resfile_info.cpp

Example program for retrieving general search information.

/*
##############################################################################
# file: resfile_info.cpp                                                     #
# 'msparser' toolkit example code                                            #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2005 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
#    $Source: parser/examples/test_cxx/resfile_info.cpp $ #
#     $Author: villek@matrixscience.com $                                                      #
#       $Date: 2018-07-30 16:23:53 +0100 $                                         #
#   $Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_2_8_1-0-gea32989045 $                                                         #
# $NoKeywords::                                                            $ #
##############################################################################
*/

#include "msparser.hpp"
#include <iostream>


// All the classes are part of the matrix_science namespace
using namespace matrix_science;


/*****************************************************************************/
/* Local functions                                                           */
/* (This test harness is 'C' and not C++)                                    */
/*****************************************************************************/
static void searchInformation(ms_mascotresfile & file);


/*****************************************************************************/
/* main                                                                      */
/* Call this program with a single argument - the name of the .dat file      */
/*****************************************************************************/
int main(int argc, char * argv[])
{
    if (argc == 2)
    {
        ms_mascotresfile file(argv[1]);

        if (file.isValid())
        {
            searchInformation(file);
        }
        else
            std::cout << "Error: " << file.getLastErrorString() << std::endl;
    }
    else 
        std::cout << "Must supply the name of a .dat file as a command line argument" << std::endl;
    return 0;
}

/*****************************************************************************/
/* searchInformation                                                         */
/* Display parameters from the ms_mascotresfile object. The functions        */
/* anyPMF, anyMSMS, anySQ should normally be used in preference to isPMF     */
/* etc. because some people submit MSMS though the sequence query window.    */
/*****************************************************************************/
static void searchInformation(ms_mascotresfile & file)
{
    time_t t = (time_t)file.getDate();
    struct tm * t1 = localtime(&t);

    std::cout << "Search information from ms_mascotresfile"       << std::endl;
    std::cout << "========================================"       << std::endl;
    std::cout << "Number of queries   : " << file.getNumQueries()  << std::endl;
    std::cout << "Number of hits      : " << file.getNumHits()     << std::endl;
    std::cout << "Number of sequences : " << file.getNumSeqs()     << std::endl;
    std::cout << "Sequences after tax : " << file.getNumSeqsAfterTax() 
                                                                  << std::endl;
    std::cout << "Number of residues  : " << file.getNumResidues() << std::endl;
    std::cout << "Execution time      : " << file.getExecTime()    << std::endl;
    std::cout << "Date (seconds)      : " << file.getDate()        << std::endl;
    std::cout << "Date                : " << asctime(t1);
    std::cout << "Mascot version      : " << file.getMascotVer()   << std::endl;
    std::cout << "Fasta version       : " << file.getFastaVer()    << std::endl;
    std::cout << "Is PMF?             : " << file.isPMF()          << std::endl;
    std::cout << "Is MSMS?            : " << file.isMSMS()         << std::endl;
    std::cout << "Is SQ?              : " << file.isSQ()           << std::endl;
    std::cout << "Is Error tolerant   : " << file.isErrorTolerant()<< std::endl;
    std::cout << "Any PMF?            : " << file.anyPMF()         << std::endl;
    std::cout << "Any MSMS?           : " << file.anyMSMS()        << std::endl;
    std::cout << "Any SQ?             : " << file.anySQ()          << std::endl;
    std::cout << "Any peptides section: " << file.doesSectionExist(ms_mascotresfile::SEC_PEPTIDES)
                                                                  << std::endl;
    std::cout << "Any peptide matches : " << file.anyPeptideSummaryMatches()
                                                                  << std::endl;
    std::cout << std::endl;
}

/*

will give the output: 



# test.exe F981123.dat

Search information from ms_mascotresfile
========================================
Number of queries   : 4
Number of hits      : 50
Number of sequences : 820227
Sequences after tax : 820227
Number of residues  : 2.55697e+008
Execution time      : 14
Date (seconds)      : 1014568786
Date                : Sun Feb 24 16:39:46 2002
Mascot version      : 1.7.17
Fasta version       : MSDB_20020121.fasta
Is PMF?             : 0
Is MSMS?            : 1
Is SQ?              : 0
Is Error tolerant   : 0
Any PMF?            : 0
Any MSMS?           : 1
Any SQ?             : 0
Any peptides section: 1
Any peptide matches : 1

*/