#include <objects/seqfeat/SubSource.hpp>

Inheritance diagram for CSubSource:

Collaboration diagram for CSubSource:

Public Types
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 }

Public Types inherited from CSubSource_Base
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

Public Types inherited from CObject
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...

Public Member Functions
	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 ()

void	RemoveCultureNotes (bool is_species_level=true)

Public Member Functions inherited from CSubSource_Base
	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...

Public Member Functions inherited from CSerialObject
	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...

Public Member Functions inherited from CObject
	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...

Public Member Functions inherited from CDebugDumpable
	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 Public Member Functions
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	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 Public Member Functions inherited from CSubSource_Base
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	ESubtype (void)
	Access to ESubtype's attributes (values, names) as defined in spec. More...

Static Public Member Functions inherited from CSerialObject
static void	SetVerifyDataThread (ESerialVerifyData verify)

static void	SetVerifyDataGlobal (ESerialVerifyData verify)

static string	UnassignedString (void)

static CStringUTF8	UnassignedStringUTF8 (void)

static char	UnassignedByte (void)

Static Public Member Functions inherited from CObject
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 Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)

Private Types
typedef CSubSource_Base	Tparent

Private Member Functions
	CSubSource (const CSubSource &value)

CSubSource &	operator= (const CSubSource &value)

Static Private Member Functions
static string	x_ParseDateRangeWithDelimiter (const string &orig_date, CTempString delim)

static vector< string >	x_GetDateTokens (const string &orig_date)

static CLatLonCountryId *	x_CalculateLatLonId (float lat_value, float lon_value, string country, string province)

static bool	x_IsFixableIsoDate (const string &orig_date)

static string	x_RemoveIsoTime (const string &orig_date)

static int	x_GetPrecision (const string &num_str)

static string	x_FormatWithPrecision (double val, int precision)

static bool	x_GenericRepliconNameValid (const string &value)

static bool	x_MeetsCommonChromosomeLinkageGroupPlasmidNameRules (const string &value, const string &taxname)

static CLatLonCountryMap &	x_GetLatLonCountryMap (void)

static CLatLonWaterMap &	x_GetLatLonWaterMap (void)

Additional Inherited Members
Static Public Attributes inherited from CSerialObject
static const char *	ms_UnassignedStr = "<unassigned>"

static const char	ms_UnassignedByte = char(0xcd)

Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...

static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...

static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...

static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...

static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...

static const TCount	eCounterStateMask
	Valid object, and object in heap. More...

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Detailed Description

Definition at line 65 of file SubSource.hpp.

Member Typedef Documentation

◆ Tparent

typedef CSubSource_Base CSubSource::Tparent

private

Definition at line 67 of file SubSource.hpp.

Member Enumeration Documentation

◆ EDateFormatFlag

enum CSubSource::EDateFormatFlag

Enumerator
eDateFormatFlag_ok
eDateFormatFlag_bad_format
eDateFormatFlag_in_future
eDateFormatFlag_out_of_order

Definition at line 111 of file SubSource.hpp.

◆ ELatLonCountryErr

enum CSubSource::ELatLonCountryErr

Enumerator
eLatLonCountryErr_None
eLatLonCountryErr_Country
eLatLonCountryErr_State
eLatLonCountryErr_Water
eLatLonCountryErr_Value

Definition at line 191 of file SubSource.hpp.

◆ EVocabulary

enum CSubSource::EVocabulary

Enumerator
eVocabulary_raw
eVocabulary_insdc

Definition at line 82 of file SubSource.hpp.

Constructor & Destructor Documentation

◆ CSubSource() [1/4]

CSubSource::CSubSource ( void )

inline

Definition at line 266 of file SubSource.hpp.

◆ CSubSource() [2/4]

CSubSource::CSubSource	(	TSubtype	subtype,
		const TName &	name
	)

inline

Definition at line 271 of file SubSource.hpp.

References CSubSource_Base::SetName(), and CSubSource_Base::SetSubtype().

◆ CSubSource() [3/4]

CSubSource::CSubSource	(	const string &	subtype,
		const TName &	name
	)

inline

Definition at line 278 of file SubSource.hpp.

References GetSubtypeValue(), CSubSource_Base::SetName(), and CSubSource_Base::SetSubtype().

◆ ~CSubSource()

CSubSource::~CSubSource ( void )

Definition at line 60 of file SubSource.cpp.

◆ CSubSource() [4/4]

CSubSource::CSubSource ( const CSubSource & value )

private

Member Function Documentation

◆ AutoFix() [1/2]

void CSubSource::AutoFix ( )

Definition at line 5158 of file SubSource.cpp.

References NStr::Equal(), CSubSource_Base::eSubtype_sex, CSubSource_Base::GetName(), CSubSource_Base::GetSubtype(), NStr::IsBlank(), CSubSource_Base::IsSetName(), CSubSource_Base::IsSetSubtype(), CSubSource_Base::SetName(), and NStr::ToLower().

Referenced by CBioSource::ShouldIgnoreConflict().

◆ AutoFix() [2/2]

string CSubSource::AutoFix	(	TSubtype	subtype,
		const string &	value
	)

static

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()

string CSubSource::CheckCellLine	(	const string &	cell_line,
		const string &	organism
	)

static

Definition at line 2998 of file SubSource.cpp.

References first(), NStr::IsBlank(), s_CellLineContaminationMap, s_InitializeCellLineContaminationMap(), and NStr::ToUpper().

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

◆ 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()

CRef< CDate > CSubSource::DateFromCollectionDate ( const string & str )

static

◆ DetectDateFormat()

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

static

Definition at line 1234 of file SubSource.cpp.

References eDay, eMonth, eYear, ITERATE, NStr::StringToInt(), and x_GetDateTokens().

Referenced by BOOST_AUTO_TEST_CASE(), CMacroFunction_FixFormat::TheFunction(), and CMacroFunction_SetPubDate::x_AddDate().

◆ FixAltitude()

string CSubSource::FixAltitude ( const string & value )

static

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 ( )

Definition at line 5104 of file SubSource.cpp.

References NStr::Equal(), CSubSource_Base::eSubtype_sex, CSubSource_Base::GetName(), CSubSource_Base::GetSubtype(), NStr::IsBlank(), CSubSource_Base::IsSetName(), CSubSource_Base::IsSetSubtype(), CSubSource_Base::SetName(), and NStr::ToLower().

◆ FixCapitalization() [2/2]

string CSubSource::FixCapitalization	(	TSubtype	subtype,
		const string &	value
	)

static

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()

string CSubSource::FixCellTypeCapitalization ( const string & value )

static

Definition at line 4931 of file SubSource.cpp.

References rapidjson::value.

Referenced by BOOST_AUTO_TEST_CASE(), FixCapitalization(), FixIsolationSourceCapitalization(), and FixTissueTypeCapitalization().

◆ FixDateFormat() [1/2]

string CSubSource::FixDateFormat ( const string & orig_date )

static

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]

string CSubSource::FixDateFormat	(	const string &	orig_date,
		bool	month_first,
		bool &	month_ambiguous
	)

static

◆ FixDevStageCapitalization()

string CSubSource::FixDevStageCapitalization ( const string & value )

static

Definition at line 4911 of file SubSource.cpp.

References rapidjson::value.

Referenced by BOOST_AUTO_TEST_CASE(), FixCapitalization(), FixIsolationSourceCapitalization(), and FixTissueTypeCapitalization().

◆ FixIsolationSourceCapitalization()

string CSubSource::FixIsolationSourceCapitalization ( const string & value )

static

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()

string CSubSource::FixLabHostCapitalization ( const string & value )

static

Definition at line 5065 of file SubSource.cpp.

References COrgMod::FixHostCapitalization(), and rapidjson::value.

Referenced by FixCapitalization().

◆ FixLatLonFormat()

string CSubSource::FixLatLonFormat	(	string	orig_lat_lon,
		bool	guess = `false`
	)

static

◆ FixLatLonPrecision()

string CSubSource::FixLatLonPrecision ( const string & orig )

static

Definition at line 1363 of file SubSource.cpp.

References fabs, IsCorrectLatLonFormat(), kEmptyStr, orig, NStr::Split(), and x_GetPrecision().

◆ FixSexQualifierValue()

string CSubSource::FixSexQualifierValue ( const string & value )

static

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()

string CSubSource::FixTissueTypeCapitalization ( const string & value )

static

Definition at line 5038 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().

◆ GetCollectionDateProblem() [1/2]

string CSubSource::GetCollectionDateProblem ( const string & date_string )

static

Definition at line 599 of file SubSource.cpp.

Referenced by BOOST_AUTO_TEST_CASE(), and CValidError_imp::ValidateSubSource().

◆ GetCollectionDateProblem() [2/2]

static string CSubSource::GetCollectionDateProblem	(	const string &	date_string,
		bool &	is_null_and_virus,
		bool	is_influenza_or_Sars2
	)

static

◆ GetDateFromISODate()

CRef< CDate > CSubSource::GetDateFromISODate ( const string & orig_date )

static

Definition at line 841 of file SubSource.cpp.

References CDate_std_Base::SetDay(), CDate_std_Base::SetMonth(), CDate_Base::SetStd(), CDate_std_Base::SetYear(), NStr::StringToInt(), and NStr::TruncateSpacesInPlace().

Referenced by CAutoColValidatordate::DoValidate().

◆ GetLabel()

void CSubSource::GetLabel ( string * str ) const

Definition at line 99 of file SubSource.cpp.

References CSubSource_Base::eSubtype_other, CSubSource_Base::GetAttrib(), CSubSource_Base::GetName(), CSubSource_Base::GetSubtype(), GetSubtypeName(), CSubSource_Base::IsSetAttrib(), str(), and type_name().

◆ GetSubtypeName()

string CSubSource::GetSubtypeName	(	CSubSource::TSubtype	stype,
		EVocabulary	vocabulary = `eVocabulary_raw`
	)

static

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()

CSubSource::TSubtype CSubSource::GetSubtypeValue	(	const string &	str,
		EVocabulary	vocabulary = `eVocabulary_raw`
	)

static

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()

bool CSubSource::HasCultureNotes ( const string & value )

static

Definition at line 5230 of file SubSource.cpp.

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

◆ IsAltitudeValid()

bool CSubSource::IsAltitudeValid ( const string & value )

static

Definition at line 2698 of file SubSource.cpp.

References NStr::EqualCase(), NStr::IsBlank(), number, s_CollectNumberAndUnits(), and rapidjson::value.

Referenced by CValidError_imp::ValidateBioSource().

◆ IsChromosomeNameValid()

bool CSubSource::IsChromosomeNameValid	(	const string &	value,
		const string &	taxname
	)

static

Definition at line 2891 of file SubSource.cpp.

References NStr::eNocase, NStr::IsBlank(), NStr::StartsWith(), rapidjson::value, and x_MeetsCommonChromosomeLinkageGroupPlasmidNameRules().

Referenced by CValidError_imp::ValidateSubSource().

◆ IsCollectionDateAfterTime() [1/3]

bool CSubSource::IsCollectionDateAfterTime	(	const CDate &	collection_date,
		CTime &	ctime
	)

static

Definition at line 446 of file SubSource.cpp.

References CTime::GetTimeT(), IsCollectionDateAfterTime(), and t.

◆ IsCollectionDateAfterTime() [2/3]

bool CSubSource::IsCollectionDateAfterTime	(	const CDate &	collection_date,
		time_t	t
	)

static

Definition at line 435 of file SubSource.cpp.

References CDate::Compare(), CDate::eCompare_after, and t.

◆ IsCollectionDateAfterTime() [3/3]

bool CSubSource::IsCollectionDateAfterTime	(	const string &	collection_date,
		time_t	t,
		bool &	bad_format
	)

static

Definition at line 412 of file SubSource.cpp.

References DateFromCollectionDate(), ITERATE, NStr::Split(), and t.

Referenced by CheckDateFormat(), IsCollectionDateAfterTime(), IsCorrectDateFormat(), and CValidError_imp::ValidateCitSub().

◆ IsCorrectDateFormat()

void CSubSource::IsCorrectDateFormat	(	const string &	date_string,
		bool &	bad_format,
		bool &	in_future
	)

static

Definition at line 453 of file SubSource.cpp.

References DateFromCollectionDate(), NStr::Find(), IsCollectionDateAfterTime(), IsISOFormatDate(), NPOS, NStr::Split(), and t.

Referenced by BOOST_AUTO_TEST_CASE(), FixDateFormat(), and GetHasCollectionDate().

◆ 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
	)