00001 /*
00002 ##############################################################################
00003 # File: msparser.hpp                                                         #
00004 # Mascot Parser toolkit                                                      #
00005 # Master include file                                                        #
00006 ##############################################################################
00007 # COPYRIGHT NOTICE                                                           #
00008 # Copyright 1998-2006 Matrix Science Limited  All Rights Reserved.           #
00009 #                                                                            #
00010 ##############################################################################
00011 #    $Source: parser/inc/msparser.hpp $
00012 #    $Author: villek@matrixscience.com $ 
00013 #      $Date: 2019-10-18 16:39:04 +0100 $ 
00014 #  $Revision: 5a6646e705a1dce6cb8493dec184ed46d0bd6c08 | MSPARSER_REL_2_8_1-0-gea32989045 $
00015 ##############################################################################
00016 */
00017 
00019 //                      Configuration files functionality                   //
00021 
00022 // Some necessary constants
00023 #include "msparser_lim.hpp"
00024 
00025 // General-purpose functionality or base classes
00026 #include "ms_logging.hpp"               // generic logging mechanism
00027 #include "ms_log.hpp"                   // log messages for internal use
00028 #include "ms_errors.hpp"                // generic error-handling mechanism
00029 #include "ms_customproperty.hpp"        // custom property functionality
00030 #include "ms_fileutilities.hpp"         // file-handling utilities
00031 #include "ms_connection_settings.hpp"   // proxy server and sessionID for config files
00032 #include "ms_tinycdb.hpp"               // cdb index files
00033 #include "ms_input_stream.hpp"          // input sream interface
00034 #include "ms_progress_info.hpp"
00035 
00036 
00037 // 'mascot.dat' file
00038 #include "ms_computeraddress.hpp"       // auxiliary definition classes
00039 #include "ms_mascotfiles.hpp"           // location of other configuration files
00040 #include "ms_clusterparams.hpp"         // 'Cluster'-section
00041 #include "ms_unigeneoptions.hpp"
00042 #include "ms_cronoptions.hpp"           // 'Cron'-section
00043 #include "ms_databaseoptions.hpp"       // 'Databases'-section
00044 #include "ms_libraryoptions.hpp"        // 'LibraryOptions' -section
00045 #include "ms_parserule.hpp"             // 'Parse'-section
00046 #include "ms_processoroptions.hpp"      // 'Processor'-section
00047 #include "ms_taxonomyrules.hpp"         // 'Taxonomy_XXX'-section
00048 #include "ms_wwwoptions.hpp"            // 'WWW'-section
00049 #include "ms_mascotoptions.hpp"         // 'Options'-section
00050 #include "ms_datfile.hpp"               // main class that represents the whole file
00051 
00052 // 'enzymes' file
00053 #include "ms_enzyme.hpp"
00054 
00055 // 'fragmentation_rules' file
00056 #include "ms_fragmentationrules.hpp"
00057 
00058 // 'mascot.license' file
00059 #include "ms_license.hpp"
00060 
00061 #include "ms_umod_configfile.hpp"
00062 
00063 // 'mod_file' and 'substitutions' files
00064 #include "ms_modfile.hpp"
00065 
00066 // 'masses file'
00067 #include "ms_masses.hpp"
00068 
00069 // CPU configuration retreival
00070 #include "ms_processors.hpp"
00071 
00072 // 'taxonomy' file
00073 #include "ms_taxonomyfile.hpp"
00074 
00075 // authentication
00076 #include "ms_security_task.hpp"
00077 #include "ms_security_tasks.hpp"
00078 #include "ms_security_user.hpp"
00079 #include "ms_security_group.hpp"
00080 #include "ms_security_options.hpp"
00081 #include "ms_security.hpp"
00082 #include "ms_security_session.hpp"
00083 
00084 // generic XML handling
00085 #include "ms_xml_typeinfo.hpp"
00086 #include "ms_xml_schema.hpp"
00087 #include "ms_xml_parameters.hpp"
00088 
00089 // crosslinking.xml programming interface
00090 #include "ms_crosslinking_accessions.hpp"
00091 #include "ms_crosslinking_accession.hpp"
00092 #include "ms_crosslinking_configfile.hpp"
00093 #include "ms_crosslinking_parameters.hpp"
00094 #include "ms_crosslinking_linkers.hpp"
00095 #include "ms_crosslinking_linker.hpp"
00096 #include "ms_crosslinking_method.hpp"
00097 #include "ms_crosslinking_monolink.hpp"
00098 #include "ms_crosslinking_does_not_pair_with.hpp"
00099 #include "ms_crosslinking_filters.hpp"
00100 #include "ms_crosslinking_scope.hpp"
00101 #include "ms_crosslinking_settings.hpp"
00102 
00103 // quantitation.xml programming interface
00104 #include "ms_quant_moverz.hpp"
00105 #include "ms_quant_correction.hpp"
00106 #include "ms_quant_isotope.hpp"
00107 #include "ms_quant_component.hpp"
00108 #include "ms_quant_composition.hpp"
00109 #include "ms_quant_parameters.hpp"
00110 #include "ms_quant_integration.hpp"
00111 #include "ms_quant_neutralloss.hpp"
00112 #include "ms_quant_specificity.hpp"
00113 #include "ms_quant_pepneutralloss.hpp"
00114 #include "ms_quant_localdef.hpp"
00115 #include "ms_quant_unmodified.hpp"
00116 #include "ms_quant_modgroup.hpp"
00117 #include "ms_quant_quality.hpp"
00118 #include "ms_quant_outliers.hpp"
00119 #include "ms_quant_normalisation.hpp"
00120 #include "ms_quant_precursor.hpp"
00121 #include "ms_quant_average.hpp"
00122 #include "ms_quant_multiplex.hpp"
00123 #include "ms_quant_reporter.hpp"
00124 #include "ms_quant_replicate.hpp"
00125 #include "ms_quant_protocol.hpp"
00126 #include "ms_quant_numerator.hpp"
00127 #include "ms_quant_ratio.hpp"
00128 #include "ms_quant_method.hpp"
00129 #include "ms_quant_configfile.hpp"
00130 #include "ms_quant_satellite.hpp"
00131 #include "ms_quant_normalisation_peptide.hpp"
00132 #include "ms_quant_normalisation_protein.hpp"
00133 #include "ms_quant_stats.hpp"
00134 #include "ms_peptide_quant_key.hpp"
00135 #include "ms_peptide_quant_key_vector.hpp"
00136 #include "ms_peptide_quant_ratio.hpp"
00137 #include "ms_protein_quant_ratio.hpp"
00138 #include "ms_quantitation.hpp"
00139 #include "ms_ms2quantitation.hpp"
00140 #include "ms_customquantitation.hpp"
00141 
00142 // unimod.xml programming interface
00143 #include "ms_umod_element.hpp"
00144 #include "ms_umod_modification.hpp"
00145 #include "ms_umod_aminoacid.hpp"
00146 #include "ms_umod_modbrick.hpp"
00147 #include "ms_umod_specificity.hpp"
00148 #include "ms_umod_composition.hpp"
00149 #include "ms_umod_neutralloss.hpp"
00150 #include "ms_umod_elemref.hpp"
00151 #include "ms_umod_xref.hpp"
00152 
00153 // HTTP connection
00154 #include "ms_http_helper_handles.hpp"
00155 #include "ms_http_helper_progress.hpp"
00156 #include "ms_http_helper_response.hpp"
00157 #include "ms_http_helper_return.hpp"
00158 #include "ms_http_helper.hpp"
00159 
00160 // remote Mascot server
00161 #include "ms_http_client_mime.hpp"
00162 #include "ms_http_client_search.hpp"
00163 #include "ms_http_client_session.hpp"
00164 #include "ms_http_client.hpp"
00165 
00166 
00168 //                      Mascot result files functionality                   //
00170 
00171 #include "ms_mascotrespeptide.hpp"
00172 #include "ms_linker_site.hpp"
00173 #include "ms_linker_site_vector.hpp"
00174 #include "ms_mascotresfile.hpp"
00175 #include "ms_mascotresprotein.hpp"
00176 #include "ms_mascotresults.hpp"
00177 #include "ms_mascotresproteinsum.hpp"
00178 #include "ms_mascotrespeptidesum.hpp"
00179 #include "ms_mascotresults_params.hpp"
00180 #include "ms_inputquery.hpp"
00181 #include "ms_mascotresparams.hpp"
00182 #include "ms_mascotresunigene.hpp"
00183 
00184 #include "ms_fragment.hpp"
00185 #include "ms_fragmentvector.hpp"
00186 
00187 #include "ms_aahelper.hpp"
00188 #include "ms_zip.hpp"
00189 #include "ms_shapiro_wilk.hpp"
00190 #include "ms_obofile.hpp"
00191 
00193 
00194 #include "ms_body.hpp"
00195 #include "ms_ms1quant_peptide_status.hpp"
00196 #include "ms_quant_helper.hpp"
00197 
00198 #include "ms_cache_file.hpp"
00199 #include "ms_cache_stream.hpp"
00200 #include "ms_matrix.hpp"
00201 #include "ms_body.hpp"
00202 #include "ms_xic.hpp"
00203 #include "ms_ms1quant_match_range.hpp"
00204 #include "ms_ms1quant_match_component.hpp"
00205 #include "ms_ms1quant_match_ratio.hpp"
00206 #include "ms_fitexy_result.hpp"
00207 #include "ms_ms1quant_charge_state.hpp"
00208 #include "ms_ms1quant_match.hpp"
00209 #include "ms_ms1quant_average_results.hpp"
00210 #include "ms_ms1quant_peptide_status.hpp"
00211 
00212 #include "ms_ms1quantitation.hpp"
00213 
00214 #include "ms_distiller_data.hpp"
00215 #include "ms_distiller_data_quant.hpp"
00216 #include "ms_distiller_data_search.hpp"
00217 #include "ms_distiller_master_project.hpp"
00218 #include "ms_distiller_subsearch.hpp"
00219 #include "ms_distiller_master_search.hpp"
00220 #include "ms_distiller_search_status.hpp"
00221 #include "ms_distiller_search_status_list.hpp"
00222 #include "ms_distiller_sub_project.hpp"
00223 
00224 #include "ms_spectral_lib_peak.hpp"
00225 #include "ms_spectral_lib_peak_list.hpp"
00226 #include "ms_spectral_lib_entry.hpp"
00227 #include "ms_spectral_lib_file.hpp"