Matrix Science Mascot Parser toolkit
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msparser.hpp
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/*
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##############################################################################
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# File: msparser.hpp #
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# Mascot Parser toolkit #
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# Master include file #
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##############################################################################
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# COPYRIGHT NOTICE #
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# Copyright 1998-2006 Matrix Science Limited All Rights Reserved. #
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# #
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##############################################################################
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# $Source: parser/inc/msparser.hpp $
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# $Author: villek@matrixscience.com $
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# $Date: 2024-04-23 13:44:38 +0100 $
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# $Revision: d68a41bc8e47b8ed51f15aa732b0a03e4685c239 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $
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##############################################################################
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*/
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// Configuration files functionality //
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// Some necessary constants
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#include "msparser_lim.hpp"
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// General-purpose functionality or base classes
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#include "ms_logging.hpp"
// generic logging mechanism
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#include "ms_log.hpp"
// log messages for internal use
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#include "ms_errors.hpp"
// generic error-handling mechanism
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#include "ms_customproperty.hpp"
// custom property functionality
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#include "ms_fileutilities.hpp"
// file-handling utilities
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#include "ms_connection_settings.hpp"
// proxy server and sessionID for config files
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#include "ms_tinycdb.hpp"
// cdb index files
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#include "ms_input_stream.hpp"
// input sream interface
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#include "ms_progress_info.hpp"
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// 'mascot.dat' file
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#include "ms_computeraddress.hpp"
// auxiliary definition classes
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#include "ms_mascotfiles.hpp"
// location of other configuration files
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#include "ms_clusterparams.hpp"
// 'Cluster'-section
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#include "ms_unigeneoptions.hpp"
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#include "ms_cronoptions.hpp"
// 'Cron'-section
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#include "ms_databaseoptions.hpp"
// 'Databases'-section
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#include "ms_libraryoptions.hpp"
// 'LibraryOptions' -section
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#include "ms_parserule.hpp"
// 'Parse'-section
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#include "ms_processoroptions.hpp"
// 'Processor'-section
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#include "ms_taxonomyrules.hpp"
// 'Taxonomy_XXX'-section
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#include "ms_wwwoptions.hpp"
// 'WWW'-section
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#include "ms_mascotoptions.hpp"
// 'Options'-section
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#include "ms_datfile.hpp"
// main class that represents the whole file
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// 'enzymes' file
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#include "ms_enzyme.hpp"
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// 'fragmentation_rules' file
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#include "ms_fragmentationrules.hpp"
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// 'mascot.license' file
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#include "ms_license.hpp"
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#include "ms_umod_configfile.hpp"
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// 'mod_file' and 'substitutions' files
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#include "ms_modfile.hpp"
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// 'masses file'
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#include "ms_masses.hpp"
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// CPU configuration retreival
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#include "ms_processors.hpp"
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// 'taxonomy' file
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#include "ms_taxonomyfile.hpp"
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// authentication
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#include "ms_security_task.hpp"
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#include "ms_security_tasks.hpp"
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#include "ms_security_user.hpp"
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#include "ms_security_group.hpp"
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#include "ms_security_options.hpp"
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#include "ms_security.hpp"
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#include "ms_security_session.hpp"
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// generic XML handling
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#include "ms_xml_typeinfo.hpp"
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#include "ms_xml_schema.hpp"
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#include "ms_xml_parameters.hpp"
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// crosslinking.xml programming interface
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#include "ms_crosslinking_accessions.hpp"
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#include "ms_crosslinking_accession.hpp"
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#include "ms_crosslinking_configfile.hpp"
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#include "ms_crosslinking_parameters.hpp"
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#include "ms_crosslinking_linkers.hpp"
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#include "ms_crosslinking_linker.hpp"
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#include "ms_crosslinking_method.hpp"
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#include "ms_crosslinking_monolink.hpp"
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#include "ms_crosslinking_does_not_pair_with.hpp"
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#include "ms_crosslinking_filters.hpp"
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#include "ms_crosslinking_scope.hpp"
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#include "ms_crosslinking_settings.hpp"
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// quantitation.xml programming interface
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#include "ms_quant_moverz.hpp"
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#include "ms_quant_correction.hpp"
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#include "ms_quant_file_index.hpp"
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#include "ms_quant_isotope.hpp"
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#include "ms_quant_component.hpp"
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#include "ms_quant_composition.hpp"
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#include "ms_quant_parameters.hpp"
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#include "ms_quant_integration.hpp"
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#include "ms_quant_neutralloss.hpp"
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#include "ms_quant_specificity.hpp"
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#include "ms_quant_pepneutralloss.hpp"
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#include "ms_quant_localdef.hpp"
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#include "ms_quant_unmodified.hpp"
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#include "ms_quant_modgroup.hpp"
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#include "ms_quant_quality.hpp"
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#include "ms_quant_outliers.hpp"
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#include "ms_quant_normalisation.hpp"
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#include "ms_quant_precursor.hpp"
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#include "ms_quant_average.hpp"
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#include "ms_quant_multiplex.hpp"
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#include "ms_quant_reporter.hpp"
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#include "ms_quant_replicate.hpp"
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#include "ms_quant_protocol.hpp"
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#include "ms_quant_numerator.hpp"
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#include "ms_quant_ratio.hpp"
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#include "ms_quant_method.hpp"
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#include "ms_quant_configfile.hpp"
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#include "ms_quant_satellite.hpp"
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#include "ms_quant_normalisation_peptide.hpp"
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#include "ms_quant_normalisation_protein.hpp"
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#include "ms_quant_stats.hpp"
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#include "ms_peptide_quant_key.hpp"
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#include "ms_peptide_quant_key_vector.hpp"
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#include "ms_peptide_quant_ratio.hpp"
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#include "ms_protein_quant_ratio.hpp"
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#include "ms_quantitation.hpp"
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#include "ms_ms2quantitation.hpp"
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#include "ms_customquantitation.hpp"
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// unimod.xml programming interface
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#include "ms_umod_element.hpp"
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#include "ms_umod_modification.hpp"
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#include "ms_umod_aminoacid.hpp"
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#include "ms_umod_modbrick.hpp"
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#include "ms_umod_specificity.hpp"
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#include "ms_umod_composition.hpp"
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#include "ms_umod_neutralloss.hpp"
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#include "ms_umod_elemref.hpp"
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#include "ms_umod_xref.hpp"
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// HTTP connection
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#include "ms_http_helper_handles.hpp"
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#include "ms_http_helper_progress.hpp"
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#include "ms_http_helper_response.hpp"
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#include "ms_http_helper_return.hpp"
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#include "ms_http_helper.hpp"
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// remote Mascot server
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#include "ms_http_client_mime.hpp"
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#include "ms_http_client_search.hpp"
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#include "ms_http_client_session.hpp"
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#include "ms_http_client.hpp"
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// Mascot result files functionality //
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#include "ms_peptide.hpp"
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#include "ms_linker_site.hpp"
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#include "ms_linker_site_vector.hpp"
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#include "ms_mascotresfilebase.hpp"
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#include "ms_mascotresfile_dat.hpp"
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#include "ms_mascotresfile_msr.hpp"
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#include "ms_protein.hpp"
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#include "ms_mascotresults.hpp"
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#include "ms_proteinsummary.hpp"
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#include "ms_peptidesummary.hpp"
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#include "ms_mascotresults_params.hpp"
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#include "ms_inputquery.hpp"
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#include "ms_searchparams.hpp"
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#include "ms_unigene.hpp"
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#include "ms_fragment.hpp"
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#include "ms_fragmentvector.hpp"
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#include "ms_aahelper.hpp"
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#include "ms_zip.hpp"
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#include "ms_shapiro_wilk.hpp"
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#include "ms_obofile.hpp"
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#include "ms_msr2dat28.hpp"
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#include "ms_body.hpp"
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#include "ms_ms1quant_peptide_status.hpp"
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#include "ms_quant_helper.hpp"
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#include "ms_cache_file.hpp"
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#include "ms_cache_stream.hpp"
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#include "ms_matrix.hpp"
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#include "ms_body.hpp"
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#include "ms_xic.hpp"
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#include "ms_ms1quant_match_range.hpp"
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#include "ms_ms1quant_match_component.hpp"
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#include "ms_ms1quant_match_ratio.hpp"
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#include "ms_fitexy_result.hpp"
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#include "ms_ms1quant_charge_state.hpp"
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#include "ms_ms1quant_match.hpp"
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#include "ms_ms1quant_average_results.hpp"
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#include "ms_ms1quant_peptide_status.hpp"
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#include "ms_ms1quant_time_align_limits.hpp"
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#include "ms_ms1quant_time_align.hpp"
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#include "ms_ms1quantitation.hpp"
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#include "ms_distiller_data.hpp"
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#include "ms_distiller_data_quant.hpp"
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#include "ms_distiller_data_search.hpp"
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#include "ms_distiller_master_project.hpp"
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#include "ms_distiller_subsearch.hpp"
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#include "ms_distiller_master_search.hpp"
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#include "ms_distiller_search_status.hpp"
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#include "ms_distiller_search_status_list.hpp"
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#include "ms_distiller_sub_project.hpp"
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#include "ms_spectral_lib_peak.hpp"
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#include "ms_spectral_lib_peak_list.hpp"
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#include "ms_spectral_lib_entry.hpp"
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#include "ms_spectral_lib_file.hpp"
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#include "ms_imputation.hpp"
inc
msparser.hpp
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