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: parser/inc/ms_ms1quant_match.hpp $
00012  * @(#)$Revision: f505c54c65f9b7a686953cde690d0fe22a5a6c85 | MSPARSER_REL_2_8_1-0-gea32989045 $
00013  * @(#)$Date: 2019-08-19 16:33:39 +0100 $
00014 ##############################################################################
00015  */
00016 
00017 #ifndef MS_MS1QUANT_MATCH_HPP
00018 #define MS_MS1QUANT_MATCH_HPP
00019 
00020 
00021 // Includes from the standard template library
00022 #include <string>
00023 
00024 namespace matrix_science
00025 {
00026     //=========================================================================
00032     class ms_ms1quant_match_body;
00033     class ms_protein;
00034     class ms_peptide;
00035     class ms_quant_component;
00036 
00038 
00045     class MS_MASCOTRESFILE_API ms_ms1quant_match :
00046         public ms_handle
00047     {
00048         public:
00050 
00053             enum chargeType
00054             {
00055                 CHARGETYPE_ORIGINAL,       
00056                 CHARGETYPE_ALL             
00057             };
00058 
00060             static std::string getXmlCode(chargeType code);
00061 
00063             static chargeType getCodeFromXml(std::string text);
00064 
00066             ms_ms1quant_match();
00067 
00069             ms_ms1quant_match(const ms_ms1quant_match_body & body);
00070 
00071 #ifndef SWIG
00072 
00073             ms_ms1quant_match_body * body();
00075             const ms_ms1quant_match_body * body() const;
00076 
00078             bool addProteinHit(const int hit, const int member);
00080             void setKey(const int id);
00082             void applyThresholds();
00083 #endif
00084 
00086             matrix_science::ms_peptide_quant_key getKey() const;
00087 
00089             bool hasIdentifiedComponent() const;
00090 
00092             bool allComponentsIdentified() const;
00093 
00095             std::string getPeptideString() const;
00096 
00098             std::string getVarMods() const;
00099 
00101             int getFirstXicScanId() const;
00102 
00104             void setFirstXicScanId(int value) ;
00105 
00107             int getLastXicScanId() const;
00108 
00110             void setLastXicScanId(int value) ;
00111 
00113             double getDisplayIntensity() const;
00114 
00116             void setDisplayIntensity(double value);
00117 
00119             int getChargeState() const;
00120 
00122             chargeType getChargeType() const;
00123 
00125             std::string getLabelFreeVarMods() const;
00126 
00128             std::string getReadableLabelFreeVarMods() const;
00129 
00131             std::string getConciseLabelFreeVarMods() const;
00132 
00134             int getDataSourceId() const;
00135 
00137             const ms_matrix & getCorrectionMatrix() const;
00138 
00139 #if !defined(SWIGJAVA) && !defined(SWIGCSHARP)
00140 
00141             ms_matrix & getCorrectionMatrix();
00142 #endif
00143 
00144             const ms_matrix & getPerfectObservedMatrix() const;
00145 
00146 #if !defined(SWIGJAVA) && !defined(SWIGCSHARP)
00147 
00148             ms_matrix & getPerfectObservedMatrix();
00149 #endif
00150 
00151             const ms_matrix & getPredictionMatrix() const;
00152 
00153 #if !defined(SWIGJAVA) && !defined(SWIGCSHARP)
00154 
00155             ms_matrix & getPredictionMatrix();
00156 #endif
00157 
00158             int getNumHits() const;
00160             const ms_protein * getHit(int index1) const;
00161 
00163             int getNumComponents() const;
00165             ms_ms1quant_match_component getComponent(int index) const;
00166 
00168             bool hasComponent(std::string componentName) const;
00170             ms_ms1quant_match_component getComponent(std::string componentName) const;
00171 
00172             ms_ms1quant_match_component * addCreatedComponent(
00173                     const matrix_science::ms_peptide & peptide,
00174                     const matrix_science::ms_quant_component & component);
00175 
00176             ms_ms1quant_match_component * addCreatedComponent(const std::string & componentName);
00177 
00179             ms_ms1quant_match_component * addCreatedComponent(
00180                 const matrix_science::ms_ms1quant_match_component & component);
00181 
00183             ms_ms1quant_match_component * addComponent(const matrix_science::ms_ms1quant_match_component & component);
00184 
00186             bool removeComponent(const std::string & componentName);
00187 
00188             ms_ms1quant_match_component * addIdentifiedComponent(
00189                     const matrix_science::ms_peptide & peptide,
00190                     const matrix_science::ms_quant_component & component);
00191 
00193             int getNumPeptideRatios() const;
00195             ms_ms1quant_match_ratio getPeptideRatio(int index) const;
00196 
00198             bool hasPeptideRatio(const std::string & ratioName) const;
00200             ms_ms1quant_match_ratio getPeptideRatio(const std::string & ratioName) const;
00202             void setPeptideRatio(const std::string & ratioName, const ms_ms1quant_match_ratio & ratio);
00203 
00205             ms_ms1quant_charge_state getChargeStateData() const;
00207             void setChargeStateData(const ms_ms1quant_charge_state & csData);
00208 
00210             bool isHitRatioOutlier(const std::string & ratioName, int hitId, int memberNumber) const;
00212             bool isHitRatioUsedForAverage(const std::string & ratioName, int hitId, int memberNumber) const;
00214             bool isHitRatioExcluded(const std::string & ratioName, int hitId, int memberNumber) const;
00215 
00217             void setHitRatioExcluded(const std::string & ratioName, int hitId, int memberNumber);
00218 
00220             void clearHitRatioExcluded(const std::string & ratioName, int hitId, int memberNumber);
00221 
00223             void setHitRatioOutlier(const std::string & ratioName, int hitId, int memberNumber);
00224 
00226             void clearHitRatioOutlier(const std::string & ratioName, int hitId, int memberNumber);
00227     };
00228 
00229  // end of quantitation_group
00231     //=========================================================================
00232 
00233 } // namespace matrix_science
00234 
00235 #endif // MS_MS1QUANT_MATCH_HPP
00236 
00237 /*------------------------------- End of File -------------------------------*/