Matrix Science header

ms_mascotresparams.hpp

00001 /*
00002 ##############################################################################
00003 # file: ms_mascotresparams.hpp                                               #
00004 # 'msparser' toolkit                                                         #
00005 # Encapsulates the parameters & masses sections from the mascot results file #
00006 ##############################################################################
00007 # COPYRIGHT NOTICE                                                           #
00008 # Copyright 1998-2002 Matrix Science Limited  All Rights Reserved.           #
00009 #                                                                            #
00010 ##############################################################################
00011 #    $Archive:: /MowseBranches/ms_mascotresfile_1.2/include/ms_mascotrespa $ #
00012 #     $Author: villek $ #
00013 #       $Date: 2016/08/23 13:18:26 $ #
00014 #   $Revision: 1.20 $ #
00015 # $NoKeywords::                                                            $ #
00016 ##############################################################################
00017 */
00018 
00019 #ifndef MS_MASCOTRESPARAMS_HPP
00020 #define MS_MASCOTRESPARAMS_HPP
00021 
00022 #ifdef _WIN32
00023 #pragma warning(disable:4251)   // Don't want all classes to be exported
00024 #pragma warning(disable:4786)   // Debug symbols too long
00025 #   ifndef _MATRIX_USE_STATIC_LIB
00026 #       ifdef MS_MASCOTRESFILE_EXPORTS
00027 #           define MS_MASCOTRESFILE_API __declspec(dllexport)
00028 #       else
00029 #           define MS_MASCOTRESFILE_API __declspec(dllimport)
00030 #       endif
00031 #   else
00032 #       define MS_MASCOTRESFILE_API
00033 #   endif
00034 #else
00035 #   define MS_MASCOTRESFILE_API
00036 #endif
00037 
00038 // for the sake of #include <string>
00039 #ifdef __ALPHA_UNIX__
00040 #include <ctype.h>
00041 #endif
00042 
00043 // Includes from the standard template library
00044 #include <string>
00045 
00046 namespace matrix_science {
00047 
00053 
00054 
00060     class MS_MASCOTRESFILE_API ms_searchparams
00061     {
00062         public:
00063 
00065 
00072             enum MULTI_SITE_MODS {
00073                 MSM_NOT_PERMITTED           = 0x0000, 
00074                 MSM_EXCLUSIVE_PLUS_VARIABLE = 0x0001  
00075             };
00076 
00078             ms_searchparams(const ms_mascotresfile &resfile);
00079 
00081             ~ms_searchparams() {};
00082 
00084             std::string  getLICENSE();
00085 
00087             std::string  getCOM();
00088 
00090             int          getSEG();
00091 
00093             double       getTOL();
00094 
00096             std::string  getTOLU();
00097 
00099             double       getITOL();
00100 
00102             std::string  getITOLU();
00103 
00105             int          getPFA();
00106 
00108             std::string  getDB(int idx = 1);
00109 
00111             int getNumberOfDatabases();
00112 
00114             std::string  getMODS();
00115 
00117             std::string  getMASS();
00118 
00120             MASS_TYPE    getMassType();
00121 
00123             std::string  getCLE();
00124 
00126             std::string  getFILENAME();
00127 
00129             std::string  getDATAURL();
00130 
00132             std::string  getQUE();
00133 
00135             std::string  getSEARCH();
00136 
00138             std::string  getUSERNAME();
00139 
00141             std::string  getUSEREMAIL();
00142 
00144             int getUSERID();
00145 
00147             std::string  getCHARGE();
00148 
00150             std::string  getINTERMEDIATE();
00151 
00153             int          getREPORT();
00154 
00156             bool         getOVERVIEW();
00157 
00159             std::string  getFORMAT();
00160 
00162             std::string  getFORMVER();
00163 
00165             std::string  getIT_MODS();
00166 
00168             std::string  getUSERField(int num);
00169 
00171             std::string getAllUSERParams() const;
00172 
00174             double       getPRECURSOR();
00175 
00177             std::string  getTAXONOMY();
00178 
00180             std::string  getREPTYPE();
00181 
00183             std::string  getACCESSION();
00184 
00186             int          getSUBCLUSTER();
00187 
00189             bool         getICAT();
00190 
00192             std::string  getINSTRUMENT();
00193 
00195             bool         getERRORTOLERANT();
00196 
00198             std::string  getRULES();
00199 
00201             double getMinInternalMass();
00202 
00204             double getMaxInternalMass();
00205 
00207             double       getResidueMass(char residue);
00208 
00210             double       getCTermMass();
00211 
00213             double       getNTermMass();
00214 
00216             double       getHydrogenMass() const;
00217 
00219             double       getOxygenMass() const;
00220 
00222             double       getCarbonMass() const;
00223 
00225             double       getNitrogenMass() const;
00226 
00228             double       getElectronMass() const;
00229 
00230             // Returns the name of the specified variable modification selected by the user.
00231             std::string  getVarModsName(int num) const;
00232 
00234             double       getVarModsDelta(int num);
00235 
00237             double       getVarModsNeutralLoss(int num);
00238 
00240             std::vector<double> getVarModsNeutralLosses(int num) const;
00241 
00243             std::vector<double> getVarModsPepNeutralLoss(int num);
00244 
00246             std::vector<double> getVarModsReqPepNeutralLoss(int num);
00247 
00248             // Returns the name of the specified fixed modification selected by the user.
00249             std::string  getFixedModsName(int num) const;
00250 
00252             double       getFixedModsDelta(int num);
00253 
00255             double       getFixedModsNeutralLoss(int num);
00256 
00258             std::string  getFixedModsResidues(int num) const;
00259 
00261             int          getNumberOfLibraryMods() const;
00262 
00264             std::string  getLibraryModName(int num) const;
00265 
00267             double       getLibraryModDelta(int num) const;
00268 
00270             std::string  getErrTolParentFilename();
00271 
00273             std::string  getQUANTITATION() const;
00274 
00276             int  getPEP_ISOTOPE_ERROR() const;
00277 
00279             int  getDECOY() const;
00280 
00282             int  getLIBRARY_SEARCH() const;
00283 
00285             unsigned int getMULTI_SITE_MODS() const;
00286 
00287         protected:
00288             const ms_mascotresfile &resfile_;
00289             // Not safe to copy or assign this object.
00290 #ifndef SWIG
00291             ms_searchparams(const ms_searchparams & rhs);
00292             ms_searchparams & operator=(const ms_searchparams & rhs);
00293 #endif
00294 
00295         private:
00296             std::string decryptNumber(const std::string & input) const;
00297             void parseLibraryMod(int num, std::string *name, double *delta) const;
00298 
00299             mutable int numDB_;
00300     }; // end of resfile_group
00302 }   // matrix_science namespace
00303 
00304 #endif // MS_MASCOTRESPARAMS_HPP
00305 
00306 /*------------------------------- End of File -------------------------------*/
Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Fri Jun 2 2017 01:44:51