00001 /*
00002 ##############################################################################
00003 # file: ms_distiller_data_search.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_distiller_data_search.hpp $
00012  * @(#)$Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_2_8_1-0-gea32989045 $
00013  * @(#)$Date: 2018-07-30 16:23:53 +0100 $
00014 ##############################################################################
00015  */
00016 
00017 #ifndef MS_DISTILLER_DATA_SEARCH_HPP
00018 #define MS_DISTILLER_DATA_SEARCH_HPP
00019 
00020 
00021 // Includes from the standard template library
00022 #include <string>
00023 
00024 
00025 namespace msparser_internal
00026 {
00027     class ms_XMLHelper;
00028     class ms_XMLElement;
00029 }
00030 
00031 namespace matrix_science
00032 {
00033     class ms_quant_configfile;
00034 
00035 
00036     //=========================================================================
00043 
00044 
00051     class MS_MASCOTRESFILE_API ms_distiller_data_search
00052     {
00053         friend class ms_distiller_data;
00054 
00055         public:
00056 
00058 
00061             enum eScoring
00062             {
00063                 eAuto = 0,            
00064                 eMudpit = 1,          
00065                 eStandard = 99999999, 
00066             };
00067 
00069 
00072             enum eGrouping
00073             {
00074                 eGroupAuto = 0,     
00075                 eGroupStandard = 1, 
00076                 eGroupFamily = 2    
00077             };
00078 
00080 
00083             enum eSpectralLibrary
00084             {
00085                 eUnknown = -1,   
00086                 eFASTA = 0,      
00087                 eLibrary = 1,    
00088                 eIntegrated = 2, 
00089             };
00090 
00092             ms_distiller_data_search();
00093 
00095             ms_distiller_data_search(
00096                 const std::string & taskId,
00097                 bool isLoaded,
00098                 const std::string & cacheFileName,
00099                 const std::string & quantMethodXml,
00100                 const std::string & mascotServerURL,
00101                 const std::string & mascotServerVersion,
00102                 unsigned int flags,
00103                 unsigned int flags2,
00104                 bool requireBoldRed,
00105                 bool showSameset,
00106                 double showSubset,
00107                 bool loadUnassigned,
00108                 double significanceThreshold,
00109                 eScoring scoring,
00110                 int reporttop,
00111                 bool errTolPeptide,
00112                 eGrouping proteinGrouping,
00113                 bool percolator,
00114                 double scoreExpectCutOff,
00115                 bool showSamesetFamily,
00116                 bool showSubsetFamily,
00117                 eSpectralLibrary libraryDisplayOption,
00118                 bool percolatorUseProteins,
00119                 bool percolatorUseRT,
00120                 int minPepLenInPepSummary
00121             );
00122 
00123             // Copying constructor for c++ programs - don't document
00124             ms_distiller_data_search(const ms_distiller_data_search &src);
00125 
00126 #ifndef SWIG
00127             // Assignment operator for c++ programs - don't document
00128             ms_distiller_data_search & operator=(const ms_distiller_data_search & right);
00129 #endif
00130 
00131             std::string getTaskId() const;
00132 
00134             bool getLoaded() const;
00135 
00137             std::string getCacheFileName() const;
00138 
00140             std::string getQuantMethodXml() const;
00141 
00143             std::string getMascotServerURL() const;
00144 
00146             bool serverVersionNewerOrSameAs(int major, int minor, int patch) const;
00147 
00149             std::string getMascotSearchURL(const std::string & resultsFilePath) const;
00150 
00152             eGrouping getProteinGrouping() const;
00153 
00155             eScoring getScoring() const;
00156 
00158             double getScoreExpectCutOff() const;
00159 
00161             double getShowSubset() const;
00162 
00164             bool getShowSubsetFamily() const;
00165 
00167             bool getRequireBoldRed() const;
00168 
00170             double getSignificanceThreshold() const; // = minProbability
00171 
00173             int getReporttop() const;
00174 
00176             bool getPercolator() const;
00177 
00179             bool getPercolatorUseProteins() const;
00180 
00182             bool getPercolatorUseRT() const;
00183 
00185             bool getErrTolPeptide() const;
00186 
00188             unsigned int getPeptideSummaryFlags() const;
00189 
00191             unsigned getPeptideSummaryFlags2() const;
00192 
00194             bool getLoadUnassigned() const;
00195 
00197             bool getShowSamesets() const;
00198 
00200             bool getShowSamesetsFamily() const;
00201 
00203             int getMinPepLenInPepSummary() const;
00204 
00206             eSpectralLibrary getSpectralLibraryDisplayOption() const;
00207 
00208         private:
00209             // Used internally to read from the rover_data XML file
00210             bool extractXml(msparser_internal::ms_XMLHelper & helper, msparser_internal::ms_XMLElement & element);
00211             void copyFrom(const ms_distiller_data_search * src);
00212             void setMissingBlueOptionValues(const std::string & mascotServerURL, 
00213                                             const std::string & mascotServerVersion,
00214                                             int minPepLenInPepSummary, 
00215                                             bool percolatorUseProteins, 
00216                                             bool percolatorUseRT);
00217 
00218             std::string taskId_;
00219             bool isLoaded_;
00220             std::string cacheFileName_;
00221             std::string quantMethodXml_;
00222             std::string mascotServerURL_;
00223             std::string mascotServerVersion_;
00224             unsigned int flags_;
00225             unsigned int flags2_;
00226 
00227             // From blueoptions (same order as schema)
00228             bool requireBoldRed_;
00229             bool showSameset_;
00230             double showSubset_;
00231             bool loadUnassigned_;
00232             double significanceThreshold_; // = minProbability
00233             eScoring scoring_;
00234             int reporttop_;
00235             bool errTolPeptide_;
00236             eGrouping proteinGrouping_;
00237             bool percolator_;
00238             double scoreExpectCutOff_;
00239             bool showSamesetFamily_;
00240             bool showSubsetFamily_;
00241             eSpectralLibrary libraryDisplayOption_;
00242             bool percolatorUseProteins_;
00243             bool percolatorUseRT_;
00244             int minPepLenInPepSummary_;
00245     };
00246  // end of quantitation_group
00248     //=========================================================================
00249 
00250 } // namespace matrix_science
00251 
00252 #endif // MS_DISTILLER_DATA_SEARCH_HPP
00253 
00254 /*------------------------------- End of File -------------------------------*/