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CGenomicCollectionsService Class Reference

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

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#include <objects/genomecoll/genomic_collections_cli.hpp>

+ Inheritance diagram for CGenomicCollectionsService:
+ Collaboration diagram for CGenomicCollectionsService:

Classes

struct  SAssemblyMode
 

Public Member Functions

 CGenomicCollectionsService (const string &cache_file="")
 
 CGenomicCollectionsService (const CArgs &args)
 
 ~CGenomicCollectionsService ()
 
CRef< CGC_AssemblyGetAssembly (const string &acc, const string &mode)
 
CRef< CGC_AssemblyGetAssembly (int releaseId, const string &mode)
 
string ValidateChrType (const string &chrType, const string &chrLoc)
 
CRef< CGCClient_AssemblyInfoFindOneAssemblyBySequences (const string &sequence_acc, int filter, CGCClient_GetAssemblyBySequenceRequest::ESort sort=CGCClient_GetAssemblyBySequenceRequest::eSort_default)
 Find assembly by sequence accession. More...
 
CRef< CGCClient_AssemblySequenceInfoFindOneAssemblyBySequences (const list< string > &sequence_acc, int filter, CGCClient_GetAssemblyBySequenceRequest::ESort sort=CGCClient_GetAssemblyBySequenceRequest::eSort_default, bool with_roles=false)
 Find assembly by sequence accessions. More...
 
CRef< CGCClient_AssembliesForSequencesFindAssembliesBySequences (const string &sequence_acc, int filter, CGCClient_GetAssemblyBySequenceRequest::ESort sort=CGCClient_GetAssemblyBySequenceRequest::eSort_default, bool with_roles=false)
 Find assemblies by sequence accession. More...
 
CRef< CGCClient_AssembliesForSequencesFindAssembliesBySequences (const list< string > &sequence_acc, int filter, CGCClient_GetAssemblyBySequenceRequest::ESort sort=CGCClient_GetAssemblyBySequenceRequest::eSort_default, bool with_roles=false)
 Find assemblies by sequence accessions. More...
 
CRef< CGCClient_EquivalentAssembliesGetEquivalentAssemblies (const string &acc, int equivalency)
 
- Public Member Functions inherited from CGenomicCollectionsService_Base
 CGenomicCollectionsService_Base (void)
 
virtual ~CGenomicCollectionsService_Base (void)
 
virtual void Ask (const TRequest &request, TReply &reply)
 
virtual void Ask (const TRequest &request, TReply &reply, TReplyChoice::E_Choice wanted)
 
virtual string AskGet_chrtype_valid (const CGCClient_ValidateChrTypeLocRequest &req, TReply *reply=0)
 
virtual CRef< CGCClient_EquivalentAssembliesAskGet_equivalent_assemblies (const CGCClient_GetEquivalentAssembliesRequest &req, TReply *reply=0)
 
virtual vector< char > AskGet_assembly_blob (const CGCClient_GetAssemblyBlobRequest &req, TReply *reply=0)
 
virtual CRef< CGCClient_AssembliesForSequencesAskGet_assembly_by_sequence (const CGCClient_GetAssemblyBySequenceRequest &req, TReply *reply=0)
 
- Public Member Functions inherited from CRPCClient< CGCClientRequest, CGCClientResponse >
 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 CGCClientRequest &request)
 
virtual void ReadReply (CObjectIStream &in, CGCClientResponse &reply)
 
EIO_Status SetTimeout (const STimeout *timeout, EIO_Event direction=eIO_ReadWrite)
 
const STimeoutGetTimeout (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...
 
CObjectoperator= (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 stringGetArgs (void) const
 Get additional connection arguments. More...
 
const stringGetService (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
 

Static Public Member Functions

static void AddArguments (CArgDescriptions &arg_desc)
 
- 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)
 

Private Member Functions

 CGenomicCollectionsService (const CGenomicCollectionsService &value)
 
CGenomicCollectionsServiceoperator= (const CGenomicCollectionsService &value)
 
CRef< CGCClient_AssembliesForSequencesx_FindAssembliesBySequences (const list< string > &sequence_acc, int filter, CGCClient_GetAssemblyBySequenceRequest::ESort sort, bool top_only, bool with_roles)
 
void x_ConfigureConnection ()
 
void x_ConfigureCache (const string &cache_file)
 

Private Attributes

string m_CacheFile
 
unique_ptr< CSQLITE_Connectionm_CacheConn
 

Additional Inherited Members

- Public Types inherited from CGenomicCollectionsService_Base
typedef CGCClientRequest TRequest
 
typedef CGCClientResponse TReply
 
typedef TRequest TRequestChoice
 
typedef TReply 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< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 
- 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...
 
- Protected Member Functions inherited from CRPCClient< CGCClientRequest, CGCClientResponse >
virtual string GetAffinity (const CGCClientRequest &) const
 
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)
 
- Static Protected Member Functions inherited from CRPCClient< CGCClientRequest, CGCClientResponse >
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< CGCClientRequest, CGCClientResponse >
const STimeoutm_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< CNcbiIostreamm_Stream
 
unique_ptr< CObjectIStreamm_In
 
unique_ptr< CObjectOStreamm_Out
 
string m_Affinity
 
unsigned int m_TryLimit
 
CHttpRetryContext m_RetryCtx
 
CConstIRef< ICanceledm_Canceler
 

Detailed Description

Definition at line 73 of file genomic_collections_cli.hpp.

Constructor & Destructor Documentation

◆ CGenomicCollectionsService() [1/3]

CGenomicCollectionsService::CGenomicCollectionsService ( const string cache_file = "")

Definition at line 75 of file genomic_collections_cli.cpp.

References x_ConfigureCache(), and x_ConfigureConnection().

◆ CGenomicCollectionsService() [2/3]

CGenomicCollectionsService::CGenomicCollectionsService ( const CArgs args)

◆ ~CGenomicCollectionsService()

CGenomicCollectionsService::~CGenomicCollectionsService ( )

◆ CGenomicCollectionsService() [3/3]

CGenomicCollectionsService::CGenomicCollectionsService ( const CGenomicCollectionsService value)
private

Member Function Documentation

◆ AddArguments()

void CGenomicCollectionsService::AddArguments ( CArgDescriptions arg_desc)
static

◆ FindAssembliesBySequences() [1/2]

CRef< CGCClient_AssembliesForSequences > CGenomicCollectionsService::FindAssembliesBySequences ( const list< string > &  sequence_acc,
int  filter,
CGCClient_GetAssemblyBySequenceRequest::ESort  sort = CGCClient_GetAssemblyBySequenceRequest::eSort_default,
bool  with_roles = false 
)

Find assemblies by sequence accessions.

Parameters
sequence_accSequence accessions in ACC.VER format
filterBitfield, OR-ed combination of eGCClient_GetAssemblyBySequenceFilter_* values: eGCClient_GetAssemblyBySequenceFilter_all - do not filter out anything eGCClient_GetAssemblyBySequenceFilter_latest - look up for latest releases only eGCClient_GetAssemblyBySequenceFilter_major - look up for major releases only eGCClient_GetAssemblyBySequenceFilter_genbank - look up for GenBank releases only eGCClient_GetAssemblyBySequenceFilter_refseq - look up for RefSeq releases only If none of genbank of refseq filters are specified then both GenBank and RefSeq releases will be returned
sortAssembly ordering: CGCClient_GetAssemblyBySequenceRequest::eSort_default - sort by number of sequences found in assembly, then by reference/representative/other, then by modification date CGCClient_GetAssemblyBySequenceRequest::eSort_latest - sort by number of sequences found in assembly, then latest first, then by reference/representative/other, then by modification date CGCClient_GetAssemblyBySequenceRequest::eSort_major - sort by number of sequences found in assembly, then major first, then by reference/representative/other, then by modification date
Returns
List of found assemblies with related sequences.

Definition at line 274 of file genomic_collections_cli.cpp.

References ct::sort(), and x_FindAssembliesBySequences().

◆ FindAssembliesBySequences() [2/2]

CRef< CGCClient_AssembliesForSequences > CGenomicCollectionsService::FindAssembliesBySequences ( const string sequence_acc,
int  filter,
CGCClient_GetAssemblyBySequenceRequest::ESort  sort = CGCClient_GetAssemblyBySequenceRequest::eSort_default,
bool  with_roles = false 
)

Find assemblies by sequence accession.

Parameters
sequence_accSequence accession in ACC.VER format
filterBitfield, OR-ed combination of eGCClient_GetAssemblyBySequenceFilter_* values: eGCClient_GetAssemblyBySequenceFilter_all - do not filter out anything eGCClient_GetAssemblyBySequenceFilter_latest - look up for latest releases only eGCClient_GetAssemblyBySequenceFilter_major - look up for major releases only eGCClient_GetAssemblyBySequenceFilter_genbank - look up for GenBank releases only eGCClient_GetAssemblyBySequenceFilter_refseq - look up for RefSeq releases only If none of genbank of refseq filters are specified then both GenBank and RefSeq releases will be returned
sortAssembly ordering: CGCClient_GetAssemblyBySequenceRequest::eSort_default - sort by number of sequences found in assembly, then by reference/representative/other, then by modification date CGCClient_GetAssemblyBySequenceRequest::eSort_latest - sort by number of sequences found in assembly, then latest first, then by reference/representative/other, then by modification date CGCClient_GetAssemblyBySequenceRequest::eSort_major - sort by number of sequences found in assembly, then major first, then by reference/representative/other, then by modification date
Returns
List of found assemblies with related sequences.

Definition at line 269 of file genomic_collections_cli.cpp.

References ct::sort().

Referenced by CClientGenomicCollectionsSvcApplication::RunWithService().

◆ FindOneAssemblyBySequences() [1/2]

CRef< CGCClient_AssemblySequenceInfo > CGenomicCollectionsService::FindOneAssemblyBySequences ( const list< string > &  sequence_acc,
int  filter,
CGCClient_GetAssemblyBySequenceRequest::ESort  sort = CGCClient_GetAssemblyBySequenceRequest::eSort_default,
bool  with_roles = false 
)

Find assembly by sequence accessions.

Parameters
sequence_accSequence accessions in ACC.VER format
filterBitfield, OR-ed combination of eGCClient_GetAssemblyBySequenceFilter_* values: eGCClient_GetAssemblyBySequenceFilter_all - do not filter out anything eGCClient_GetAssemblyBySequenceFilter_latest - look up for latest releases only eGCClient_GetAssemblyBySequenceFilter_major - look up for major releases only eGCClient_GetAssemblyBySequenceFilter_genbank - look up for GenBank releases only eGCClient_GetAssemblyBySequenceFilter_refseq - look up for RefSeq releases only If none of genbank of refseq filters are specified then both GenBank and RefSeq releases will be returned
sortAssembly ordering: CGCClient_GetAssemblyBySequenceRequest::eSort_default - sort by number of sequences found in assembly, then by reference/representative/other, then by modification date CGCClient_GetAssemblyBySequenceRequest::eSort_latest - sort by number of sequences found in assembly, then latest first, then by reference/representative/other, then by modification date CGCClient_GetAssemblyBySequenceRequest::eSort_major - sort by number of sequences found in assembly, then major first, then by reference/representative/other, then by modification date
Returns
If assembly is found then return it with list of related sequences. NULL otherwise.

Definition at line 260 of file genomic_collections_cli.cpp.

References ct::sort(), and x_FindAssembliesBySequences().

◆ FindOneAssemblyBySequences() [2/2]

CRef< CGCClient_AssemblyInfo > CGenomicCollectionsService::FindOneAssemblyBySequences ( const string sequence_acc,
int  filter,
CGCClient_GetAssemblyBySequenceRequest::ESort  sort = CGCClient_GetAssemblyBySequenceRequest::eSort_default 
)

Find assembly by sequence accession.

Parameters
sequence_accSequence accession in ACC.VER format
filterBitfield, OR-ed combination of eGCClient_GetAssemblyBySequenceFilter_* values: eGCClient_GetAssemblyBySequenceFilter_all - do not filter out anything eGCClient_GetAssemblyBySequenceFilter_latest - look up for latest releases only eGCClient_GetAssemblyBySequenceFilter_major - look up for major releases only eGCClient_GetAssemblyBySequenceFilter_genbank - look up for GenBank releases only eGCClient_GetAssemblyBySequenceFilter_refseq - look up for RefSeq releases only If none of genbank of refseq filters are specified then both GenBank and RefSeq releases will be returned
sortAssembly ordering: CGCClient_GetAssemblyBySequenceRequest::eSort_default - sort by number of sequences found in assembly, then by reference/representative/other, then by modification date CGCClient_GetAssemblyBySequenceRequest::eSort_latest - sort by number of sequences found in assembly, then latest first, then by reference/representative/other, then by modification date CGCClient_GetAssemblyBySequenceRequest::eSort_major - sort by number of sequences found in assembly, then major first, then by reference/representative/other, then by modification date
Returns
Assembly if found, NULL otherwise.

Definition at line 253 of file genomic_collections_cli.cpp.

References ct::sort().

Referenced by CClientGenomicCollectionsSvcApplication::RunWithService().

◆ GetAssembly() [1/2]

CRef< CGC_Assembly > CGenomicCollectionsService::GetAssembly ( const string acc,
const string mode 
)

◆ GetAssembly() [2/2]

CRef< CGC_Assembly > CGenomicCollectionsService::GetAssembly ( int  releaseId,
const string mode 
)

◆ GetEquivalentAssemblies()

CRef< CGCClient_EquivalentAssemblies > CGenomicCollectionsService::GetEquivalentAssemblies ( const string acc,
int  equivalency 
)

◆ operator=()

CGenomicCollectionsService& CGenomicCollectionsService::operator= ( const CGenomicCollectionsService value)
private

◆ ValidateChrType()

string CGenomicCollectionsService::ValidateChrType ( const string chrType,
const string chrLoc 
)

◆ x_ConfigureCache()

void CGenomicCollectionsService::x_ConfigureCache ( const string cache_file)
private

◆ x_ConfigureConnection()

void CGenomicCollectionsService::x_ConfigureConnection ( )
private

◆ x_FindAssembliesBySequences()

CRef< CGCClient_AssembliesForSequences > CGenomicCollectionsService::x_FindAssembliesBySequences ( const list< string > &  sequence_acc,
int  filter,
CGCClient_GetAssemblyBySequenceRequest::ESort  sort,
bool  top_only,
bool  with_roles 
)
private

Member Data Documentation

◆ m_CacheConn

unique_ptr<CSQLITE_Connection> CGenomicCollectionsService::m_CacheConn
private

◆ m_CacheFile

string CGenomicCollectionsService::m_CacheFile
private

The documentation for this class was generated from the following files:
Modified on Sat Feb 24 07:50:07 2024 by modify_doxy.py rev. 669887