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NCBI C++ ToolKit: CSubSource Class Reference

Represents ASN.1 type SubSource defined in file seqfeat.asn

#include <objects/seqfeat/SubSource.hpp>

enum EVocabulary { eVocabulary_raw , eVocabulary_insdc } enum EDateFormatFlag { eDateFormatFlag_ok = 0 , eDateFormatFlag_bad_format = 1 , eDateFormatFlag_in_future = 2 , eDateFormatFlag_out_of_order = 4 } enum ELatLonCountryErr {
  eLatLonCountryErr_None = 0 , eLatLonCountryErr_Country , eLatLonCountryErr_State , eLatLonCountryErr_Water ,
  eLatLonCountryErr_Value
} enum ESubtype {
  eSubtype_chromosome = 1 , eSubtype_map = 2 , eSubtype_clone = 3 , eSubtype_subclone = 4 ,
  eSubtype_haplotype = 5 , eSubtype_genotype = 6 , eSubtype_sex = 7 , eSubtype_cell_line = 8 ,
  eSubtype_cell_type = 9 , eSubtype_tissue_type = 10 , eSubtype_clone_lib = 11 , eSubtype_dev_stage = 12 ,
  eSubtype_frequency = 13 , eSubtype_germline = 14 , eSubtype_rearranged = 15 , eSubtype_lab_host = 16 ,
  eSubtype_pop_variant = 17 , eSubtype_tissue_lib = 18 , eSubtype_plasmid_name = 19 , eSubtype_transposon_name = 20 ,
  eSubtype_insertion_seq_name = 21 , eSubtype_plastid_name = 22 , eSubtype_country = 23 , eSubtype_segment = 24 ,
  eSubtype_endogenous_virus_name = 25 , eSubtype_transgenic = 26 , eSubtype_environmental_sample = 27 , eSubtype_isolation_source = 28 ,
  eSubtype_lat_lon = 29 , eSubtype_collection_date = 30 , eSubtype_collected_by = 31 , eSubtype_identified_by = 32 ,
  eSubtype_fwd_primer_seq = 33 , eSubtype_rev_primer_seq = 34 , eSubtype_fwd_primer_name = 35 , eSubtype_rev_primer_name = 36 ,
  eSubtype_metagenomic = 37 , eSubtype_mating_type = 38 , eSubtype_linkage_group = 39 , eSubtype_haplogroup = 40 ,
  eSubtype_whole_replicon = 41 , eSubtype_phenotype = 42 , eSubtype_altitude = 43 , eSubtype_other = 255
} enum class E_memberIndex { e__allMandatory = 0 , e_subtype , e_name , e_attrib } typedef int TSubtype typedef string TName typedef string TAttrib typedef Tparent::CMemberIndex< E_memberIndex, 4 > TmemberIndex enum EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern } Control filling of newly allocated memory. More...
typedef CObjectCounterLocker TLockerType Default locker type for CRef. More...
typedef atomic< Uint8 > TCounter Counter type is CAtomiCounter. More...
typedef Uint8 TCount Alias for value type of counter. More...
CSubSource (void) CSubSource (TSubtype subtype, const TName &name) CSubSource (const string &subtype, const TName &name) ~CSubSource (void) void GetLabel (string *str) const void FixCapitalization () void AutoFix () bool IsDeprecated () const void RemoveCultureNotes (bool is_species_level=true) CSubSource_Base (void) virtual ~CSubSource_Base (void) DECLARE_INTERNAL_TYPE_INFO () bool IsSetSubtype (void) const Check if a value has been assigned to Subtype data member. More...
bool CanGetSubtype (void) const Check if it is safe to call GetSubtype method. More...
void ResetSubtype (void) Reset Subtype data member. More...
TSubtype GetSubtype (void) const Get the Subtype member data. More...
void SetSubtype (TSubtype value) Assign a value to Subtype data member. More...
TSubtype & SetSubtype (void) Assign a value to Subtype data member. More...
bool IsSetName (void) const Check if a value has been assigned to Name data member. More...
bool CanGetName (void) const Check if it is safe to call GetName method. More...
void ResetName (void) Reset Name data member. More...
const TName & GetName (void) const Get the Name member data. More...
void SetName (const TName &value) Assign a value to Name data member. More...
void SetName (TName &&value) TName & SetName (void) Assign a value to Name data member. More...
bool IsSetAttrib (void) const attribution/source of this name Check if a value has been assigned to Attrib data member. More...
bool CanGetAttrib (void) const Check if it is safe to call GetAttrib method. More...
void ResetAttrib (void) Reset Attrib data member. More...
const TAttrib & GetAttrib (void) const Get the Attrib member data. More...
void SetAttrib (const TAttrib &value) Assign a value to Attrib data member. More...
void SetAttrib (TAttrib &&value) TAttrib & SetAttrib (void) Assign a value to Attrib data member. More...
virtual void Reset (void) Reset the whole object. More...
CSerialObject (void) virtual ~CSerialObject (void) virtual const CTypeInfo * GetThisTypeInfo (void) const =0 virtual void Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive) Set object to copy of another one. More...
virtual bool Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const Check if both objects contain the same values. More...
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const Define method for dumping debug information. More...
void ThrowUnassigned (TMemberIndex index) const void ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const bool HasNamespaceName (void) const Check if object data type has namespace name. More...
const string & GetNamespaceName (void) const Get namespace name. More...
bool HasNamespacePrefix (void) const Check if data type has namespace prefix. More...
const string & GetNamespacePrefix (void) const Get namespace prefix. More...
CObject (void) Constructor. More...
CObject (const CObject &src) Copy constructor. More...
virtual ~CObject (void) Destructor. More...
CObject & operator= (const CObject &src) THROWS_NONE Assignment operator. More...
bool CanBeDeleted (void) const THROWS_NONE Check if object can be deleted. More...
bool IsAllocatedInPool (void) const THROWS_NONE Check if object is allocated in memory pool (not system heap) More...
bool Referenced (void) const THROWS_NONE Check if object is referenced. More...
bool ReferencedOnlyOnce (void) const THROWS_NONE Check if object is referenced only once. More...
void AddReference (void) const Add reference to object. More...
void RemoveReference (void) const Remove reference to object. More...
void ReleaseReference (void) const Remove reference without deleting object. More...
virtual void DoNotDeleteThisObject (void) Mark this object as not allocated in heap – do not delete this object. More...
virtual void DoDeleteThisObject (void) Mark this object as allocated in heap – object can be deleted. More...
void * operator new (size_t size) Define new operator for memory allocation. More...
void * operator new[] (size_t size) Define new[] operator for 'array' memory allocation. More...
void operator delete (void *ptr) Define delete operator for memory deallocation. More...
void operator delete[] (void *ptr) Define delete[] operator for memory deallocation. More...
void * operator new (size_t size, void *place) Define new operator. More...
void operator delete (void *ptr, void *place) Define delete operator. More...
void * operator new (size_t size, CObjectMemoryPool *place) Define new operator using memory pool. More...
void operator delete (void *ptr, CObjectMemoryPool *place) Define delete operator. More...
CDebugDumpable (void) virtual ~CDebugDumpable (void) void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const void DumpToConsole (void) const static bool NCBI_UseGeoLocNameForCountry (void) static TSubtype GetSubtypeValue (const string &str, EVocabulary vocabulary=eVocabulary_raw) static string GetSubtypeName (CSubSource::TSubtype stype, EVocabulary vocabulary=eVocabulary_raw) static bool IsValidSubtypeName (const string &str, EVocabulary vocabulary=eVocabulary_raw) static bool IsMultipleValuesAllowed (TSubtype) static bool NeedsNoText (const TSubtype &subtype) static bool IsDiscouraged (const TSubtype subtype) static CRef< CDate > DateFromCollectionDate (const string &str) THROWS((CException)) static void IsCorrectDateFormat (const string &date_string, bool &bad_format, bool &in_future) static size_t CheckDateFormat (const string &date_string) static string GetCollectionDateProblem (const string &date_string) static string GetCollectionDateProblem (const string &date_string, bool &is_null_and_virus, bool is_influenza_or_Sars2) static bool IsCollectionDateAfterTime (const string &collection_date, time_t t, bool &bad_format) static bool IsCollectionDateAfterTime (const CDate &collection_date, time_t t) static bool IsCollectionDateAfterTime (const CDate &collection_date, CTime &ctime) static bool IsISOFormatTime (const string &orig_time, int &hour, int &min, int &sec, bool require_time_zone=true) static bool IsISOFormatDateOnly (const string &date) static bool IsISOFormatDate (const string &orig_date) static CRef< CDate > GetDateFromISODate (const string &orig_date) static bool IsDayValueOkForMonth (int day, int month, int year) Determine whether day number could occur in month. More...
static string FixDateFormat (const string &orig_date) Attempt to fix the format of the date Returns a blank if the format of the date cannot be determined. More...
static string FixDateFormat (const string &orig_date, bool month_first, bool &month_ambiguous) static void DetectDateFormat (const string &orig_date, bool &ambiguous, bool &day_first) static void IsCorrectLatLonFormat (string lat_lon, bool &format_correct, bool &precision_correct, bool &lat_in_range, bool &lon_in_range, double &lat_value, double &lon_value) static string FixLatLonFormat (string orig_lat_lon, bool guess=false) static string MakeLatLon (double lat_value, double lon_value, int lat_precision=2, int lon_precision=2) static string FixLatLonPrecision (const string &orig) static string ValidateLatLonCountry (const string &countryname, string &lat_lon, bool check_state, ELatLonCountryErr &errcode) static bool IsValidSexQualifierValue (const string &value) static string FixSexQualifierValue (const string &value) static bool IsAltitudeValid (const string &value) static string FixAltitude (const string &value) static bool IsPlasmidNameValid (const string &value, const string &taxname) static bool IsChromosomeNameValid (const string &value, const string &taxname) static bool IsLinkageGroupNameValid (const string &value, const string &taxname) static bool IsSegmentValid (const string &value) static bool IsEndogenousVirusNameValid (const string &value) static string FixDevStageCapitalization (const string &value) static string FixCellTypeCapitalization (const string &value) static string FixIsolationSourceCapitalization (const string &value) static string FixTissueTypeCapitalization (const string &value) static string FixLabHostCapitalization (const string &value) static string FixCapitalization (TSubtype subtype, const string &value) static string AutoFix (TSubtype subtype, const string &value) static bool IsDeprecated (TSubtype subtype) static bool HasCultureNotes (const string &value) static void RemoveCultureNotes (string &value, bool is_species_level=true) static string CheckCellLine (const string &cell_line, const string &organism) static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() ESubtype (void) Access to ESubtype's attributes (values, names) as defined in spec. More...
static void SetVerifyDataThread (ESerialVerifyData verify) static void SetVerifyDataGlobal (ESerialVerifyData verify) static string UnassignedString (void) static CStringUTF8 UnassignedStringUTF8 (void) static char UnassignedByte (void) static NCBI_XNCBI_EXPORT void ThrowNullPointerException (void) Define method to throw null pointer exception. More...
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (const type_info &type) static EAllocFillMode GetAllocFillMode (void) static void SetAllocFillMode (EAllocFillMode mode) static void SetAllocFillMode (const string &value) Set mode from configuration parameter value. More...
static void EnableDebugDump (bool on)

Definition at line 65 of file SubSource.hpp.

◆ Tparent ◆ EDateFormatFlag Enumerator eDateFormatFlag_ok eDateFormatFlag_bad_format eDateFormatFlag_in_future eDateFormatFlag_out_of_order

Definition at line 111 of file SubSource.hpp.

◆ ELatLonCountryErr Enumerator eLatLonCountryErr_None eLatLonCountryErr_Country eLatLonCountryErr_State eLatLonCountryErr_Water eLatLonCountryErr_Value

Definition at line 191 of file SubSource.hpp.

◆ EVocabulary Enumerator eVocabulary_raw eVocabulary_insdc

Definition at line 82 of file SubSource.hpp.

◆ CSubSource() [1/4] CSubSource::CSubSource ( void ) inline

Definition at line 269 of file SubSource.hpp.

◆ CSubSource() [2/4] ◆ CSubSource() [3/4] ◆ ~CSubSource() CSubSource::~CSubSource ( void )

Definition at line 60 of file SubSource.cpp.

◆ CSubSource() [4/4] ◆ AutoFix() [1/2] void CSubSource::AutoFix ( ) ◆ AutoFix() [2/2]

Definition at line 5132 of file SubSource.cpp.

References CSubSource_Base::eSubtype_altitude, CSubSource_Base::eSubtype_collection_date, CSubSource_Base::eSubtype_country, CSubSource_Base::eSubtype_lat_lon, CSubSource_Base::eSubtype_sex, FixAltitude(), FixDateFormat(), FixLatLonFormat(), FixSexQualifierValue(), CCountries::NewFixCountry(), and rapidjson::value.

Referenced by BOOST_AUTO_TEST_CASE(), and CNewCleanup_imp::x_SubSourceBC().

◆ CheckCellLine() ◆ CheckDateFormat() size_t CSubSource::CheckDateFormat ( const string & date_string ) static

Definition at line 504 of file SubSource.cpp.

References CDate::Compare(), DateFromCollectionDate(), CDate::eCompare_before, eDateFormatFlag_bad_format, eDateFormatFlag_in_future, eDateFormatFlag_ok, eDateFormatFlag_out_of_order, NStr::Find(), IsCollectionDateAfterTime(), IsISOFormatDate(), NPOS, NStr::Split(), and t.

◆ DateFromCollectionDate()

Definition at line 285 of file SubSource.cpp.

References eUnknown, NStr::Find(), NStr::IsBlank(), CTime::MonthNameToNum(), NCBI_THROW, NPOS, CDate_std_Base::SetDay(), CDate_std_Base::SetMonth(), CDate_Base::SetStd(), CDate_std_Base::SetYear(), str(), NStr::StringToInt(), t, test, and NStr::TruncateSpaces().

Referenced by BOOST_AUTO_TEST_CASE(), CheckDateFormat(), CApplyPubQualTreeItemData::GetVariables(), IsCollectionDateAfterTime(), IsCorrectDateFormat(), CCleanup::s_CleanupGenomeAssembly(), CBioSource::ShouldIgnoreConflict(), and CMacroFunction_SetPubDate::x_AddDate().

◆ DetectDateFormat() void CSubSource::DetectDateFormat ( const string & orig_date, bool & ambiguous, bool & day_first ) static ◆ FixAltitude()

Definition at line 2735 of file SubSource.cpp.

References NStr::Equal(), NStr::IsBlank(), kEmptyStr, number, precision, s_CollectNumberAndUnits(), NStr::StringToDouble(), val, rapidjson::value, x_FormatWithPrecision(), and x_GetPrecision().

Referenced by AutoFix(), BOOST_AUTO_TEST_CASE(), and CMacroFunction_FixFormat::s_ConvertAltitudeToMeters().

◆ FixCapitalization() [1/2] void CSubSource::FixCapitalization ( ) ◆ FixCapitalization() [2/2]

Definition at line 5071 of file SubSource.cpp.

References CSubSource_Base::eSubtype_cell_type, CSubSource_Base::eSubtype_dev_stage, CSubSource_Base::eSubtype_isolation_source, CSubSource_Base::eSubtype_lab_host, CSubSource_Base::eSubtype_sex, CSubSource_Base::eSubtype_tissue_type, FixCellTypeCapitalization(), FixDevStageCapitalization(), FixIsolationSourceCapitalization(), FixLabHostCapitalization(), FixSexQualifierValue(), FixTissueTypeCapitalization(), NStr::IsBlank(), and rapidjson::value.

Referenced by BOOST_AUTO_TEST_CASE().

◆ FixCellTypeCapitalization() ◆ FixDateFormat() [1/2]

Attempt to fix the format of the date Returns a blank if the format of the date cannot be determined.

Parameters: orig_date The original date [in] Rules: First, check to see if the string matches the ISO format (YYYY-MM-DD); if so then just return original string as this is valid. Second, try to split the string into tokens using the following delimiters: * space * comma (,) * dash (-) * slash (/) * underscore (_) * equals (=) * period (.) If more than three tokens are generated, fail and return empty string. Of the tokens that are generated, look for a token that contains letters. If there is such a token, this token is assumed to be the month, and will be checked to see if it begins with any of the three-letter abbreviations for months (Jan, Feb, Mar, etc.). If so, the month is known. If none of the abbreviations produce a match, fail and return an empty string. If more than one token that contains letters is found, return an empty string. If there are no tokens that contain letters, try to determine which token is the month by eliminating tokens that would be year or day. Any token that is a number and has a value greater than 31 will be assumed to be the year. If there is more than one such token, return an empty string. After making this initial pass, try to guess the identities of the remaining tokens. Numbers between 1 and 12 could be considered months, if no month token containing letters was already identified. If two or more such tokens are found, the date is ambiguous: return an empty string, unless one of these two conditions are met: a) the numbers are equal, in which case ambiguity about placement is irrelevant b) if one token is NOT zero-padded and less than 10, and the other is either 10 or more or IS zero-padded, then the token that is not padded and less than 10 is the day, and the other is the year, to which we should add 2000 If a number is between 1 and 31, it could be considered the day. If two such tokens are found, the date is ambiguous: return an empty string. If there is a number that cannot be the month or the day, assume that this is the year. If the year is less than 100, this may be a two-digit representation. If 2000 + the value is not in the future, use this as the year, otherwise use 1900 + the value for the year. If all tokens can be identified, arrange them in the output string in one of the following formats: YYYY Mmm-YYYY DD-Mmm-YYYY

Definition at line 630 of file SubSource.cpp.

References ArraySize(), i, NStr::IsBlank(), and x_ParseDateRangeWithDelimiter().

Referenced by AutoFix(), BOOST_AUTO_TEST_CASE(), CCleanup::CleanupCollectionDates(), CCleanup::s_CleanupGenomeAssembly(), CMacroFunction_FixFormat::TheFunction(), CMacroFunction_SetPubDate::x_AddDate(), CParseCollectionDateFormats::x_ApplyToBioSource(), and x_ParseDateRangeWithDelimiter().

◆ FixDateFormat() [2/2]

Definition at line 1012 of file SubSource.cpp.

References CTime::eAbbr, NStr::EndsWith(), NStr::EqualNocase(), isalpha(), NStr::IsBlank(), IsCorrectDateFormat(), IsDayValueOkForMonth(), isdigit(), IsISOFormatDate(), kEmptyStr, max(), min(), CTime::MonthNameToNum(), CTime::MonthNumToName(), NStr::NumericToString(), RepairSingleDigitMonth(), s_ChooseMonthAndDay(), NStr::StartsWith(), NStr::StringToInt(), test, NStr::TruncateSpacesInPlace(), val, x_GetDateTokens(), x_IsFixableIsoDate(), and x_RemoveIsoTime().

◆ FixDevStageCapitalization() ◆ FixIsolationSourceCapitalization()

Definition at line 5011 of file SubSource.cpp.

References NStr::EqualNocase(), FixCellTypeCapitalization(), FixDevStageCapitalization(), COrgMod::FixHostCapitalization(), i, max(), s_InitializeQualMaps(), s_IsolationSourceMap, sm_ValidSexQualifierTokens, and rapidjson::value.

Referenced by BOOST_AUTO_TEST_CASE(), and FixCapitalization().

◆ FixLabHostCapitalization() ◆ FixLatLonFormat()

Definition at line 1921 of file SubSource.cpp.

References CUtf8::AsUTF8(), CUtf8::GuessEncoding(), MakeLatLon(), NStr::ParseEscapes(), precision, NStr::ReplaceInPlace(), s_GetLatLong(), s_InsertSpacesBetweenTokens(), s_RemoveSpacesWithinNumbers(), s_ShortenLatLon(), NStr::Sanitize(), NStr::StartsWith(), NStr::TrimPrefixInPlace(), and NStr::TrimSuffixInPlace().

Referenced by AutoFix(), BOOST_AUTO_TEST_CASE(), CLatLonTool::GetValuesTableFromSeqEntry(), and CMacroFunction_FixFormat::s_FixLatLonFormat().

◆ FixLatLonPrecision() ◆ FixSexQualifierValue()

Definition at line 2572 of file SubSource.cpp.

References ArraySize(), NStr::Equal(), NStr::EqualNocase(), i, ITERATE, kEmptyStr, max(), s_IsValidSexQualifierPhrase(), sm_ValidSexQualifierTokens, NStr::Split(), str(), NStr::ToLower(), and rapidjson::value.

Referenced by AutoFix(), BOOST_AUTO_TEST_CASE(), and FixCapitalization().

◆ FixTissueTypeCapitalization()

Definition at line 5038 of file SubSource.cpp.

Referenced by BOOST_AUTO_TEST_CASE(), and FixCapitalization().

◆ GetCollectionDateProblem() [1/2] ◆ GetCollectionDateProblem() [2/2] ◆ GetDateFromISODate() ◆ GetLabel() void CSubSource::GetLabel ( string * str ) const ◆ GetSubtypeName()

Definition at line 183 of file SubSource.cpp.

References ENUM_METHOD_NAME, CSubSource_Base::eSubtype_insertion_seq_name, CSubSource_Base::eSubtype_other, CSubSource_Base::eSubtype_plasmid_name, CSubSource_Base::eSubtype_subclone, CSubSource_Base::eSubtype_transposon_name, eVocabulary_insdc, and NStr::Replace().

Referenced by AddBioSourceToAttributes(), CFieldChoicePanel::AutoMatchSrc(), GetLabel(), GetSeqTableFromSeqEntry(), CWriteUtil::GetSubSourceSubType(), GetSubtypeName(), CGuiObjectInfoComponent::GetToolTip(), UpdateBiosourceFromBiosample(), CValidError_imp::ValidateBioSource(), CValidError_imp::ValidateSubSource(), CSourceFieldNamePanel::x_ChooseTextQualifier(), CSrcModListPanel::x_FillDataList(), CMacroEditorContext::x_GetBsrcTextFieldnames(), CBioSource::x_GetSubtypeNameValPairs(), and CAutoDefOptions::x_MakeModifierList().

◆ GetSubtypeValue()

Definition at line 126 of file SubSource.cpp.

References ENUM_METHOD_NAME, NStr::EqualNocase(), CSubSource_Base::eSubtype_insertion_seq_name, CSubSource_Base::eSubtype_other, CSubSource_Base::eSubtype_plasmid_name, CSubSource_Base::eSubtype_subclone, CSubSource_Base::eSubtype_transposon_name, eVocabulary_insdc, str(), NStr::ToLower(), and NStr::TruncateSpaces().

Referenced by CFieldChoicePanel::AutoMatchSrc(), CSrcTableColumnBaseFactory::Create(), CreateActionBiosource(), CSubSource(), CSubSrcQual::CSubSrcQual(), CAutoColValidatorsubsource::DoValidate(), CSourceFieldNamePanel::GetChoices(), SrcEditDialog::GetLabelForTitle(), CColumnValidator::IsDiscouraged(), CCompareWithBiosample::OnClickOk(), s_SetBioSourceField(), s_StringHasSubSourcePrefix(), CSourceFieldNamePanel::SetFieldName(), CBioSource::ShouldIgnoreConflict(), CBioSource::UpdateWithBioSample(), CMacroFunction_AddorSetContElement::x_AddBioSrcModifier(), CMacroFunction_Autodef::x_IsRequested(), CMacroFunction_AutodefComplete::x_IsRequested(), CSrcModListPanel::x_SetBioSourceModifier(), CAutoDefOptions::x_SetModifierList(), and CSrcWriter::xGatherSubtypeFeat().

◆ HasCultureNotes() ◆ IsAltitudeValid() ◆ IsChromosomeNameValid() ◆ IsCollectionDateAfterTime() [1/3] ◆ IsCollectionDateAfterTime() [2/3] bool CSubSource::IsCollectionDateAfterTime ( const CDate & collection_date, time_t t ) static ◆ IsCollectionDateAfterTime() [3/3] bool CSubSource::IsCollectionDateAfterTime ( const string & collection_date, time_t t, bool & bad_format ) static ◆ IsCorrectDateFormat() void CSubSource::IsCorrectDateFormat ( const string & date_string, bool & bad_format, bool & in_future ) static ◆ IsCorrectLatLonFormat() void CSubSource::IsCorrectLatLonFormat ( string lat_lon, bool & format_correct, bool & precision_correct, bool & lat_in_range, bool & lon_in_range, double & lat_value, double & lon_value ) static

Definition at line 1296 of file SubSource.cpp.

References NStr::IsBlank(), len, NStr::Split(), NStr::StartsWith(), and x_GetPrecision().

Referenced by BOOST_AUTO_TEST_CASE(), FixLatLonPrecision(), CMacroFunction_FixFormat::s_FixLatLonFormat(), CBioSource::ShouldIgnoreConflict(), CValidError_imp::ValidateBioSource(), ValidateLatLonCountry(), and CValidError_imp::ValidateSubSource().

◆ IsDayValueOkForMonth() bool CSubSource::IsDayValueOkForMonth ( int day, int month, int year ) static ◆ IsDeprecated() [1/2] bool CSubSource::IsDeprecated ( ) const ◆ IsDeprecated() [2/2] ◆ IsDiscouraged()

Definition at line 245 of file SubSource.cpp.

References CSubSource_Base::eSubtype_frequency, CSubSource_Base::eSubtype_fwd_primer_name, CSubSource_Base::eSubtype_fwd_primer_seq, CSubSource_Base::eSubtype_insertion_seq_name, CSubSource_Base::eSubtype_phenotype, CSubSource_Base::eSubtype_plastid_name, CSubSource_Base::eSubtype_rev_primer_name, CSubSource_Base::eSubtype_rev_primer_seq, CSubSource_Base::eSubtype_transposon_name, and CSubSource_Base::eSubtype_whole_replicon.

Referenced by CSrcModPanel::DoNotListSubSrc(), CColumnValidator::IsDiscouraged(), s_MustCopy(), s_StringHasSubSourcePrefix(), CSourceFieldNamePanel::x_ChooseTextQualifier(), CMacroEditorContext::x_GetBsrcTextFieldnames(), and CSrcWriter::xIsSubsourceTypeSuppressed().

◆ IsEndogenousVirusNameValid() ◆ IsISOFormatDate() ◆ IsISOFormatDateOnly() ◆ IsISOFormatTime() ◆ IsLinkageGroupNameValid() ◆ IsMultipleValuesAllowed() bool CSubSource::IsMultipleValuesAllowed ( TSubtype subtype ) static

Definition at line 206 of file SubSource.cpp.

Referenced by CValidError_imp::ValidateBioSource(), and CSourceModParser::x_ApplyMods().

◆ IsPlasmidNameValid() ◆ IsSegmentValid() ◆ IsValidSexQualifierValue()

Definition at line 2533 of file SubSource.cpp.

References NStr::Equal(), ITERATE, max(), s_IsValidSexQualifierPhrase(), sm_ValidSexQualifierTokens, NStr::Split(), str(), NStr::ToLower(), and rapidjson::value.

Referenced by BOOST_AUTO_TEST_CASE(), CBioSource::FixSexMatingTypeInconsistencies(), and CValidError_imp::ValidateBioSource().

◆ IsValidSubtypeName()

Definition at line 155 of file SubSource.cpp.

References ENUM_METHOD_NAME, NStr::EqualNocase(), eVocabulary_insdc, str(), NStr::ToLower(), and NStr::TruncateSpaces().

Referenced by CFieldChoicePanel::AutoMatchSrc(), CSrcTableColumnBaseFactory::Create(), CreateActionBiosource(), CSourceFieldNamePanel::GetChoices(), NMItemData::GetEditableFieldForPair(), SrcEditDialog::GetLabelForTitle(), CSourceFieldNamePanel::GetMacroFieldName(), NMacroUtil::IsBiosourceModifier(), s_SetBioSourceField(), CSourceFieldNamePanel::SetFieldName(), CMacroFunction_AddorSetContElement::x_AddBioSrcModifier(), CMacroEditorContext::x_GetAsnPathToBsrcText(), CMacroEditorContext::x_GetGUIFieldForBsrcText(), CMacroFunction_Autodef::x_IsRequested(), CMacroFunction_AutodefComplete::x_IsRequested(), and CSrcModListPanel::x_SetBioSourceModifier().

◆ MakeLatLon() string CSubSource::MakeLatLon ( double lat_value, double lon_value, int lat_precision = 2, int lon_precision = 2 ) static ◆ NCBI_UseGeoLocNameForCountry() bool CSubSource::NCBI_UseGeoLocNameForCountry ( void ) static

Definition at line 92 of file SubSource.cpp.

References s_init_UseGeoLocNameForCountry(), and rapidjson::value.

Referenced by BOOST_AUTO_TEST_CASE(), CValidator::ConvertCode(), CValidErrorFormat::GetSubmitterFormatErrorGroupTitle(), CDiscrepancyVisitorImpl< _Name >::Summarize(), TestOneLatLonCountry(), CValidError_imp::ValidateBioSource(), CValidError_imp::ValidateOrgModVoucher(), CValidError_imp::ValidateSubSource(), CSourceFeatureItem::x_FormatQuals(), CDeflineGenerator::x_GetModifiers(), and CSrcWriter::xFormatTabDelimited().

◆ NeedsNoText()

Definition at line 231 of file SubSource.cpp.

References CSubSource_Base::eSubtype_environmental_sample, CSubSource_Base::eSubtype_germline, CSubSource_Base::eSubtype_metagenomic, CSubSource_Base::eSubtype_rearranged, and CSubSource_Base::eSubtype_transgenic.

Referenced by AddBioSourceToAttributes(), CBioSource::AutoFix(), CNewCleanup_imp::BiosourceBC(), CSourceFieldNamePanel::GetChoices(), GetSeqTableFromSeqEntry(), CSrcTableSubSourceColumn::GetValsFromBioSource(), s_StringHasSubSourcePrefix(), s_SubsourceEqual(), s_SubsourceEquivalent(), CBioSource::UpdateWithBioSample(), CValidError_imp::ValidateSubSource(), CSourceModParser::x_ApplyMods(), CBioSource::x_GetSubtypeNameValPairs(), CNewCleanup_imp::x_PostBiosource(), CDescrModApply::x_SetSubtype(), and CSrcWriter::xGatherSubtypeFeat().

◆ operator=() ◆ RemoveCultureNotes() [1/2] void CSubSource::RemoveCultureNotes ( bool is_species_level = true ) ◆ RemoveCultureNotes() [2/2] void CSubSource::RemoveCultureNotes ( string & value, bool is_species_level = true ) static

Definition at line 5287 of file SubSource.cpp.

References NStr::EndsWith(), NStr::EqualNocase(), NStr::FindNoCase(), i, NStr::IsBlank(), NPOS, NULL, s_RemovableCultureNotes, s_ReplaceableCultureNotes, NStr::StartsWith(), and rapidjson::value.

Referenced by BOOST_AUTO_TEST_CASE(), CBioSource::RemoveCultureNotes(), and RemoveCultureNotes().

◆ ValidateLatLonCountry()

Definition at line 2160 of file SubSource.cpp.

Referenced by BOOST_AUTO_TEST_CASE(), CCountryConflict::GetValuesTableFromSeqEntry(), and CValidError_imp::ValidateLatLonCountry().

◆ x_CalculateLatLonId()

Definition at line 1971 of file SubSource.cpp.

References NStr::EqualNocase(), ErrorDistance(), CLatLonMap_Base::FindClosestToLatLon(), CLatLonCountryId::GetClosestCountry(), CLatLonCountryId::GetClosestWater(), CCountryExtreme::GetCountry(), CLatLonCountryId::GetGuessCountry(), CLatLonCountryId::GetGuessProvince(), CLatLonCountryId::GetGuessWater(), CCountryExtreme::GetLevel0(), CCountryExtreme::GetLevel1(), CLatLonMap_Base::GuessRegionForLatLon(), NStr::IsBlank(), CLatLonMap_Base::IsNearLatLon(), x_GetLatLonCountryMap(), and x_GetLatLonWaterMap().

Referenced by ValidateLatLonCountry().

◆ x_FormatWithPrecision() string CSubSource::x_FormatWithPrecision ( double val, int precision ) staticprivate ◆ x_GenericRepliconNameValid() ◆ x_GetDateTokens() ◆ x_GetLatLonCountryMap() ◆ x_GetLatLonWaterMap() ◆ x_GetPrecision() ◆ x_IsFixableIsoDate() ◆ x_MeetsCommonChromosomeLinkageGroupPlasmidNameRules() ◆ x_ParseDateRangeWithDelimiter() ◆ x_RemoveIsoTime()

The documentation for this class was generated from the following files:

include/objects/seqfeat/SubSource.hpp
src/objects/seqfeat/SubSource.cpp

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