Search Toolkit Book for CSrcWriter

Used to generate tables showing qualifier-field entries occuring in the BioSources of instances of Bioseq and Seq-entry. More...

#include <objtools/writers/src_writer.hpp>

Inheritance diagram for CSrcWriter:

Collaboration diagram for CSrcWriter:

Public Types
typedef map< string, size_t >	COLUMNMAP

typedef map< string, string >	NAMEMAP

typedef list< string >	NAMELIST

typedef vector< string >	FIELDS

typedef bool(CSrcWriter::*	HANDLER) (const CBioSource &, const string &, ILineErrorListener *)

typedef map< string, CSrcWriter::HANDLER >	HANDLERMAP

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
	CSrcWriter (unsigned int flags=0)

virtual	~CSrcWriter ()

virtual bool	WriteBioseqHandle (CBioseq_Handle, const FIELDS &, CNcbiOstream &)
	Write a table of the specified qualifier-field entries found in the BioSource of a given Bioseq. More...

virtual bool	WriteBioseqHandles (const vector< pair< string, CBioseq_Handle > > &, const FIELDS &, CNcbiOstream &, ILineErrorListener *=nullptr)
	Write a table of the specified qualifier-field entries found in the BioSources of a vector of Bioseqs. More...

void	SetDelimiter (const string &delimiter)
	Set the column delimiter for the output table. More...

virtual bool	WriteSeqEntry (const CSeq_entry &, CScope &, CNcbiOstream &, bool=false)
	Write a table of all qualifier-field entries occurring in the BioSources for a given Seq-entry, with columns appearing in a canonical order. 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...

virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. 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	ValidateFields (const FIELDS &fields, ILineErrorListener *=nullptr)
	Verify that each string in fields is a valid qualifier name. More...

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)

Static Public Attributes
static const FIELDS	sDefaultSrcCheckFields
	Default fields processed by srcchk application, in their canonical order. More...

static const FIELDS	sAllSrcCheckFields
	All possible fields processed by srchck application, in their canonical order. More...

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
void	xInit ()

virtual bool	xGather (CBioseq_Handle, string id, const FIELDS &, ILineErrorListener *=nullptr)

virtual bool	xGatherId (CBioseq_Handle, ILineErrorListener *=nullptr)

virtual bool	xGatherGi (CBioseq_Handle, ILineErrorListener *=nullptr)

virtual bool	xGatherLocalId (CBioseq_Handle, ILineErrorListener *=nullptr)

virtual bool	xGatherBankitId (CBioseq_Handle, ILineErrorListener *=nullptr)

virtual bool	xGatherDefline (CBioseq_Handle, ILineErrorListener *=nullptr)

virtual bool	xTryDefaultId (const string &id, ILineErrorListener *=nullptr)

virtual bool	xHandleSourceField (const CBioSource &, const string &, ILineErrorListener *=nullptr)

virtual bool	xGatherTaxname (const CBioSource &, const string &, ILineErrorListener *=nullptr)

virtual bool	xGatherDivision (const CBioSource &, const string &, ILineErrorListener *=nullptr)

virtual bool	xGatherGenome (const CBioSource &, const string &, ILineErrorListener *=nullptr)

virtual bool	xGatherOrigin (const CBioSource &, const string &, ILineErrorListener *=nullptr)

virtual bool	xGatherSubtypeFeat (const CBioSource &, const string &, ILineErrorListener *=nullptr)

virtual bool	xGatherOrgModFeat (const CBioSource &, const string &, ILineErrorListener *=nullptr)

virtual bool	xGatherOrgCommon (const CBioSource &, const string &, ILineErrorListener *=nullptr)

virtual bool	xGatherOrgnameLineage (const CBioSource &, const string &, ILineErrorListener *=nullptr)

virtual bool	xGatherPcrPrimers (const CBioSource &, const string &, ILineErrorListener *=nullptr)

virtual bool	xGatherDb (const CBioSource &, const string &, ILineErrorListener *=nullptr)

virtual bool	xGatherTaxonId (const CBioSource &, const string &, ILineErrorListener *=nullptr)

virtual bool	xFormatTabDelimited (const FIELDS &, CNcbiOstream &)

void	xPrepareTableColumn (const string &, const string &, const string &="")

void	xAppendColumnValue (const string &, const string &)

bool	xValueNeedsQuoting (const string &)

string	xDequotedValue (const string &)

string	xGetColStub (const string &)

string	xGetOriginalId (const CBioseq_Handle &) const

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

Static Protected Member Functions
static FIELDS	xGetOrderedFieldNames (const FIELDS &)

static HANDLER	xGetHandler (const string &)

static string	xPrimerSetNames (const CPCRPrimerSet &)

static string	xPrimerSetSequences (const CPCRPrimerSet &)

static bool	xIsSubsourceTypeSuppressed (CSubSource::TSubtype)

static bool	xIsOrgmodTypeSuppressed (COrgMod::TSubtype)

static NAMELIST	xGetOrgModSubtypeNames ()

static NAMELIST	xGetSubSourceSubtypeNames ()

static string	xCompressFieldName (const string &)

static FIELDS	xProcessFieldNames (const FIELDS &)

Protected Attributes
CRef< CSeq_table >	mSrcTable

COLUMNMAP	mColnameToIndex

unsigned int	mFlags

string	mDelimiter

Static Protected Attributes
static const FIELDS	sDefaultSeqEntryFields

static const FIELDS	sAllSeqEntryFields

static HANDLERMAP	sHandlerMap

static NAMEMAP	sFieldnameToColname

Detailed Description

Used to generate tables showing qualifier-field entries occuring in the BioSources of instances of Bioseq and Seq-entry.

Definition at line 70 of file src_writer.hpp.

Member Typedef Documentation

◆ COLUMNMAP

typedef map<string, size_t> CSrcWriter::COLUMNMAP

Definition at line 75 of file src_writer.hpp.

◆ FIELDS

typedef vector<string> CSrcWriter::FIELDS

Definition at line 78 of file src_writer.hpp.

◆ HANDLER

typedef bool(CSrcWriter::* CSrcWriter::HANDLER) (const CBioSource &, const string &, ILineErrorListener *)

Definition at line 79 of file src_writer.hpp.

◆ HANDLERMAP

typedef map<string, CSrcWriter::HANDLER> CSrcWriter::HANDLERMAP

Definition at line 80 of file src_writer.hpp.

◆ NAMELIST

typedef list<string> CSrcWriter::NAMELIST

Definition at line 77 of file src_writer.hpp.

◆ NAMEMAP

typedef map<string, string> CSrcWriter::NAMEMAP

Definition at line 76 of file src_writer.hpp.

Constructor & Destructor Documentation

◆ CSrcWriter()

CSrcWriter::CSrcWriter ( unsigned int flags = 0 )

inline

Definition at line 83 of file src_writer.hpp.

References xInit().

◆ ~CSrcWriter()

virtual CSrcWriter::~CSrcWriter ( )

inlinevirtual

Definition at line 90 of file src_writer.hpp.

Member Function Documentation

◆ SetDelimiter()

void CSrcWriter::SetDelimiter ( const string & delimiter )

inline

Set the column delimiter for the output table.

Definition at line 111 of file src_writer.hpp.

References delimiter, and mDelimiter.

Referenced by sRunTest(), sUpdateCase(), and CSrcChkApp::xInitWriter().

◆ ValidateFields()

bool CSrcWriter::ValidateFields	(	const FIELDS &	fields,
		ILineErrorListener *	= `nullptr`
	)

static

Verify that each string in fields is a valid qualifier name.

Definition at line 1407 of file src_writer.cpp.

References CSrcError::Create(), eDiag_Error, map_checker< Container >::end(), map_checker< Container >::find(), ILineErrorListener::PutError(), sFieldnameToColname, and xCompressFieldName().

Referenced by CSrcChkApp::xGetDesiredFields().

◆ WriteBioseqHandle()

bool CSrcWriter::WriteBioseqHandle	(	CBioseq_Handle	,
		const FIELDS &	,
		CNcbiOstream &
	)

virtual

Write a table of the specified qualifier-field entries found in the BioSource of a given Bioseq.

Definition at line 146 of file src_writer.cpp.

References out(), xFormatTabDelimited(), xGather(), and xProcessFieldNames().

◆ WriteBioseqHandles()

bool CSrcWriter::WriteBioseqHandles	(	const vector< pair< string, CBioseq_Handle > > &	,
		const FIELDS &	,
		CNcbiOstream &	,
		ILineErrorListener *	= `nullptr`
	)

virtual

Write a table of the specified qualifier-field entries found in the BioSources of a vector of Bioseqs.

Definition at line 165 of file src_writer.cpp.

References out(), xFormatTabDelimited(), xGather(), and xProcessFieldNames().

Referenced by sRunTest(), sUpdateCase(), WriteSeqEntry(), and CSrcChkApp::xTryProcessIdFile().

◆ WriteSeqEntry()

bool CSrcWriter::WriteSeqEntry	(	const CSeq_entry &	seqEntry,
		CScope &	scope,
		CNcbiOstream &	out,
		bool	nucsOnly = `false`
	)

virtual

Write a table of all qualifier-field entries occurring in the BioSources for a given Seq-entry, with columns appearing in a canonical order.

Definition at line 189 of file src_writer.cpp.

References CScope::AddTopLevelSeqEntry(), out(), sAllSeqEntryFields, and WriteBioseqHandles().

Referenced by sRunTest(), sUpdateCase(), and CSrcChkApp::xTryProcessSeqEntry().

◆ xAppendColumnValue()

void CSrcWriter::xAppendColumnValue	(	const string &	colName,
		const string &	colValue
	)

protected

Definition at line 1395 of file src_writer.cpp.

References column, mColnameToIndex, mSrcTable, and CSeq_table_Base::SetColumns().

Referenced by xGather(), xGatherBankitId(), xGatherDb(), xGatherDefline(), xGatherDivision(), xGatherGenome(), xGatherGi(), xGatherId(), xGatherLocalId(), xGatherOrgCommon(), xGatherOrgModFeat(), xGatherOrgnameLineage(), xGatherOrigin(), xGatherPcrPrimers(), xGatherSubtypeFeat(), xGatherTaxname(), xGatherTaxonId(), and xTryDefaultId().

◆ xCompressFieldName()

string CSrcWriter::xCompressFieldName ( const string & fieldName )

staticprotected

Definition at line 458 of file src_writer.cpp.

References NStr::ReplaceInPlace(), NStr::ToLower(), and NStr::TruncateSpaces().

Referenced by ValidateFields(), xGetOrderedFieldNames(), xInit(), and xProcessFieldNames().

◆ xDequotedValue()

string CSrcWriter::xDequotedValue ( const string & value )

protected

Definition at line 1438 of file src_writer.cpp.

References NStr::Replace(), and value.

Referenced by xFormatTabDelimited().

◆ xFormatTabDelimited()

bool CSrcWriter::xFormatTabDelimited	(	const FIELDS &	,
		CNcbiOstream &
	)

protectedvirtual

Definition at line 1312 of file src_writer.cpp.

References map_checker< Container >::begin(), column, map_checker< Container >::end(), map_checker< Container >::find(), CSeq_table::GetColumn(), CSeq_table_Base::GetNum_rows(), mColnameToIndex, mDelimiter, mSrcTable, out(), xDequotedValue(), xGetColStub(), and xValueNeedsQuoting().

Referenced by WriteBioseqHandle(), and WriteBioseqHandles().

◆ xGather()

bool CSrcWriter::xGather	(	CBioseq_Handle	,
		string	id,
		const FIELDS &	,
		ILineErrorListener *	= `nullptr`
	)

protectedvirtual

Definition at line 560 of file src_writer.cpp.

References CDate::Compare(), rapidjson::defaultValue, CSeqdesc_Base::e_Pub, CSeqdesc_Base::e_Source, CPub_Base::e_Sub, CDate::eCompare_before, CPub_equiv_Base::Get(), CAffil_Base::C_Std::GetAffil(), CAuth_list_Base::GetAffil(), CCit_sub_Base::GetAuthors(), CPerson_id_Base::GetConsortium(), CCit_sub_Base::GetDate(), CName_std_Base::GetInitials(), CName_std_Base::GetLast(), CAuthor_Base::GetName(), CPerson_id_Base::GetName(), CAuth_list_Base::GetNames(), CSeq_table_Base::GetNum_rows(), CPubdesc_Base::GetPub(), CAffil_Base::GetStd(), CAffil_Base::GetStr(), CPerson_id_Base::IsConsortium(), CPerson_id_Base::IsName(), CPub_equiv_Base::IsSet(), CAffil_Base::C_Std::IsSetAffil(), CAuth_list_Base::IsSetAffil(), CCit_sub_Base::IsSetAuthors(), CCit_sub_Base::IsSetDate(), CName_std_Base::IsSetInitials(), CName_std_Base::IsSetLast(), CAuthor_Base::IsSetName(), CAuth_list_Base::IsSetNames(), CPubdesc_Base::IsSetPub(), CAffil_Base::IsStd(), CAffil_Base::IsStr(), ITERATE, mSrcTable, names, CSeq_table_Base::SetNum_rows(), xAppendColumnValue(), xGatherBankitId(), xGatherDefline(), xGatherGi(), xGatherId(), xGatherLocalId(), xHandleSourceField(), xPrepareTableColumn(), and xTryDefaultId().

Referenced by WriteBioseqHandle(), and WriteBioseqHandles().

◆ xGatherBankitId()

bool CSrcWriter::xGatherBankitId	(	CBioseq_Handle	bsh,
		ILineErrorListener *	= `nullptr`
	)

protectedvirtual

Definition at line 832 of file src_writer.cpp.

References rapidjson::defaultValue, CBioseq_Handle::GetId(), ITERATE, xAppendColumnValue(), and xPrepareTableColumn().

Referenced by xGather().

◆ xGatherDb()

bool CSrcWriter::xGatherDb	(	const CBioSource &	src,
		const string &	colName,
		ILineErrorListener *	= `nullptr`
	)

protectedvirtual

Definition at line 1113 of file src_writer.cpp.

References rapidjson::defaultValue, CObject_id_Base::e_Id, CObject_id_Base::e_Str, COrg_ref_Base::GetDb(), CObject_id_Base::GetId(), CBioSource_Base::GetOrg(), CObject_id_Base::GetStr(), NStr::IntToString(), COrg_ref_Base::IsSetDb(), CBioSource_Base::IsSetOrg(), tag, CObject_id_Base::Which(), xAppendColumnValue(), and xPrepareTableColumn().

Referenced by xInit().

◆ xGatherDefline()

bool CSrcWriter::xGatherDefline	(	CBioseq_Handle	bsh,
		ILineErrorListener *	= `nullptr`
	)

protectedvirtual

Definition at line 871 of file src_writer.cpp.

References rapidjson::defaultValue, label, xAppendColumnValue(), and xPrepareTableColumn().

Referenced by xGather().

◆ xGatherDivision()

bool CSrcWriter::xGatherDivision	(	const CBioSource &	src,
		const string &	colName,
		ILineErrorListener *	= `nullptr`
	)

protectedvirtual

Definition at line 958 of file src_writer.cpp.

References rapidjson::defaultValue, COrg_ref::GetDivision(), CBioSource_Base::GetOrg(), COrg_ref::IsSetDivision(), CBioSource_Base::IsSetOrg(), value, xAppendColumnValue(), and xPrepareTableColumn().

Referenced by xInit().

◆ xGatherGenome()

bool CSrcWriter::xGatherGenome	(	const CBioSource &	src,
		const string &	colName,
		ILineErrorListener *	= `nullptr`
	)

protectedvirtual

Definition at line 978 of file src_writer.cpp.

References rapidjson::defaultValue, CBioSource_Base::GetGenome(), CBioSource::GetOrganelleByGenome(), CBioSource_Base::IsSetGenome(), value, xAppendColumnValue(), and xPrepareTableColumn().

Referenced by xInit().

◆ xGatherGi()

bool CSrcWriter::xGatherGi	(	CBioseq_Handle	bsh,
		ILineErrorListener *	= `nullptr`
	)

protectedvirtual

Definition at line 739 of file src_writer.cpp.

References rapidjson::defaultValue, CSeq_id::eContent, CBioseq_Handle::GetId(), ITERATE, label, xAppendColumnValue(), and xPrepareTableColumn().

Referenced by xGather().

◆ xGatherId()

bool CSrcWriter::xGatherId	(	CBioseq_Handle	bsh,
		ILineErrorListener *	= `nullptr`
	)

protectedvirtual

Definition at line 715 of file src_writer.cpp.

References rapidjson::defaultValue, GetAccessionForId(), CBioseq_Handle::GetScope(), CBioseq_Handle::GetSeqId(), label, xAppendColumnValue(), and xPrepareTableColumn().

Referenced by xGather().

◆ xGatherLocalId()

bool CSrcWriter::xGatherLocalId	(	CBioseq_Handle	bsh,
		ILineErrorListener *	= `nullptr`
	)

protectedvirtual

Definition at line 800 of file src_writer.cpp.

References rapidjson::defaultValue, CSeq_id::eContent, CSeq_id::GetLabel(), CBioseq_Handle::GetLocalIdOrNull(), NStr::IsBlank(), xAppendColumnValue(), xGetOriginalId(), and xPrepareTableColumn().

Referenced by xGather().

◆ xGatherOrgCommon()

bool CSrcWriter::xGatherOrgCommon	(	const CBioSource &	src,
		const string &	colName,
		ILineErrorListener *	= `nullptr`
	)

protectedvirtual

Definition at line 917 of file src_writer.cpp.

References rapidjson::defaultValue, COrg_ref_Base::GetCommon(), CBioSource_Base::GetOrg(), COrg_ref_Base::IsSetCommon(), CBioSource_Base::IsSetOrg(), value, xAppendColumnValue(), and xPrepareTableColumn().

Referenced by xInit().

◆ xGatherOrgModFeat()

bool CSrcWriter::xGatherOrgModFeat	(	const CBioSource &	src,
		const string &	colName,
		ILineErrorListener *	= `nullptr`
	)

protectedvirtual

Definition at line 1070 of file src_writer.cpp.

References COrgMod::eVocabulary_raw, COrgName_Base::GetMod(), CBioSource::GetOrgname(), COrgMod_Base::GetSubname(), COrgMod_Base::GetSubtype(), COrgMod::GetSubtypeValue(), NStr::IntToString(), CBioSource::IsSetOrgMod(), ncbi::grid::netcache::search::fields::key, value, xAppendColumnValue(), xIsOrgmodTypeSuppressed(), and xPrepareTableColumn().

Referenced by xInit().

◆ xGatherOrgnameLineage()

bool CSrcWriter::xGatherOrgnameLineage	(	const CBioSource &	src,
		const string &	colName,
		ILineErrorListener *	= `nullptr`
	)

protectedvirtual

Definition at line 937 of file src_writer.cpp.

References rapidjson::defaultValue, COrgName_Base::GetLineage(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), COrgName_Base::IsSetLineage(), CBioSource_Base::IsSetOrg(), COrg_ref_Base::IsSetOrgname(), value, xAppendColumnValue(), and xPrepareTableColumn().

Referenced by xInit().

◆ xGatherOrigin()

bool CSrcWriter::xGatherOrigin	(	const CBioSource &	src,
		const string &	colName,
		ILineErrorListener *	= `nullptr`
	)

protectedvirtual

Definition at line 998 of file src_writer.cpp.

References rapidjson::defaultValue, CBioSource_Base::GetOrigin(), CBioSource::GetStringFromOrigin(), CBioSource_Base::IsSetOrigin(), value, xAppendColumnValue(), and xPrepareTableColumn().

Referenced by xInit().

◆ xGatherPcrPrimers()

bool CSrcWriter::xGatherPcrPrimers	(	const CBioSource &	src,
		const string &	colName,
		ILineErrorListener *	= `nullptr`
	)

protectedvirtual

Definition at line 1205 of file src_writer.cpp.

References CPCRReactionSet_Base::Get(), CPCRReaction_Base::GetForward(), CBioSource_Base::GetPcr_primers(), CPCRReaction_Base::GetReverse(), NStr::IntToString(), CPCRReaction_Base::IsSetForward(), CBioSource_Base::IsSetPcr_primers(), CPCRReaction_Base::IsSetReverse(), xAppendColumnValue(), xPrepareTableColumn(), xPrimerSetNames(), and xPrimerSetSequences().

Referenced by xInit().

◆ xGatherSubtypeFeat()

bool CSrcWriter::xGatherSubtypeFeat	(	const CBioSource &	src,
		const string &	colName,
		ILineErrorListener *	= `nullptr`
	)

protectedvirtual

Definition at line 1018 of file src_writer.cpp.

References CSubSource::eVocabulary_raw, CSubSource_Base::GetName(), CBioSource_Base::GetSubtype(), CSubSource_Base::GetSubtype(), CSubSource::GetSubtypeValue(), NStr::IntToString(), CSubSource_Base::IsSetName(), CBioSource_Base::IsSetSubtype(), ncbi::grid::netcache::search::fields::key, CSubSource::NeedsNoText(), value, xAppendColumnValue(), xIsSubsourceTypeSuppressed(), and xPrepareTableColumn().

Referenced by xInit().

◆ xGatherTaxname()

bool CSrcWriter::xGatherTaxname	(	const CBioSource &	src,
		const string &	colName,
		ILineErrorListener *	= `nullptr`
	)

protectedvirtual

Definition at line 897 of file src_writer.cpp.

References rapidjson::defaultValue, CBioSource::GetTaxname(), CBioSource::IsSetTaxname(), value, xAppendColumnValue(), and xPrepareTableColumn().

Referenced by xInit().

◆ xGatherTaxonId()

bool CSrcWriter::xGatherTaxonId	(	const CBioSource &	src,
		const string &	colName,
		ILineErrorListener *	= `nullptr`
	)

protectedvirtual

Definition at line 1160 of file src_writer.cpp.

References rapidjson::defaultValue, CObject_id_Base::e_Id, CObject_id_Base::e_Str, COrg_ref_Base::GetDb(), CObject_id_Base::GetId(), CBioSource_Base::GetOrg(), CObject_id_Base::GetStr(), NStr::IntToString(), COrg_ref_Base::IsSetDb(), CBioSource_Base::IsSetOrg(), tag, CObject_id_Base::Which(), xAppendColumnValue(), and xPrepareTableColumn().

Referenced by xInit().

◆ xGetColStub()

string CSrcWriter::xGetColStub ( const string & colName )

protected

Definition at line 1376 of file src_writer.cpp.

References NStr::Find(), and NPOS.

Referenced by xFormatTabDelimited().

◆ xGetHandler()

CSrcWriter::HANDLER CSrcWriter::xGetHandler ( const string & fieldName )

staticprotected

Definition at line 501 of file src_writer.cpp.

References sHandlerMap.

Referenced by xHandleSourceField().

◆ xGetOrderedFieldNames()

CSrcWriter::FIELDS CSrcWriter::xGetOrderedFieldNames ( const FIELDS & )

staticprotected

Definition at line 360 of file src_writer.cpp.

References set< Key, Compare >::end(), set< Key, Compare >::find(), set< Key, Compare >::insert(), ct::sort(), xCompressFieldName(), xGetOrgModSubtypeNames(), and xGetSubSourceSubtypeNames().

◆ xGetOrgModSubtypeNames()

CSrcWriter::NAMELIST CSrcWriter::xGetOrgModSubtypeNames ( )

staticprotected

Definition at line 424 of file src_writer.cpp.

References ENUM_METHOD_NAME.

Referenced by xGetOrderedFieldNames(), and xInit().

◆ xGetOriginalId()

string CSrcWriter::xGetOriginalId ( const CBioseq_Handle & bsh ) const

protected

Definition at line 770 of file src_writer.cpp.

References NStr::EqualNocase(), FIELD_IS_SET_AND_IS, FOR_EACH_SEQDESC_ON_SEQDESCR, FOR_EACH_USERFIELD_ON_USEROBJECT, GET_FIELD, CUser_field_Base::GetData(), CUser_field_Base::GetLabel(), CObject_id_Base::GetStr(), CUser_field_Base::C_Data::GetStr(), CUser_object_Base::GetType(), CSeqdesc_Base::GetUser(), CUser_field_Base::IsSetData(), CUser_object_Base::IsSetType(), CObject_id_Base::IsStr(), CUser_field_Base::C_Data::IsStr(), and CSeqdesc_Base::IsUser().

Referenced by xGatherLocalId().

◆ xGetSubSourceSubtypeNames()

CSrcWriter::NAMELIST CSrcWriter::xGetSubSourceSubtypeNames ( )

staticprotected

Definition at line 441 of file src_writer.cpp.

References ENUM_METHOD_NAME.

Referenced by xGetOrderedFieldNames(), and xInit().

◆ xHandleSourceField()

bool CSrcWriter::xHandleSourceField	(	const CBioSource &	src,
		const string &	fieldName,
		ILineErrorListener *	pEC = `nullptr`
	)

protectedvirtual

Definition at line 510 of file src_writer.cpp.

References CSrcError::Create(), eDiag_Error, ILineErrorListener::PutError(), and xGetHandler().

Referenced by xGather().

◆ xInit()

void CSrcWriter::xInit ( )

protected

◆ xIsOrgmodTypeSuppressed()

bool CSrcWriter::xIsOrgmodTypeSuppressed ( COrgMod::TSubtype subtype )

staticprotected

Definition at line 486 of file src_writer.cpp.

References COrgMod_Base::eSubtype_old_name, and COrgMod::IsDiscouraged().

Referenced by xGatherOrgModFeat().

◆ xIsSubsourceTypeSuppressed()

bool CSrcWriter::xIsSubsourceTypeSuppressed ( CSubSource::TSubtype subtype )

staticprotected

Definition at line 474 of file src_writer.cpp.

References CSubSource::IsDiscouraged().

Referenced by xGatherSubtypeFeat().

◆ xPrepareTableColumn()

void CSrcWriter::xPrepareTableColumn	(	const string &	colName,
		const string &	colTitle,
		const string &	colDefault = `""`
	)

protected

◆ xPrimerSetNames()

string CSrcWriter::xPrimerSetNames ( const CPCRPrimerSet & pset )

staticprotected

Definition at line 1274 of file src_writer.cpp.

References CPCRPrimerSet_Base::Get(), CPCRPrimer_Base::GetName(), CPCRPrimer_Base::IsSetName(), and names.

Referenced by xGatherPcrPrimers().

◆ xPrimerSetSequences()

string CSrcWriter::xPrimerSetSequences ( const CPCRPrimerSet & pset )

staticprotected

Definition at line 1293 of file src_writer.cpp.

References CPCRPrimerSet_Base::Get(), CPCRPrimer_Base::GetSeq(), and CPCRPrimer_Base::IsSetSeq().

Referenced by xGatherPcrPrimers().

◆ xProcessFieldNames()

CSrcWriter::FIELDS CSrcWriter::xProcessFieldNames ( const FIELDS & )

staticprotected

Definition at line 210 of file src_writer.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), sFieldnameToColname, and xCompressFieldName().

Referenced by WriteBioseqHandle(), and WriteBioseqHandles().

◆ xTryDefaultId()

bool CSrcWriter::xTryDefaultId	(	const string &	id,
		ILineErrorListener *	= `nullptr`
	)

protectedvirtual

Definition at line 532 of file src_writer.cpp.

References rapidjson::defaultValue, ctll::empty(), NStr::fConvErr_NoThrow, CSeq_table_Base::GetNum_rows(), mSrcTable, CSeq_table_Base::SetNum_rows(), xAppendColumnValue(), and xPrepareTableColumn().

Referenced by xGather().

◆ xValueNeedsQuoting()

bool CSrcWriter::xValueNeedsQuoting ( const string & value )

protected

Definition at line 1429 of file src_writer.cpp.

References mDelimiter, and value.

Referenced by xFormatTabDelimited().

Member Data Documentation

◆ mColnameToIndex

COLUMNMAP CSrcWriter::mColnameToIndex

protected

Definition at line 187 of file src_writer.hpp.

Referenced by xAppendColumnValue(), xFormatTabDelimited(), and xPrepareTableColumn().

◆ mDelimiter

string CSrcWriter::mDelimiter

protected

Definition at line 189 of file src_writer.hpp.

Referenced by SetDelimiter(), xFormatTabDelimited(), and xValueNeedsQuoting().

◆ mFlags

unsigned int CSrcWriter::mFlags

protected

Definition at line 188 of file src_writer.hpp.

◆ mSrcTable

CRef<CSeq_table> CSrcWriter::mSrcTable

protected

Definition at line 186 of file src_writer.hpp.

Referenced by xAppendColumnValue(), xFormatTabDelimited(), xGather(), xInit(), xPrepareTableColumn(), and xTryDefaultId().

◆ sAllSeqEntryFields

const CSrcWriter::FIELDS CSrcWriter::sAllSeqEntryFields

staticprotected

Definition at line 183 of file src_writer.hpp.

Referenced by WriteSeqEntry().

◆ sAllSrcCheckFields

const CSrcWriter::FIELDS CSrcWriter::sAllSrcCheckFields

static

All possible fields processed by srchck application, in their canonical order.

Definition at line 179 of file src_writer.hpp.

Referenced by CSrcChkApp::Run(), sRunTest(), sUpdateCase(), and CSrcChkApp::xGetDesiredFields().

◆ sDefaultSeqEntryFields

const CSrcWriter::FIELDS CSrcWriter::sDefaultSeqEntryFields

staticprotected

Definition at line 182 of file src_writer.hpp.

◆ sDefaultSrcCheckFields

const CSrcWriter::FIELDS CSrcWriter::sDefaultSrcCheckFields

static

Default fields processed by srcchk application, in their canonical order.

Definition at line 178 of file src_writer.hpp.

Referenced by CSrcChkApp::xGetDesiredFields().

◆ sFieldnameToColname

CSrcWriter::NAMEMAP CSrcWriter::sFieldnameToColname

staticprotected

Definition at line 185 of file src_writer.hpp.

Referenced by ValidateFields(), xInit(), and xProcessFieldNames().

◆ sHandlerMap

CSrcWriter::HANDLERMAP CSrcWriter::sHandlerMap

staticprotected

Definition at line 184 of file src_writer.hpp.

Referenced by xGetHandler(), and xInit().

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

include/objtools/writers/src_writer.hpp
src/objtools/writers/src_writer.cpp

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Member Typedef Documentation

◆ COLUMNMAP

◆ FIELDS

◆ HANDLER

◆ HANDLERMAP

◆ NAMELIST

◆ NAMEMAP

Constructor & Destructor Documentation

◆ CSrcWriter()

◆ ~CSrcWriter()

Member Function Documentation

◆ SetDelimiter()

◆ ValidateFields()

◆ WriteBioseqHandle()

◆ WriteBioseqHandles()

◆ WriteSeqEntry()

◆ xAppendColumnValue()

◆ xCompressFieldName()

◆ xDequotedValue()

◆ xFormatTabDelimited()

◆ xGather()

◆ xGatherBankitId()

◆ xGatherDb()

◆ xGatherDefline()

◆ xGatherDivision()

◆ xGatherGenome()

◆ xGatherGi()

◆ xGatherId()

◆ xGatherLocalId()

◆ xGatherOrgCommon()

◆ xGatherOrgModFeat()

◆ xGatherOrgnameLineage()

◆ xGatherOrigin()

◆ xGatherPcrPrimers()

◆ xGatherSubtypeFeat()

◆ xGatherTaxname()

◆ xGatherTaxonId()

◆ xGetColStub()

◆ xGetHandler()

◆ xGetOrderedFieldNames()

◆ xGetOrgModSubtypeNames()

◆ xGetOriginalId()

◆ xGetSubSourceSubtypeNames()

◆ xHandleSourceField()

◆ xInit()

◆ xIsOrgmodTypeSuppressed()

◆ xIsSubsourceTypeSuppressed()

◆ xPrepareTableColumn()

◆ xPrimerSetNames()

◆ xPrimerSetSequences()

◆ xProcessFieldNames()

◆ xTryDefaultId()

◆ xValueNeedsQuoting()

Member Data Documentation

◆ mColnameToIndex

◆ mDelimiter

◆ mFlags

◆ mSrcTable

◆ sAllSeqEntryFields

◆ sAllSrcCheckFields

◆ sDefaultSeqEntryFields

◆ sDefaultSrcCheckFields

◆ sFieldnameToColname

◆ sHandlerMap