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: 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> #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_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()) { 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_mascotresfile & 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 */
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