Options parseOptions(int _argc, char * _argv[], Options defaults) {
/******************************************
* Pass the array of argument and the name of
* a configuration file to the ArgumentParser
* object. Then ask for the value of the argument
* and collect error and warnings.
*
* This function returns a Options structure
* defined at the head of this file
******************************************/
Options opt;
/******************************************
* Set the allowed and required options:
*
* Example of configuartion file:
*
******************************************/
vector<string> required;
vector<string> allowed;
opt.required.push_back("pdbFile");
opt.required.push_back("segment");
opt.required.push_back("proteinId");
opt.required.push_back("topFile");
opt.required.push_back("parFile");
opt.required.push_back("solvFile");
opt.required.push_back("hBondFile");
opt.allowed.push_back("configfile");
//OptionParser OP(_argc, _argv);
OptionParser OP;
OP.setShortOptionEquivalent(opt.equivalent);
OP.readArgv(_argc, _argv);
OP.setDefaultArguments(opt.defaultArgs); // a pdb file value can be given as a default argument without the --pdbfile option
OP.setRequired(opt.required);
OP.setAllowed(opt.allowed);
OP.autoExtendOptions(); // if you give option "solvat" it will be autocompleted to "solvationfile"
if (OP.countOptions() == 0) {
usage();
exit(0);
}
opt.configfile = OP.getString("configfile");
if (opt.configfile != "") {
OP.readFile(opt.configfile);
if (OP.fail()) {
opt.errorFlag = true;
opt.errorMessages += "Cannot read configuration file " + opt.configfile + "\n";
exit(1);
}
}
/*****************************************
* VERSION AND HELP
*
* --version or -v arguments print the version number
* --help prints the usage and help
*****************************************/
opt.version = OP.getBool("version");
//if (OP.fail()) {
// opt.version = OP.getBool("v");
//}
if (opt.version) {
version();
exit(0);
}
opt.help = OP.getBool("help");
if (OP.fail()) {
opt.help = OP.getBool("h");
}
if (opt.help) {
help(defaults);
exit(0);
}
/*****************************************
* CHECK THE GIVEN OPTIONS
*****************************************/
if (!OP.checkOptions()) {
opt.errorFlag = true;
opt.OPerrors = OP.getErrors();
return opt;
}
opt.errorFlag = false;
opt.warningFlag = false;
opt.errorMessages = "";
opt.warningMessages = "";
/*****************************************
* CHECK THE GIVEN OPTIONS
*****************************************/
opt.pdbFile = OP.getString("pdbFile");
if (OP.fail()) {
opt.errorMessages += "pdbFile not specified\n";
opt.errorFlag = true;
}
opt.segment = OP.getMultiString("segment");
if (OP.fail()) {
opt.errorMessages += "segment not specified\n";
opt.errorFlag = true;
}
opt.proteinId = OP.getString("proteinId");
if (OP.fail()) {
opt.errorMessages += "proteinId not specified\n";
opt.errorFlag = true;
}
opt.topFile = OP.getString("topFile");
if (OP.fail()) {
opt.errorMessages += "topFile not specified\n";
opt.errorFlag = true;
}
opt.parFile = OP.getString("parFile");
if (OP.fail()) {
opt.errorMessages += "parFile not specified\n";
opt.errorFlag = true;
}
opt.solvFile = OP.getString("solvFile");
if (OP.fail()) {
opt.errorMessages += "solvFile not specified\n";
opt.errorFlag = true;
}
opt.hBondFile = OP.getString("hBondFile");
if (OP.fail()) {
opt.errorMessages += "hBondFile not specified\n";
opt.errorFlag = true;
}
// return the Options structure
return opt;
}
