Matrix Science header

ms_distiller_data_search.hpp

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: /vol/cvsroot/parser/inc/ms_distiller_data_search.hpp,v $
00012  * @(#)$Revision: 1.4 $
00013  * @(#)$Date: 2016/03/30 09:37:21 $
00014 ##############################################################################
00015  */
00016 
00017 #ifndef MS_DISTILLER_DATA_SEARCH_HPP
00018 #define MS_DISTILLER_DATA_SEARCH_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 
00040 namespace msparser_internal
00041 {
00042     class ms_XMLHelper;
00043     class ms_XMLElement;
00044 }
00045 
00046 namespace matrix_science
00047 {
00048     //=========================================================================
00054     class ms_quant_configfile;
00055 
00057 
00060     class MS_MASCOTRESFILE_API ms_distiller_data_search
00061     {
00062         public:
00063 
00065 
00068             enum eScoring
00069             {
00070                 eAuto = 0,            
00071                 eMudpit = 1,          
00072                 eStandard = 99999999, 
00073             };
00074 
00076 
00079             enum eGrouping
00080             {
00081                 eGroupAuto = 0,     
00082                 eGroupStandard = 1, 
00083                 eGroupFamily = 2    
00084             };
00085 
00086             // used internally
00087             ms_distiller_data_search();
00088             bool extractXml(msparser_internal::ms_XMLHelper & helper, msparser_internal::ms_XMLElement & element);
00089 
00091             std::string getTaskId() const;
00092 
00094             bool getLoaded() const;
00095 
00097             std::string getCacheFileName() const;
00098 
00100             std::string getQuantMethodXml() const;
00101 
00103             const matrix_science::ms_quant_configfile & getQuantConfigFile() const;
00105             eGrouping getProteinGrouping() const;
00107             eScoring getScoring() const;
00109             double getScoreExpectCutOff() const;
00111             double getShowSubset() const;
00113             bool getShowSubsetFamily() const;
00115             bool getRequireBoldRed() const;
00117             double getSignificanceThreshold() const; // = minProbability
00119             int getReporttop() const;
00121             bool getPercolator() const;
00123             bool getErrTolPeptide() const;
00124 
00126             int getPeptideSummaryFlags() const;
00128             int getPeptideSummaryFlags2() const;
00130             bool getLoadUnassigned() const;
00132             bool getShowSamesets() const;
00134             bool getShowSamesetsFamily() const;
00135 
00136         private:
00137             std::string taskId;
00138             bool isLoaded;
00139             std::string cacheFileName;
00140             std::string quantMethodXml;
00141             matrix_science::ms_quant_configfile quantConfigFile;
00142             eGrouping proteinGrouping;
00143             eScoring scoring;
00144             double scoreExpectCutOff;
00145             double showSubset;
00146             bool showSubsetFamily;
00147             bool requireBoldRed;
00148             double significanceThreshold; // = minProbability
00149             int reporttop;
00150             bool percolator;
00151             bool errTolPeptide;
00152             bool loadUnassigned;
00153             bool showSameset;
00154             bool showSamesetFamily;
00155     };
00156  // end of quantitation_group
00158     //=========================================================================
00159 
00160 } // namespace matrix_science
00161 
00162 #endif // MS_DISTILLER_DATA_SEARCH_HPP
00163 
00164 /*------------------------------- End of File -------------------------------*/
Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Fri Jun 2 2017 01:44:50