Matrix Science header

ms_ms1quant_match.hpp

00001 /*
00002 ##############################################################################
00003 # file: ms_ms1quant_match.hpp
00004 # 'msparser' toolkit
00005 # An extracted ion chromatogram
00006 ##############################################################################
00007 # COPYRIGHT NOTICE
00008 # Copyright 1998-2014 Matrix Science Limited  All Rights Reserved.
00009 #
00010 ##############################################################################
00011  * @(#)$Source: /vol/cvsroot/parser/inc/ms_ms1quant_match.hpp,v $
00012  * @(#)$Revision: 1.7 $
00013  * @(#)$Date: 2017/01/31 13:10:16 $
00014 ##############################################################################
00015  */
00016 
00017 #ifndef MS_MS1QUANT_MATCH_HPP
00018 #define MS_MS1QUANT_MATCH_HPP
00019 
00020 #ifdef _WIN32
00021 #pragma warning(disable:4251)   // Don't want all classes to be exported
00022 #pragma warning(disable:4786)   // Debug symbols too long
00023 #   ifndef _MATRIX_USE_STATIC_LIB
00024 #       ifdef MS_MASCOTRESFILE_EXPORTS
00025 #           define MS_MASCOTRESFILE_API __declspec(dllexport)
00026 #       else
00027 #           define MS_MASCOTRESFILE_API __declspec(dllimport)
00028 #       endif
00029 #   else
00030 #       define MS_MASCOTRESFILE_API
00031 #   endif
00032 #else
00033 #   define MS_MASCOTRESFILE_API
00034 #endif
00035 
00036 // Includes from the standard template library
00037 #include <string>
00038 
00039 namespace matrix_science
00040 {
00041     //=========================================================================
00047     class ms_ms1quant_match_body;
00048     class ms_protein;
00049     class ms_peptide;
00050     class ms_quant_component;
00051 
00053 
00060     class MS_MASCOTRESFILE_API ms_ms1quant_match :
00061         public ms_handle
00062     {
00063         public:
00065 
00068             enum chargeType
00069             {
00070                 CHARGETYPE_ORIGINAL,       
00071                 CHARGETYPE_ALL             
00072             };
00073 
00075             static std::string getXmlCode(chargeType code);
00076 
00078             static chargeType getCodeFromXml(std::string text);
00079 
00081             ms_ms1quant_match();
00082 
00084             ms_ms1quant_match(const ms_ms1quant_match_body & body);
00085 
00086 #ifndef SWIG
00087 
00088             ms_ms1quant_match_body * body();
00090             const ms_ms1quant_match_body * body() const;
00091 
00093             bool addProteinHit(const int hit, const int member);
00095             void setKey(const int id);
00096 #endif
00097 
00099             matrix_science::ms_peptide_quant_key getKey() const;
00100 
00102             bool hasIdentifiedComponent() const;
00103 
00105             bool allComponentsIdentified() const;
00106 
00108             std::string getPeptideString() const;
00109 
00111             std::string getVarMods() const;
00112 
00114             int getFirstXicScanId() const;
00115 
00117             void setFirstXicScanId(int value) ;
00118 
00120             int getLastXicScanId() const;
00121 
00123             void setLastXicScanId(int value) ;
00124 
00126             double getDisplayIntensity() const;
00127 
00129             void setDisplayIntensity(double value);
00130 
00132             int getChargeState() const;
00133 
00135             chargeType getChargeType() const;
00136 
00138             std::string getLabelFreeVarMods() const;
00139 
00141             std::string getReadableLabelFreeVarMods() const;
00142 
00144             std::string getConciseLabelFreeVarMods() const;
00145 
00147             int getDataSourceId() const;
00148 
00150             const ms_matrix & getCorrectionMatrix() const;
00151 
00153             ms_matrix & getCorrectionMatrix();
00154 
00156             const ms_matrix & getPerfectObservedMatrix() const;
00157 
00159             ms_matrix & getPerfectObservedMatrix();
00160 
00162             const ms_matrix & getPredictionMatrix() const;
00163 
00165             ms_matrix & getPredictionMatrix();
00166 
00168             int getNumHits() const;
00170             const ms_protein * getHit(int index1) const;
00171 
00173             int getNumComponents() const;
00175             ms_ms1quant_match_component getComponent(int index) const;
00176 
00178             bool hasComponent(std::string componentName) const;
00180             ms_ms1quant_match_component getComponent(std::string componentName) const;
00181 
00182             ms_ms1quant_match_component * addCreatedComponent(
00183                     const matrix_science::ms_peptide & peptide,
00184                     const matrix_science::ms_quant_component & component);
00185 
00186             ms_ms1quant_match_component * addIdentifiedComponent(
00187                     const matrix_science::ms_peptide & peptide,
00188                     const matrix_science::ms_quant_component & component);
00189 
00191             int getNumPeptideRatios() const;
00193             ms_ms1quant_match_ratio getPeptideRatio(int index) const;
00194 
00196             bool hasPeptideRatio(const std::string & ratioName) const;
00198             ms_ms1quant_match_ratio getPeptideRatio(const std::string & ratioName) const;
00200             void setPeptideRatio(const std::string & ratioName, const ms_ms1quant_match_ratio & ratio);
00201 
00203             ms_ms1quant_charge_state getChargeStateData() const;
00205             void setChargeStateData(const ms_ms1quant_charge_state & csData);
00206 
00208             bool isHitRatioOutlier(const std::string & ratioName, int hitId, int memberNumber) const;
00210             bool isHitRatioUsedForAverage(const std::string & ratioName, int hitId, int memberNumber) const;
00212             bool isHitRatioExcluded(const std::string & ratioName, int hitId, int memberNumber) const;
00213 
00215             void setHitRatioExcluded(const std::string & ratioName, int hitId, int memberNumber);
00216 
00218             void setHitRatioOutlier(const std::string & ratioName, int hitId, int memberNumber);
00219 
00221             void clearHitRatioOutlier(const std::string & ratioName, int hitId, int memberNumber);
00222     };
00223 
00224  // end of quantitation_group
00226     //=========================================================================
00227 
00228 } // namespace matrix_science
00229 
00230 #endif // MS_MS1QUANT_MATCH_HPP
00231 
00232 /*------------------------------- End of File -------------------------------*/
Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Fri Jun 2 2017 01:44:51