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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/reader__id1_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/data_loaders/genbank/id1/reader_id1.cpp Source File

fail_recover = 0;

( fail_recover > 0 ) {

stream.setstate(ios::badbit);

(2,

);

& driver_name)

(2,

);

( service_name.empty() ) {

service_name =

(GENBANK,ID1_SERVICE_NAME)::GetDefault();

( service_name.empty() ) {

( stream.bad() ) {

tmout.

= 0; tmout.

= 1;

( ids_lock.IsLoaded() ) {

sc_SatMap.find(dbtag.

().c_str()) != sc_SatMap.end() ) {

seq_ids.push_back(seq_id);

( !gi_lock.IsLoaded() ) {

( !gi_ids_lock.IsLoaded() ) {

( ids.IsLoaded() ) {

( seq_id.

() ) {

gi = seq_id.

();

( !id1_reply.

() ) {

(

& s : accs ) {

( s.first !=

) {

( ids.IsLoaded() ) {

(

.GetGeneral().GetTag().GetId8(num) && num != 0 ) {

& dbtag =

.GetGeneral();

& db = dbtag.

();

( iter != sc_SatMap.end() ) {

sat = iter->second.first;

sub_sat = iter->second.second;

sat_key =

(num);

sub_sat |=

((num>>32)<<16);

blob_id->SetSat(sat);

blob_id->SetSatKey(sat_key);

blob_id->SetSubSat(sub_sat);

( !gi_lock.IsLoaded() ) {

( !gi_ids_lock.IsLoaded() ) {

( ids.IsLoaded() ) {

( seq_id.

() ) {

gi = seq_id.

();

(

.GetBlob_state() < 0 ) {

(

.GetSuppress() & 5 ) {

(

.GetSuppress() == 4)

(

.GetWithdrawn() > 0) {

(

.GetConfidential() > 0) {

(

.GetSat() < 0 ||

.GetSat_key() < 0 ) {

blob_id->SetSat(

.GetSat());

blob_id->SetSatKey(

.GetSat_key());

(

.IsSetExtfeatmask() ) {

blob_id->SetSat(

.GetSat());

blob_id->SetSatKey(

.GetSat_key());

(

.IsSetExtfeatmask() ) {

blob_id->SetSubSat(

.GetExtfeatmask());

( reply.

() ) {

);

);

<<

);

<<

);

+

s <<

;

+

s <<

;

s <<

;

+

s <<

;

objects::CReader* drv = 0;

drv =

objects::CId1Reader(params, driver);

TSatKey GetSatKey() const

TSubSat GetSubSat() const

Base class, inherited from "std::iostream", does both input and output, using the specified CONNECTOR...

@ID1server_back.hpp User-defined methods of the data storage class.

CID1server_maxcomplex –.

static TIntId GetExtAnnotGi(const CBlob_id &blob_id)

static void CreateExtAnnotBlob_ids(TBlobIds &blob_ids, TIntId gi, int ext_feat)

static bool IsAnnotSat(int sat)

static int GetExtAnnotSubSat(const CBlob_id &blob_id)

Class factory for ID1 reader.

CSimpleClassFactoryImpl< objects::CReader, objects::CId1Reader > TParent

objects::CReader * CreateInstance(const string &driver=kEmptyStr, CVersionInfo version=NCBI_INTERFACE_VERSION(objects::CReader), const TPluginManagerParamTree *params=0) const

Create instance of TDriver.

void GetBlobVersion(CReaderRequestResult &result, const CBlob_id &blob_id)

CReaderServiceConnector m_Connector

void GetBlobState(CReaderRequestResult &result, const CBlob_id &blob_id)

virtual void x_AddConnectionSlot(TConn conn)

void x_SetParams(CID1server_maxcomplex &params, const CBlob_id &blob_id)

TBlobState x_ResolveId(CReaderRequestResult &result, CID1server_back &id1_reply, CID1server_request &id1_request)

void x_ReceiveReply(TConn conn, CID1server_back &reply)

bool LoadSeq_idSeq_ids(CReaderRequestResult &result, const CSeq_id_Handle &id)

bool LoadSeq_idBlob_ids(CReaderRequestResult &result, const CSeq_id_Handle &id, const SAnnotSelector *sel)

All LoadXxx() methods should return false if there is no requested data in the reader.

void x_SendRequest(TConn conn, CID1server_request &request)

CId1Reader(int max_connections=0)

virtual void x_RemoveConnectionSlot(TConn conn)

void x_SetBlobRequest(CID1server_request &request, const CBlob_id &blob_id)

void GetBlob(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id)

CConn_IOStream * x_GetConnection(TConn conn)

bool LoadSeq_idGi(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

string x_ConnDescription(CConn_IOStream &stream) const

virtual void x_ConnectAtSlot(TConn conn)

virtual void x_DisconnectAtSlot(TConn conn, bool failed)

TConnections m_Connections

bool LoadGiBlob_ids(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const SAnnotSelector *sel)

bool LoadGiSeq_ids(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

int GetMaximumConnectionsLimit(void) const

bool SetNoBlob_ids(const CFixedBlob_ids::TState &state, TExpirationTime expiration_time)

bool SetLoadedBlob_ids(const TData &data, TExpirationTime expiration_time)

bool IsLoadedChunk(void) const

bool IsLoadedGi(void) const

static bool IsFound(const TData &data)

static TGi GetGi(const TData &data)

bool SetLoadedSeq_ids(const TData &data)

Data loader exceptions, used by GenBank loader.

CObjectIStreamAsnBinary –.

CObjectOStreamAsnBinary –.

static TGi ConvertGiFromOM(TGi gi)

static void OffsetAllGisToOM(CBeginInfo obj, CTSE_SetObjectInfo *set_info=0)

virtual void ProcessStream(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, CNcbiIstream &stream) const

static bool TrySNPSplit(void)

static void OffsetAllGisFromOM(CBeginInfo obj)

const CProcessor & GetProcessor(CProcessor::EType type) const

void LoadSeq_idGi(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

void LoadSeq_idSeq_ids(CReaderRequestResult &result, const CSeq_id_Handle &seq_id)

void LoadSeq_idBlob_ids(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const SAnnotSelector *sel)

void RememberIfBad(SConnInfo &conn_info)

void SetTimeoutTo(STimeout *tmout) const

void InitTimeouts(CConfig &conf, const string &driver_name)

SConnInfo Connect(int error_count=0)

string GetConnDescription(CConn_IOStream &stream) const

void SetServiceName(const string &service_name)

vector< CSeq_id_Handle > TSeqIds

CReadDispatcher * m_Dispatcher

void SetAndSaveNoSeq_idBlob_ids(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const SAnnotSelector *sel, const CLoadLockGi &gi_lock) const

void SetAndSaveSeq_idGi(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const TSequenceGi &gi) const

void SetAndSaveBlobVersion(CReaderRequestResult &result, const TBlobId &blob_id, TBlobVersion version) const

vector< CBlob_Info > TBlobIds

void SetAndSaveBlobState(CReaderRequestResult &result, const TBlobId &blob_id, TBlobState blob_state) const

void SetAndSaveSeq_idSeq_ids(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const CFixedSeq_ids &seq_ids) const

void x_ReportDisconnect(const char *reader, const char *server, TConn conn, bool failed) const

virtual void OpenConnection(TConn conn)

void SetAndSaveSeq_idBlob_ids(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const SAnnotSelector *sel, CLoadLockBlobIds &lock, const CLoadLockBlobIds &blob_ids) const

void InitParams(CConfig &conf, const string &driver_name, int default_max_conn)

int SetMaximumConnections(int max)

virtual bool LoadSeq_idBlob_ids(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const SAnnotSelector *sel)

All LoadXxx() methods should return false if there is no requested data in the reader.

void SetAndSaveNoSeq_idSeq_ids(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, TState state) const

Template class helps to implement one driver class factory.

class CStaticArrayMap<> is an array adaptor that provides an STLish interface to statically-defined a...

TBase::const_iterator const_iterator

definition of a Culling tree

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

main entry point for tests

static CS_CONNECTION * conn

void reset(element_type *p=0, EOwnership ownership=eTakeOwnership)

Reset will delete the old pointer (if owned), set content to the new value, and assume the ownership ...

#define GI_FROM(T, value)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

element_type * get(void) const

Get pointer.

@ eTakeOwnership

An object can take ownership of another.

EIO_Status CONN_SetTimeout(CONN conn, EIO_Event event, const STimeout *timeout)

Specify timeout for the connection I/O, including "Connect" (aka "Open") and "Close".

#define LOG_POST_X(err_subcode, message)

#define ERR_POST_X_ONCE(err_subcode, message)

Error posting only once during program execution with default error code and given error subcode.

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

#define NCBI_THROW(exception_class, err_code, message)

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

void Warning(CExceptionArgs_Base &args)

#define NCBI_THROW_FMT(exception_class, err_code, message)

The same as NCBI_THROW but with message processed as output to ostream.

#define NCBI_RETHROW(prev_exception, exception_class, err_code, message)

Generic macro to re-throw an exception.

#define MSerial_AsnText

I/O stream manipulators –.

string GetString(const string &driver_name, const string &param_name, EErrAction on_error, const string &default_value, const list< string > *synonyms=NULL)

Utility function to get an element of parameter tree Throws an exception when mandatory parameter is ...

@ eErr_NoThrow

Return default value on error.

CConstRef< CSeq_id > GetSeqId(void) const

static CSeq_id_Handle GetGiHandle(TGi gi)

Faster way to create a handle for a gi.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

CSeq_id::E_Choice Which(void) const

CBeginInfo Begin(C &obj)

Get starting point of object hierarchy.

bool IsIncludedAnyNamedAnnotAccession(void) const

check if any named annot accession is included in the search

const TNamedAnnotAccessions & GetNamedAnnotAccessions(void) const

#define NCBI_PARAM_TYPE(section, name)

Generate typename for a parameter from its {section, name} attributes.

@ eParam_NoThread

Do not use per-thread values.

static void NCBI_EntryPointImpl(TDriverInfoList &info_list, EEntryPointRequest method)

Entry point implementation.

#define NCBI_INTERFACE_VERSION(iface)

Macro to construct CVersionInfo class using interface name (relies on CInterfaceVersion class)

list< SDriverInfo > TDriverInfoList

List of driver information.

EEntryPointRequest

Actions performed by the entry point.

int32_t Int4

4-byte (32-bit) signed integer

int64_t Int8

8-byte (64-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

unsigned int usec

microseconds (modulo 1,000,000)

@ eIO_ReadWrite

eIO_Read | eIO_Write (also, eCONN_OnFlush)

@ eIO_Close

also serves as an error indicator in SOCK_Poll

@ eNonCompatible

major, minor does not match

const TTag & GetTag(void) const

Get the Tag member data.

const TDb & GetDb(void) const

Get the Db member data.

void SetEnt(TEnt value)

Assign a value to Ent data member.

const TGotblobinfo & GetGotblobinfo(void) const

Get the variant data.

void SetGi(TGi value)

Assign a value to Gi data member.

bool IsIds(void) const

Check if variant Ids is selected.

TBlob_state GetBlob_state(void) const

Get the Blob_state member data.

TGetsefromgi & SetGetsefromgi(void)

Select the variant.

E_Choice Which(void) const

Which variant is currently selected.

TError GetError(void) const

Get the variant data.

bool IsError(void) const

Check if variant Error is selected.

bool IsGotgi(void) const

Check if variant Gotgi is selected.

const TGotsewithinfo & GetGotsewithinfo(void) const

Get the variant data.

void SetSat(const TSat &value)

Assign a value to Sat data member.

TGotgi GetGotgi(void) const

Get the variant data.

const TIds & GetIds(void) const

Get the variant data.

TGetblobinfo & SetGetblobinfo(void)

Select the variant.

void SetMaxplex(TMaxplex value)

Assign a value to Maxplex data member.

TGetseqidsfromgi & SetGetseqidsfromgi(void)

Select the variant.

TGetsewithinfo & SetGetsewithinfo(void)

Select the variant.

TGetgi & SetGetgi(void)

Select the variant.

list< CRef< CSeq_id > > TIds

bool IsGotblobinfo(void) const

Check if variant Gotblobinfo is selected.

const TBlob_info & GetBlob_info(void) const

Get the Blob_info member data.

@ eEntry_complexities_entry

the "natural" entry for this (nuc-prot)

TGi GetGi(void) const

Get the variant data.

const TGeneral & GetGeneral(void) const

Get the variant data.

@ e_General

for other databases

@ e_Gi

GenInfo Integrated Database.

const string version

version string

string s_Value(TValue value)

Multi-threading – mutexes; rw-locks; semaphore.

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

Helper classes and templates to implement plugins.

static const TSI sc_SatIndex[]

static bool sx_IsSNPOnly(const SAnnotSelector::TNamedAnnotAccessions &accs)

#define GENBANK_ID1_RANDOM_FAILS_RECOVER

void NCBI_EntryPoint_xreader_id1(CPluginManager< objects::CReader >::TDriverInfoList &info_list, CPluginManager< objects::CReader >::EEntryPointRequest method)

DEFINE_STATIC_ARRAY_MAP(TSatMap, sc_SatMap, sc_SatIndex)

void GenBankReaders_Register_Id1(void)

NCBI_PARAM_DECL(int, GENBANK, ID1_DEBUG)

SStaticPair< TRDR::ESat, TRDR::ESubSat > TSK

static int GetDebugLevel(void)

void NCBI_EntryPoint_Id1Reader(CPluginManager< objects::CReader >::TDriverInfoList &info_list, CPluginManager< objects::CReader >::EEntryPointRequest method)

#define GENBANK_ID1_RANDOM_FAILS_FREQUENCY

SStaticPair< const char *, TSK > TSI

#define SetRandomFail(stream)

NCBI_PARAM_DEF_EX(int, GENBANK, ID1_DEBUG, 0, eParam_NoThread, GENBANK_ID1_DEBUG)

CStaticPairArrayMap< const char *, TSK, PNocase_CStr > TSatMap

#define NCBI_GBLOADER_READER_ID1_PARAM_SERVICE_NAME

#define NCBI_GBLOADER_READER_ID1_DRIVER_NAME

Better replacement of GetGi(), this method should be defined in data loaders, GetGi() is left for com...

AutoPtr< CConn_IOStream > m_Stream

Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...

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