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NCBI C++ ToolKit: src/objects/seqfeat/SubSource.cpp File Reference

#include <ncbi_pch.hpp>
#include <serial/enumvalues.hpp>
#include <objects/seqfeat/SubSource.hpp>
#include <math.h>
#include <objects/misc/sequence_util_macros.hpp>
#include <util/row_reader_ncbi_tsv.hpp>
#include <corelib/ncbi_safe_static.hpp>
#include <util/compile_time.hpp>
#include "cell_line.inc"
#include "isolation_sources.inc"
#include "lat_lon_country.inc"
#include "lat_lon_water.inc"

Go to the source code of this file.

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Definition at line 6038 of file SubSource.cpp.

◆ EPSILON ◆ TCellLineContaminationMap ◆ TContaminatingCellLine ◆ TCStringPairsMap ◆ TCStrSet ◆ TNCBITSVStream ◆ TParishMap ◆ TParishMapEntry ◆ TQualFixMap ◆ TSpeciesContaminant ◆ TStateMap ◆ TStateMapEntry ◆ TStaticQualFixMap ◆ TStaticQualFixPair ◆ TWaterPairElem ◆ TWaterPairMap ◆ DEFINE_STATIC_ARRAY_MAP() [1/9] ◆ DEFINE_STATIC_ARRAY_MAP() [2/9] ◆ DEFINE_STATIC_ARRAY_MAP() [3/9] ◆ DEFINE_STATIC_ARRAY_MAP() [4/9] ◆ DEFINE_STATIC_ARRAY_MAP() [5/9] ◆ DEFINE_STATIC_ARRAY_MAP() [6/9] ◆ DEFINE_STATIC_ARRAY_MAP() [7/9] ◆ DEFINE_STATIC_ARRAY_MAP() [8/9] ◆ DEFINE_STATIC_ARRAY_MAP() [9/9] ◆ DEFINE_STATIC_FAST_MUTEX() [1/2] DEFINE_STATIC_FAST_MUTEX ( s_CellLineContaminationMutex ) ◆ DEFINE_STATIC_FAST_MUTEX() [2/2] DEFINE_STATIC_FAST_MUTEX ( s_QualFixMutex ) ◆ DegreesToRadians() static double DegreesToRadians ( double degrees ) static ◆ DistanceOnGlobe() static double DistanceOnGlobe ( double latA, double lonA, double latB, double lonB ) static ◆ ErrorDistance() double ErrorDistance ( double latA, double lonA, double scale ) ◆ MAKE_CONST_SET() MAKE_CONST_SET ( s_Null_CollectionDatesSet , ct::tagStrCase , { "missing", "missing: control sample", "missing: data agreement established pre-2023", "missing: endangered species", "missing: human-identifiable", "missing: lab stock", "missing: sample group", "missing: synthetic construct", "missing: third party data", "not applicable", "not collected", "not provided", "restricted access", } ) ◆ RepairSingleDigitMonth() ◆ s_AddOneDataFile()

Definition at line 4959 of file SubSource.cpp.

References ERR_POST, file, file_name, g_FindDataFile(), i, lr(), NCBI_CATCH, ILineReader::New(), Note, NULL, and s_ProcessQualMapLine().

Referenced by s_InitializeQualMaps().

◆ s_ChooseMonthAndDay() ◆ s_CollectNumberAndUnits() ◆ s_CompressRunsOfSpaces() ◆ s_ContainsWholeWord() ◆ s_DoUSAStateCleanup()

Definition at line 4507 of file SubSource.cpp.

References CCountries::e_Ambiguous, CCountries::e_Corrected, CCountries::e_Missing, CCountries::e_NoResult, CCountries::e_NotUSA, CCountries::e_Valid, NStr::EndsWith(), NStr::eNocase, NStr::Equal(), NStr::EqualNocase(), match(), CCountries::NewFixCountry(), s_CompressRunsOfSpaces(), s_IsParish(), s_IsState(), NStr::Split(), NStr::SplitInTwo(), NStr::StartsWith(), and NStr::TruncateSpacesInPlace().

Referenced by CCountries::USAStateCleanup().

◆ s_FailsGenusOrSpeciesTest() ◆ s_GetLatLong() static void s_GetLatLong ( const string & new_str, vector< double > & numbers, vector< int > & precision ) static ◆ s_init_UseGeoLocNameForCountry() static bool s_init_UseGeoLocNameForCountry ( void ) static ◆ s_InitializeCellLineContaminationMap() static void s_InitializeCellLineContaminationMap ( void ) static ◆ s_InitializeQualMaps() static void s_InitializeQualMaps ( void ) static ◆ s_InsertSpacesBetweenTokens() ◆ s_IsNumber() ◆ s_IsParish() ◆ s_IsState() ◆ s_IsValidSexQualifierPhrase() ◆ s_NormalizeTokens() static string s_NormalizeTokens ( vector< string > & tokens, vector< double > & numbers, vector< string > & anum, vector< int > & precision, vector< string > & lat_long, vector< string > & nsew ) static

Definition at line 1492 of file SubSource.cpp.

References NStr::EndsWith(), NStr::EqualNocase(), NStr::Find(), i, NStr::Join(), kEmptyStr, NPOS, precision, s_IsNumber(), NStr::Split(), and tmp.

Referenced by s_GetLatLong().

◆ s_ProcessCellLineLine() ◆ s_ProcessQualMapLine() ◆ s_RemoveSpacesWithinNumbers() ◆ s_ReorderNorthSouthEastWest() static void s_ReorderNorthSouthEastWest ( vector< double > & numbers, vector< int > & precision, const vector< string > & lat_long, vector< string > & nsew ) static ◆ s_ShortenLatLon() ◆ s_SuppressCountryFix() ◆ x_FindSurroundingOcean() ◆ exception_map ◆ exceptions_initialized ◆ k_NumLatLonCountryText const size_t k_NumLatLonCountryText = ArraySize(s_DefaultLatLonCountryText) static ◆ k_NumLatLonWaterText const size_t k_NumLatLonWaterText = ArraySize(s_DefaultLatLonWaterText) static ◆ k_water_pair_map ◆ kCellTypePairs Initial value:

= {

{ "hemocyte", "hemocyte" },

{ "hepatocyte", "hepatocyte" },

{ "lymphocyte", "lymphocyte" },

{ "neuroblast", "neuroblast" }

}

Definition at line 4923 of file SubSource.cpp.

◆ kDevStagePairs Initial value:

= {

{ "adult", "adult" },

{ "egg", "egg" },

{ "juvenile", "juvenile" },

{ "larva", "larva" }

}

Definition at line 4902 of file SubSource.cpp.

◆ parish_abbrev_array ◆ s_CellLineContaminationMap ◆ s_CellLineContaminationMapInitialized bool s_CellLineContaminationMapInitialized = false static ◆ s_Countries ◆ s_CountriesSet ◆ s_Former_Countries Initial value:

= {

"Belgian Congo",

"British Guiana",

"Burma",

"Czech Republic",

"Czechoslovakia",

"East Timor",

"Korea",

"Macedonia",

"Micronesia",

"Netherlands Antilles",

"Serbia and Montenegro",

"Siam",

"Swaziland",

"The former Yugoslav Republic of Macedonia",

"USSR",

"Yugoslavia",

"Zaire"

}

Definition at line 3308 of file SubSource.cpp.

◆ s_Former_CountriesSet ◆ s_IsolationSourceMap ◆ s_map_country_name_fixes ◆ s_map_old_country_name_fixes Initial value:

= {

{"Burma", "Myanmar"},

{"Siam", "Thailand"}

}

Definition at line 3786 of file SubSource.cpp.

◆ s_map_subregion_fixes ◆ s_map_whole_country_fixes Initial value:

{

{"england", "United Kingdom: England"},

{"great britain", "United Kingdom: Great Britain"},

{"new jersey, usa", "USA: New Jersey"}

}

Definition at line 3474 of file SubSource.cpp.

◆ s_Null_Countries Initial value:

= {

"missing",

"missing: control sample",

"missing: data agreement established pre-2023",

"missing: endangered species",

"missing: human-identifiable",

"missing: lab stock",

"missing: sample group",

"missing: synthetic construct",

"missing: third party data",

"not applicable",

"not collected",

"not provided",

"restricted access"

}

Definition at line 3330 of file SubSource.cpp.

◆ s_Null_CountriesSet ◆ s_QualFixupMapsInitialized ◆ s_RemovableCultureNotes const char* s_RemovableCultureNotes[] static ◆ s_ReplaceableCultureNotes const char* s_ReplaceableCultureNotes[] static Initial value:

= {

"[BankIt_uncultured16S_wizard]; [species_specific primers]; [tgge]",

"[BankIt_uncultured16S_wizard]; [species_specific primers]; [dgge]",

"[BankIt_uncultured16S_wizard]; [species_specific primers]",

"[uncultured (with species-specific primers)]",

"[uncultured]; [amplified with species-specific primers]",

"[uncultured (using species-specific primers) bacterial source]",

"[amplified with species-specific primers]",

}

Definition at line 5258 of file SubSource.cpp.

Referenced by CSubSource::HasCultureNotes(), and CSubSource::RemoveCultureNotes().

◆ s_USAStates const char* s_USAStates[] static ◆ sm_ValidSexQualifierPhrases const char* sm_ValidSexQualifierPhrases[] ◆ sm_ValidSexQualifierTokens const char* sm_ValidSexQualifierTokens[] Initial value:

= {

"asexual",

"bisexual",

"diecious",

"dioecious",

"f",

"female",

"gelding",

"hermaphrodite",

"intersex",

"m",

"male",

"mixed",

"monecious",

"monoecious",

"neuter",

"unisexual",

}

Definition at line 2492 of file SubSource.cpp.

Referenced by CSubSource::FixIsolationSourceCapitalization(), CSubSource::FixSexQualifierValue(), CSubSource::FixTissueTypeCapitalization(), and CSubSource::IsValidSexQualifierValue().

◆ state_abbrev_array

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