CTaxon1 Class Reference

Search Toolkit Book for CTaxon1

#include <objects/taxon1/taxon1.hpp>

Collaboration diagram for CTaxon1:

Public Types
enum	EOrgRefStatus {   eStatus_Ok = COrg_ref::eOrgref_nothing , eStatus_WrongTaxId = COrg_ref::eOrgref_db_taxid , eStatus_NoOrgname = COrg_ref::eOrgref_orgname , eStatus_WrongTaxname = COrg_ref::eOrgref_taxname ,   eStatus_WrongOrgrefMod = COrg_ref::eOrgref_mod , eStatus_WrongCommonName = COrg_ref::eOrgref_common , eStatus_WrongOrgname = COrg_ref::eOrgref_on_name , eStatus_WrongOrgmod = COrg_ref::eOrgref_on_mod ,   eStatus_WrongLineage = COrg_ref::eOrgref_on_lin , eStatus_WrongDivision = COrg_ref::eOrgref_on_div , eStatus_WrongGC = COrg_ref::eOrgref_on_gc , eStatus_WrongMGC = COrg_ref::eOrgref_on_mgc ,   eStatus_WrongPGC = COrg_ref::eOrgref_on_pgc , eStatus_WrongOrgnameAttr = COrg_ref::eOrgref_on_attr , eStatus_WrongONASpecified = COrg_ref::eOrgref_on_attr_spec , eStatus_WrongONANoModFwd = COrg_ref::eOrgref_on_attr_nofwd ,   eStatus_WrongONAUncultured = COrg_ref::eOrgref_on_attr_uncult , eStatus_WrongNomenclature = COrg_ref::eOrgref_on_mod_nom , eStatus_WrongModOldname = COrg_ref::eOrgref_on_mod_oldname , eStatus_WrongModTypeMaterial = COrg_ref::eOrgref_on_mod_tm }
enum	ESearch { eSearch_Exact , eSearch_TokenSet , eSearch_WildCard , eSearch_Phonetic }
enum	ESpeciesMode { eSpeciesMode_RankOnly , eSpeciesMode_Flag }
enum	EIteratorMode {   eIteratorMode_FullTree , eIteratorMode_LeavesBranches , eIteratorMode_Best , eIteratorMode_Blast ,   eIteratorMode_Default = eIteratorMode_FullTree }
typedef list< string >	TNameList
typedef vector< TTaxId >	TTaxIdList
typedef list< CRef< CTaxon1_info > >	TInfoList
typedef unsigned	TOrgRefStatus

Public Member Functions
	CTaxon1 ()
	~CTaxon1 ()
bool	Init (void)
bool	Init (unsigned cache_capacity)
bool	Init (const STimeout *timeout, unsigned reconnect_attempts=def_reconnect_attempts, unsigned cache_capacity=def_cache_capacity)
void	Fini (void)
CRef< CTaxon2_data >	GetById (TTaxId tax_id)
bool	GetScientificName (TTaxId tax_id, string &name_out)
CRef< CTaxon2_data >	Lookup (const COrg_ref &inp_orgRef, string *psLog=0)
CConstRef< CTaxon2_data >	LookupMerge (COrg_ref &inp_orgRef, string *psLog=0, TOrgRefStatus *pStatusOut=0)
TTaxId	GetTaxIdByOrgRef (const COrg_ref &inp_orgRef)
bool	CheckOrgRef (const COrg_ref &orgRef, TOrgRefStatus &stat_out, string *psLog=0)
TTaxId	GetTaxIdByName (const string &orgname)
TTaxId	FindTaxIdByName (const string &orgname)
TTaxId	SearchTaxIdByName (const string &orgname, ESearch mode=eSearch_TokenSet, list< CRef< CTaxon1_name > > *name_list_out=NULL)
int	GetAllTaxIdByName (const string &orgname, TTaxIdList &lIds)
CConstRef< COrg_ref >	GetOrgRef (TTaxId tax_id, bool &is_species, bool &is_uncultured, string &blast_name, bool *is_specified=NULL)
bool	SetSynonyms (bool on_off)
TTaxId	GetParent (TTaxId id_tax)
TTaxId	GetSpecies (TTaxId id_tax, ESpeciesMode mode=eSpeciesMode_Flag)
TTaxId	GetGenus (TTaxId id_tax)
TTaxId	GetSuperkingdom (TTaxId id_tax)
TTaxId	GetAncestorByRank (TTaxId id_tax, const char *rank_name)
TTaxId	GetAncestorByRank (TTaxId id_tax, TTaxRank rank_id)
int	GetChildren (TTaxId id_tax, TTaxIdList &children_ids)
bool	GetGCName (TTaxGeneticCode gc_id, string &gc_name_out)
bool	GetRankName (TTaxRank rank_id, string &rank_name_out)
TTaxRank	GetRankIdByName (const string &rank_name)
bool	GetDivisionName (TTaxDivision div_id, string &div_name_out, string *div_code_out=NULL)
TTaxDivision	GetDivisionIdByName (const string &div_name)
bool	GetNameClass (TTaxNameClass nameclass_id, string &class_name_out)
TTaxNameClass	GetNameClassId (const string &class_name)
TTaxId	Join (TTaxId taxid1, TTaxId taxid2)
int	GetAllNames (TTaxId tax_id, TNameList &lNames, bool unique)
bool	GetAllNamesEx (TTaxId tax_id, list< CRef< CTaxon1_name > > &lNames)
bool	DumpNames (TTaxNameClass name_class, list< CRef< CTaxon1_name > > &out)
bool	IsAlive (void)
bool	GetTaxId4GI (TGi gi, TTaxId &tax_id_out)
bool	GetBlastName (TTaxId tax_id, string &blast_name_out)
const string &	GetLastError () const
bool	GetPopsetJoin (const TTaxIdList &ids_in, TTaxIdList &ids_out)
bool	LoadNode (TTaxId tax_id, const ITaxon1Node **ppNode=NULL)
bool	LoadChildren (TTaxId tax_id, const ITaxon1Node **ppNode=NULL)
bool	LoadSubtree (TTaxId tax_id, const ITaxon1Node **ppNode=NULL)
CRef< ITreeIterator >	GetTreeIterator (EIteratorMode mode=eIteratorMode_Default)
CRef< ITreeIterator >	GetTreeIterator (TTaxId tax_id, EIteratorMode mode=eIteratorMode_Default)
bool	GetNodeProperty (TTaxId tax_id, const string &prop_name, bool &prop_val)
bool	GetNodeProperty (TTaxId tax_id, const string &prop_name, int &prop_val)
bool	GetNodeProperty (TTaxId tax_id, const string &prop_name, string &prop_val)
bool	GetInheritedPropertyDefines (const string &prop_name, TInfoList &results_out, TTaxId subtree_root=TAX_ID_CONST(1))
bool	GetTypeMaterial (TTaxId tax_id, TNameList &type_material_list_out)
TTaxId	GetMaxTaxId (void)
bool	GetDisplayCommonName (TTaxId tax_id, string &disp_name_out)

Static Public Attributes
static const unsigned	def_reconnect_attempts = 5
static const unsigned	def_cache_capacity = 1000

Private Types
typedef map< TTaxGeneticCode, string >	TGCMap

Private Member Functions
void	Reset (void)
bool	SendRequest (CTaxon1_req &req, CTaxon1_resp &resp, bool bShouldReconnect=true)
void	SetLastError (const char *err_msg)
bool	LoadSubtreeEx (TTaxId tax_id, int type, const ITaxon1Node **ppNode)
TOrgRefStatus	x_ConvertOrgrefProps (CTaxon2_data &data)

Private Attributes
ESerialDataFormat	m_eDataFormat
const char *	m_pchService
STimeout *	m_timeout
STimeout	m_timeout_value
CConn_ServiceStream *	m_pServer
CObjectOStream *	m_pOut
CObjectIStream *	m_pIn
unsigned	m_nReconnectAttempts
COrgRefCache *	m_plCache
bool	m_bWithSynonyms
string	m_sLastError
TGCMap	m_gcStorage

Friends
class	COrgRefCache

Detailed Description

Definition at line 67 of file taxon1.hpp.

Member Typedef Documentation

TGCMap

typedef map<TTaxGeneticCode, string> CTaxon1::TGCMap

private

Definition at line 610 of file taxon1.hpp.

TInfoList

typedef list< CRef< CTaxon1_info > > CTaxon1::TInfoList

Definition at line 71 of file taxon1.hpp.

TNameList

typedef list< string > CTaxon1::TNameList

Definition at line 69 of file taxon1.hpp.

TOrgRefStatus

typedef unsigned CTaxon1::TOrgRefStatus

Definition at line 113 of file taxon1.hpp.

TTaxIdList

typedef vector< TTaxId > CTaxon1::TTaxIdList

Definition at line 70 of file taxon1.hpp.

Member Enumeration Documentation

EIteratorMode

enum CTaxon1::EIteratorMode

Enumerator
eIteratorMode_FullTree
eIteratorMode_LeavesBranches
eIteratorMode_Best
eIteratorMode_Blast
eIteratorMode_Default

Definition at line 510 of file taxon1.hpp.

EOrgRefStatus

enum CTaxon1::EOrgRefStatus

Enumerator
eStatus_Ok
eStatus_WrongTaxId
eStatus_NoOrgname
eStatus_WrongTaxname
eStatus_WrongOrgrefMod
eStatus_WrongCommonName
eStatus_WrongOrgname
eStatus_WrongOrgmod
eStatus_WrongLineage
eStatus_WrongDivision
eStatus_WrongGC
eStatus_WrongMGC
eStatus_WrongPGC
eStatus_WrongOrgnameAttr
eStatus_WrongONASpecified
eStatus_WrongONANoModFwd
eStatus_WrongONAUncultured
eStatus_WrongNomenclature
eStatus_WrongModOldname
eStatus_WrongModTypeMaterial

Definition at line 152 of file taxon1.hpp.

ESearch

enum CTaxon1::ESearch

Enumerator
eSearch_Exact
eSearch_TokenSet
eSearch_WildCard
eSearch_Phonetic

Definition at line 181 of file taxon1.hpp.

ESpeciesMode

enum CTaxon1::ESpeciesMode

Enumerator
eSpeciesMode_RankOnly
eSpeciesMode_Flag

Definition at line 270 of file taxon1.hpp.

Constructor & Destructor Documentation

CTaxon1()

CTaxon1::CTaxon1

(

)

Definition at line 60 of file taxon1.cpp.

~CTaxon1()

CTaxon1::~CTaxon1

(

)

Definition at line 71 of file taxon1.cpp.

References Fini().

Member Function Documentation

CheckOrgRef()

bool CTaxon1::CheckOrgRef	(	const COrg_ref &	orgRef,
		TOrgRefStatus &	stat_out,
		string *	psLog = 0
	)

Definition at line 2145 of file taxon1.cpp.

References eStatus_Ok, CTaxon1_resp_Base::GetLookup(), CTaxon1_data_Base::GetOrg(), CTaxon2_data::GetProperty(), Init(), CTaxon1_resp_Base::IsLookup(), NULL, SendRequest(), SetLastError(), CTaxon1_req_Base::SetLookup(), CTaxon2_data_Base::SetOrg(), COrgrefProp::SetOrgrefProp(), TAXON1_IS_INITED, and x_ConvertOrgrefProps().

Referenced by BOOST_AUTO_TEST_CASE().

DumpNames()

bool CTaxon1::DumpNames	(	TTaxNameClass	name_class,
		list< CRef< CTaxon1_name > > &	out
	)

Definition at line 1327 of file taxon1.cpp.

References Init(), CTaxon1_resp_Base::IsDumpnames4class(), NULL, SendRequest(), CTaxon1_req_Base::SetDumpnames4class(), CTaxon1_resp_Base::SetDumpnames4class(), SetLastError(), and TAXON1_IS_INITED.

FindTaxIdByName()

TTaxId CTaxon1::FindTaxIdByName

(

const string &

orgname

)

Definition at line 548 of file taxon1.cpp.

References CTaxon1_resp_Base::GetGetunique(), GetTaxIdByName(), Init(), INVALID_TAX_ID, CTaxon1_resp_Base::IsGetunique(), NULL, SendRequest(), CTaxon1_req_Base::SetGetunique(), SetLastError(), TAX_ID_CONST, TAXON1_IS_INITED, and ZERO_TAX_ID.

Referenced by BOOST_AUTO_TEST_CASE().

Fini()

void CTaxon1::Fini

(

void

)

Definition at line 203 of file taxon1.cpp.

References CTaxon1_resp_Base::IsFini(), NULL, Reset(), SendRequest(), CTaxon1_req_Base::SetFini(), SetLastError(), and TAXON1_IS_INITED.

Referenced by fta_replace_org(), NCBITEST_AUTO_FINI(), CTaxFormat::~CTaxFormat(), ~CTaxon1(), and TaxClient::~TaxClient().

GetAllNames()

int CTaxon1::GetAllNames	(	TTaxId	tax_id,
		TNameList &	lNames,
		bool	unique
	)

Definition at line 1248 of file taxon1.cpp.

References CTaxon1_resp_Base::GetGetorgnames(), i, Init(), CTaxon1_resp_Base::IsGetorgnames(), NULL, SendRequest(), CTaxon1_req_Base::SetGetorgnames(), SetLastError(), TAX_ID_TO, and TAXON1_IS_INITED.

Referenced by BOOST_AUTO_TEST_CASE().

GetAllNamesEx()

bool CTaxon1::GetAllNamesEx	(	TTaxId	tax_id,
		list< CRef< CTaxon1_name > > &	lNames
	)

Definition at line 1293 of file taxon1.cpp.

References CTaxon1_resp_Base::GetGetorgnames(), i, Init(), CTaxon1_resp_Base::IsGetorgnames(), NULL, SendRequest(), CTaxon1_req_Base::SetGetorgnames(), SetLastError(), TAX_ID_TO, and TAXON1_IS_INITED.

Referenced by GetDisplayCommonName(), and GetTypeMaterial().

GetAllTaxIdByName()

int CTaxon1::GetAllTaxIdByName	(	const string &	orgname,
		TTaxIdList &	lIds
	)

Definition at line 659 of file taxon1.cpp.

References CTaxon1_resp_Base::GetFindname(), i, Init(), CTaxon1_resp_Base::IsFindname(), NULL, SendRequest(), CTaxon1_req_Base::SetFindname(), SetLastError(), and TAXON1_IS_INITED.

Referenced by BOOST_AUTO_TEST_CASE().

GetAncestorByRank() [1/2]

TTaxId CTaxon1::GetAncestorByRank	(	TTaxId	id_tax,
		const char *	rank_name
	)

Definition at line 942 of file taxon1.cpp.

References ERR_POST_X, COrgRefCache::FindRankByName(), GetLastError(), Init(), m_plCache, NULL, SetLastError(), TAX_ID_CONST, and TAXON1_IS_INITED.

Referenced by CScore_Taxid::Get(), CLocalTaxon::GetGenus(), CLocalTaxon::GetOrder(), and CLocalTaxon::GetSpecies().

GetAncestorByRank() [2/2]

TTaxId CTaxon1::GetAncestorByRank	(	TTaxId	id_tax,
		TTaxRank	rank_id
	)

Definition at line 962 of file taxon1.cpp.

References CTaxon1Node::GetParent(), CTaxon1Node::GetRank(), CTaxon1Node::GetTaxId(), Init(), INVALID_TAX_ID, CTaxon1Node::IsRoot(), COrgRefCache::LookupAndAdd(), m_plCache, NULL, SetLastError(), TAX_ID_CONST, TAXON1_IS_INITED, and ZERO_TAX_ID.

GetBlastName()

bool CTaxon1::GetBlastName	(	TTaxId	tax_id,
		string &	blast_name_out
	)

Definition at line 1405 of file taxon1.cpp.

References CTaxon1Node::GetBlastName(), CTaxon1Node::GetParent(), Init(), CTaxon1Node::IsRoot(), COrgRefCache::LookupAndAdd(), m_plCache, NULL, SetLastError(), and TAXON1_IS_INITED.

Referenced by BOOST_AUTO_TEST_CASE(), GetDisplayCommonName(), CTaxFormat::x_InitBlastNameTaxInfo(), and CPhyTreeFormatter::x_InitTreeFeatures().

GetById()

CRef< CTaxon2_data > CTaxon1::GetById

(

TTaxId

tax_id

)

Definition at line 230 of file taxon1.cpp.

References Init(), COrgRefCache::LookupAndInsert(), m_plCache, NULL, s_achInvalTaxid, SetLastError(), TAXON1_IS_INITED, and ZERO_TAX_ID.

Referenced by BOOST_AUTO_TEST_CASE(), fta_get_orgref_byid(), TaxClient::GetTaxNameForTaxID(), and CAgpconvertApplication::x_HandleTaxArgs().

GetChildren()

int CTaxon1::GetChildren	(	TTaxId	id_tax,
		TTaxIdList &	children_ids
	)

Definition at line 992 of file taxon1.cpp.

References CTreeIterator::AddChild(), CTreeCont::GetIterator(), CTaxon1Node::GetTaxId(), COrgRefCache::GetTree(), CTreeIterator::GoNode(), i, Init(), CTaxon1_resp_Base::IsTaxachildren(), COrgRefCache::LookupAndAdd(), m_plCache, NULL, SendRequest(), COrgRefCache::SetIndexEntry(), SetLastError(), CTaxon1_req_Base::SetTaxachildren(), CTaxon1_resp_Base::SetTaxachildren(), TAX_ID_TO, and TAXON1_IS_INITED.

Referenced by BOOST_AUTO_TEST_CASE().

GetDisplayCommonName()

bool CTaxon1::GetDisplayCommonName	(	TTaxId	tax_id,
		string &	disp_name_out
	)

Definition at line 2296 of file taxon1.cpp.

References GetAllNamesEx(), GetBlastName(), COrgRefCache::GetCommonNameClass(), COrgRefCache::GetPreferredCommonNameClass(), GetSpecies(), CTaxon1Node::GetTaxId(), Init(), COrgRefCache::InitNameClasses(), ITERATE, COrgRefCache::LookupAndAdd(), m_plCache, NULL, SetLastError(), TAXON1_IS_INITED, and ZERO_TAX_ID.

Referenced by TaxClient::GetDisplayCommonName().

GetDivisionIdByName()

TTaxDivision CTaxon1::GetDivisionIdByName

(

const string &

div_name

)

Definition at line 1154 of file taxon1.cpp.

References COrgRefCache::FindDivisionByCode(), COrgRefCache::FindDivisionByName(), Init(), m_plCache, NULL, SetLastError(), and TAXON1_IS_INITED.

Referenced by BOOST_AUTO_TEST_CASE().

GetDivisionName()

bool CTaxon1::GetDivisionName	(	TTaxDivision	div_id,
		string &	div_name_out,
		string *	div_code_out = NULL
	)

Definition at line 1126 of file taxon1.cpp.

References COrgRefCache::GetDivisionCode(), COrgRefCache::GetDivisionName(), Init(), m_plCache, NULL, SetLastError(), and TAXON1_IS_INITED.

Referenced by BOOST_AUTO_TEST_CASE().

GetGCName()

bool CTaxon1::GetGCName	(	TTaxGeneticCode	gc_id,
		string &	gc_name_out
	)

Definition at line 1036 of file taxon1.cpp.

References map_checker< Container >::empty(), map_checker< Container >::end(), map_checker< Container >::find(), CTaxon1_resp_Base::GetGetgcs(), i, Init(), map_checker< Container >::insert(), CTaxon1_resp_Base::IsGetgcs(), m_gcStorage, NULL, SendRequest(), CTaxon1_req_Base::SetGetgcs(), SetLastError(), and TAXON1_IS_INITED.

Referenced by BOOST_AUTO_TEST_CASE().

GetGenus()

TTaxId CTaxon1::GetGenus

(

TTaxId

id_tax

)

Definition at line 843 of file taxon1.cpp.

References COrgRefCache::GetGenusRank(), CTaxon1Node::GetParent(), CTaxon1Node::GetRank(), CTaxon1Node::GetTaxId(), Init(), COrgRefCache::InitRanks(), INVALID_TAX_ID, CTaxon1Node::IsRoot(), COrgRefCache::LookupAndAdd(), m_plCache, NULL, SetLastError(), TAXON1_IS_INITED, and ZERO_TAX_ID.

Referenced by BOOST_AUTO_TEST_CASE().

GetInheritedPropertyDefines()

bool CTaxon1::GetInheritedPropertyDefines	(	const string &	prop_name,
		CTaxon1::TInfoList &	results,
		TTaxId	subtree_root = TAX_ID_CONST(1)
	)

Definition at line 1927 of file taxon1.cpp.

References CTaxon1_error_Base::eLevel_none, ERR_POST_X, CTaxon1_resp_Base::GetError(), CTaxon1_error::GetErrorText(), CTaxon1_resp_Base::GetGetorgprop(), GetLastError(), CTaxon1_error_Base::GetLevel(), Init(), CTaxon1_resp_Base::IsError(), CTaxon1_resp_Base::IsGetorgprop(), NULL, SendRequest(), CTaxon1_req_Base::SetGetorgprop(), CTaxon1_resp_Base::SetGetorgprop(), SetLastError(), TAX_ID_TO, and TAXON1_IS_INITED.

Referenced by s_InitializeViralMap().

GetLastError()

const string& CTaxon1::GetLastError ( void  ) const

inline

Definition at line 471 of file taxon1.hpp.

References m_sLastError.

Referenced by GetAncestorByRank(), GetInheritedPropertyDefines(), GetNodeProperty(), GetTaxId4GI(), GetTypeMaterial(), SearchTaxIdByName(), CTaxTreeToolJob::x_CreateProjectItems(), CTreeBuilderJob::x_CreateProjectItems(), CTaxFormat::x_InitTaxClient(), and CTaxFormat::x_LoadTaxTree().

GetMaxTaxId()

TTaxId CTaxon1::GetMaxTaxId

(

void

)

Definition at line 2273 of file taxon1.cpp.

References Init(), INVALID_TAX_ID, COrgRefCache::m_nMaxTaxId, m_plCache, NULL, SetLastError(), TAX_ID_FROM, and TAXON1_IS_INITED.

Referenced by BOOST_AUTO_TEST_CASE().

GetNameClass()

bool CTaxon1::GetNameClass	(	TTaxNameClass	nameclass_id,
		string &	class_name_out
	)

Definition at line 1176 of file taxon1.cpp.

References COrgRefCache::GetNameClassName(), Init(), m_plCache, NULL, SetLastError(), and TAXON1_IS_INITED.

GetNameClassId()

TTaxNameClass CTaxon1::GetNameClassId

(

const string &

class_name

)

Definition at line 1199 of file taxon1.cpp.

References COrgRefCache::FindNameClassByName(), Init(), COrgRefCache::InitNameClasses(), m_plCache, NULL, SetLastError(), and TAXON1_IS_INITED.

Referenced by GetTypeMaterial(), and CTaxFormat::x_InitBlastNameTaxInfo().

GetNodeProperty() [1/3]

bool CTaxon1::GetNodeProperty	(	TTaxId	tax_id,
		const string &	prop_name,
		bool &	prop_val
	)

Definition at line 1821 of file taxon1.cpp.

References CTaxon1_error_Base::eLevel_none, ERR_POST_X, CTaxon1_resp_Base::GetError(), CTaxon1_error::GetErrorText(), CTaxon1_resp_Base::GetGetorgprop(), GetLastError(), CTaxon1_error_Base::GetLevel(), Init(), CTaxon1_resp_Base::IsError(), CTaxon1_resp_Base::IsGetorgprop(), NULL, SendRequest(), CTaxon1_req_Base::SetGetorgprop(), SetLastError(), TAX_ID_TO, and TAXON1_IS_INITED.

Referenced by GetOrgRef().

GetNodeProperty() [2/3]

bool CTaxon1::GetNodeProperty	(	TTaxId	tax_id,
		const string &	prop_name,
		int &	prop_val
	)

Definition at line 1874 of file taxon1.cpp.

References CTaxon1_error_Base::eLevel_none, ERR_POST_X, CTaxon1_resp_Base::GetError(), CTaxon1_error::GetErrorText(), CTaxon1_resp_Base::GetGetorgprop(), GetLastError(), CTaxon1_error_Base::GetLevel(), Init(), CTaxon1_resp_Base::IsError(), CTaxon1_resp_Base::IsGetorgprop(), NULL, SendRequest(), CTaxon1_req_Base::SetGetorgprop(), SetLastError(), TAX_ID_TO, and TAXON1_IS_INITED.

GetNodeProperty() [3/3]

bool CTaxon1::GetNodeProperty	(	TTaxId	tax_id,
		const string &	prop_name,
		string &	prop_val
	)

Definition at line 1768 of file taxon1.cpp.

References CTaxon1_error_Base::eLevel_none, ERR_POST_X, CTaxon1_resp_Base::GetError(), CTaxon1_error::GetErrorText(), CTaxon1_resp_Base::GetGetorgprop(), GetLastError(), CTaxon1_error_Base::GetLevel(), Init(), CTaxon1_resp_Base::IsError(), CTaxon1_resp_Base::IsGetorgprop(), NULL, SendRequest(), CTaxon1_req_Base::SetGetorgprop(), SetLastError(), TAX_ID_TO, and TAXON1_IS_INITED.

GetOrgRef()

CConstRef< COrg_ref > CTaxon1::GetOrgRef	(	TTaxId	tax_id,
		bool &	is_species,
		bool &	is_uncultured,
		string &	blast_name,
		bool *	is_specified = NULL
	)

Definition at line 704 of file taxon1.cpp.

References CTaxon2_data_Base::GetBlast_name(), CTaxon2_data_Base::GetIs_species_level(), CTaxon2_data_Base::GetIs_uncultured(), GetNodeProperty(), CTaxon2_data_Base::GetOrg(), Init(), CTaxon2_data_Base::IsSetBlast_name(), COrgRefCache::LookupAndInsert(), m_plCache, NULL, SetLastError(), TAXON1_IS_INITED, and ZERO_TAX_ID.

Referenced by BOOST_AUTO_TEST_CASE(), GetCommonTax(), TaxClient::GetOrgRef(), GetTypeMaterial(), CTaxonCache::Initialize(), IsLikelyTaxname(), CTreeBuilderJob::x_CreateProjectItems(), CAltValidator::x_GetTaxonSpecies(), and CTaxonCache::x_QueryTaxonService().

GetParent()

TTaxId CTaxon1::GetParent

(

TTaxId

id_tax

)

Definition at line 761 of file taxon1.cpp.

References CTaxon1Node::GetParent(), CTaxon1Node::GetTaxId(), Init(), COrgRefCache::LookupAndAdd(), m_plCache, NULL, SetLastError(), TAXON1_IS_INITED, and ZERO_TAX_ID.

Referenced by BOOST_AUTO_TEST_CASE(), TaxClient::GetParentTaxID(), and CAltValidator::x_GetTaxonSpecies().

GetPopsetJoin()

bool CTaxon1::GetPopsetJoin	(	const TTaxIdList &	ids_in,
		TTaxIdList &	ids_out
	)

Definition at line 1546 of file taxon1.cpp.

References CTreeIterator::AddChild(), map_checker< Container >::end(), map_checker< Container >::find(), CTreeCont::GetIterator(), CTreeIterator::GetNode(), CTaxon1Node::GetParent(), CTreeCont::GetRoot(), CTaxon1Node::GetTaxId(), COrgRefCache::GetTree(), CTreeIterator::GoChild(), CTreeIterator::GoNode(), CTreeIterator::GoParent(), CTreeIterator::GoRoot(), CTreeIterator::GoSibling(), i, Init(), map_checker< Container >::insert(), COrgRefCache::LookupAndAdd(), m_plCache, NULL, s_StoreResidueTaxid(), SetLastError(), CTreeCont::SetRoot(), and TAXON1_IS_INITED.

Referenced by TaxClient::GetFullLineage(), CTaxTreeToolJob::x_CreateProjectItems(), and CTaxFormat::x_LoadTaxTree().

GetRankIdByName()

TTaxRank CTaxon1::GetRankIdByName

(

const string &

rank_name

)

Definition at line 1105 of file taxon1.cpp.

References COrgRefCache::FindRankByName(), Init(), m_plCache, NULL, SetLastError(), and TAXON1_IS_INITED.

Referenced by BOOST_AUTO_TEST_CASE().

GetRankName()

bool CTaxon1::GetRankName	(	TTaxRank	rank_id,
		string &	rank_name_out
	)

Definition at line 1081 of file taxon1.cpp.

References COrgRefCache::GetRankName(), Init(), m_plCache, NULL, SetLastError(), and TAXON1_IS_INITED.

Referenced by TaxClient::GetRankID().

GetScientificName()

bool CTaxon1::GetScientificName	(	TTaxId	tax_id,
		string &	name_out
	)

Definition at line 2390 of file taxon1.cpp.

References CTaxon1Node::GetName(), Init(), COrgRefCache::LookupAndAdd(), m_plCache, NULL, SetLastError(), and TAXON1_IS_INITED.

Referenced by BOOST_AUTO_TEST_CASE(), and s_InitializeViralMap().

GetSpecies()

TTaxId CTaxon1::GetSpecies	(	TTaxId	id_tax,
		ESpeciesMode	mode = eSpeciesMode_Flag
	)

Definition at line 789 of file taxon1.cpp.

References eSpeciesMode_RankOnly, CTaxon2_data_Base::GetIs_species_level(), CTaxon1Node::GetParent(), CTaxon1Node::GetRank(), COrgRefCache::GetSpeciesRank(), CTaxon1Node::GetTaxId(), Init(), COrgRefCache::InitRanks(), INVALID_TAX_ID, CTaxon1Node::IsRoot(), CTaxon2_data_Base::IsSetIs_species_level(), COrgRefCache::LookupAndAdd(), COrgRefCache::LookupAndInsert(), m_plCache, NULL, SetLastError(), TAXON1_IS_INITED, and ZERO_TAX_ID.

Referenced by GetDisplayCommonName().

GetSuperkingdom()

TTaxId CTaxon1::GetSuperkingdom

(

TTaxId

id_tax

)

Definition at line 875 of file taxon1.cpp.

References CTaxon1Node::GetParent(), CTaxon1Node::GetRank(), COrgRefCache::GetSuperkingdomRank(), CTaxon1Node::GetTaxId(), Init(), COrgRefCache::InitRanks(), INVALID_TAX_ID, CTaxon1Node::IsRoot(), COrgRefCache::LookupAndAdd(), m_plCache, NULL, SetLastError(), TAXON1_IS_INITED, and ZERO_TAX_ID.

Referenced by TaxClient::GetSuperKingdom().

GetTaxId4GI()

bool CTaxon1::GetTaxId4GI	(	TGi	gi,
		TTaxId &	tax_id_out
	)

Definition at line 1371 of file taxon1.cpp.

References CTaxon1_error_Base::eLevel_error, NStr::EqualNocase(), CTaxon1_resp_Base::GetError(), CTaxon1_resp_Base::GetId4gi(), GetLastError(), CTaxon1_error_Base::GetLevel(), CTaxon1_error_Base::GetMsg(), Init(), CTaxon1_resp_Base::IsError(), CTaxon1_resp_Base::IsId4gi(), CTaxon1_error_Base::IsSetLevel(), CTaxon1_error_Base::IsSetMsg(), NULL, SendRequest(), CTaxon1_req_Base::SetId4gi(), SetLastError(), TAXON1_IS_INITED, and ZERO_TAX_ID.

Referenced by BOOST_AUTO_TEST_CASE(), GetCommonTax(), TaxClient::GetTaxIDForGI(), CGi2TaxIdApp::Run(), CTaxTreeToolJob::x_CreateProjectItems(), CTreeBuilderJob::x_CreateProjectItems(), and CSFTranslationJob::x_InitGeneticCode().

GetTaxIdByName()

TTaxId CTaxon1::GetTaxIdByName

(

const string &

orgname

)

Definition at line 523 of file taxon1.cpp.

References eSearch_Exact, INVALID_TAX_ID, NULL, SearchTaxIdByName(), SetLastError(), TAX_ID_TO, and ZERO_TAX_ID.

Referenced by BOOST_AUTO_TEST_CASE(), FindTaxIdByName(), and IsLikelyTaxname().

GetTaxIdByOrgRef()

TTaxId CTaxon1::GetTaxIdByOrgRef

(

const COrg_ref &

inp_orgRef

)

Definition at line 489 of file taxon1.cpp.

References CTaxon1_resp_Base::GetGetidbyorg(), Init(), INVALID_TAX_ID, CTaxon1_resp_Base::IsGetidbyorg(), NULL, SendRequest(), CTaxon1_req_Base::SetGetidbyorg(), SetLastError(), TAX_ID_FROM, TAXON1_IS_INITED, and ZERO_TAX_ID.

Referenced by BOOST_AUTO_TEST_CASE(), fta_replace_org(), and TaxClient::GetTaxIDFromBioseq().

GetTreeIterator() [1/2]

CRef< ITreeIterator > CTaxon1::GetTreeIterator

(

CTaxon1::EIteratorMode

mode = eIteratorMode_Default

)

Definition at line 1715 of file taxon1.cpp.

References eIteratorMode_Best, eIteratorMode_Blast, eIteratorMode_FullTree, eIteratorMode_LeavesBranches, CTreeCont::GetConstIterator(), COrgRefCache::GetTree(), Init(), m_plCache, NULL, CRef< C, Locker >::Reset(), SetLastError(), and TAXON1_IS_INITED.

Referenced by TaxClient::GetRankID(), GetTreeIterator(), Join(), CTaxTreeToolJob::x_CreateProjectItems(), and CTaxFormat::x_LoadTaxTree().

GetTreeIterator() [2/2]

CRef< ITreeIterator > CTaxon1::GetTreeIterator	(	TTaxId	tax_id,
		CTaxon1::EIteratorMode	mode = eIteratorMode_Default
	)

Definition at line 1746 of file taxon1.cpp.

References GetTreeIterator(), ITreeIterator::GoNode(), Init(), COrgRefCache::LookupAndAdd(), m_plCache, NULL, CRef< C, Locker >::Reset(), SetLastError(), and TAXON1_IS_INITED.

GetTypeMaterial()

bool CTaxon1::GetTypeMaterial	(	TTaxId	tax_id,
		TNameList &	type_material_list_out
	)

Definition at line 2196 of file taxon1.cpp.

References a, b, NStr::EqualNocase(), ERR_POST_X, GetAllNamesEx(), COrgName_Base::C_Name::GetBinomial(), GetLastError(), GetNameClassId(), GetOrgRef(), CTaxon1Node::GetParent(), CTaxon1Node::GetRank(), CBinomialOrgName_Base::GetSpecies(), COrgRefCache::GetSpeciesRank(), CBinomialOrgName_Base::GetSubspecies(), COrgRefCache::GetSubspeciesRank(), CTaxon1Node::GetTaxId(), i, Init(), COrgRefCache::InitRanks(), COrgName_Base::C_Name::IsBinomial(), CTaxon1Node::IsRoot(), CBinomialOrgName_Base::IsSetSpecies(), CBinomialOrgName_Base::IsSetSubspecies(), ITERATE, COrgRefCache::LookupAndAdd(), m_plCache, NULL, SetLastError(), and TAXON1_IS_INITED.

Init() [1/3]

bool CTaxon1::Init	(	const STimeout *	timeout,
		unsigned	reconnect_attempts = def_reconnect_attempts,
		unsigned	cache_capacity = def_cache_capacity
	)

Definition at line 113 of file taxon1.cpp.

References ConnNetInfo_Create(), ConnNetInfo_Destroy(), ConnNetInfo_SetTimeout(), COrgRefCache, eFNP_Allow, eSerial_AsnBinary, eSerial_AsnText, fSERV_Any, COrgRefCache::Init(), CTaxon1_resp_Base::IsInit(), m_eDataFormat, m_nReconnectAttempts, m_pchService, m_pIn, m_plCache, m_pOut, m_pServer, m_timeout, m_timeout_value, SConnNetInfo::max_try, NULL, CObjectIStream::Open(), CObjectOStream::Open(), SendRequest(), CTaxon1_req_Base::SetInit(), SetLastError(), TAXON1_IS_INITED, and tmp.

Init() [2/3]

bool CTaxon1::Init

(

unsigned

cache_capacity

)

Definition at line 107 of file taxon1.cpp.

References def_reconnect_attempts, def_timeout, and Init().

Init() [3/3]

bool CTaxon1::Init

(

void

)

Definition at line 101 of file taxon1.cpp.

References def_cache_capacity, def_reconnect_attempts, and def_timeout.

Referenced by BOOST_AUTO_TEST_CASE(), CheckOrgRef(), TaxClient::ConnectToTaxServer(), DumpNames(), FindTaxIdByName(), fta_get_orgref_byid(), fta_init_tax_server(), fta_replace_org(), CScore_Taxid::Get(), GetAllNames(), GetAllNamesEx(), GetAllTaxIdByName(), GetAncestorByRank(), GetBlastName(), GetById(), GetChildren(), GetCommonTax(), GetDisplayCommonName(), GetDivisionIdByName(), GetDivisionName(), GetGCName(), GetGenus(), GetInheritedPropertyDefines(), GetMaxTaxId(), GetNameClass(), GetNameClassId(), GetNodeProperty(), GetOrgRef(), GetParent(), GetPopsetJoin(), GetRankIdByName(), GetRankName(), GetScientificName(), GetSpecies(), GetSuperkingdom(), GetTaxId4GI(), GetTaxIdByOrgRef(), GetTreeIterator(), GetTypeMaterial(), Init(), CTaxonCache::Initialize(), IsLikelyTaxname(), Join(), LoadSubtreeEx(), Lookup(), LookupMerge(), CGi2TaxIdApp::Run(), SearchTaxIdByName(), CTaxTreeToolJob::x_CreateProjectItems(), CTreeBuilderJob::x_CreateProjectItems(), COrfSearchJob::x_DoSearch(), CAltValidator::x_GetTaxonSpecies(), CAgpconvertApplication::x_HandleTaxArgs(), CSFTranslationJob::x_InitGeneticCode(), CTaxFormat::x_InitTaxClient(), and CPhyTreeFormatter::x_InitTreeFeatures().

IsAlive()

bool CTaxon1::IsAlive

(

void

)

Definition at line 1354 of file taxon1.cpp.

References CObjectIStream::InGoodState(), CObjectOStream::InGoodState(), m_pIn, m_pOut, NULL, SetLastError(), and TAXON1_IS_INITED.

Referenced by TaxClient::ConnectToTaxServer(), TaxClient::IsAlive(), CTaxTreeToolJob::x_CreateProjectItems(), CTreeBuilderJob::x_CreateProjectItems(), CTaxFormat::x_InitBlastNameTaxInfo(), CTaxFormat::x_InitTaxClient(), and CTaxFormat::x_LoadTaxTree().

Join()

TTaxId CTaxon1::Join	(	TTaxId	taxid1,
		TTaxId	taxid2
	)

Definition at line 1220 of file taxon1.cpp.

References ITreeIterator::GetNode(), ITaxon1Node::GetTaxId(), GetTreeIterator(), ITreeIterator::GoAncestor(), ITreeIterator::GoNode(), Init(), INVALID_TAX_ID, COrgRefCache::LookupAndAdd(), m_plCache, NULL, SetLastError(), TAXON1_IS_INITED, and ZERO_TAX_ID.

Referenced by BOOST_AUTO_TEST_CASE(), GetCommonTax(), TaxClient::IsTaxDescendant(), and TaxClient::Join().

LoadChildren()

bool CTaxon1::LoadChildren ( TTaxId  tax_id, const ITaxon1Node **  ppNode = NULL  )

inline

Definition at line 498 of file taxon1.hpp.

References LoadSubtreeEx().

LoadNode()

bool CTaxon1::LoadNode ( TTaxId  tax_id, const ITaxon1Node **  ppNode = NULL  )

inline

Definition at line 488 of file taxon1.hpp.

References LoadSubtreeEx().

Referenced by CTaxTreeToolJob::x_CreateProjectItems(), COrfSearchJob::x_DoSearch(), CSFTranslationJob::x_InitGeneticCode(), and CTaxFormat::x_LoadTaxTree().

LoadSubtree()

bool CTaxon1::LoadSubtree ( TTaxId  tax_id, const ITaxon1Node **  ppNode = NULL  )

inline

Definition at line 507 of file taxon1.hpp.

References LoadSubtreeEx().

LoadSubtreeEx()

bool CTaxon1::LoadSubtreeEx ( TTaxId  tax_id, int  type, const ITaxon1Node **  ppNode  )

private

Definition at line 1639 of file taxon1.cpp.

References CTreeIterator::AddChild(), CTreeCont::GetIterator(), CTaxon1Node::GetTaxId(), COrgRefCache::GetTree(), CTreeIterator::GoNode(), i, Init(), CTaxon1Node::IsSubtreeLoaded(), CTaxon1_resp_Base::IsTaxachildren(), COrgRefCache::Lookup(), COrgRefCache::LookupAndAdd(), m_plCache, NULL, NStr::NumericToString(), SendRequest(), COrgRefCache::SetIndexEntry(), SetLastError(), CTaxon1Node::SetSubtreeLoaded(), CTaxon1_req_Base::SetTaxachildren(), CTaxon1_resp_Base::SetTaxachildren(), TAX_ID_TO, and TAXON1_IS_INITED.

Referenced by LoadChildren(), LoadNode(), and LoadSubtree().

Lookup()

CRef< CTaxon2_data > CTaxon1::Lookup	(	const COrg_ref &	inp_orgRef,
		string *	psLog = 0
	)

Definition at line 384 of file taxon1.cpp.

References CTaxon1_resp_Base::GetLookup(), CTaxon1_data_Base::GetOrg(), CTaxon2_data::GetProperty(), Init(), CTaxon1_resp_Base::IsLookup(), m_bWithSynonyms, NULL, CRef< C, Locker >::Reset(), SendRequest(), SetLastError(), CTaxon1_req_Base::SetLookup(), CTaxon2_data_Base::SetOrg(), COrgrefProp::SetOrgrefProp(), TAXON1_IS_INITED, and x_ConvertOrgrefProps().

Referenced by BOOST_AUTO_TEST_CASE(), and fta_replace_org().

LookupMerge()

CConstRef< CTaxon2_data > CTaxon1::LookupMerge	(	COrg_ref &	inp_orgRef,
		string *	psLog = 0,
		TOrgRefStatus *	pStatusOut = 0
	)

Definition at line 429 of file taxon1.cpp.

References CTaxon1_resp_Base::GetLookup(), CTaxon1_data_Base::GetOrg(), CTaxon2_data_Base::GetOrg(), CTaxon2_data::GetProperty(), Init(), CTaxon1_resp_Base::IsLookup(), m_bWithSynonyms, NULL, CRef< C, Locker >::Reset(), SendRequest(), SetLastError(), CTaxon1_req_Base::SetLookup(), CTaxon2_data_Base::SetOrg(), COrgrefProp::SetOrgrefProp(), TAXON1_IS_INITED, and x_ConvertOrgrefProps().

Referenced by BOOST_AUTO_TEST_CASE(), fta_replace_org(), and CAgpconvertApplication::x_HandleTaxArgs().

Reset()

void CTaxon1::Reset ( void  )

private

Definition at line 78 of file taxon1.cpp.

References m_pIn, m_plCache, m_pOut, m_pServer, NULL, and SetLastError().

Referenced by Fini().

SearchTaxIdByName()

TTaxId CTaxon1::SearchTaxIdByName	(	const string &	orgname,
		ESearch	mode = eSearch_TokenSet,
		list< CRef< CTaxon1_name > > *	name_list_out = NULL
	)

Definition at line 595 of file taxon1.cpp.

References eSearch_Exact, eSearch_Phonetic, eSearch_TokenSet, eSearch_WildCard, GetLastError(), CTaxon1_resp_Base::GetSearchname(), Init(), INVALID_TAX_ID, CTaxon1_resp_Base::IsSearchname(), NULL, SendRequest(), SetLastError(), CTaxon1_req_Base::SetSearchname(), CTaxon1_resp_Base::SetSearchname(), TAX_ID_CONST, TAXON1_IS_INITED, and ZERO_TAX_ID.

Referenced by GetTaxIdByName(), and CTaxFormat::x_InitBlastNameTaxInfo().

SendRequest()

bool CTaxon1::SendRequest ( CTaxon1_req &  req, CTaxon1_resp &  resp, bool  bShouldReconnect = true  )

private

Definition at line 1429 of file taxon1.cpp.

References CObjectIStream::eFail, CObjectOStream::eFail, eFNP_Allow, CObjectIStream::eNotOpen, CObjectOStream::eNotOpen, CObjectIStream::eReadError, CObjectOStream::eWriteError, CObjectOStream::Flush(), fSERV_Any, CTaxon1_resp_Base::GetError(), CTaxon1_error::GetErrorText(), CObjectIStream::GetFailFlags(), CObjectOStream::GetFailFlags(), CObjectIStream::InGoodState(), m_eDataFormat, m_nReconnectAttempts, m_pchService, m_pIn, m_pOut, m_pServer, m_timeout, NULL, CObjectIStream::Open(), CObjectOStream::Open(), and SetLastError().

Referenced by CheckOrgRef(), DumpNames(), FindTaxIdByName(), Fini(), GetAllNames(), GetAllNamesEx(), GetAllTaxIdByName(), GetChildren(), GetGCName(), GetInheritedPropertyDefines(), GetNodeProperty(), GetTaxId4GI(), GetTaxIdByOrgRef(), Init(), COrgRefCache::Init(), COrgRefCache::InitDomain(), COrgRefCache::InitNameClasses(), COrgRefCache::Insert2(), LoadSubtreeEx(), Lookup(), COrgRefCache::LookupAndAdd(), LookupMerge(), and SearchTaxIdByName().

SetLastError()

void CTaxon1::SetLastError ( const char *  err_msg )

private

Definition at line 1516 of file taxon1.cpp.

References m_sLastError.

Referenced by CheckOrgRef(), DumpNames(), FindTaxIdByName(), Fini(), GetAllNames(), GetAllNamesEx(), GetAllTaxIdByName(), GetAncestorByRank(), GetBlastName(), GetById(), GetChildren(), GetDisplayCommonName(), GetDivisionIdByName(), GetDivisionName(), GetGCName(), GetGenus(), GetInheritedPropertyDefines(), GetMaxTaxId(), GetNameClass(), GetNameClassId(), GetNodeProperty(), GetOrgRef(), GetParent(), GetPopsetJoin(), GetRankIdByName(), GetRankName(), GetScientificName(), GetSpecies(), GetSuperkingdom(), GetTaxId4GI(), GetTaxIdByName(), GetTaxIdByOrgRef(), GetTreeIterator(), GetTypeMaterial(), Init(), COrgRefCache::Init(), COrgRefCache::InitDomain(), COrgRefCache::InitNameClasses(), COrgRefCache::InitRanks(), COrgRefCache::Insert2(), IsAlive(), Join(), LoadSubtreeEx(), Lookup(), COrgRefCache::LookupAndAdd(), LookupMerge(), Reset(), SearchTaxIdByName(), SendRequest(), and SetSynonyms().

SetSynonyms()

bool CTaxon1::SetSynonyms

(

bool

on_off

)

Definition at line 746 of file taxon1.cpp.

References m_bWithSynonyms, NULL, and SetLastError().

Referenced by fix_synonyms(), and TaxClient::SetSynonyms().

x_ConvertOrgrefProps()

CTaxon1::TOrgRefStatus CTaxon1::x_ConvertOrgrefProps ( CTaxon2_data &  data )

private

Definition at line 271 of file taxon1.cpp.

References data, CObject_id_Base::e_Id, CObject_id_Base::e_Str, NStr::EndsWith(), NStr::Equal(), NStr::EqualNocase(), eStatus_WrongCommonName, eStatus_WrongDivision, eStatus_WrongGC, eStatus_WrongLineage, eStatus_WrongMGC, eStatus_WrongOrgmod, eStatus_WrongOrgname, eStatus_WrongOrgnameAttr, eStatus_WrongOrgrefMod, eStatus_WrongPGC, eStatus_WrongTaxId, eStatus_WrongTaxname, NStr::fSplit_Tokenize, i, NON_CONST_ITERATE, result, s_GetBoolValue(), COrg_ref_Base::SetDb(), NStr::Split(), NStr::StartsWith(), and NStr::TruncateSpacesInPlace().

Referenced by CheckOrgRef(), COrgRefCache::Insert2(), Lookup(), and LookupMerge().

Friends And Related Function Documentation

COrgRefCache

friend class COrgRefCache

friend

Definition at line 591 of file taxon1.hpp.

Referenced by Init().

Member Data Documentation

def_cache_capacity

const unsigned CTaxon1::def_cache_capacity = 1000

static

Definition at line 84 of file taxon1.hpp.

Referenced by Init().

def_reconnect_attempts

const unsigned CTaxon1::def_reconnect_attempts = 5

static

Definition at line 83 of file taxon1.hpp.

Referenced by Init().

m_bWithSynonyms

bool CTaxon1::m_bWithSynonyms

private

Definition at line 607 of file taxon1.hpp.

Referenced by COrgRefCache::Insert2(), Lookup(), LookupMerge(), and SetSynonyms().

m_eDataFormat

ESerialDataFormat CTaxon1::m_eDataFormat

private

Definition at line 593 of file taxon1.hpp.

Referenced by Init(), and SendRequest().

m_gcStorage

TGCMap CTaxon1::m_gcStorage

private

Definition at line 611 of file taxon1.hpp.

Referenced by GetGCName().

m_nReconnectAttempts

unsigned CTaxon1::m_nReconnectAttempts

private

Definition at line 603 of file taxon1.hpp.

Referenced by Init(), and SendRequest().

m_pchService

const char* CTaxon1::m_pchService

private

Definition at line 594 of file taxon1.hpp.

Referenced by Init(), and SendRequest().

m_pIn

CObjectIStream* CTaxon1::m_pIn

private

Definition at line 601 of file taxon1.hpp.

Referenced by Init(), IsAlive(), Reset(), and SendRequest().

m_plCache

COrgRefCache* CTaxon1::m_plCache

private

Definition at line 605 of file taxon1.hpp.

Referenced by GetAncestorByRank(), GetBlastName(), GetById(), GetChildren(), GetDisplayCommonName(), GetDivisionIdByName(), GetDivisionName(), GetGenus(), GetMaxTaxId(), GetNameClass(), GetNameClassId(), GetOrgRef(), GetParent(), GetPopsetJoin(), GetRankIdByName(), GetRankName(), GetScientificName(), GetSpecies(), GetSuperkingdom(), GetTreeIterator(), GetTypeMaterial(), Init(), Join(), LoadSubtreeEx(), and Reset().

m_pOut

CObjectOStream* CTaxon1::m_pOut

private

Definition at line 600 of file taxon1.hpp.

Referenced by Init(), IsAlive(), Reset(), and SendRequest().

m_pServer

CConn_ServiceStream* CTaxon1::m_pServer

private

Definition at line 598 of file taxon1.hpp.

Referenced by Init(), Reset(), and SendRequest().

m_sLastError

string CTaxon1::m_sLastError

private

Definition at line 608 of file taxon1.hpp.

Referenced by GetLastError(), and SetLastError().

m_timeout

STimeout* CTaxon1::m_timeout

private

Definition at line 595 of file taxon1.hpp.

Referenced by Init(), and SendRequest().

m_timeout_value

STimeout CTaxon1::m_timeout_value

private

Definition at line 596 of file taxon1.hpp.

Referenced by Init().

---

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

• include/objects/taxon1/taxon1.hpp
• src/objects/taxon1/taxon1.cpp