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DEFINE_STATIC_ARRAY_MAP (TGenomeMap, sm_GenomeKeys, genome_key_to_subtype) DEFINE_STATIC_ARRAY_MAP (TOriginMap, sm_OriginKeys, origin_key_to_subtype) DEFINE_STATIC_ARRAY_MAP (TOriginMap, sm_OriginSynonyms, origin_synonyms) bool s_MustCopy (int subtype) int s_iCompareNameVals (const CBioSource::TNameVal &f1, const CBioSource::TNameVal &f2) bool s_CompareNameVals (const CBioSource::TNameVal &f1, const CBioSource::TNameVal &f2) bool s_MayIgnoreCase (const string &value) bool s_IsTaxNameElement (const string &value) bool s_SameExceptPrecision (double val1, double val2) void CompareValLists (TFieldDiffList &list, const string &val_name, bool is_local_copy, const vector< string > &list1, const vector< string > &list2) void GetFieldDiffsFromNameValLists (TFieldDiffList &list, CBioSource::TNameValList &list1, CBioSource::TNameValList &list2, bool is_local_copy) void RemoveDiffByName (TFieldDiffList &diff_list, string pair_name) set< string > GetINSDCMissingValues () static bool s_IsPunct (char ch) static void s_GetWordListFromText (string &str, TWordList &word_list) static bool s_DoesTextContainOnlyTheseWords (const string &text, const TWordList &word_list) ◆ MAKE_COMMON_INT #define MAKE_COMMON_INT ( o1, o2, o3, Field ) if (o1.IsSet##Field() && o2.IsSet##Field() && o1.Get##Field() == o2.Get##Field()) o3.Set##Field(o1.Get##Field());Definition at line 2061 of file BioSource.cpp.
◆ IgnoreConflictData ◆ TCIgnoreCaseQualsSet ◆ TCStopWordStrSet ◆ TCTaxNameElementQualsSet ◆ TGenomeKey ◆ TGenomeMap ◆ TOriginKey ◆ TOriginMap ◆ TWordList ◆ EConflictIgnoreType Enumerator eConflictIgnoreAll eConflictIgnoreMissingInBioSource eConflictIgnoreMissingInBioSampleDefinition at line 981 of file BioSource.cpp.
◆ CompareValLists() ◆ DEFINE_STATIC_ARRAY_MAP() [1/3] ◆ DEFINE_STATIC_ARRAY_MAP() [2/3] ◆ DEFINE_STATIC_ARRAY_MAP() [3/3] ◆ GetFieldDiffsFromNameValLists() ◆ GetINSDCMissingValues() ◆ RemoveDiffByName() ◆ s_CompareNameVals() ◆ s_DoesTextContainOnlyTheseWords() ◆ s_GetWordListFromText() ◆ s_iCompareNameVals() ◆ s_IsPunct() ◆ s_IsTaxNameElement() ◆ s_MayIgnoreCase() ◆ s_MustCopy() ◆ s_SameExceptPrecision() bool s_SameExceptPrecision ( double val1, double val2 ) ◆ genome_key_to_subtype ◆ kDisableStrainForwardAttrib const char* kDisableStrainForwardAttrib = "nomodforward" static ◆ kOrganismName const char* kOrganismName = "Organism Name" static ◆ kOrgModNote const char* kOrgModNote = "orgmod_note" static ◆ kSubSrcNote const char* kSubSrcNote = "subsrc_note" static ◆ kTaxId const char* kTaxId = "Tax ID" static ◆ origin_key_to_subtype Initial value:= {
}
@ eOrigin_synthetic
purely synthetic
@ eOrigin_mut
artificially mutagenized
@ eOrigin_artificial
artificially engineered
@ eOrigin_natmut
naturally occurring mutant
@ eOrigin_natural
normal biological entity
Definition at line 233 of file BioSource.cpp.
◆ origin_synonyms ◆ s_IgnoreCaseQuals Initial value:= {
"cell-type",
"collected-by",
"dev-stage",
"frequency",
"group",
"identified-by",
"isolation-source",
"map",
"metagenome-source",
"note",
"phenotype",
"sex",
"subgroup",
"tissue-type"
}
Definition at line 933 of file BioSource.cpp.
◆ s_IgnoreCaseQualsSet ◆ s_insdcNullTerms Initial value:= {
"-",
"?",
"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",
"missing",
"n/a",
"na",
"none",
"not applicable",
"not available",
"not collected",
"not determined",
"not provided",
"not recorded",
"null",
"restricted access",
"unk",
"unknown",
"unspecified"
}
Definition at line 1362 of file BioSource.cpp.
Referenced by GetINSDCMissingValues().
◆ s_SpecialLineageWords const char* s_SpecialLineageWords[] static Initial value:= {
"Class",
"Classification",
"Domain",
"Family",
"Genus",
"Kingdom",
"Lineage",
"Note",
"Order",
"Organism",
"Phylum",
"Species",
"Superfamily",
"Tax class/lineage",
"Taxonomic classification",
"Taxonomic Classification is",
"Taxonomy"
}
Definition at line 1496 of file BioSource.cpp.
Referenced by CBioSource::RemoveLineageSourceNotes().
◆ s_StopWords 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",
"n/a",
"na",
"none",
"not applicable",
"not available",
"not collected",
"not determined",
"not provided",
"not recorded",
"null",
"restricted access",
"unk",
"unknown",
"unspecified"
}
Definition at line 1396 of file BioSource.cpp.
◆ s_StopWordsSet ◆ s_TaxNameElementQuals Initial value:= {
"biovar",
"chemovar",
"forma",
"forma-specialis",
"genotype",
"pathovar",
"serotype",
"serovar",
"subspecies",
"variety"
}
Definition at line 959 of file BioSource.cpp.
◆ s_TaxNameElementQualsSet ◆ sIgnoreConflictListRetroSearch is an open source project built by @garambo | Open a GitHub Issue
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