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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cdd__client_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/data_loaders/cdd/cdd_access/cdd_client.cpp Source File

{

, objects::CCDDClient::eSemiBinary },

{

, objects::CCDDClient::eBinary }

objects::CCDDClient::eBinary);

data_format = TDataFormatParam::GetDefault();

m_DataFormat(data_format)

(

.SetFormattingFlags(kJSONFlags);

}

(!next_reply->IsSetEnd_of_reply());

cdd_request->SetSerial_number(serial_number);

cdd_request->SetRequest().SetGet_blob_id().Assign(seq_id);

cdd_packet.

().push_back(cdd_request);

(cdd_packet, *cdd_reply);

cdd_request->SetSerial_number(serial_number);

cdd_request->SetRequest().SetGet_blob().Assign(blob_id);

cdd_packet.

().push_back(cdd_request);

(cdd_packet, *cdd_reply);

shared_ptr<SCDDCacheInfo>

= found->second;

shared_ptr<SCDDCacheInfo>

= found->second;

shared_ptr<SCDDCacheInfo>

= make_shared<SCDDCacheInfo>(idh, blob);

(s_Counter.

(1));

pool_soft_limit,

time_t pool_age_limit,

exclude_nucleotides)

(ret.

)

ret;

cdd_request->SetSerial_number(serial);

cdd_request->SetRequest().SetGet_blob_by_seq_id(*nc_id);

cdd_packet.

().push_back(cdd_request);

.Get().Ask(cdd_packet, *cdd_reply);

& cdd_blob = cdd_reply->SetReply().SetGet_blob_by_seq_id();

ret.

.

(&cdd_blob.SetBlob_id());

(ret.

)

;

(ret.

)

ret;

cdd_request->SetSerial_number(serial);

list<CRef<CSeq_id>>& req_ids = cdd_request->SetRequest().SetGet_blob_by_seq_ids();

req_ids.push_back(nc_id);

(req_ids.empty())

ret;

cdd_packet.

().push_back(cdd_request);

.Get().Ask(cdd_packet, *cdd_reply);

& cdd_blob = cdd_reply->SetReply().SetGet_blob_by_seq_id();

ret.

.

(&cdd_blob.SetBlob_id());

(blob.

)

blob.

;

cdd_request->SetSerial_number(serial);

cdd_request->SetRequest().SetGet_blob_id().Assign(*

);

cdd_packet.

().push_back(cdd_request);

.Get().Ask(cdd_packet, *cdd_reply);

blob.

.

(&cdd_reply->SetReply().SetGet_blob_id());

(blob.

)

blob.

;

cdd_request->SetSerial_number(serial);

& req = cdd_request->SetRequest().SetGet_blob();

req.SetSat(blob_id.

());

cdd_packet.

().push_back(cdd_request);

.Get().Ask(cdd_packet, *cdd_reply);

ret.

(&cdd_reply->SetReply().SetGet_blob());

(!reply)

;

(reply->GetReply().IsEmpty() && !reply->IsSetError())

;

(reply->IsSetError()) {

(reply->GetSerial_number() != serial) {

(

<< serial <<

<< reply->GetSerial_number());

(reply->GetReply().Which() != choice) {

(

<< reply->GetReply().Which() <<

<< choice);

(

.Which()) {

(

->first >= cutoff

s << (

)blob_id.

() <<

vector<string> parts;

(parts.size() != 3)

ret;

blob_id->SetSat((

)NStr::StringToNumeric<unsigned int>(parts[0]));

blob_id->SetSub_sat((

)NStr::StringToNumeric<unsigned int>(parts[1]));

blob_id->SetSat_key((

)NStr::StringToNumeric<unsigned int>(parts[2]));

User-defined methods of the data storage class.

User-defined methods of the data storage class.

const size_t kMaxCacheSize

const int kMaxCacheLifespanSeconds

static ESerialDataFormat s_GetSerialFormat(CCDDClient::EDataFormat &data_format)

NCBI_PARAM_DEF(double, CDD, client_timeout, -1.0)

NCBI_PARAM_ENUM_ARRAY(objects::CCDDClient::EDataFormat, CDD, data_format)

NCBI_PARAM_DECL(double, CDD, client_timeout)

typedef NCBI_PARAM_TYPE(CDD, data_format) TDataFormatParam

NCBI_PARAM_ENUM_DEF(objects::CCDDClient::EDataFormat, CDD, data_format, objects::CCDDClient::eBinary)

NCBI_PARAM_ENUM_DECL(objects::CCDDClient::EDataFormat, CDD, data_format)

#define DEFAULT_CDD_SERVICE_NAME

CAtomicCounter_WithAutoInit –.

void x_UpdateDeadline(shared_ptr< SCDDCacheInfo > &info)

CCDDClientPool::SCDDBlob TBlob

TBlob Get(const CSeq_id_Handle &seq_id)

list< shared_ptr< SCDDCacheInfo > > TInfoQueue

CCDDClientPool::TBlobId TBlobId

map< CSeq_id_Handle, shared_ptr< SCDDCacheInfo > > TSeqIdMap

map< string, shared_ptr< SCDDCacheInfo > > TBlobIdMap

virtual const char * GetErrCodeString(void) const override

Get error code interpreted as text.

CCDDClientGuard(CCDDClientPool &pool)

CCDDClientPool::TClient m_Client

static CRef< TBlobId > StringToBlobId(const string &s)

SCDDBlob GetBlobBySeq_ids(const TSeq_idSet &ids)

TBlobData GetBlobByBlobId(const TBlobId &blob_id)

TBlobData x_RequestBlobData(const TBlobId &blob_id)

CCDDClientPool(const string &service_name="getCddSeqAnnot", size_t pool_soft_limit=10, time_t pool_age_limit=900, bool exclude_nucleotides=true)

void x_ReleaseClient(TClient &client)

static string BlobIdToString(const TBlobId &blob_id)

SCDDBlob GetBlobBySeq_id(CSeq_id_Handle idh)

bool IsValidId(const CSeq_id &id)

unique_ptr< CCDDBlobCache > m_Cache

static int x_NextSerialNumber(void)

TClientPool::iterator TClient

bool m_ExcludeNucleotides

void x_DiscardClient(TClient &client)

TBlobInfo GetBlobIdBySeq_id(CSeq_id_Handle idh)

bool x_CheckReply(CRef< CCDD_Reply > &reply, int serial, CCDD_Reply::TReply::E_Choice choice)

CRef< CCDD_Reply > AskBlob(int serial_number, const CID2_Blob_Id &blob_id)

CRef< CCDD_Reply > AskBlobId(int serial_number, const CSeq_id &seq_id)

EDataFormat

Serial data format for requests and replies.

@ eSemiBinary

JSON requests, binary ASN.1 replies.

@ eDefaultFormat

Determined by [CCddClient] data_format.

@ eJSON

Bidirectional JSON.

@ eBinary

Bidirectional binary ASN.1.

CCDDClient(const string &service_name=kEmptyStr, EDataFormat data_format=eDefaultFormat)

virtual void ReadReply(CObjectIStream &in, CCDD_Reply &reply)

virtual void Ask(const CCDD_Request_Packet &request, CCDD_Reply &reply)

virtual void WriteRequest(CObjectOStream &out, const CCDD_Request_Packet &request)

void JustAsk(const CCDD_Request_Packet &request)

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

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

CTimeout – Timeout interval.

const_iterator end() const

const_iterator find(const key_type &key) const

const_iterator lower_bound(const key_type &key) const

const_iterator end() const

iterator insert(const value_type &val)

const_iterator begin() const

container_type::iterator iterator

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

main entry point for tests

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

@ eNoOwnership

No ownership is assumed.

EIO_Status Fetch(const STimeout *timeout=kDefaultTimeout)

Flush the stream and fetch the response (w/o extracting any user data)

TValue Add(int delta) THROWS_NONE

Atomically add value (=delta), and return new counter value.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

TErrCode GetErrCode(void) const

Get error code.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

virtual void Ask(const CCDD_Request_Packet &request, CCDD_Reply &reply)

void SetArgs(const string &args)

Set additional connection arguments.

unique_ptr< CObjectOStream > m_Out

virtual void x_Connect(void) override

virtual void WriteRequest(CObjectOStream &out, const CCDD_Request_Packet &request)

unsigned int TSerial_Format_Flags

MSerial_Format –.

ESerialDataFormat

Data file format.

@ fSerial_Json_NoIndentation

do not use indentation

@ fSerial_Json_NoEol

do not write end-of-line symbol

@ eSerial_AsnBinary

ASN.1 binary.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Optimized implementation of CSerialObject::Assign, which is not so efficient.

CConstRef< CSeq_id > GetSeqId(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

virtual void SetFormattingFlags(TSerial_Format_Flags flags)

Set output formatting flags.

void Reset(void)

Reset reference object.

EIO_Status SetTimeout(EIO_Event event, const STimeout *timeout)

Specify timeout for the pipe I/O (see Open|Read|Write functions).

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static string URLEncode(const CTempString str, EUrlEncode flag=eUrlEnc_SkipMarkChars)

URL-encode string.

@ eUrlEnc_URIQueryValue

Encode query part of an URI, arg value.

void Set(EType type)

Set special value.

static void GetCurrentTimeT(time_t *sec, long *nanosec=0)

Get current UTC time in time_t format (with nanoseconds).

@ eDefault

Default timeout (to be interpreted by the client code)

const STimeout * g_CTimeoutToSTimeout(const CTimeout &cto, STimeout &sto)

CTimeout/STimeout adapters.

const TBlob_id & GetBlob_id(void) const

Get the Blob_id member data.

const TMessage & GetMessage(void) const

Get the Message member data.

E_Choice

Choice variants.

TSeverity GetSeverity(void) const

Get the Severity member data.

Tdata & Set(void)

Assign a value to data member.

const TSeq_id & GetSeq_id(void) const

Get the Seq_id member data.

TCode GetCode(void) const

Get the Code member data.

@ e_Get_blob_by_seq_id

return (Seq-annot + blob-id) for get-blob-by-seq-id OR get-blob-by-seq-ids request

@ e_Get_blob_id

return blob-id for get-blob-id request

@ e_Get_blob

return Seq-annot for get-blob request

TSat_key GetSat_key(void) const

Get the Sat_key member data.

TSub_sat GetSub_sat(void) const

Get the Sub_sat member data.

TSat GetSat(void) const

Get the Sat member data.

@ e_Gibbmt

Geninfo backbone moltype.

@ e_Giim

Geninfo import id.

@ e_Gpipe

Internal NCBI genome pipeline processing ID.

@ e_Gibbsq

Geninfo backbone seqid.

@ e_General

for other databases

@ e_Gi

GenInfo Integrated Database.

@ e_Named_annot_track

Internal named annotation tracking ID.

@ e_not_set

No variant selected.

unsigned int

A callback function used to compare two keys in a database.

constexpr bool empty(list< Ts... >) noexcept

static const STimeout kZeroTimeout

std::istream & in(std::istream &in_, double &x_)

static CNamedPipeClient * client

CCDDClientPool::SCDDBlob TBlob

SCDDCacheInfo & operator=(const SCDDCacheInfo &)

SCDDCacheInfo(const SCDDCacheInfo &)

SCDDCacheInfo(const CSeq_id_Handle idh, const TBlob &b)

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