int main ( int argc, char** argv )
{
initialiseProspector ();
ParameterList pList ( argc, argv );
try {
if ( pList.getBoolValue ( "save_params" ) ) {
init_html ( cout, "Saving Search Compare Parameters" );
pList.removeName ( "save_params" );
ParameterList cookieParamList ( "", false, false ); // Create empty parameter set
cookieParamList.appendParameters ( pList );
cookieParamList.removeName ( "accession_nums" );
cookieParamList.removeName ( "remove" );
cookieParamList.removeName ( "id_filter_list" );
cookieParamList.removeName ( "data" );
cookieParamList.removeName ( "version" );
bool ret = cookieParamList.copyToCookie ( cout, "search_compare_params" );
if ( !ret ) {
ErrorHandler::genError ()->error ( "Could not save the parameters as their length exceeds the maximum cookie length.\n" );
}
cout << "<p>Settings saved</p>" << endl;
cout << "<input type=\"button\" value=\"Search Form\" onclick=\"history.go(-1)\">" << endl;
exit ( 0 );
}
if ( pList.empty () ) {
ErrorHandler::genError ()->error ( "No parameters passed to Search Compare.\n" );
}
ProgramLink::setParams ( &pList );
init_html_premature_stop ( "Search Compare", true );
SearchCompareParams params ( &pList );
sresFPR = params.getReportType () == "False Positive Rate";
sresTime = params.getReportType () == "Time" || sresFPR;
sresXLinks = params.getReportType () == "Crosslinked Peptides";
sresMods = params.getReportType () == "Modifications";
sresProt = params.getReportType () == "Protein";
sresKeepReplicates = params.getPeptideFilter () == "Keep Replicates" || sresTime;
sresKeepCharges = params.getPeptideFilter () == "Best Per Charge";
sresKeepTimeReplicates = params.getPeptideFilter () == "Keep Replicates";
sresViewer = params.getSaveFormat () == 'V';
ujm = new UpdatingJavascriptMessage;
vector <SearchResults*> searchResults;
getSearchResults ( params, searchResults );
writeReport ( params, searchResults );
delete ujm;
printProgramInformationHTML ( cout, "Search Compare" );
ProteinInfo::deleteTempDirs ();
}
catch ( runtime_error e ) {
pList.writeLogError ( e.what () );
}
return 0;
}
int main ( int argc, char** argv )
{
initialiseProspector ();
ParameterList paramList ( argc, argv ); // Process the cgi input including the uploaded file
try {
ostream& os = cout;
if ( paramList.getBoolValue ( "save_params" ) )
saveParams ( os, paramList );
else
batchSubmission ( os, paramList );
}
catch ( runtime_error e ) {
paramList.writeLogError ( e.what () );
}
MySQLPPSDDBase::instance ( false, true );
return 0;
}
