} else if (Arguments[i].compare("metabolites") == 0) {
if (int(Arguments.size()) < i+2) {
cout << "Insufficient arguments" << endl;
FErrorFile() << "Insufficient arguments" << endl;
FlushErrorFile();
} else {
SetParameter("metabolites to optimize",Arguments[i+1].data());
}
} else if (Arguments[i].compare("WebGCM") == 0) {
if (int(Arguments.size()) < i+3) {
cout << "Insufficient arguments" << endl;
FErrorFile() << "Insufficient arguments" << endl;
FlushErrorFile();
} else {
RunWebGCM(Arguments[i+1].data(),Arguments[i+2].data());
}
} else if (Arguments[i].compare("ProcessMolfiles") == 0) {
if (int(Arguments.size()) < i+3) {
cout << "Insufficient arguments" << endl;
FErrorFile() << "Insufficient arguments" << endl;
FlushErrorFile();
} else {
ProcessMolfileDirectory(Arguments[i+1].data(),Arguments[i+2].data());
}
} else if (Arguments[i].compare("ProcessMolfileList") == 0) {
ProcessMolfiles();
}
}
}
//---------------------------------------------------------------------------------
// Purpose: Initialise the database fields
//---------------------------------------------------------------------------------
bool ManiDatabase::Init(void)
{
LoadDatabaseFile();
return true;
}
