Matrix Science Mascot Parser toolkit
 
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msparser.hpp
1/*
2##############################################################################
3# File: msparser.hpp #
4# Mascot Parser toolkit #
5# Master include file #
6##############################################################################
7# COPYRIGHT NOTICE #
8# Copyright 1998-2006 Matrix Science Limited All Rights Reserved. #
9# #
10##############################################################################
11# $Source: parser/inc/msparser.hpp $
12# $Author: villek@matrixscience.com $
13# $Date: 2024-04-23 13:44:38 +0100 $
14# $Revision: d68a41bc8e47b8ed51f15aa732b0a03e4685c239 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $
15##############################################################################
16*/
17
19// Configuration files functionality //
21
22// Some necessary constants
23#include "msparser_lim.hpp"
24
25// General-purpose functionality or base classes
26#include "ms_logging.hpp" // generic logging mechanism
27#include "ms_log.hpp" // log messages for internal use
28#include "ms_errors.hpp" // generic error-handling mechanism
29#include "ms_customproperty.hpp" // custom property functionality
30#include "ms_fileutilities.hpp" // file-handling utilities
31#include "ms_connection_settings.hpp" // proxy server and sessionID for config files
32#include "ms_tinycdb.hpp" // cdb index files
33#include "ms_input_stream.hpp" // input sream interface
34#include "ms_progress_info.hpp"
35
36
37// 'mascot.dat' file
38#include "ms_computeraddress.hpp" // auxiliary definition classes
39#include "ms_mascotfiles.hpp" // location of other configuration files
40#include "ms_clusterparams.hpp" // 'Cluster'-section
41#include "ms_unigeneoptions.hpp"
42#include "ms_cronoptions.hpp" // 'Cron'-section
43#include "ms_databaseoptions.hpp" // 'Databases'-section
44#include "ms_libraryoptions.hpp" // 'LibraryOptions' -section
45#include "ms_parserule.hpp" // 'Parse'-section
46#include "ms_processoroptions.hpp" // 'Processor'-section
47#include "ms_taxonomyrules.hpp" // 'Taxonomy_XXX'-section
48#include "ms_wwwoptions.hpp" // 'WWW'-section
49#include "ms_mascotoptions.hpp" // 'Options'-section
50#include "ms_datfile.hpp" // main class that represents the whole file
51
52// 'enzymes' file
53#include "ms_enzyme.hpp"
54
55// 'fragmentation_rules' file
56#include "ms_fragmentationrules.hpp"
57
58// 'mascot.license' file
59#include "ms_license.hpp"
60
61#include "ms_umod_configfile.hpp"
62
63// 'mod_file' and 'substitutions' files
64#include "ms_modfile.hpp"
65
66// 'masses file'
67#include "ms_masses.hpp"
68
69// CPU configuration retreival
70#include "ms_processors.hpp"
71
72// 'taxonomy' file
73#include "ms_taxonomyfile.hpp"
74
75// authentication
76#include "ms_security_task.hpp"
77#include "ms_security_tasks.hpp"
78#include "ms_security_user.hpp"
79#include "ms_security_group.hpp"
80#include "ms_security_options.hpp"
81#include "ms_security.hpp"
82#include "ms_security_session.hpp"
83
84// generic XML handling
85#include "ms_xml_typeinfo.hpp"
86#include "ms_xml_schema.hpp"
87#include "ms_xml_parameters.hpp"
88
89// crosslinking.xml programming interface
90#include "ms_crosslinking_accessions.hpp"
91#include "ms_crosslinking_accession.hpp"
92#include "ms_crosslinking_configfile.hpp"
93#include "ms_crosslinking_parameters.hpp"
94#include "ms_crosslinking_linkers.hpp"
95#include "ms_crosslinking_linker.hpp"
96#include "ms_crosslinking_method.hpp"
97#include "ms_crosslinking_monolink.hpp"
98#include "ms_crosslinking_does_not_pair_with.hpp"
99#include "ms_crosslinking_filters.hpp"
100#include "ms_crosslinking_scope.hpp"
101#include "ms_crosslinking_settings.hpp"
102
103// quantitation.xml programming interface
104#include "ms_quant_moverz.hpp"
105#include "ms_quant_correction.hpp"
106#include "ms_quant_file_index.hpp"
107#include "ms_quant_isotope.hpp"
108#include "ms_quant_component.hpp"
109#include "ms_quant_composition.hpp"
110#include "ms_quant_parameters.hpp"
111#include "ms_quant_integration.hpp"
112#include "ms_quant_neutralloss.hpp"
113#include "ms_quant_specificity.hpp"
114#include "ms_quant_pepneutralloss.hpp"
115#include "ms_quant_localdef.hpp"
116#include "ms_quant_unmodified.hpp"
117#include "ms_quant_modgroup.hpp"
118#include "ms_quant_quality.hpp"
119#include "ms_quant_outliers.hpp"
120#include "ms_quant_normalisation.hpp"
121#include "ms_quant_precursor.hpp"
122#include "ms_quant_average.hpp"
123#include "ms_quant_multiplex.hpp"
124#include "ms_quant_reporter.hpp"
125#include "ms_quant_replicate.hpp"
126#include "ms_quant_protocol.hpp"
127#include "ms_quant_numerator.hpp"
128#include "ms_quant_ratio.hpp"
129#include "ms_quant_method.hpp"
130#include "ms_quant_configfile.hpp"
131#include "ms_quant_satellite.hpp"
132#include "ms_quant_normalisation_peptide.hpp"
133#include "ms_quant_normalisation_protein.hpp"
134#include "ms_quant_stats.hpp"
135#include "ms_peptide_quant_key.hpp"
136#include "ms_peptide_quant_key_vector.hpp"
137#include "ms_peptide_quant_ratio.hpp"
138#include "ms_protein_quant_ratio.hpp"
139#include "ms_quantitation.hpp"
140#include "ms_ms2quantitation.hpp"
141#include "ms_customquantitation.hpp"
142
143// unimod.xml programming interface
144#include "ms_umod_element.hpp"
145#include "ms_umod_modification.hpp"
146#include "ms_umod_aminoacid.hpp"
147#include "ms_umod_modbrick.hpp"
148#include "ms_umod_specificity.hpp"
149#include "ms_umod_composition.hpp"
150#include "ms_umod_neutralloss.hpp"
151#include "ms_umod_elemref.hpp"
152#include "ms_umod_xref.hpp"
153
154// HTTP connection
155#include "ms_http_helper_handles.hpp"
156#include "ms_http_helper_progress.hpp"
157#include "ms_http_helper_response.hpp"
158#include "ms_http_helper_return.hpp"
159#include "ms_http_helper.hpp"
160
161// remote Mascot server
162#include "ms_http_client_mime.hpp"
163#include "ms_http_client_search.hpp"
164#include "ms_http_client_session.hpp"
165#include "ms_http_client.hpp"
166
167
169// Mascot result files functionality //
171
172#include "ms_peptide.hpp"
173#include "ms_linker_site.hpp"
174#include "ms_linker_site_vector.hpp"
175#include "ms_mascotresfilebase.hpp"
176#include "ms_mascotresfile_dat.hpp"
177#include "ms_mascotresfile_msr.hpp"
178#include "ms_protein.hpp"
179#include "ms_mascotresults.hpp"
180#include "ms_proteinsummary.hpp"
181#include "ms_peptidesummary.hpp"
182#include "ms_mascotresults_params.hpp"
183#include "ms_inputquery.hpp"
184#include "ms_searchparams.hpp"
185#include "ms_unigene.hpp"
186
187#include "ms_fragment.hpp"
188#include "ms_fragmentvector.hpp"
189
190#include "ms_aahelper.hpp"
191#include "ms_zip.hpp"
192#include "ms_shapiro_wilk.hpp"
193#include "ms_obofile.hpp"
194#include "ms_msr2dat28.hpp"
195
197
198#include "ms_body.hpp"
199#include "ms_ms1quant_peptide_status.hpp"
200#include "ms_quant_helper.hpp"
201
202#include "ms_cache_file.hpp"
203#include "ms_cache_stream.hpp"
204#include "ms_matrix.hpp"
205#include "ms_body.hpp"
206#include "ms_xic.hpp"
207#include "ms_ms1quant_match_range.hpp"
208#include "ms_ms1quant_match_component.hpp"
209#include "ms_ms1quant_match_ratio.hpp"
210#include "ms_fitexy_result.hpp"
211#include "ms_ms1quant_charge_state.hpp"
212#include "ms_ms1quant_match.hpp"
213#include "ms_ms1quant_average_results.hpp"
214#include "ms_ms1quant_peptide_status.hpp"
215#include "ms_ms1quant_time_align_limits.hpp"
216#include "ms_ms1quant_time_align.hpp"
217
218#include "ms_ms1quantitation.hpp"
219
220#include "ms_distiller_data.hpp"
221#include "ms_distiller_data_quant.hpp"
222#include "ms_distiller_data_search.hpp"
223#include "ms_distiller_master_project.hpp"
224#include "ms_distiller_subsearch.hpp"
225#include "ms_distiller_master_search.hpp"
226#include "ms_distiller_search_status.hpp"
227#include "ms_distiller_search_status_list.hpp"
228#include "ms_distiller_sub_project.hpp"
229
230#include "ms_spectral_lib_peak.hpp"
231#include "ms_spectral_lib_peak_list.hpp"
232#include "ms_spectral_lib_entry.hpp"
233#include "ms_spectral_lib_file.hpp"
234
235#include "ms_imputation.hpp"