TaxClient Class Reference

Search Toolkit Book for TaxClient

#include <algo/structure/cd_utils/cuTaxClient.hpp>

Collaboration diagram for TaxClient:

Public Member Functions
	TaxClient (bool refresh=REFRESH_DEFAULT)
virtual	~TaxClient ()
virtual bool	init ()
virtual bool	IsAlive ()
virtual TTaxId	GetTaxIDForSeqId (CConstRef< CSeq_id > sid)
virtual TTaxId	GetTaxIDForGI (TGi gi)
virtual bool	GetOrgRef (TTaxId taxId, COrg_ref &orgRef)
virtual bool	GetOrgRef (TTaxId taxId, CRef< COrg_ref > &orgRef)
virtual bool	SetSynonyms (bool on_off)
virtual short	GetRankID (TTaxId taxId, string &rankName)
virtual TTaxId	GetTaxIDFromBioseq (const CBioseq &bioseq, bool lookInBioseq)
virtual string	GetTaxNameForTaxID (TTaxId taxid)
virtual string	GetSuperKingdom (TTaxId taxid)
virtual bool	GetDisplayCommonName (TTaxId taxid, string &displayCommonName)
virtual TTaxId	GetParentTaxID (TTaxId taxid)
virtual bool	IsTaxDescendant (TTaxId tax1, TTaxId tax2)
virtual bool	GetFullLineage (TTaxId taxid, vector< TTaxId > &lineageFromRoot)
virtual bool	GetFullLineage (TTaxId taxid, vector< pair< TTaxId, string > > &lineageFromRoot, bool useCommonName=false)
virtual bool	ConnectToTaxServer ()
CConstRef< COrg_ref >	GetOrgRef (TTaxId tax_id, bool &is_species, bool &is_uncultured, string &blast_name)
TTaxId	Join (TTaxId taxid1, TTaxId taxid2)

Private Attributes
CTaxon1 *	m_taxonomyClient
CScope *	m_scope

Static Private Attributes
static const bool	REFRESH_DEFAULT = false

Detailed Description

Definition at line 50 of file cuTaxClient.hpp.

Constructor & Destructor Documentation

TaxClient()

TaxClient::TaxClient

(

bool

refresh = REFRESH_DEFAULT

)

Definition at line 62 of file cuTaxClient.cpp.

~TaxClient()

TaxClient::~TaxClient ( )

virtual

Definition at line 67 of file cuTaxClient.cpp.

References CTaxon1::Fini(), m_scope, and m_taxonomyClient.

Member Function Documentation

ConnectToTaxServer()

bool TaxClient::ConnectToTaxServer ( )

virtual

Definition at line 82 of file cuTaxClient.cpp.

References CTaxon1::Init(), CTaxon1::IsAlive(), and m_taxonomyClient.

Referenced by CTaxNRCriteria::ConnectToServer(), and init().

GetDisplayCommonName()

bool TaxClient::GetDisplayCommonName ( TTaxId  taxid, string &  displayCommonName  )

virtual

Definition at line 276 of file cuTaxClient.cpp.

References CTaxon1::GetDisplayCommonName(), IsAlive(), and m_taxonomyClient.

Referenced by GetFullLineage().

GetFullLineage() [1/2]

bool TaxClient::GetFullLineage ( TTaxId  taxid, vector< pair< TTaxId, string > > &  lineageFromRoot, bool  useCommonName = false  )

virtual

Definition at line 329 of file cuTaxClient.cpp.

References GetDisplayCommonName(), GetFullLineage(), GetTaxNameForTaxID(), ITERATE, kEmptyStr, and TAX_ID_CONST.

GetFullLineage() [2/2]

bool TaxClient::GetFullLineage ( TTaxId  taxid, vector< TTaxId > &  lineageFromRoot  )

virtual

Definition at line 314 of file cuTaxClient.cpp.

References CTaxon1::GetPopsetJoin(), IsAlive(), m_taxonomyClient, and TAX_ID_CONST.

Referenced by GetFullLineage().

GetOrgRef() [1/3]

CConstRef< COrg_ref > TaxClient::GetOrgRef	(	TTaxId	tax_id,
		bool &	is_species,
		bool &	is_uncultured,
		string &	blast_name
	)

Definition at line 295 of file cuTaxClient.cpp.

References CTaxon1::GetOrgRef(), IsAlive(), m_taxonomyClient, and null.

GetOrgRef() [2/3]

bool TaxClient::GetOrgRef ( TTaxId  taxId, COrg_ref &  orgRef  )

virtual

Definition at line 145 of file cuTaxClient.cpp.

References CSerialObject::Assign(), CTaxon1::GetOrgRef(), IsAlive(), m_taxonomyClient, COrg_ref_Base::Reset(), result, and ZERO_TAX_ID.

Referenced by GetOrgRef(), and CPriorityTaxNodes::TaxIdsToCddOrgRefSet().

GetOrgRef() [3/3]

bool TaxClient::GetOrgRef ( TTaxId  taxId, CRef< COrg_ref > &  orgRef  )

virtual

Definition at line 162 of file cuTaxClient.cpp.

References GetOrgRef(), and CRef< C, Locker >::NotEmpty().

GetParentTaxID()

TTaxId TaxClient::GetParentTaxID ( TTaxId  taxid )

virtual

Definition at line 262 of file cuTaxClient.cpp.

References CTaxon1::GetParent(), IsAlive(), m_taxonomyClient, and ZERO_TAX_ID.

Referenced by TaxTreeData::growAndInsertLineage().

GetRankID()

short TaxClient::GetRankID ( TTaxId  taxId, string &  rankName  )

virtual

Definition at line 227 of file cuTaxClient.cpp.

References ITreeIterator::GetNode(), ITaxon1Node::GetRank(), CTaxon1::GetRankName(), CTaxon1::GetTreeIterator(), IsAlive(), and m_taxonomyClient.

Referenced by TaxTreeData::addSeqTax(), and TaxTreeData::growAndInsertLineage().

GetSuperKingdom()

string TaxClient::GetSuperKingdom ( TTaxId  taxid )

virtual

Definition at line 270 of file cuTaxClient.cpp.

References CTaxon1::GetSuperkingdom(), GetTaxNameForTaxID(), INVALID_TAX_ID, kEmptyStr, and m_taxonomyClient.

Referenced by SeqTreeAPI::annotateLeafNode().

GetTaxIDForGI()

TTaxId TaxClient::GetTaxIDForGI ( TGi  gi )

virtual

Definition at line 137 of file cuTaxClient.cpp.

References CTaxon1::GetTaxId4GI(), IsAlive(), m_taxonomyClient, and ZERO_TAX_ID.

Referenced by GetTaxIDForSeqId(), and TaxTreeData::GetTaxIDForSequence().

GetTaxIDForSeqId()

TTaxId TaxClient::GetTaxIDForSeqId ( CConstRef< CSeq_id >  sid )

virtual

Definition at line 101 of file cuTaxClient.cpp.

References CScope::AddDefaults(), CConstRef< C, Locker >::Empty(), CSeq_id_Base::GetGi(), CSeq_id_Handle::GetHandle(), CScope::GetIds(), CObjectManager::GetInstance(), GetTaxIDForGI(), CSeq_id_Base::IsGi(), ITERATE, m_scope, CGBDataLoader::RegisterInObjectManager(), ZERO_GI, and ZERO_TAX_ID.

Referenced by SeqTreeAPI::annotateLeafNode().

GetTaxIDFromBioseq()

TTaxId TaxClient::GetTaxIDFromBioseq ( const CBioseq &  bioseq, bool  lookInBioseq  )

virtual

Definition at line 177 of file cuTaxClient.cpp.

References CSeq_descr_Base::Get(), COrg_ref_Base::GetDb(), CBioseq_Base::GetDescr(), CTaxon1::GetTaxIdByOrgRef(), IsAlive(), CBioseq_Base::IsSetDescr(), m_taxonomyClient, NULL, TAX_ID_FROM, and ZERO_TAX_ID.

Referenced by TaxTreeData::GetTaxIDForSequence(), and CTaxNRCriteria::GetTaxIdFromClient().

GetTaxNameForTaxID()

std::string TaxClient::GetTaxNameForTaxID ( TTaxId  taxid )

virtual

Definition at line 240 of file cuTaxClient.cpp.

References data, CTaxon1::GetById(), IsAlive(), kEmptyStr, m_taxonomyClient, string, TAX_ID_CONST, and ZERO_TAX_ID.

Referenced by TaxTreeData::addSeqTax(), GetFullLineage(), GetSuperKingdom(), TaxTreeData::GetTaxIDForSequence(), and TaxTreeData::growAndInsertLineage().

init()

bool TaxClient::init ( )

virtual

Definition at line 77 of file cuTaxClient.cpp.

References ConnectToTaxServer().

Referenced by SeqTreeAPI::annotateLeafNode(), and TaxTreeData::TaxTreeData().

IsAlive()

bool TaxClient::IsAlive ( )

virtual

Definition at line 95 of file cuTaxClient.cpp.

References CTaxon1::IsAlive(), and m_taxonomyClient.

Referenced by CTaxNRCriteria::ConnectToServer(), GetDisplayCommonName(), GetFullLineage(), GetOrgRef(), GetParentTaxID(), GetRankID(), GetTaxIDForGI(), GetTaxIDFromBioseq(), GetTaxNameForTaxID(), IsTaxDescendant(), Join(), and TaxTreeData::makeTaxonomyTree().

IsTaxDescendant()

bool TaxClient::IsTaxDescendant ( TTaxId  tax1, TTaxId  tax2  )

virtual

Definition at line 286 of file cuTaxClient.cpp.

References IsAlive(), CTaxon1::Join(), and m_taxonomyClient.

Referenced by CPriorityTaxNodes::findAncestor().

Join()

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

Definition at line 305 of file cuTaxClient.cpp.

References IsAlive(), CTaxon1::Join(), m_taxonomyClient, and ZERO_TAX_ID.

SetSynonyms()

bool TaxClient::SetSynonyms ( bool  on_off )

virtual

Definition at line 171 of file cuTaxClient.cpp.

References m_taxonomyClient, and CTaxon1::SetSynonyms().

Member Data Documentation

m_scope

CScope* TaxClient::m_scope

private

Definition at line 114 of file cuTaxClient.hpp.

Referenced by GetTaxIDForSeqId(), and ~TaxClient().

m_taxonomyClient

CTaxon1* TaxClient::m_taxonomyClient

private

Definition at line 113 of file cuTaxClient.hpp.

Referenced by ConnectToTaxServer(), GetDisplayCommonName(), GetFullLineage(), GetOrgRef(), GetParentTaxID(), GetRankID(), GetSuperKingdom(), GetTaxIDForGI(), GetTaxIDFromBioseq(), GetTaxNameForTaxID(), IsAlive(), IsTaxDescendant(), Join(), SetSynonyms(), and ~TaxClient().

REFRESH_DEFAULT

const bool TaxClient::REFRESH_DEFAULT = false

staticprivate

Definition at line 53 of file cuTaxClient.hpp.

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

• include/algo/structure/cd_utils/cuTaxClient.hpp
• src/algo/structure/cd_utils/cuTaxClient.cpp