CEntrez2Client Class Reference

Client for ASN.1-based protocol defined in file entrez2.asn

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#include <objects/entrez2/entrez2_client.hpp>

Inheritance diagram for CEntrez2Client:

Collaboration diagram for CEntrez2Client:

Public Types
typedef TIntId	TUid
Public Types inherited from CEntrez2Client_Base
typedef CEntrez2_request	TRequest
typedef CEntrez2_reply	TReply
typedef CE2Request	TRequestChoice
typedef CE2Reply	TReplyChoice
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
	CEntrez2Client (void)
	~CEntrez2Client (void)
void	GetNeighbors (TUid query_uid, const string &db_from, const string &db_to, vector< TUid > &neighbor_uids)
	A simplified interface for getting neighbors (links) More...
void	GetNeighbors (const vector< TUid > &query_uids, const string &db, const string &link_type, vector< TUid > &neighbor_uids)
	This form just yields a vector of UIDs, taking a vector of UIDs. More...
CRef< CEntrez2_link_set >	GetNeighbors (TUid query_uid, const string &db_from, const string &db_to)
	This form returns the entire CEntrez2_link_set object, which includes scores. More...
CRef< CEntrez2_link_set >	GetNeighbors (const vector< TUid > &query_uids, const string &db_from, const string &db_to)
	This form returns the entire CEntrez2_link_set object, which includes scores. More...
CRef< CEntrez2_link_count_list >	GetNeighborCounts (TUid query_uid, const string &db)
	Retrieve counts of the various types of neighbors available. More...
void	Query (const string &query, const string &db, vector< TUid > &result_uids, size_t start_offs=0, size_t count=0, TReply *reply=0)
	Some other simplified interfaces. More...
void	FilterIds (const vector< TUid > &query_uids, const string &db, const string &query_string, vector< TUid > &result_uids)
	Given some uids, a database, and an entrez query string, determine which of these uids match the query string. More...
CRef< CEntrez2_docsum_list >	GetDocsums (const vector< TUid > &uids, const string &db)
	Retrieve the docsums for a set of UIDs. More...
CRef< CEntrez2_docsum_list >	GetDocsums (TUid uid, const string &db)
	Retrieve the docsums for a single UID. More...
void	GetNeighbors (TGi query_uid, const string &db_from, const string &db_to, vector< TGi > &neighbor_uids)
void	GetNeighbors (const vector< TGi > &query_uids, const string &db, const string &link_type, vector< TGi > &neighbor_uids)
CRef< CEntrez2_link_set >	GetNeighbors (TGi query_uid, const string &db_from, const string &db_to)
CRef< CEntrez2_link_set >	GetNeighbors (const vector< TGi > &query_uids, const string &db_from, const string &db_to)
CRef< CEntrez2_link_count_list >	GetNeighborCounts (TGi query_uid, const string &db)
void	Query (const string &query, const string &db, vector< TGi > &result_uids, size_t start_offs=0, size_t count=0, TReply *reply=0)
void	FilterIds (const vector< TGi > &query_uids, const string &db, const string &query_string, vector< TGi > &result_uids)
CRef< CEntrez2_docsum_list >	GetDocsums (const vector< TGi > &uids, const string &db)
CRef< CEntrez2_docsum_list >	GetDocsums (TGi uid, const string &db)
Public Member Functions inherited from CEntrez2Client_Base
	CEntrez2Client_Base (void)
virtual	~CEntrez2Client_Base (void)
virtual void	Ask (const TRequest &request, TReply &reply)
virtual void	Ask (const TRequest &request, TReply &reply, TReplyChoice::E_Choice wanted)
virtual const TRequest &	GetDefaultRequest (void) const
virtual TRequest &	SetDefaultRequest (void)
virtual void	SetDefaultRequest (const TRequest &request)
virtual void	Ask (const TRequestChoice &req, TReply &reply)
virtual void	Ask (const TRequestChoice &req, TReply &reply, TReplyChoice::E_Choice wanted)
virtual CRef< CEntrez2_info >	AskGet_info (TReply *reply=0)
virtual CRef< CEntrez2_boolean_reply >	AskEval_boolean (const CEntrez2_eval_boolean &req, TReply *reply=0)
virtual CRef< CEntrez2_docsum_list >	AskGet_docsum (const CEntrez2_id_list &req, TReply *reply=0)
virtual int	AskGet_term_pos (const CEntrez2_term_query &req, TReply *reply=0)
virtual CRef< CEntrez2_term_list >	AskGet_term_list (const CEntrez2_term_pos &req, TReply *reply=0)
virtual CRef< CEntrez2_hier_node >	AskGet_term_hierarchy (const CEntrez2_hier_query &req, TReply *reply=0)
virtual CRef< CEntrez2_link_set >	AskGet_links (const CEntrez2_get_links &req, TReply *reply=0)
virtual CRef< CEntrez2_id_list >	AskGet_linked (const CEntrez2_get_links &req, TReply *reply=0)
virtual CRef< CEntrez2_link_count_list >	AskGet_link_counts (const CEntrez2_id &req, TReply *reply=0)
Public Member Functions inherited from CRPCClient< CEntrez2_request, CEntrez2_reply >
	CRPCClient (const string &service=kEmptyStr)
	CRPCClient (const string &service, ESerialDataFormat format)
	CRPCClient (const string &service, ESerialDataFormat format, unsigned int try_limit)
virtual	~CRPCClient (void)
virtual void	WriteRequest (CObjectOStream &out, const CEntrez2_request &request)
virtual void	ReadReply (CObjectIStream &in, CEntrez2_reply &reply)
EIO_Status	SetTimeout (const STimeout *timeout, EIO_Event direction=eIO_ReadWrite)
const STimeout *	GetTimeout (EIO_Event direction=eIO_Read) const
EIO_Status	AsyncConnect (void *handle_buf, size_t handle_size)
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
Public Member Functions inherited from CRPCClient_Base
	CRPCClient_Base (const string &service, ESerialDataFormat format)
	CRPCClient_Base (const string &service, ESerialDataFormat format, unsigned int try_limit)
virtual	~CRPCClient_Base (void)
void	Connect (void)
void	Disconnect (void)
void	Reset (void)
void	SetArgs (const string &args)
	Set additional connection arguments. More...
void	SetArgs (const CUrlArgs &args)
const string &	GetArgs (void) const
	Get additional connection arguments. More...
const string &	GetService (void) const
void	SetService (const string &service)
ESerialDataFormat	GetFormat (void) const
void	SetFormat (ESerialDataFormat fmt)
unsigned int	GetTryLimit (void) const
	Get number of request attempts. More...
void	SetTryLimit (unsigned int n)
unsigned int	GetRetryLimit (void) const
void	SetRetryLimit (unsigned int n)
const CTimeSpan	GetRetryDelay (void) const
	Get retry delay. More...
void	SetRetryDelay (const CTimeSpan &ts)
void	SetCanceledCallback (const ICanceled *canceled)
	Set request canceler. More...
bool	IsCanceled (void) const

Protected Member Functions
virtual string	GetAffinity (const CEntrez2_request &request) const
	Get DB affinity of the request. More...
Protected Member Functions inherited from CRPCClient< CEntrez2_request, CEntrez2_reply >
virtual void	x_WriteRequest (CObjectOStream &out, const CSerialObject &request) override
virtual void	x_ReadReply (CObjectIStream &in, CSerialObject &reply) override
virtual string	x_GetAffinity (const CSerialObject &request) const override
virtual void	x_Connect (void) override
	These run with m_Mutex already acquired. More...
void	x_ConnectURL (const string &url)
	Connect to a URL. More...
Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...
Protected Member Functions inherited from CRPCClient_Base
void	SetAffinity (const string &affinity)
virtual void	x_Disconnect (void)
	Disconnect as cleanly as possible. More...
void	x_SetStream (CNcbiIostream *stream)
void	x_Ask (const CSerialObject &request, CSerialObject &reply)
virtual bool	x_ShouldRetry (unsigned int tries)
CTimeSpan	x_GetRetryDelay (double max_delay) const
Protected Member Functions inherited from CConnIniter
	CConnIniter (void)

Private Types
typedef CEntrez2Client_Base	Tparent

Private Member Functions
	CEntrez2Client (const CEntrez2Client &value)
CEntrez2Client &	operator= (const CEntrez2Client &value)

Additional Inherited Members
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 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...
Static Protected Member Functions inherited from CRPCClient< CEntrez2_request, CEntrez2_reply >
static EHTTP_HeaderParse	sx_ParseHeader (const char *http_header, void *user_data, int server_error)
static bool	sx_IsSpecial (const STimeout *timeout)
Static Protected Member Functions inherited from CRPCClient_Base
static const char *	GetContentTypeHeader (ESerialDataFormat format)
Protected Attributes inherited from CRPCClient< CEntrez2_request, CEntrez2_reply >
const STimeout *	m_Timeout
	Cloned if not special. More...
Protected Attributes inherited from CRPCClient_Base
string	m_Service
	Used by default Connect(). More...
string	m_Args
unique_ptr< CNcbiIostream >	m_Stream
unique_ptr< CObjectIStream >	m_In
unique_ptr< CObjectOStream >	m_Out
string	m_Affinity
unsigned int	m_TryLimit
CHttpRetryContext	m_RetryCtx
CConstIRef< ICanceled >	m_Canceler

Detailed Description

Definition at line 56 of file entrez2_client.hpp.

Member Typedef Documentation

Tparent

typedef CEntrez2Client_Base CEntrez2Client::Tparent

private

Definition at line 58 of file entrez2_client.hpp.

TUid

typedef TIntId CEntrez2Client::TUid

Definition at line 60 of file entrez2_client.hpp.

Constructor & Destructor Documentation

CEntrez2Client() [1/2]

CEntrez2Client::CEntrez2Client ( void  )

inline

Definition at line 175 of file entrez2_client.hpp.

References CEntrez2Client_Base::SetDefaultRequest(), CEntrez2_request_Base::SetTool(), and CEntrez2_request_Base::SetVersion().

~CEntrez2Client()

CEntrez2Client::~CEntrez2Client

(

void

)

Definition at line 66 of file entrez2_client.cpp.

CEntrez2Client() [2/2]

CEntrez2Client::CEntrez2Client ( const CEntrez2Client &  value )

private

Member Function Documentation

FilterIds() [1/2]

void CEntrez2Client::FilterIds	(	const vector< TGi > &	query_uids,
		const string &	db,
		const string &	query_string,
		vector< TGi > &	result_uids
	)

Definition at line 375 of file entrez2_client.cpp.

References FilterIds(), GI_FROM, GI_TO, and ITERATE.

FilterIds() [2/2]

void CEntrez2Client::FilterIds	(	const vector< TUid > &	query_uids,
		const string &	db,
		const string &	query_string,
		vector< TUid > &	result_uids
	)

Given some uids, a database, and an entrez query string, determine which of these uids match the query string.

Note: If a uid appears more than once in query_uids and matches the query string, it may or may not appear more more than once in the result.

Definition at line 199 of file entrez2_client.cpp.

References i, ITERATE, min(), NStr::NumericToString(), and Query().

Referenced by FilterIds(), and CTestProtProd_EntrezNeighbors::RunTest().

GetAffinity()

string CEntrez2Client::GetAffinity ( const CEntrez2_request &  request ) const

protectedvirtual

Get DB affinity of the request.

Reimplemented from CRPCClient< CEntrez2_request, CEntrez2_reply >.

Definition at line 265 of file entrez2_client.cpp.

References CE2Request_Base::e_Eval_boolean, CE2Request_Base::e_Get_docsum, CE2Request_Base::e_Get_link_counts, CE2Request_Base::e_Get_linked, CE2Request_Base::e_Get_links, CE2Request_Base::e_Get_term_hierarchy, CE2Request_Base::e_Get_term_list, CE2Request_Base::e_Get_term_pos, CAliasBase< TPrim >::Get(), CEntrez2_boolean_exp_Base::GetDb(), CEntrez2_hier_query_Base::GetDb(), CEntrez2_id_Base::GetDb(), CEntrez2_id_list_Base::GetDb(), CEntrez2_term_pos_Base::GetDb(), CEntrez2_term_query_Base::GetDb(), CE2Request_Base::GetEval_boolean(), CE2Request_Base::GetGet_docsum(), CE2Request_Base::GetGet_link_counts(), CE2Request_Base::GetGet_linked(), CE2Request_Base::GetGet_links(), CE2Request_Base::GetGet_term_hierarchy(), CE2Request_Base::GetGet_term_list(), CE2Request_Base::GetGet_term_pos(), CEntrez2_eval_boolean_Base::GetQuery(), CEntrez2_request_Base::GetRequest(), CEntrez2_get_links_Base::GetUids(), kEmptyStr, and CE2Request_Base::Which().

GetDocsums() [1/4]

CRef< CEntrez2_docsum_list > CEntrez2Client::GetDocsums	(	const vector< TGi > &	uids,
		const string &	db
	)

Definition at line 391 of file entrez2_client.cpp.

References GetDocsums(), GI_TO, and ITERATE.

GetDocsums() [2/4]

CRef< CEntrez2_docsum_list > CEntrez2Client::GetDocsums	(	const vector< TUid > &	uids,
		const string &	db
	)

Retrieve the docsums for a set of UIDs.

Definition at line 244 of file entrez2_client.cpp.

References CEntrez2Client_Base::AskGet_docsum(), CEntrez2_id_list::AssignUids(), and CEntrez2_id_list_Base::SetDb().

Referenced by GetDocsums(), and CGeneModelFeatJob::x_ProcessLandMarkFeatures().

GetDocsums() [3/4]

CRef< CEntrez2_docsum_list > CEntrez2Client::GetDocsums	(	TGi	uid,
		const string &	db
	)

Definition at line 401 of file entrez2_client.cpp.

References GetDocsums(), and GI_TO.

GetDocsums() [4/4]

CRef< CEntrez2_docsum_list > CEntrez2Client::GetDocsums	(	TUid	uid,
		const string &	db
	)

Retrieve the docsums for a single UID.

Definition at line 256 of file entrez2_client.cpp.

References GetDocsums().

GetNeighborCounts() [1/2]

CRef< CEntrez2_link_count_list > CEntrez2Client::GetNeighborCounts	(	TGi	query_uid,
		const string &	db
	)

Definition at line 355 of file entrez2_client.cpp.

References GetNeighborCounts(), and GI_TO.

GetNeighborCounts() [2/2]

CRef< CEntrez2_link_count_list > CEntrez2Client::GetNeighborCounts	(	TUid	query_uid,
		const string &	db
	)

Retrieve counts of the various types of neighbors available.

Definition at line 141 of file entrez2_client.cpp.

References CEntrez2Client_Base::AskGet_link_counts(), ENTREZ_ID_FROM, CEntrez2_id_Base::SetDb(), and CEntrez2_id_Base::SetUid().

Referenced by GetNeighborCounts().

GetNeighbors() [1/8]

void CEntrez2Client::GetNeighbors	(	const vector< TGi > &	query_uids,
		const string &	db,
		const string &	link_type,
		vector< TGi > &	neighbor_uids
	)

Definition at line 321 of file entrez2_client.cpp.

References GetNeighbors(), GI_FROM, GI_TO, and ITERATE.

GetNeighbors() [2/8]

CRef< CEntrez2_link_set > CEntrez2Client::GetNeighbors	(	const vector< TGi > &	query_uids,
		const string &	db_from,
		const string &	db_to
	)

Definition at line 344 of file entrez2_client.cpp.

References GetNeighbors(), GI_TO, and ITERATE.

GetNeighbors() [3/8]

void CEntrez2Client::GetNeighbors	(	const vector< TUid > &	query_uids,
		const string &	db,
		const string &	link_type,
		vector< TUid > &	neighbor_uids
	)

This form just yields a vector of UIDs, taking a vector of UIDs.

This form just yields a vector of UIDs.

Definition at line 86 of file entrez2_client.cpp.

References CConstResizingIterator< TSeq, TOut >::AtEnd(), and GetNeighbors().

GetNeighbors() [4/8]

CRef< CEntrez2_link_set > CEntrez2Client::GetNeighbors	(	const vector< TUid > &	query_uids,
		const string &	db,
		const string &	link_type
	)

This form returns the entire CEntrez2_link_set object, which includes scores.

Definition at line 122 of file entrez2_client.cpp.

References CEntrez2Client_Base::AskGet_links(), CEntrez2_id_list::AssignUids(), CEntrez2_id_list_Base::SetDb(), CEntrez2_get_links_Base::SetLinktype(), and CEntrez2_get_links_Base::SetUids().

GetNeighbors() [5/8]

CRef< CEntrez2_link_set > CEntrez2Client::GetNeighbors	(	TGi	query_uid,
		const string &	db_from,
		const string &	db_to
	)

Definition at line 337 of file entrez2_client.cpp.

References GetNeighbors(), and GI_TO.

GetNeighbors() [6/8]

void CEntrez2Client::GetNeighbors	(	TGi	query_uid,
		const string &	db_from,
		const string &	db_to,
		vector< TGi > &	neighbor_uids
	)

Definition at line 309 of file entrez2_client.cpp.

References GetNeighbors(), GI_FROM, GI_TO, and ITERATE.

GetNeighbors() [7/8]

CRef< CEntrez2_link_set > CEntrez2Client::GetNeighbors	(	TUid	query_uid,
		const string &	db,
		const string &	link_type
	)

This form returns the entire CEntrez2_link_set object, which includes scores.

Definition at line 109 of file entrez2_client.cpp.

References GetNeighbors().

GetNeighbors() [8/8]

void CEntrez2Client::GetNeighbors	(	TUid	query_uid,
		const string &	db,
		const string &	link_type,
		vector< TUid > &	neighbor_uids
	)

A simplified interface for getting neighbors (links)

Get ids of neigbors of a specified type. db is, e.g., "nucleotide" or "protein" (depending on the query). link_type is, for example, "nucleotide_nucleotide". This form just yields a vector of UIDs

This form just yields a vector of UIDs

Definition at line 74 of file entrez2_client.cpp.

Referenced by GetNeighbors(), and CTestProtProd_EntrezNeighbors::RunTest().

operator=()

CEntrez2Client& CEntrez2Client::operator= ( const CEntrez2Client &  value )

private

Query() [1/2]

void CEntrez2Client::Query	(	const string &	query,
		const string &	db,
		vector< TGi > &	result_uids,
		size_t	start_offs = 0,
		size_t	count = 0,
		TReply *	reply = 0
	)

Definition at line 361 of file entrez2_client.cpp.

References GI_FROM, ITERATE, Query(), and query.

Query() [2/2]

void CEntrez2Client::Query	(	const string &	query,
		const string &	db,
		vector< TUid > &	result_uids,
		size_t	start_offs = 0,
		size_t	count = 0,
		TReply *	reply = 0
	)

Some other simplified interfaces.

Query a db with a string, returning uids as integers.

Query a db with a string, returning uids as integers

Definition at line 152 of file entrez2_client.cpp.

References CEntrez2Client_Base::AskEval_boolean(), query, CEntrez2_boolean_exp_Base::SetDb(), CEntrez2_boolean_exp_Base::SetExp(), CEntrez2_boolean_exp_Base::SetLimits(), CEntrez2_eval_boolean_Base::SetQuery(), and CEntrez2_eval_boolean_Base::SetReturn_UIDs().

Referenced by BOOST_AUTO_TEST_CASE(), FilterIds(), and Query().

---

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

• include/objects/entrez2/entrez2_client.hpp
• src/objects/entrez2/entrez2_client.cpp