CPriorityTaxNodes Class Reference

Search Toolkit Book for CPriorityTaxNodes

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

Collaboration diagram for CPriorityTaxNodes:

Public Types
enum	TaxNodeInputType {   eCddPrefNodes = 1 , eCddModelOrgs = 2 , eCddOptional = 4 , eCddPrefNodesAll = 7 ,   eRawTaxIds = 8 }

Public Member Functions
	CPriorityTaxNodes (TaxNodeInputType inputType)
	CPriorityTaxNodes (const string &prefTaxnodeFileName, TaxNodeInputType inputType)
	CPriorityTaxNodes (const CCdd_pref_nodes &prefNodes, TaxNodeInputType inputType)
	CPriorityTaxNodes (const vector< TTaxId > &taxids, TaxClient &taxClient, TaxNodeInputType inputType=eRawTaxIds)
virtual	~CPriorityTaxNodes ()
bool	LoadFromFile (const string &prefTaxnodeFileName, bool doReset=false)
unsigned int	Load (const CCdd_pref_nodes &prefNodes, bool doReset=false)
void	Reset (TaxNodeInputType *inputType=NULL, bool forceClearAncestorMap=false)
bool	IsLoaded ()
string	GetLastError ()
TaxNodeInputType	GetNodeInputType () const
bool	IsPriorityTaxnode (TTaxId taxid)
bool	GetPriorityTaxid (TTaxId taxidIn, TTaxId &priorityTaxid, TaxClient &taxClient)
bool	GetPriorityTaxidAndName (TTaxId taxidIn, TTaxId &priorityTaxid, string &nodeName, TaxClient &taxClient)
int	GetPriorityTaxnode (TTaxId taxid, string &nodeName, TaxClient *taxClient=NULL)
int	GetPriorityTaxnode (TTaxId taxid, const OrgNode *&orgNode, TaxClient *taxClient=NULL)

Static Public Member Functions
static string	getTaxName (const CRef< CCdd_org_ref > &orgRef)
static TTaxId	getTaxId (const CRef< CCdd_org_ref > &orgRef)
static bool	isActive (const CRef< CCdd_org_ref > &orgRef)
static unsigned int	CddOrgRefSetToTaxIds (const CCdd_org_ref_set &cddOrgRefSet, vector< TTaxId > &taxids, vector< int > *notAddedIndices=NULL)
static unsigned int	TaxIdsToCddOrgRefSet (const vector< TTaxId > &taxids, CCdd_org_ref_set &cddOrgRefSet, TaxClient &taxClient, vector< TTaxId > *notAddedTaxids=NULL)

Protected Attributes
string	m_err

Private Types
typedef map< TTaxId, TTaxId >	TAncestorMap

Private Member Functions
TaxidToOrgMap::iterator	findAncestor (TTaxId taxid, TaxClient *taxClient)
void	putIntoMap (const CCdd_org_ref_set &orgRefs)
void	BuildMap (const CCdd_pref_nodes &prefNodes, bool reset=false)
bool	ReadPreferredTaxnodes (const string &fileName, bool reset=false)

Private Attributes
bool	m_loaded
TaxNodeInputType	m_inputType
TaxidToOrgMap	m_selectedTaxNodesMap
TAncestorMap	m_ancestralTaxNodeMap

Static Private Attributes
static const char *	PREF_TAXNODE_FILE = "data/txnodes.asn"

Detailed Description

Definition at line 56 of file cuPrefTaxNodes.hpp.

Member Typedef Documentation

TAncestorMap

typedef map<TTaxId, TTaxId> CPriorityTaxNodes::TAncestorMap

private

Definition at line 153 of file cuPrefTaxNodes.hpp.

Member Enumeration Documentation

TaxNodeInputType

enum CPriorityTaxNodes::TaxNodeInputType

Enumerator
eCddPrefNodes
eCddModelOrgs
eCddOptional
eCddPrefNodesAll
eRawTaxIds

Definition at line 61 of file cuPrefTaxNodes.hpp.

Constructor & Destructor Documentation

CPriorityTaxNodes() [1/4]

CPriorityTaxNodes::CPriorityTaxNodes

(

TaxNodeInputType

inputType

)

Definition at line 48 of file cuPrefTaxNodes.cpp.

References LoadFromFile(), and PREF_TAXNODE_FILE.

CPriorityTaxNodes() [2/4]

CPriorityTaxNodes::CPriorityTaxNodes	(	const string &	prefTaxnodeFileName,
		TaxNodeInputType	inputType
	)

Definition at line 54 of file cuPrefTaxNodes.cpp.

References LoadFromFile().

CPriorityTaxNodes() [3/4]

CPriorityTaxNodes::CPriorityTaxNodes	(	const CCdd_pref_nodes &	prefNodes,
		TaxNodeInputType	inputType
	)

Definition at line 59 of file cuPrefTaxNodes.cpp.

References BuildMap(), and m_loaded.

CPriorityTaxNodes() [4/4]

CPriorityTaxNodes::CPriorityTaxNodes	(	const vector< TTaxId > &	taxids,
		TaxClient &	taxClient,
		TaxNodeInputType	inputType = eRawTaxIds
	)

Definition at line 66 of file cuPrefTaxNodes.cpp.

References m_loaded, putIntoMap(), Reset(), and TaxIdsToCddOrgRefSet().

~CPriorityTaxNodes()

CPriorityTaxNodes::~CPriorityTaxNodes ( )

virtual

Definition at line 76 of file cuPrefTaxNodes.cpp.

Member Function Documentation

BuildMap()

void CPriorityTaxNodes::BuildMap ( const CCdd_pref_nodes &  prefNodes, bool  reset = false  )

private

Definition at line 126 of file cuPrefTaxNodes.cpp.

References CCdd_pref_nodes_Base::CanGetModel_organisms(), CCdd_pref_nodes_Base::CanGetOptional_nodes(), CCdd_pref_nodes_Base::CanGetPreferred_nodes(), eCddModelOrgs, eCddOptional, eCddPrefNodes, eRawTaxIds, CCdd_pref_nodes_Base::GetModel_organisms(), CCdd_pref_nodes_Base::GetOptional_nodes(), CCdd_pref_nodes_Base::GetPreferred_nodes(), m_inputType, putIntoMap(), and Reset().

Referenced by CPriorityTaxNodes(), Load(), and ReadPreferredTaxnodes().

CddOrgRefSetToTaxIds()

unsigned int CPriorityTaxNodes::CddOrgRefSetToTaxIds ( const CCdd_org_ref_set &  cddOrgRefSet, vector< TTaxId > &  taxids, vector< int > *  notAddedIndices = NULL  )

static

Definition at line 208 of file cuPrefTaxNodes.cpp.

References CCdd_org_ref_set_Base::Get(), getTaxId(), and ZERO_TAX_ID.

findAncestor()

TaxidToOrgMap::iterator CPriorityTaxNodes::findAncestor ( TTaxId  taxid, TaxClient *  taxClient  )

private

Definition at line 230 of file cuPrefTaxNodes.cpp.

References map_checker< Container >::begin(), map_checker< Container >::end(), map_checker< Container >::find(), map_checker< Container >::insert(), TaxClient::IsTaxDescendant(), m_ancestralTaxNodeMap, m_selectedTaxNodesMap, and ZERO_TAX_ID.

Referenced by GetPriorityTaxidAndName(), and GetPriorityTaxnode().

GetLastError()

string CPriorityTaxNodes::GetLastError ( )

inline

Definition at line 105 of file cuPrefTaxNodes.hpp.

References m_err.

GetNodeInputType()

TaxNodeInputType CPriorityTaxNodes::GetNodeInputType ( ) const

inline

Definition at line 106 of file cuPrefTaxNodes.hpp.

References m_inputType.

GetPriorityTaxid()

bool CPriorityTaxNodes::GetPriorityTaxid	(	TTaxId	taxidIn,
		TTaxId &	priorityTaxid,
		TaxClient &	taxClient
	)

Definition at line 264 of file cuPrefTaxNodes.cpp.

References GetPriorityTaxidAndName().

GetPriorityTaxidAndName()

bool CPriorityTaxNodes::GetPriorityTaxidAndName	(	TTaxId	taxidIn,
		TTaxId &	priorityTaxid,
		string &	nodeName,
		TaxClient &	taxClient
	)

Definition at line 270 of file cuPrefTaxNodes.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), findAncestor(), getTaxName(), kEmptyStr, m_selectedTaxNodesMap, result, and ZERO_TAX_ID.

Referenced by GetPriorityTaxid().

GetPriorityTaxnode() [1/2]

int CPriorityTaxNodes::GetPriorityTaxnode	(	TTaxId	taxid,
		const OrgNode *&	orgNode,
		TaxClient *	taxClient = NULL
	)

Definition at line 297 of file cuPrefTaxNodes.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), findAncestor(), m_selectedTaxNodesMap, NULL, OrgNode::order, and ZERO_TAX_ID.

GetPriorityTaxnode() [2/2]

int CPriorityTaxNodes::GetPriorityTaxnode	(	TTaxId	taxid,
		string &	nodeName,
		TaxClient *	taxClient = NULL
	)

Definition at line 322 of file cuPrefTaxNodes.cpp.

References getTaxName(), kEmptyStr, NULL, OrgNode::order, and OrgNode::orgRef.

Referenced by CTaxNRCriteria::Apply().

getTaxId()

TTaxId CPriorityTaxNodes::getTaxId ( const CRef< CCdd_org_ref > &  orgRef )

static

Definition at line 164 of file cuPrefTaxNodes.cpp.

References CCdd_org_ref_Base::CanGetReference(), CCdd_org_ref_Base::GetReference(), COrg_ref::GetTaxId(), and ZERO_TAX_ID.

Referenced by CddOrgRefSetToTaxIds(), and putIntoMap().

getTaxName()

string CPriorityTaxNodes::getTaxName ( const CRef< CCdd_org_ref > &  orgRef )

static

Definition at line 151 of file cuPrefTaxNodes.cpp.

References CCdd_org_ref_Base::CanGetReference(), CCdd_org_ref_Base::GetReference(), COrg_ref_Base::GetTaxname(), COrg_ref_Base::IsSetTaxname(), and kEmptyStr.

Referenced by GetPriorityTaxidAndName(), and GetPriorityTaxnode().

isActive()

bool CPriorityTaxNodes::isActive ( const CRef< CCdd_org_ref > &  orgRef )

static

Definition at line 175 of file cuPrefTaxNodes.cpp.

References CCdd_org_ref_Base::GetActive().

IsLoaded()

bool CPriorityTaxNodes::IsLoaded ( )

inline

Definition at line 104 of file cuPrefTaxNodes.hpp.

References m_loaded.

IsPriorityTaxnode()

bool CPriorityTaxNodes::IsPriorityTaxnode

(

TTaxId

taxid

)

Definition at line 258 of file cuPrefTaxNodes.cpp.

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

Load()

unsigned int CPriorityTaxNodes::Load	(	const CCdd_pref_nodes &	prefNodes,
		bool	doReset = false
	)

Definition at line 107 of file cuPrefTaxNodes.cpp.

References BuildMap(), m_selectedTaxNodesMap, and map_checker< Container >::size().

LoadFromFile()

bool CPriorityTaxNodes::LoadFromFile	(	const string &	prefTaxnodeFileName,
		bool	doReset = false
	)

Definition at line 96 of file cuPrefTaxNodes.cpp.

References m_err, m_loaded, ReadPreferredTaxnodes(), and result.

Referenced by CPriorityTaxNodes().

putIntoMap()

void CPriorityTaxNodes::putIntoMap ( const CCdd_org_ref_set &  orgRefs )

private

Definition at line 139 of file cuPrefTaxNodes.cpp.

References CCdd_org_ref_set_Base::Get(), getTaxId(), i, map_checker< Container >::insert(), m_selectedTaxNodesMap, and map_checker< Container >::size().

Referenced by BuildMap(), and CPriorityTaxNodes().

ReadPreferredTaxnodes()

bool CPriorityTaxNodes::ReadPreferredTaxnodes ( const string &  fileName, bool  reset = false  )

private

Definition at line 114 of file cuPrefTaxNodes.cpp.

References BuildMap(), m_err, and ReadASNFromFile().

Referenced by LoadFromFile().

Reset()

void CPriorityTaxNodes::Reset	(	TaxNodeInputType *	inputType = NULL,
		bool	forceClearAncestorMap = false
	)

Definition at line 80 of file cuPrefTaxNodes.cpp.

References map_checker< Container >::clear(), m_ancestralTaxNodeMap, m_err, m_inputType, m_loaded, and m_selectedTaxNodesMap.

Referenced by BuildMap(), and CPriorityTaxNodes().

TaxIdsToCddOrgRefSet()

unsigned int CPriorityTaxNodes::TaxIdsToCddOrgRefSet ( const vector< TTaxId > &  taxids, CCdd_org_ref_set &  cddOrgRefSet, TaxClient &  taxClient, vector< TTaxId > *  notAddedTaxids = NULL  )

static

Definition at line 180 of file cuPrefTaxNodes.cpp.

References TaxClient::GetOrgRef(), i, CRef< C, Locker >::NotEmpty(), CCdd_org_ref_set_Base::Set(), CCdd_org_ref_Base::SetActive(), and CCdd_org_ref_Base::SetReference().

Referenced by CPriorityTaxNodes().

Member Data Documentation

m_ancestralTaxNodeMap

TAncestorMap CPriorityTaxNodes::m_ancestralTaxNodeMap

private

Definition at line 154 of file cuPrefTaxNodes.hpp.

Referenced by findAncestor(), and Reset().

m_err

string CPriorityTaxNodes::m_err

protected

Definition at line 141 of file cuPrefTaxNodes.hpp.

Referenced by GetLastError(), LoadFromFile(), ReadPreferredTaxnodes(), and Reset().

m_inputType

TaxNodeInputType CPriorityTaxNodes::m_inputType

private

Definition at line 145 of file cuPrefTaxNodes.hpp.

Referenced by BuildMap(), GetNodeInputType(), and Reset().

m_loaded

bool CPriorityTaxNodes::m_loaded

private

Definition at line 144 of file cuPrefTaxNodes.hpp.

Referenced by CPriorityTaxNodes(), IsLoaded(), LoadFromFile(), and Reset().

m_selectedTaxNodesMap

TaxidToOrgMap CPriorityTaxNodes::m_selectedTaxNodesMap

private

Definition at line 148 of file cuPrefTaxNodes.hpp.

Referenced by findAncestor(), GetPriorityTaxidAndName(), GetPriorityTaxnode(), IsPriorityTaxnode(), Load(), putIntoMap(), and Reset().

PREF_TAXNODE_FILE

const char * CPriorityTaxNodes::PREF_TAXNODE_FILE = "data/txnodes.asn"

staticprivate

Definition at line 58 of file cuPrefTaxNodes.hpp.

Referenced by CPriorityTaxNodes().

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

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