config_fragrules.cpp

Read in the fragmentation_rules file.

/*
##############################################################################
# file: config_fragrules.cpp                                                 #
# 'msparser' toolkit example code                                            #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2005 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
#    $Source: parser/examples/test_cxx/config_fragrules.cpp $ #
#     $Author: villek@matrixscience.com $                                                      #
#       $Date: 2018-07-30 16:23:53 +0100 $                                         #
#   $Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $                                                         #
# $NoKeywords::                                                            $ #
##############################################################################
*/
 
#include "msparser.hpp"
 
#include <iostream>
 
 
// All the classes are part of the matrix_science namespace
using namespace matrix_science;
 
int main(int argc, char * argv[])
{
    if ( argc < 2 )
    {
        std::cout << "The location of fragmentation_rules file has to be specified as a parameter" << std::endl;
        std::cout << "The location should either be the full path to the fragmentation_rules file" << std::endl;
        std::cout << "or a URL to a Mascot server - e.g. http://mascot-server/mascot/cgi" << std::endl;
        return 1;
    }
 
    // A sessionID can optionally be passed as the second parameter
    // This will only be required if the 'file' is a URL
    ms_connection_settings cs;
    if (argc > 2) 
    {
        cs.setSessionID(argv[2]);
    }
 
    ms_fragrulesfile file(argv[1], &cs);
 
    if ( !file.isValid() )
    {
        std::cout << "There are errors. Cannot continue. The last error description:" << std::endl;
        std::cout << file.getLastErrorString() << std::endl;
        return 1;
    }
 
    int n = file.getNumberOfInstruments();
    std::cout << n << " instruments are configured:" << std::endl;
 
    int i;
    for(i=0; i < n; i++)
    {
        std::cout << file.getInstrumentName(i) << std::endl;
    }
 
    // Now change ESI-QUAD-TOF
    ms_fragmentationrules instrument = *file.getInstrumentByName("ESI-QUAD-TOF");
    instrument.setSeriesUsed(23, true);  // Add v series
    file.updateInstrumentByName("ESI-QUAD-TOF", instrument);
 
    // And delete MALDI-QIT-TOF
    file.deleteInstrumentByName("MALDI-QIT-TOF");
 
    //Finally, save the file under a new name - but only if not http:
    if (strncmp("http:", argv[1], 5) != 0) {
        std::string filename = argv[1];
        filename +=  ".new";
        file.setFileName(filename.c_str());
        file.save_file();
    }
    std::cout << "There are now " << file.getNumberOfInstruments() << " instruments configured." << std::endl;
    return 0;
}
 
 
 
 
 
 
/*
will give the output: 
 
 
# config_fragrules.exe ../config/fragmentation_rules
 
11 instruments are configured:
Default
ESI-QUAD-TOF
MALDI-TOF-PSD
ESI-TRAP
ESI-QUAD
ESI-FTICR
MALDI-TOF-TOF
ESI-4SECTOR
FTMS-ECD
MALDI-QUAD-TOF
LCQ
There are now 10 instruments configured.
*/