Example program for retrieving search parameter data.
/* ############################################################################## # file: resfile_params.cs # # 'msparser' toolkit example code # ############################################################################## # COPYRIGHT NOTICE # # Copyright 1998-2015 Matrix Science Limited All Rights Reserved. # # # ############################################################################## # $Source: parser/examples/test_csharp/resfile_params.cs $ # # $Author: villek@matrixscience.com $ # # $Date: 2018-07-30 16:23:53 +0100 $ # # $Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_2_8_1-0-gea32989045 $ # # $NoKeywords:: $ # ############################################################################## */ using System; using matrix_science.msparser; namespace MsParserExamples { public class resfile_params { public static void Main(string[] argv) { // ----- Object creation ----- if (argv.Length < 1) { Console.WriteLine("Must specify results filename as parameter"); return; } ms_mascotresfile file = new ms_mascotresfile(argv[0], 0, ""); if (file.isValid()) { searchParameters(file); } else { Console.WriteLine("Error number: {0}", file.getLastError()); Console.WriteLine("Error string: {0}", file.getLastErrorString()); return; } } private static void searchParameters(ms_mascotresfile file) { int i; char ch; ms_searchparams p = file._params(); Console.WriteLine("Search parameters from ms_searchparams"); Console.WriteLine("========================================="); Console.WriteLine("License : {0}", p.getLICENSE()); Console.WriteLine("Search title : {0}", p.getCOM()); Console.WriteLine("SEG mass : {0}", p.getSEG()); Console.WriteLine("Peptide tol : {0}", p.getTOL()); Console.WriteLine("Peptide tol units : {0}", p.getTOLU()); Console.WriteLine("Fragment tol : {0}", p.getITOL()); Console.WriteLine("Fragment tol units : {0}", p.getITOLU()); Console.WriteLine("Missed cleavages : {0}", p.getPFA()); Console.WriteLine("Database : {0}", p.getDB()); Console.WriteLine("Static mods : {0}", p.getMODS()); Console.WriteLine("Average/monoisotopic: {0}", p.getMASS()); Console.WriteLine("Enzyme : {0}", p.getCLE()); Console.WriteLine("Raw data file name : {0}", p.getFILENAME()); Console.WriteLine("Input data : {0}", p.getQUE()); Console.WriteLine("Type of search : {0}", p.getSEARCH()); Console.WriteLine("User name : {0}", p.getUSERNAME()); Console.WriteLine("User email : {0}", p.getUSEREMAIL()); Console.WriteLine("Charge state : {0}", p.getCHARGE()); Console.WriteLine("Repeat searhc file : {0}", p.getINTERMEDIATE()); Console.WriteLine("Num hits to display : {0}", p.getREPORT()); Console.WriteLine("Show overview : {0}", ((p.getOVERVIEW()) ? 1 : 0)); Console.WriteLine("Data file format : {0}", p.getFORMAT()); Console.WriteLine("Form version : {0}", p.getFORMVER()); Console.WriteLine("Variable mods : {0}", p.getIT_MODS()); for (i = 0; i <= 12; i++) { Console.WriteLine("User{0} : {1}", "" + i.ToString("D2"), p.getUSERField(i)); } Console.WriteLine("Precursor mass : {0:#}", p.getPRECURSOR()); Console.WriteLine("Taxonomy filter : {0}", p.getTAXONOMY()); Console.WriteLine("Type of report : {0}", p.getREPTYPE()); Console.WriteLine("Accessions to search: {0}", p.getACCESSION()); Console.WriteLine("Subcluster used : {0}", p.getSUBCLUSTER()); Console.WriteLine("ICAT search? : {0}", ((p.getICAT()) ? 1 : 0)); Console.WriteLine("Instrument type : {0}", p.getINSTRUMENT()); Console.WriteLine("Error tolerant? : {0}", ((p.getERRORTOLERANT()) ? 1 : 0)); Console.WriteLine("Rules (ions series) : {0}", p.getRULES()); Console.WriteLine("Quantitation method : {0}", p.getQUANTITATION()); Console.WriteLine("Peptide isotope err : {0}", p.getPEP_ISOTOPE_ERROR()); Console.WriteLine("Decoy database : {0}", p.getDECOY()); for (ch = 'A'; ch <= 'Z'; ch++) { Console.WriteLine("Residue {0} : {1:#}", ch, p.getResidueMass(ch)); } Console.WriteLine("C terminus mass : {0:#}", p.getCTermMass()); Console.WriteLine("N terminus mass : {0:#}", p.getNTermMass()); Console.WriteLine("Mass of hydrogen : {0:#}", p.getHydrogenMass()); Console.WriteLine("Mass of oxygen : {0:#}", p.getOxygenMass()); Console.WriteLine("Mass of carbon : {0:#}", p.getCarbonMass()); Console.WriteLine("Mass of nitrogen : {0:#}", p.getNitrogenMass()); Console.WriteLine("Mass of electron : {0:#}", p.getElectronMass()); i = 1; while (p.getVarModsName(i).Length > 0) { Console.WriteLine("Variable mod name : {0}", p.getVarModsName(i)); Console.WriteLine("Variable mod delta : {0:#}", p.getVarModsDelta(i)); Console.WriteLine("Variable mod neutral: {0:#}", p.getVarModsNeutralLoss(i)); i++; } Console.WriteLine(); } } } /* resfile_params.exe c:\inetpub\mascot\data\F981123.dat Will give the following output: Search parameters from ms_searchparams ========================================= License : Matrix Science (ECUK-U3C2-5RS5-AAQL-H2X5) Search title : MS/MS Example SEG mass : -1 Peptide tol : 0.2 Peptide tol units : Da Fragment tol : 0.2 Fragment tol units : Da Missed cleavages : 1 Database : SwissProt Static mods : Average/monoisotopic: Monoisotopic Enzyme : Trypsin Raw data file name : Input data : Type of search : MIS User name : User email : Charge state : 2+ Repeat searhc file : ../data/F981123.dat Num hits to display : 0 Show overview : 0 Data file format : Mascot generic Form version : 1.01 Variable mods : Oxidation (M) User00 : User01 : User02 : User03 : User04 : User05 : User06 : User07 : User08 : User09 : User10 : User11 : User12 : Precursor mass : 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 : None Peptide isotope err : 0 Decoy database : -1 Residue A : 71 Residue B : 115 Residue C : 103 Residue D : 115 Residue E : 129 Residue F : 147 Residue G : 57 Residue H : 137 Residue I : 113 Residue J : 113 Residue K : 128 Residue L : 113 Residue M : 131 Residue N : 114 Residue O : 237 Residue P : 97 Residue Q : 128 Residue R : 156 Residue S : 87 Residue T : 101 Residue U : 151 Residue V : 99 Residue W : 186 Residue X : 111 Residue Y : 163 Residue Z : 129 C terminus mass : 17 N terminus mass : 1 Mass of hydrogen : 1 Mass of oxygen : 16 Mass of carbon : 12 Mass of nitrogen : 14 Mass of electron : Variable mod name : Oxidation (M) Variable mod delta : 16 Variable mod neutral: */
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