//------------------------------------------------------------------------------
int main(int argc, char **argv) {
prgm_opt::variables_map option_map;
prgm_opt::options_description options("Options");
try {
prgm_opt::arg="[File]";
options.add_options()
(CMDOPTIONS::HELP_OPTION,CMDOPTIONS::HELP_TEXT)
(CMDOPTIONS::PERCOLATORFILE_OPTION,prgm_opt::value<string>()->required(),CMDOPTIONS::PERCOLATORFILE_TEXT)
(CMDOPTIONS::MZIDFILE_OPTION,prgm_opt::value<string>()->required(),CMDOPTIONS::MZIDFILE_TEXT)
(CMDOPTIONS::MZIDOUTPUT_OPTION,prgm_opt::value<string>()->required(),CMDOPTIONS::MZIDOUTPUT_TEXT)
(CMDOPTIONS::MZIDFILES_OPTION,prgm_opt::value<string>()->required(),CMDOPTIONS::MZIDFILES_TEXT)
(CMDOPTIONS::DECOY_OPTION,CMDOPTIONS::DECOY_TEXT)
(CMDOPTIONS::VALIDATION_OPTION,CMDOPTIONS::VALIDATION_TEXT)
(CMDOPTIONS::WARNING_OPTION,CMDOPTIONS::WARNING_TEXT);
prgm_opt::store(prgm_opt::parse_command_line(argc,argv,options),option_map);
if (option_map.count(CMDOPTIONS::HELP_TEST)) {
printVersion();
cout << options;
CleanUp(EXIT_SUCCESS);
}
if (option_map.count(CMDOPTIONS::DECOY_TEST))
percolator.setDecoy();
if (option_map.count(CMDOPTIONS::VALIDATION_TEST)) {
percolator.unsetValidation();
mzid.unsetValidation();
}
if (option_map.count(CMDOPTIONS::MZIDOUTPUT_TEST))
mzid.setOutputFileEnding(option_map[CMDOPTIONS::MZIDOUTPUT_TEST].as<string>());
if (option_map.count(CMDOPTIONS::PERCOLATORFILE_TEST))
if (!percolator.setFilename(option_map[CMDOPTIONS::PERCOLATORFILE_TEST].as<string>()))
THROW_ERROR_VALUE(PRINT_TEXT::NO_PERCOLATOR_FILE,option_map[CMDOPTIONS::PERCOLATORFILE_TEST].as<string>());
if (option_map.count(CMDOPTIONS::MZIDFILE_TEST))
mzid.setFilename(option_map[CMDOPTIONS::MZIDFILE_TEST].as<string>());
if (option_map.count(CMDOPTIONS::MZIDFILES_TEST))
if (!mzid.addFilenames(option_map[CMDOPTIONS::MZIDFILES_TEST].as<string>()))
THROW_ERROR_VALUE(PRINT_TEXT::NO_MZID_FILE,option_map[CMDOPTIONS::MZIDFILES_TEST].as<string>());
if (option_map.count(CMDOPTIONS::WARNING_TEST))
mzid.unsetWarningFlag();
if (!mzid.checkFilenames())
CleanUp(EXIT_FAILURE);
if (percolator.noFilename())
THROW_ERROR(PRINT_TEXT::PERCOLATOR_FILE_NOT_ENTERED);
xercesc::XMLPlatformUtils::Initialize();
percolator.setFirstMzIDFilename(mzid.getFirstFilename());
if (!percolator.getPoutValues(pout_values))
THROW_ERROR(PRINT_TEXT::CANNOT_LOAD_PERCOLATOR_FILE);
if (!mzid.insertMZIDValues(pout_values))
THROW_ERROR(PRINT_TEXT::CANNOT_INSERT);
CleanUp(EXIT_SUCCESS);
}
catch(exception &e) {
cerr << e.what() << endl;
CleanUp(EXIT_FAILURE);
}
}
//------------------------------------------------------------------------------
bool MzIDIO::insertMZIDValues(boost::unordered_map<PercolatorOutFeatures, string, PercolatorOutFeatures> &pout_values,
vector <string> &filenames, bool multiplemzidfiles) {
ifstream fpr;
ofstream fpw;
ostream *wout;
string mzidname,s1,psmid;
int i1,vi1,n,xmlindent;
n=0;
psmid="";
try {
for (vi1=0; vi1<filenames.size(); vi1++) {
mzidname=boost::lexical_cast<boost::filesystem::path>(filenames[vi1]).stem().string();
if (!multiplemzidfiles)
mzidname="";
fpr.open(filenames[vi1].c_str());
if (outputfileending.length()>0) {
fpw.open(setOutputFileName(filenames[vi1]).c_str());
wout=&fpw;
}
else
wout=&cout;
while (getline(fpr,s1)) {
if (s1.find(MZID_PARAM::END_INSERT_TAG)!=string::npos) {
if (psmid.length()==0)
THROW_ERROR_VALUE(PRINT_TEXT::BAD_XML,filenames[vi1]);
for (i1=0; i1<ARRAYSIZE(MZID_PARAM::ELEMENT_DATA::ELEMENTS); i1++) {
if (pout_values.find(PercolatorOutFeatures(mzidname,psmid,i1))==pout_values.end())
continue;
n++;
switch (MZID_PARAM::ELEMENT_DATA::ELEMENTS[i1]) {
case MZID_PARAM::CVPARAM: {
*wout << boost::format(MZID_PARAM::CVPARAM_TAG) % string(xmlindent,' ')
% MZID_PARAM::ELEMENT_DATA::ACCESSIONS[i1]
% MZID_PARAM::ELEMENT_DATA::CVREFS[i1]
% MZID_PARAM::ELEMENT_DATA::NAMES[i1]
% pout_values[PercolatorOutFeatures(mzidname,psmid,i1)];
break;
}
case MZID_PARAM::USERPARAM: {
*wout << boost::format(MZID_PARAM::USERPARAM_TAG) % string(xmlindent,' ')
% MZID_PARAM::ELEMENT_DATA::NAMES[i1]
% pout_values[PercolatorOutFeatures(mzidname,psmid,i1)];
break;
}
}
pout_values.erase(PercolatorOutFeatures(mzidname,psmid,i1));
}
psmid="";
}
xmlindent=s1.find_first_not_of(" ");
*wout << s1 << endl;
if (s1.find(MZID_PARAM::PSMID_TAG)!=string::npos && s1.find(MZID_PARAM::START_INSERT_TAG)!=string::npos) {
i1=s1.find(MZID_PARAM::PSMID_TAG)+strlen(MZID_PARAM::PSMID_TAG);
psmid=s1.substr(i1,s1.find("\"",i1)-i1);
}
}
fpr.close();
fpw.close();
}
clog << boost::format(PRINT_TEXT::INSERTED) % n << endl;
for (boost::unordered_map<PercolatorOutFeatures, string, PercolatorOutFeatures>::iterator
it=pout_values.begin(); it!=pout_values.end(); it++)
cerr << boost::format(PRINT_TEXT::PSM_NOT_ENTERED) % it->first.filename % it->first.psmid << endl;
return true;
}
catch (exception &e) {
cerr << e.what() << endl;
fpr.close();
fpw.close();
return false;
}
}
