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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/taxon1_8hpp_source.html below:

NCBI C++ ToolKit: include/objects/taxon1/taxon1.hpp Source File

1 #ifndef NCBI_TAXON1_HPP 2 #define NCBI_TAXON1_HPP 83 static const unsigned

def_reconnect_attempts = 5;

84 static const unsigned

def_cache_capacity = 1000;

86 bool Init

(

unsigned

cache_capacity);

87 bool Init

(

const STimeout

* timeout,

unsigned

reconnect_attempts=def_reconnect_attempts,

88 unsigned

cache_capacity=def_cache_capacity);

111 bool

GetScientificName(

TTaxId

tax_id,

string

& name_out);

179 bool

CheckOrgRef(

const COrg_ref

& orgRef, TOrgRefStatus& stat_out,

string

* psLog = 0 );

195 TTaxId

GetTaxIdByName(

const string

& orgname);

205 TTaxId

FindTaxIdByName(

const string

& orgname);

216 TTaxId

SearchTaxIdByName(

const string

& orgname,

217

ESearch

mode

= eSearch_TokenSet,

225 int

GetAllTaxIdByName(

const string

& orgname, TTaxIdList& lIds);

238 bool

& is_uncultured,

240 bool

* is_specified =

NULL

);

248 bool

SetSynonyms(

bool

on_off);

332 TTaxId

GetAncestorByRank(

TTaxId

id_tax,

const char

* rank_name);

340 int

GetChildren(

TTaxId

id_tax, TTaxIdList& children_ids);

350 bool

GetRankName(

TTaxRank

rank_id,

string

& rank_name_out );

357 TTaxRank

GetRankIdByName(

const string

& rank_name);

362 bool

GetDivisionName(

TTaxDivision

div_id,

string

& div_name_out,

string

* div_code_out =

NULL

);

369 TTaxDivision

GetDivisionIdByName(

const string

& div_name);

374 bool

GetNameClass(

TTaxNameClass

nameclass_id,

string

& class_name_out );

420 int

GetAllNames(

TTaxId

tax_id, TNameList& lNames,

bool

unique);

444 bool

IsAlive(

void

);

455 bool

GetTaxId4GI(

TGi

gi,

TTaxId

& tax_id_out);

465 bool

GetBlastName(

TTaxId

tax_id,

string

& blast_name_out);

480 bool

GetPopsetJoin(

const

TTaxIdList& ids_in, TTaxIdList& ids_out );

489

{

return

LoadSubtreeEx( tax_id, 0, ppNode ); }

499

{

return

LoadSubtreeEx( tax_id, 1, ppNode ); }

508

{

return

LoadSubtreeEx( tax_id, -1, ppNode ); }

517

eIteratorMode_Default = eIteratorMode_FullTree

526

= eIteratorMode_Default );

534

= eIteratorMode_Default );

543 bool

GetNodeProperty(

TTaxId

tax_id,

const string

& prop_name,

545 bool

GetNodeProperty(

TTaxId

tax_id,

const string

& prop_name,

547 bool

GetNodeProperty(

TTaxId

tax_id,

const string

& prop_name,

558 bool

GetInheritedPropertyDefines(

const string

& prop_name,

559

TInfoList& results_out,

569 bool

GetTypeMaterial(

TTaxId

tax_id, TNameList& type_material_list_out );

575 TTaxId

GetMaxTaxId(

void

);

588 bool

GetDisplayCommonName(

TTaxId

tax_id,

string

& disp_name_out );

615 void

SetLastError(

const char

* err_msg);

793

EAction TraverseDownward(I4Each&,

unsigned

levels =

kMax_UInt

);

809

EAction TraverseUpward(I4Each&,

unsigned

levels =

kMax_UInt

);

826

EAction TraverseLevelByLevel(I4Each&,

unsigned

levels =

kMax_UInt

);

836

EAction TraverseAncestors(I4Each&);

852 EAction

TraverseLevelByLevelInternal(

I4Each

& cb,

unsigned

levels,

853

vector< const ITaxon1Node* >& skp);

This stream exchanges data with a named service, in a constraint that the service is implemented as o...

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

const string & GetLastError() const

vector< TTaxId > TTaxIdList

const char * m_pchService

ESerialDataFormat m_eDataFormat

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

CConn_ServiceStream * m_pServer

@ eIteratorMode_LeavesBranches

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

unsigned m_nReconnectAttempts

list< CRef< CTaxon1_info > > TInfoList

map< TTaxGeneticCode, string > TGCMap

virtual TTaxGeneticCode GetMGC() const =0

virtual bool IsUncultured() const =0

virtual const string & GetName() const =0

virtual bool IsGenBankHidden() const =0

virtual TTaxDivision GetDivision() const =0

virtual const string & GetBlastName() const =0

virtual bool IsRoot() const =0

virtual TTaxId GetTaxId() const =0

virtual TTaxGeneticCode GetGC() const =0

virtual TTaxRank GetRank() const =0

virtual EAction LevelEnd(const ITaxon1Node *)

virtual EAction LevelBegin(const ITaxon1Node *)

virtual EAction Execute(const ITaxon1Node *pNode)=0

virtual bool GoSibling()=0

virtual bool GoNode(const ITaxon1Node *pNode)=0

virtual bool IsFirstChild() const =0

virtual const ITaxon1Node * GetNode() const =0

virtual bool IsLastChild() const =0

virtual bool GoParent()=0

const ITaxon1Node * operator->() const

virtual bool AboveNode(const ITaxon1Node *node) const =0

virtual CTaxon1::EIteratorMode GetMode() const =0

virtual bool IsTerminal() const =0

virtual bool BelongSubtree(const ITaxon1Node *subtree_root) const =0

virtual bool GoAncestor(const ITaxon1Node *pNode)=0

std::ofstream out("events_result.xml")

main entry point for tests

SStrictId_Tax::TId TTaxId

Taxon id type.

ESerialDataFormat

Data file format.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_TAXON1_EXPORT

@ eSkip

Unicode to be skipped in translation. Usually it is combined mark.

Miscellaneous common-use basic types and functionality.

short int TTaxRank

Primitive types for some taxon1 object fields.

short int TTaxGeneticCode

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