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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/reader__pubseq_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/data_loaders/genbank/pubseq/reader_pubseq.cpp Source File

(

(

) !=

) {

.SetParam(param, &idIn);

.SetParam(param, &idIn);

(

(

) !=

) {

dbr.

(pos) <<

<<

);

& server,

& dbapi_driver)

: m_Server(server) , m_User(user), m_Password(pswd),

m_DbapiDriver(dbapi_driver),

m_SetCubbyUser(

)

(1,

);

& driver_name)

m_SetCubbyUser(

)

(1,

);

( stream.

() ) {

stream.

();

CPubseqValidator(

allow_gzip,

excl_wgs_master)

: m_AllowGzip(allow_gzip),

m_ExclWGSMaster(excl_wgs_master)

(

.LangCmd(

));

( m_ExclWGSMaster ) {

(

.LangCmd(

));

GetName(

)

{

;

m_AllowGzip, m_ExclWGSMaster;

.release();

(

.Fetch() ) {

(

pos = 0; pos <

.NofItems(); ++pos ) {

(

.ItemName(pos) == name ) {

( !sx_FetchNextItem(*

,

) ) {

args[

]=

;

args[

]=

;

vector<string> driver_list;

driver_count = driver_list.size();

vector<string> errmsg(driver_count);

(

= 0;

< driver_count; ++

) {

&errmsg[

], &args);

( exception& exc ) {

errmsg[

] = exc.what();

(

= 0;

< driver_count; ++

) {

(2,

<<driver_list[

]<<

<<errmsg[

]);

+

( !

.get() ) {

s <<

<<

->ServerName();

( lock.IsLoaded() ) {

( lock.IsLoaded() ) {

( !gi_ids.IsLoaded() ) {

( blob_ids.IsLoaded() ) {

(all_blob_ids.IsLoaded());

( seq_id.

() ) {

(

<< gi);

(

->HasMoreResults() ) {

( !dbr.

() ) {

status = v.

();

( status == 100 ) {

sx_FetchNextItem(*dbr,

) ) {

.sequence_found =

;

( dbr->

() )

( exception&

) {

( dbr->

() )

(

<< seq_id.

());

( seq_id.

() ) {

result_count = 0;

->SetParam(

, &asnIn);

(

->HasMoreResults()) {

( !dbr.

() ) {

( dbr->

() )

( dbr->

() ) {

(

pos = 0; pos < dbr->

(); ++pos ) {

& name = dbr->

(pos);

(

<< name);

(name ==

) {

(name ==

) {

(name ==

|| name ==

) {

( extFeatGot.

() ) {

(

);

(name ==

) {

dbr->

(&namedAnnotsGot);

(

<<namedAnnotsGot.

());

( namedAnnotsGot.

() ) {

sat = satGot.

();

sat_key = sat_keyGot.

();

<< sat_key <<

( extFeatGot.

() ) {

s << extFeatGot.

();

( gi ==

&& !sat && !sat_key ) {

.sequence_found =

;

blob_id->SetSat(sat);

blob_id->SetSatKey(sat_key);

( !extFeatGot.

() ) {

blob_id->SetSat(sat);

blob_id->SetSatKey(sat_key);

( !extFeatGot.

() ) {

blob_id->SetSubSat(extFeatGot.

());

( with_named_accs && named_gi !=

) {

(

<<named_gi);

(

->HasMoreResults()) {

( !dbr.

() ) {

( dbr->

() )

( dbr->

() ) {

(

pos = 0; pos < dbr->

(); ++pos ) {

& name = dbr->

(pos);

(

<< name);

(name ==

) {

(name ==

) {

(name ==

) {

(name ==

) {

blob_id->SetSat(satGot.

());

blob_id->SetSatKey(satKeyGot.

());

annot_info->AddNamedAnnotName(nameGot.

());

.SetAnnotInfo(annot_info);

blob_ids.push_back(

);

( result_count == 0 ) {

result_count > 0;

( load_lock.IsLoaded() ) {

(

<< gi);

->SetParam(

, &binIn);

(

->HasMoreResults() ) {

( !dbr.

() ) {

( dbr->

() ) {

status = v.

();

( status == 100 ) {

sx_FetchNextItem(*dbr,

) ) {

(

.HaveMoreData() ) {

(

.HaveMoreData() ) {

(4,

);

( dbr->

() )

( dbr->

() )

ids.push_back(seq_id);

( lock.IsLoaded() ) {

( lock.IsLoaded() ) {

( !gi_lock.

(gi) ) {

.sequence_found =

;

( load_lock.IsLoaded() ) {

(

<< gi);

->SetParam(

, &hashIn);

(

->HasMoreResults() ) {

( !dbr.

() ) {

sx_FetchNextItem(*dbr,

) ) {

.sequence_found =

;

.hash_known =

;

( dbr->

() )

(3,

);

.SetAndSaveBlobState(blob_id, 0);

(5,

);

.SetAndSaveBlobVersion(blob_id, 0);

( exception& ) {

.SetAndSaveBlobVersion(blob_id, 0);

( stream.read(

, 1) && stream.gcount() ) {

(6,

<<blob_id);

->DumpResults();

->SetParam(

, &idIn);

->SetParam(

, &satIn);

->SetParam(

, &ext_feat);

->SetParam(

, &satIn);

->SetParam(

, &satKeyIn);

->SetParam(

, &ext_feat);

.release();

( !ret.

&&

.HasMoreResults() ) {

(

);

(

.HasFailed() ) {

( !dbr.

() ) {

( dbr->

() )

( !ret.

&& dbr->

() ) {

(

pos = 0; pos < dbr->

(); ++pos ) {

& name = dbr->

(pos);

(

<< name);

( name ==

) {

( v.

() ) {

( name ==

) {

( v.

() & 5 ) {

( name ==

) {

( v.

() ) {

( name ==

) {

( name ==

) {

( v.

() == kState_dead ) {

( name ==

) {

( name ==

) {

(

<< item->GetType());

( item->GetType() ) {

( !ret.

&& force_blob ) {

(

);

( !web_cookie.empty() ) {

objects::CPubseqReader>

objects::CReader* drv = 0;

drv =

objects::CPubseqReader(params, driver);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

bool IsMainBlob(void) const

TSatKey GetSatKey() const

TSubSat GetSubSat() const

string ToString(void) const

Get string representation of blob id.

ERW_Result PendingCount(size_t *)

Via parameter "count" (which is guaranteed to be supplied non-NULL) return the number of bytes that a...

ERW_Result Read(void *buf, size_t count, size_t *bytes_read)

Read as many as "count" bytes into a buffer pointed to by the "buf" argument.

CDB_Result_Reader(CDB_Result *db_result)

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)

bool IsLoadedAccVer(void) const

bool IsLoadedChunk(void) const

bool IsLoadedGi(void) const

static bool IsFound(const TData &data)

static TGi GetGi(const TData &data)

bool IsLoadedHash(void) const

static int GetHash(const TData &data)

TData::TState GetState(void) const

Data loader exceptions, used by GenBank loader.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

CObjectIStreamAsnBinary –.

static TGi ConvertGiFromOM(TGi gi)

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

static void OffsetGiToOM(TGi &gi)

static bool TrySNPSplit(void)

static void OffsetIdToOM(CSeq_id &id)

static CSeq_id_Handle ConvertIdFromOM(CSeq_id_Handle id)

Class factory for Pubseq reader.

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

Create instance of TDriver.

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

atomic< I_DriverContext * > m_Context

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

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

virtual ~CPubseqReader() override

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

virtual int GetMaximumConnectionsLimit(void) const override

virtual void x_ConnectAtSlot(TConn conn) override

I_BaseCmd * x_SendRequest(const CBlob_id &blob_id, CDB_Connection *db_conn, const char *rpc)

virtual void x_DisconnectAtSlot(TConn conn, bool failed) override

bool LoadSeq_idInfo(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const SAnnotSelector *with_named_accs)

virtual void x_RemoveConnectionSlot(TConn conn) override

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

CDB_Connection * x_GetConnection(TConn conn)

virtual bool LoadSeq_idAccVer(CReaderRequestResult &result, const CSeq_id_Handle &seq_id) override

virtual void x_AddConnectionSlot(TConn conn) override

virtual bool LoadSeq_idSeq_ids(CReaderRequestResult &result, const CSeq_id_Handle &seq_id) override

void x_ReceiveData(CReaderRequestResult &result, SPubseqReaderReceiveData &data, const TBlobId &blob_id, I_BaseCmd &cmd, bool force_blob)

virtual void SetIncludeHUP(bool include_hup=true, const string &web_cookie=NcbiEmptyString) override

virtual bool LoadSequenceHash(CReaderRequestResult &result, const CSeq_id_Handle &seq_id) override

TConnections m_Connections

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

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

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

CPubseqReader(int max_connections=0, const string &server=kEmptyStr, const string &user=kEmptyStr, const string &pswd=kEmptyStr, const string &dbapi_driver=kEmptyStr)

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

Note about the "buf_size" parameter for streams in this API.

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

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

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

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

vector< CSeq_id_Handle > TSeqIds

CReadDispatcher * m_Dispatcher

void SetAndSaveSeq_idAccVer(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const TSequenceAcc &acc_id) const

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

vector< CBlob_Info > TBlobIds

void SetAndSaveNoBlob(CReaderRequestResult &result, const TBlobId &blob_id, TChunkId chunk_id, TBlobState blob_state)

void x_SetIncludeHUP(bool include_hup)

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

virtual void OpenConnection(TConn conn)

CDataLoader::SHashFound TSequenceHash

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

void SetAndSaveSequenceHash(CReaderRequestResult &result, const CSeq_id_Handle &seq_id, const TSequenceHash &hash) const

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

int SetMaximumConnections(int max)

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

CDataLoader::SGiFound TSequenceGi

Template class helps to implement one driver class factory.

static string GetUserName(void)

Get actual user name for the current process.

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

definition of a Culling tree

CZipStreamDecompressor – zlib based decompression stream processor.

A very basic data-read interface.

#define DBLB_INSTALL_DEFAULT_EX(if_set)

Easy-to-use macro to install the default DBAPI service mapper, with control over what to do if a conn...

static CS_CONNECTION * conn

static const char * str(char *buf, int n)

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)

element_type * get(void) const

Get pointer.

element_type * release(void)

Release will release ownership of pointer to caller.

@ eTakeOwnership

An object can take ownership of another.

I_DriverContext * GetDriverContext(const string &driver_name, string *err_msg=0, const map< string, string > *attr=0)

virtual EDB_ResType ResultType() const

Get type of the result.

virtual bool SkipItem()

Skip result item.

virtual CDB_LangCmd * LangCmd(const string &lang_query)

Make language command.

virtual size_t ReadItem(void *buffer, size_t buffer_size, bool *is_null=0)

Read a result item body (for BLOB columns, mostly).

virtual CDB_Object * GetItem(CDB_Object *item_buf=0, EGetItem policy=eAppendLOB)

Get a result item (you can use either GetItem or ReadItem).

virtual const char * ItemName(unsigned int item_num) const

Get name of a result item.

virtual unsigned int NofItems() const

Get # of items (columns) in the result.

virtual CDB_RPCCmd * RPC(const string &rpc_name)

Make remote procedure call command.

virtual bool Fetch()

Fetch next row.

virtual void AssignValue(const CDB_Object &v)

const char * Value(void) const

virtual void AssignValue(const CDB_Object &v)

#define LOG_POST_X_ONCE(err_subcode, message)

#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.

#define NCBI_THROW_FMT(exception_class, err_code, message)

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

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 ...

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

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

@ 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.

string AsString(void) const

CSeq_id::E_Choice Which(void) const

bool IsIncludedAnyNamedAnnotAccession(void) const

check if any named annot accession is included in the search

bool IsIncludedNamedAnnotAccession(const string &acc) const

check if named annot accession is included in the search

SAnnotSelector & IncludeNamedAnnotAccession(const string &acc, int zoom_level=0)

#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.

ERW_Result

Result codes for I/O operations.

@ eRW_NotImplemented

Action / information is not available.

@ eRW_Eof

End of data, should be considered permanent.

@ eRW_Success

Everything is okay, I/O completed.

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 CStringUTF8 SQLEncode(const CStringUTF8 &str, ESqlEncode flag)

SQL-encode string.

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.

@ eSqlEnc_TagNonASCII

Produce N'...' when input's not pure ASCII.

#define DEFINE_STATIC_FAST_MUTEX(id)

Define static fast mutex and initialize it.

@ eNonCompatible

major, minor does not match

@ e_Gi

GenInfo Integrated Database.

const string version

version string

string s_Value(TValue value)

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

Helper classes and templates to implement plugins.

#define DEFAULT_DB_PASSWORD

#define DEFAULT_DB_DRIVER

static TIntId sx_GetIntId(CDB_Result &dbr, int pos)

#define DEFAULT_EXCL_WGS_MASTER

static void sx_SetIntId(CDB_RPCCmd &cmd, const char *param, TIntId id)

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

#define DEFAULT_DB_SERVER

NCBI_PARAM_DECL(int, GENBANK, PUBSEQOS_DEBUG)

NCBI_PARAM_DEF_EX(int, GENBANK, PUBSEQOS_DEBUG, 0, eParam_NoThread, GENBANK_PUBSEQOS_DEBUG)

static int GetDebugLevel(void)

void GenBankReaders_Register_Pubseq(void)

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

#define RPC_GET_BLOB_INFO

#define DEFAULT_ALLOW_GZIP

#define NCBI_GBLOADER_READER_PUBSEQ_PARAM_SERVER

#define NCBI_GBLOADER_READER_PUBSEQ_PARAM_USER

#define NCBI_GBLOADER_READER_PUBSEQ_PARAM_EXCL_WGS_MASTER

#define NCBI_GBLOADER_READER_PUBSEQ_DRIVER_NAME

#define NCBI_GBLOADER_READER_PUBSEQ_PARAM_GZIP

#define NCBI_GBLOADER_READER_PUBSEQ_PARAM_PASSWORD

#define NCBI_GBLOADER_READER_PUBSEQ_PARAM_DRIVER

Reader-writer based streams.

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

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

Better replacement of GetSequenceHash(), this method should be defined in data loaders,...

AutoPtr< CDB_Result > dbr

CReader::TBlobState blob_state

CReader::TBlobVersion blob_version

SPubseqReaderReceiveData()

static CS_CONTEXT * context

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