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

m_Preopen(ePreopenByConfig),

m_UsePSGInitialized(

),

m_PSGNoSplit(

),

m_HasHUPIncluded(

)

( method.empty() ) {

method = TGenbankLoaderMethod::GetDefault();

use_psg =

;

vector<string> str_list;

(

s : str_list) {

(str_list.size() == 1) {

+ loader_method +

);

+ loader_method +

);

atomic<bool> initialized;

atomic<bool> loader_psg;

( !initialized.load(memory_order_acquire) ) {

new_value =

;

( TGenbankLoaderPsg::GetDefault() ) {

loader_psg.store(new_value, memory_order_relaxed);

initialized.store(

, memory_order_release);

loader_psg.load(memory_order_relaxed);

( !loader_psg_param.empty() ) {

<<

<< ex.what());

( !loader_method.empty() ) {

(loader_method.empty()) {

(loader_method.empty()) {

& reader_name,

& web_cookie,

& web_cookie)

& reader_name,

is_default, priority);

& reader_name,

& web_cookie,

& web_cookie)

.Set(

,

);

(web_cookie.empty()) {

.Update(web_cookie.data(), web_cookie.size());

m_HasHUPIncluded(params.HasHUPIncluded()),

m_WebCookie(params.GetWebCookie())

TParams* FindSubNode(TParams* params,

TParams* FindSubNode(

TParams* params,

& subnode_name)

( params->

(subnode_name) ) {

subnode = FindSubNode(params, subnode_name);

& subnode_name)

( params->

(subnode_name) ) {

subnode = FindSubNode(params, subnode_name);

& reader_name)

& reader_name)

& param_name,

& param_value)

* subnode = FindSubNode(params, param_name);

subnode->

().value = param_value;

& param_name)

* subnode = FindSubNode(params, param_name);

TSatKey GetSatKey() const

CObjectManager::TPriority GetPriority(const TPluginManagerParamTree *params) const

CObjectManager::EIsDefault GetIsDefault(const TPluginManagerParamTree *params) const

bool ValidParams(const TPluginManagerParamTree *params) const

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, const CGBLoaderParams &params, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

virtual TRealBlobId x_GetRealBlobId(const TBlobId &blob_id) const =0

static void SetParam(TParamTree *params, const string &param_name, const string &param_value)

CConstRef< CSeqref > GetSatSatkey(const CSeq_id_Handle &idh)

CGBDataLoader(const string &loader_name, const CGBLoaderParams &params)

static TParamTree * GetReaderParams(TParamTree *params, const string &reader_name)

virtual bool GetTrackSplitSeq() const override

static string GetLoaderNameFromArgs(CReader *reader=0)

TRealBlobId GetRealBlobId(const TBlobId &blob_id) const

static TParamTree * GetParamsSubnode(TParamTree *params, const string &subnode_name)

bool HasHUPIncluded(void) const

virtual CObjectManager::TPriority GetDefaultPriority(void) const override

static bool IsUsingPSGLoader(void)

static string x_GetLoaderMethod(const TParamTree *params)

static string GetParam(const TParamTree *params, const string &param_name)

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

virtual ~CGBDataLoader(void)

static TParamTree * GetLoaderParams(TParamTree *params)

const string & GetLoaderMethod(void) const

CReader * GetReaderPtr(void) const

EPreopenConnection m_Preopen

const string & GetLoaderName(void) const

const TParamTree * m_ParamTree

bool IsSetEnableCDD(void) const

void SetEnableSNP(bool enable)

const TParamTree * GetParamTree(void) const

CRef< CReader > m_ReaderPtr

CNullable< bool > m_EnableCDD

void SetEnableWGS(bool enable)

void SetParamTree(const TParamTree *params)

CNullable< bool > m_EnableSNP

void SetEnableCDD(bool enable)

bool IsSetEnableSNP(void) const

const string & GetWebCookie(void) const

bool GetEnableWGS(void) const

CNullable< bool > m_EnableWGS

bool HasHUPIncluded(void) const

bool GetEnableCDD(void) const

CGBLoaderParams & operator=(const CGBLoaderParams &)

const string & GetReaderName(void) const

void SetHUPIncluded(bool include_hup=true, const string &web_cookie=NcbiEmptyString)

bool GetEnableSNP(void) const

bool IsSetEnableWGS(void) const

void SetReaderPtr(CReader *reader_ptr)

virtual ~CGB_DataLoaderCF(void)

virtual CDataLoader * CreateAndRegister(CObjectManager &om, const TPluginManagerParamTree *params) const

Data loader exceptions, used by GenBank loader.

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

CDataSource & GetDataSource(void) const

const TBlobId & GetBlobId(void) const

definition of a Culling tree

static void md5(const char *src, const char *out)

NCBI_PARAM_DECL(bool, GENBANK, LOADER_PSG)

#define NCBI_GBLOADER_PARAM_LOADER_PSG

#define NCBI_PSG_READER_NAME

static bool s_GetDefaultUsePSG()

void DataLoaders_Register_GenBank(void)

#define GBLOADER_HUP_NAME

void NCBI_EntryPoint_DataLoader_GB(CPluginManager< CDataLoader >::TDriverInfoList &info_list, CPluginManager< CDataLoader >::EEntryPointRequest method)

void NCBI_EntryPoint_xloader_genbank(CPluginManager< objects::CDataLoader >::TDriverInfoList &info_list, CPluginManager< objects::CDataLoader >::EEntryPointRequest method)

static bool s_CheckPSGMethod(const string &loader_method)

typedef NCBI_PARAM_TYPE(GENBANK, LOADER_PSG) TGenbankLoaderPsg

NCBI_PARAM_DEF_EX(bool, GENBANK, LOADER_PSG, false, eParam_NoThread, GENBANK_LOADER_PSG)

#define NCBI_GBLOADER_PARAM_LOADER_METHOD

#define NCBI_GBLOADER_DRIVER_NAME

bool IsNull(void) const

Check if the object is unassigned.

const TValue & GetValue(void) const

Get a const reference to the current value.

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

void Critical(CExceptionArgs_Base &args)

#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.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

virtual CObjectManager::TPriority GetDefaultPriority(void) const

TLoader * GetLoader(void) const

Get pointer to the loader.

CDataSource * GetDataSource(void) const

EIsDefault

Flag defining if the data loader is included in the "default" group.

virtual TBlobId GetBlobId(const CSeq_id_Handle &idh)

TObjectType * GetNCPointerOrNull(void) const THROWS_NONE

Get pointer value.

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

@ eParam_NoThread

Do not use per-thread values.

static void NCBI_EntryPointImpl(TDriverInfoList &info_list, EEntryPointRequest method)

Entry point implementation.

list< SDriverInfo > TDriverInfoList

List of driver information.

EEntryPointRequest

Actions performed by the entry point.

#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 bool StringToBool(const CTempString str)

Convert string to bool.

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 SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

bool KeyEqual(const TKeyType &key) const

Check if the node's key is equal to the argument.

void AddNode(TTreeType *subnode)

Add new subnode.

const TTreeType * FindSubNode(const TKeyType &key) const

Non recursive linear scan of all subnodes, with key comparison.

const TValue & GetValue(void) const

Return node's value.

CMD5 - class for computing Message Digest version 5 checksums.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Multi-threading – classes, functions, and features.

Helper classes and templates to implement plugins.

CRef< objects::CObjectManager > om

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