resfile_params.cpp

Example program for retrieving search parameter data.

/*
##############################################################################
# file: resfile_params.cpp                                                   #
# 'msparser' toolkit example code                                            #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2005 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
#    $Source: parser/examples/test_cxx/resfile_params.cpp $ #
#     $Author: robertog@matrixscience.com $                                                      #
#       $Date: 2024-09-04 10:23:46 +0100 $                                         #
#   $Revision: 526921a73137894bb1eae0b0fc8ccb4bb52ea662 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $                                                         #
# $NoKeywords::                                                            $ #
##############################################################################
*/
#include "msparser.hpp"
#include <iostream>
#include <iomanip>
 
 
// 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 searchParameters(ms_mascotresfilebase & 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_mascotresfilebase file = ms_mascotresfilebase::createResfile(argv[1]);
 
        if (file.isValid())
        {
            searchParameters(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;
}
 
/*****************************************************************************/
/* searchParameters                                                          */
/* Display parameters from the ms_searchparams object.                       */
/* The values come from the parameters and the masses sections of the file   */
/*****************************************************************************/
static void searchParameters(ms_mascotresfilebase & file)
{
    ms_searchparams p(file);
 
    std::cout << "Search parameters from ms_searchparams"             << std::endl;
    std::cout << "========================================="          << std::endl;
    std::cout << "License             : " << p.getLICENSE()           << std::endl;
    std::cout << "Search title        : " << p.getCOM()               << std::endl;
    std::cout << "SEG mass            : " << p.getSEG()               << std::endl;
    std::cout << "Peptide tol         : " << p.getTOL()               << std::endl;
    std::cout << "Peptide tol units   : " << p.getTOLU()              << std::endl;
    std::cout << "Fragment tol        : " << p.getITOL()              << std::endl;
    std::cout << "Fragment tol units  : " << p.getITOLU()             << std::endl;
    std::cout << "Missed cleavages    : " << p.getPFA()               << std::endl;
    std::cout << "Database            : " << p.getDB()                << std::endl;
    std::cout << "Static mods         : " << p.getMODS()              << std::endl;
    std::cout << "Average/monoisotopic: " << p.getMASS()              << std::endl;
    std::cout << "Enzyme              : " << p.getCLE()               << std::endl;
    std::cout << "Raw data file name  : " << p.getFILENAME()          << std::endl;
    std::cout << "Input data          : " << p.getQUE()               << std::endl;
    std::cout << "Type of search      : " << p.getSEARCH()            << std::endl;
    std::cout << "User name           : " << p.getUSERNAME()          << std::endl;
    std::cout << "User email          : " << p.getUSEREMAIL()         << std::endl;
    std::cout << "Charge state        : " << p.getCHARGE()            << std::endl;
    std::cout << "Repeat search file  : " << p.getINTERMEDIATE()      << std::endl;
    std::cout << "Num hits to display : " << p.getREPORT()            << std::endl;
    std::cout << "Show overview       : " << p.getOVERVIEW()          << std::endl;
    std::cout << "Data file format    : " << p.getFORMAT()            << std::endl;
    std::cout << "Form version        : " << p.getFORMVER()           << std::endl;
    std::cout << "Variable mods       : " << p.getIT_MODS()           << std::endl;
 
    for (int u=0; u <=12; u++)
        std::cout << "User" 
        << std::setw(2) << std::setfill('0')  << u 
              <<       "              : " << p.getUSERField(u)        << std::endl;
    std::cout << "Precursor mass      : " << p.getPRECURSOR()         << std::endl;
    std::cout << "Taxonomy filter     : " << p.getTAXONOMY()          << std::endl;
    std::cout << "Type of report      : " << p.getREPTYPE()           << std::endl;
    std::cout << "Accessions to search: " << p.getACCESSION()         << std::endl;
    std::cout << "Subcluster used     : " << p.getSUBCLUSTER()        << std::endl;
    std::cout << "ICAT search?        : " << p.getICAT()              << std::endl;
    std::cout << "Instrument type     : " << p.getINSTRUMENT()        << std::endl;
    std::cout << "Error tolerant?     : " << p.getERRORTOLERANT()     << std::endl;
    std::cout << "Rules (ions series) : " << p.getRULES()             << std::endl;
    std::cout << "Quantitation method : " << p.getQUANTITATION()      << std::endl;
    std::cout << "Peptide isotope err : " << p.getPEP_ISOTOPE_ERROR() << std::endl;
    std::cout << "Decoy database      : " << p.getDECOY()             << std::endl;
 
    for (char ch='A'; ch <= 'Z'; ch++)
    {
        std::cout << "Residue " << ch << "           : " 
                  << p.getResidueMass(ch)
                  << std::endl;
    }
    std::cout << "C terminus mass     : " << p.getCTermMass()         << std::endl;
    std::cout << "N terminus mass     : " << p.getNTermMass()         << std::endl;
    std::cout << "Mass of hydrogen    : " << p.getHydrogenMass()      << std::endl;
    std::cout << "Mass of oxygen      : " << p.getOxygenMass()        << std::endl;
    std::cout << "Mass of carbon      : " << p.getCarbonMass()        << std::endl;
    std::cout << "Mass of nitrogen    : " << p.getNitrogenMass()      << std::endl;
    std::cout << "Mass of electron    : " << p.getElectronMass()      << std::endl;
 
 
    int i = 1;
    while (p.getVarModsName(i).length())
    {
    std::cout << "Variable mod name   : " << p.getVarModsName(i)      << std::endl;
    std::cout << "Variable mod delta  : " << p.getVarModsDelta(i)     << std::endl;
    std::cout << "Variable mod neutral: " << p.getVarModsNeutralLoss(i)<< std::endl;
    i++;
    }
    std::cout << std::endl << std::endl;
}
 
/*
will give the output: 
 
Search parameters from ms_searchparams
=========================================
License             :
Search title        : A few peptides from an LCMS run
SEG mass            : -1
Peptide tol         : 2
Peptide tol units   : Da
Fragment tol        : 1
Fragment tol units  : Da
Missed cleavages    : 1
Database            : MSDB
Static mods         : Oxidation (M),SMA (K),SMA (N-term)
Average/monoisotopic: Monoisotopic
Enzyme              : Trypsin
Raw data file name  : U:\\Mascot test data\\TSQ\\dyckall_1.asc
Input data          :
Type of search      : MIS
User name           : Cat R. Piller
User email          : crp@brassica.com
Charge state        : 2+
Repeat search file  :
Num hits to display : 5
Show overview       : 0
Data file format    : Finnigan (.ASC)
Form version        : 1.01
Variable mods       :
User00              :
User01              :
User02              :
User03              :
User04              :
User05              :
User06              :
User07              :
User08              :
User09              :
User10              :
User11              :
User12              :
Precursor mass      : 0
Taxonomy filter     : All entries
Type of report      : peptide
Accessions to search:
Subcluster used     : -1
ICAT search?        : 0
Instrument type     : ESI-QUAD-TOF
Error tolerant?     : 0
Rules (ions series) : 1,2,8,9,10,13,14,15
Quantitation method : ICAT
Peptide isotope err : 2
Decoy database      : 1
Residue A           : 71.0371
Residue B           : 114.535
Residue C           : 103.009
Residue D           : 115.027
Residue E           : 129.043
Residue F           : 147.068
Residue G           : 57.0215
Residue H           : 137.059
Residue I           : 113.084
Residue J           : 0
Residue K           : 255.158
Residue L           : 113.084
Residue M           : 147.035
Residue N           : 114.043
Residue O           : 0
Residue P           : 97.0528
Residue Q           : 128.059
Residue R           : 156.101
Residue S           : 87.032
Residue T           : 101.048
Residue U           : 0
Residue V           : 99.0684
Residue W           : 186.079
Residue X           : 111
Residue Y           : 163.063
Residue Z           : 128.551
C terminus mass     : 17.0027
N terminus mass     : 128.071
Mass of hydrogen    : 1.00783
Mass of oxygen      : 15.9949
Mass of carbon      : 12
Mass of nitrogen    : 14.0031
Mass of electron    : 0
 
*/