NCBI C++ ToolKit
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Search Toolkit Book for CSubSource
#include <objects/seqfeat/SubSource.hpp>
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 |
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 Private Attributes | |
static unique_ptr< CLatLonCountryMap > | m_LatLonCountryMap |
static unique_ptr< CLatLonCountryMap > | m_LatLonWaterMap |
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... | |
Definition at line 64 of file SubSource.hpp.
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Definition at line 66 of file SubSource.hpp.
Enumerator | |
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eDateFormatFlag_ok | |
eDateFormatFlag_bad_format | |
eDateFormatFlag_in_future | |
eDateFormatFlag_out_of_order |
Definition at line 110 of file SubSource.hpp.
Enumerator | |
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eLatLonCountryErr_None | |
eLatLonCountryErr_Country | |
eLatLonCountryErr_State | |
eLatLonCountryErr_Water | |
eLatLonCountryErr_Value |
Definition at line 189 of file SubSource.hpp.
Enumerator | |
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eVocabulary_raw | |
eVocabulary_insdc |
Definition at line 81 of file SubSource.hpp.
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Definition at line 256 of file SubSource.hpp.
Definition at line 261 of file SubSource.hpp.
References CSubSource_Base::SetName(), and CSubSource_Base::SetSubtype().
Definition at line 268 of file SubSource.hpp.
References GetSubtypeValue(), CSubSource_Base::SetName(), and CSubSource_Base::SetSubtype().
CSubSource::~CSubSource | ( | void | ) |
Definition at line 63 of file SubSource.cpp.
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void CSubSource::AutoFix | ( | ) |
Definition at line 5103 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().
Definition at line 5077 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().
Definition at line 2955 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().
Definition at line 505 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.
Definition at line 287 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().
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Definition at line 1176 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().
Definition at line 2690 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().
void CSubSource::FixCapitalization | ( | ) |
Definition at line 5049 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().
Definition at line 5016 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().
Definition at line 4876 of file SubSource.cpp.
References rapidjson::value.
Referenced by BOOST_AUTO_TEST_CASE(), FixCapitalization(), FixIsolationSourceCapitalization(), and FixTissueTypeCapitalization().
Attempt to fix the format of the date Returns a blank if the format of the date cannot be determined.
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 620 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().
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Definition at line 957 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(), s_ChooseMonthAndDay(), NStr::StartsWith(), NStr::StringToInt(), test, NStr::TruncateSpacesInPlace(), val, x_GetDateTokens(), x_IsFixableIsoDate(), and x_RemoveIsoTime().
Definition at line 4855 of file SubSource.cpp.
References rapidjson::value.
Referenced by BOOST_AUTO_TEST_CASE(), FixCapitalization(), FixIsolationSourceCapitalization(), and FixTissueTypeCapitalization().
Definition at line 4956 of file SubSource.cpp.
References map_checker< Container >::end(), NStr::EqualNocase(), map_checker< Container >::find(), FixCellTypeCapitalization(), FixDevStageCapitalization(), COrgMod::FixHostCapitalization(), i, max(), s_InitializeQualMaps(), s_IsolationSourceMap, sm_ValidSexQualifierTokens, and rapidjson::value.
Referenced by BOOST_AUTO_TEST_CASE(), and FixCapitalization().
Definition at line 5010 of file SubSource.cpp.
References COrgMod::FixHostCapitalization(), and rapidjson::value.
Referenced by FixCapitalization().
Definition at line 1862 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().
Definition at line 1304 of file SubSource.cpp.
References fabs, IsCorrectLatLonFormat(), kEmptyStr, orig, NStr::Split(), and x_GetPrecision().
Definition at line 2527 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().
Definition at line 4983 of file SubSource.cpp.
References map_checker< Container >::end(), NStr::EqualNocase(), map_checker< Container >::find(), FixCellTypeCapitalization(), FixDevStageCapitalization(), COrgMod::FixHostCapitalization(), i, max(), s_InitializeQualMaps(), s_IsolationSourceMap, sm_ValidSexQualifierTokens, and rapidjson::value.
Referenced by BOOST_AUTO_TEST_CASE(), and FixCapitalization().
Referenced by BOOST_AUTO_TEST_CASE(), and CValidError_imp::ValidateSubSource().
Definition at line 831 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().
void CSubSource::GetLabel | ( | string * | str | ) | const |
Definition at line 101 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().
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Definition at line 185 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().
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Definition at line 128 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().
Definition at line 5175 of file SubSource.cpp.
References NStr::EqualNocase(), NStr::FindNoCase(), i, NULL, s_RemovableCultureNotes, s_ReplaceableCultureNotes, and rapidjson::value.
Definition at line 2653 of file SubSource.cpp.
References NStr::EqualCase(), NStr::IsBlank(), number, s_CollectNumberAndUnits(), and rapidjson::value.
Referenced by CValidError_imp::ValidateBioSource().
Definition at line 2846 of file SubSource.cpp.
References NStr::eNocase, NStr::IsBlank(), NStr::StartsWith(), rapidjson::value, and x_MeetsCommonChromosomeLinkageGroupPlasmidNameRules().
Referenced by CValidError_imp::ValidateSubSource().
Definition at line 447 of file SubSource.cpp.
References CTime::GetTimeT(), IsCollectionDateAfterTime(), and t.
Definition at line 436 of file SubSource.cpp.
References CDate::Compare(), CDate::eCompare_after, and t.
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Definition at line 414 of file SubSource.cpp.
References DateFromCollectionDate(), ITERATE, NStr::Split(), and t.
Referenced by CheckDateFormat(), IsCollectionDateAfterTime(), IsCorrectDateFormat(), and CValidError_imp::ValidateCitSub().
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Definition at line 454 of file SubSource.cpp.
References DateFromCollectionDate(), NStr::Find(), IsCollectionDateAfterTime(), IsISOFormatDate(), NPOS, NStr::Split(), and t.
Referenced by BOOST_AUTO_TEST_CASE(), FixDateFormat(), and GetHasCollectionDate().
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Definition at line 1237 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().
Determine whether day number could occur in month.
day | The number of the day, 1-based [in] |
month | The number of the month, 1-based [in] |
year | The number of the year, 1-based [in] |
Definition at line 266 of file SubSource.cpp.
References CTime::DaysInMonth().
Referenced by FixDateFormat(), and IsISOFormatDateOnly().
Definition at line 247 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().
Definition at line 2753 of file SubSource.cpp.
References rapidjson::value, and x_GenericRepliconNameValid().
Referenced by CValidError_imp::ValidateSubSource().
Definition at line 816 of file SubSource.cpp.
References NStr::Find(), IsISOFormatDateOnly(), IsISOFormatTime(), NPOS, and NStr::TruncateSpacesInPlace().
Referenced by CheckDateFormat(), CAutoColValidatordate::DoValidate(), FixDateFormat(), and IsCorrectDateFormat().
Definition at line 739 of file SubSource.cpp.
References IsDayValueOkForMonth(), isdigit(), and NStr::StringToInt().
Referenced by IsISOFormatDate(), and x_IsFixableIsoDate().
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Definition at line 644 of file SubSource.cpp.
References NStr::Find(), isdigit(), min(), NPOS, NStr::StringToInt(), and suffix.
Referenced by BOOST_AUTO_TEST_CASE(), IsISOFormatDate(), and x_IsFixableIsoDate().
Definition at line 2859 of file SubSource.cpp.
References NStr::IsBlank(), rapidjson::value, and x_MeetsCommonChromosomeLinkageGroupPlasmidNameRules().
Referenced by CValidError_imp::ValidateSubSource().
Definition at line 208 of file SubSource.cpp.
References CSubSource_Base::eSubtype_altitude, CSubSource_Base::eSubtype_chromosome, CSubSource_Base::eSubtype_clone, CSubSource_Base::eSubtype_collected_by, CSubSource_Base::eSubtype_collection_date, CSubSource_Base::eSubtype_country, CSubSource_Base::eSubtype_environmental_sample, CSubSource_Base::eSubtype_fwd_primer_name, CSubSource_Base::eSubtype_fwd_primer_seq, CSubSource_Base::eSubtype_germline, CSubSource_Base::eSubtype_identified_by, CSubSource_Base::eSubtype_lat_lon, CSubSource_Base::eSubtype_metagenomic, CSubSource_Base::eSubtype_plasmid_name, CSubSource_Base::eSubtype_rearranged, CSubSource_Base::eSubtype_rev_primer_name, CSubSource_Base::eSubtype_rev_primer_seq, CSubSource_Base::eSubtype_segment, CSubSource_Base::eSubtype_sex, and CSubSource_Base::eSubtype_transgenic.
Referenced by CValidError_imp::ValidateBioSource(), and CSourceModParser::x_ApplyMods().
Definition at line 2871 of file SubSource.cpp.
References NStr::Equal(), NStr::Find(), set< Key, Compare >::find(), NStr::FindNoCase(), NStr::IsBlank(), NPOS, NStr::StartsWith(), rapidjson::value, and x_MeetsCommonChromosomeLinkageGroupPlasmidNameRules().
Referenced by BOOST_AUTO_TEST_CASE(), and CValidError_imp::ValidateSubSource().
Definition at line 2747 of file SubSource.cpp.
References rapidjson::value, and x_GenericRepliconNameValid().
Referenced by CValidError_imp::ValidateSubSource().
Definition at line 2488 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().
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Definition at line 157 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().
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Definition at line 1890 of file SubSource.cpp.
References NStr::DoubleToString(), and NStr::TrimSuffixInPlace().
Referenced by FixLatLonFormat(), and ValidateLatLonCountry().
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Definition at line 94 of file SubSource.cpp.
References s_init_UseGeoLocNameForCountry(), and rapidjson::value.
Referenced by BOOST_AUTO_TEST_CASE(), CDiscrepancyVisitorImpl< _Name >::Summarize(), CValidError_imp::ValidateOrgModVoucher(), CValidError_imp::ValidateSubSource(), CSourceFeatureItem::x_FormatQuals(), CDeflineGenerator::x_GetModifiers(), and CSrcWriter::xFormatTabDelimited().
Definition at line 233 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().
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Definition at line 5227 of file SubSource.cpp.
References CSubSource_Base::GetName(), NStr::IsBlank(), CSubSource_Base::IsSetName(), RemoveCultureNotes(), CSubSource_Base::ResetName(), and CSubSource_Base::SetName().
Definition at line 5192 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().
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Definition at line 2101 of file SubSource.cpp.
References check_state(), CLatLonCountryId::Classify(), eLatLonCountryErr_Country, eLatLonCountryErr_None, eLatLonCountryErr_State, eLatLonCountryErr_Value, eLatLonCountryErr_Water, NStr::eNocase, NStr::Equal(), NStr::EqualNocase(), NStr::eReverseSearch, NStr::eTrunc_Both, CLatLonCountryId::fCountryClosest, CLatLonCountryId::fCountryMatch, CLatLonCountryMap::fFlip, NStr::Find(), flags, CLatLonCountryMap::fNegateLat, CLatLonCountryMap::fNegateLon, CLatLonCountryMap::fNone, CLatLonCountryId::fProvinceClosest, CLatLonCountryId::fProvinceMatch, CLatLonCountryId::fWaterMatch, g(), CLatLonCountryId::GetClaimedDistance(), CLatLonCountryId::GetClaimedFull(), CLatLonCountryId::GetClosestCountry(), CLatLonCountryId::GetClosestWater(), CLatLonCountryId::GetGuessCountry(), CLatLonCountryId::GetGuessProvince(), CLatLonCountryId::GetGuessWater(), CLatLonCountryId::GetLandDistance(), NStr::IntToString(), NStr::IsBlank(), IsCorrectLatLonFormat(), kEmptyStr, m_LatLonCountryMap, m_LatLonWaterMap, MakeLatLon(), NPOS, NULL, NStr::StartsWith(), NStr::TruncateSpacesInPlace(), x_CalculateLatLonId(), and x_FindSurroundingOcean().
Referenced by BOOST_AUTO_TEST_CASE(), CCountryConflict::GetValuesTableFromSeqEntry(), and CValidError_imp::ValidateLatLonCountry().
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Definition at line 1912 of file SubSource.cpp.
References NStr::EqualNocase(), ErrorDistance(), CLatLonCountryId::GetClosestCountry(), CLatLonCountryId::GetClosestWater(), CCountryExtreme::GetCountry(), CLatLonCountryId::GetGuessCountry(), CLatLonCountryId::GetGuessProvince(), CLatLonCountryId::GetGuessWater(), CCountryExtreme::GetLevel0(), CCountryExtreme::GetLevel1(), NStr::IsBlank(), m_LatLonCountryMap, and m_LatLonWaterMap.
Referenced by ValidateLatLonCountry().
Definition at line 2682 of file SubSource.cpp.
References precision, and val.
Referenced by FixAltitude().
Definition at line 2727 of file SubSource.cpp.
References isalnum(), NStr::IsBlank(), isprint(), and rapidjson::value.
Referenced by IsEndogenousVirusNameValid(), IsSegmentValid(), and x_MeetsCommonChromosomeLinkageGroupPlasmidNameRules().
Definition at line 852 of file SubSource.cpp.
References NStr::EqualNocase(), isalpha(), NStr::IsBlank(), isdigit(), ITERATE, NPOS, and NStr::TruncateSpacesInPlace().
Referenced by DetectDateFormat(), and FixDateFormat().
Definition at line 2671 of file SubSource.cpp.
References NStr::Find(), int, NPOS, and precision.
Referenced by FixAltitude(), FixLatLonPrecision(), and IsCorrectLatLonFormat().
Definition at line 779 of file SubSource.cpp.
References NStr::Find(), IsISOFormatDateOnly(), IsISOFormatTime(), NPOS, and NStr::TruncateSpacesInPlace().
Referenced by FixDateFormat().
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Definition at line 2805 of file SubSource.cpp.
References NStr::FindNoCase(), NPOS, s_FailsGenusOrSpeciesTest(), NStr::StartsWith(), rapidjson::value, and x_GenericRepliconNameValid().
Referenced by IsChromosomeNameValid(), IsLinkageGroupNameValid(), and IsPlasmidNameValid().
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Definition at line 596 of file SubSource.cpp.
References NStr::eNocase, NStr::Find(), FixDateFormat(), NStr::IsBlank(), kEmptyStr, CTempString::length(), and NPOS.
Referenced by FixDateFormat().
Definition at line 804 of file SubSource.cpp.
References NStr::Find(), NPOS, and NStr::TruncateSpacesInPlace().
Referenced by FixDateFormat().
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Definition at line 247 of file SubSource.hpp.
Referenced by ValidateLatLonCountry(), and x_CalculateLatLonId().
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Definition at line 248 of file SubSource.hpp.
Referenced by ValidateLatLonCountry(), and x_CalculateLatLonId().