Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/snploader__impl_8cpp_source.html below:

NCBI C++ ToolKit: src/sra/data_loaders/snp/snploader_impl.cpp Source File

=

=

m_IsPrimaryTrack(

),

m_IsPrimaryTrackGraph(

),

m_FilterIndex(

(filter_index)),

m_IsPrimaryTrack(

),

m_IsPrimaryTrackGraph(

),

m_SeqIndex(

(seq_index)),

m_FilterIndex(

(filter_index))

(

.IsValidNA() ) {

SetSatNA(

.GetAccession());

m_Accession =

.GetAccession();

SetSeqAndFilterIndex(seq_index, filter_index);

na_index > 0 && na_index < 1000000000;

pair<size_t, size_t> ret(0, 0);

( acc.

() < 13 || acc.

() > 15 ||

acc[0] !=

|| acc[1] !=

|| acc[11] !=

) {

na_index = NStr::StringToNumeric<size_t>(acc.

(2, 9),

na_version = NStr::StringToNumeric<size_t>(acc.

(12),

ret.first = na_index;

ret.second = na_version;

pair<size_t, size_t> na =

(acc);

= s.size();

( pos &&

(s[pos-1]) ) {

num_len =

- pos;

index = NStr::StringToNumeric<size_t>(s.substr(pos));

dot1 =

.find(

);

( dot1 ==

) {

dot2 =

.find(

, dot1+1);

( dot2 ==

) {

sat = NStr::StringToNumeric<size_t>(

.substr(0, dot1),

subsat = NStr::StringToNumeric<size_t>(

.substr(dot1+1, dot2-dot1-1),

is_primary_track_graph = is_primary_track && subsat >=

;

na_index = subsat - (is_primary_track_graph?

: 0);

satkey = NStr::StringToNumeric<size_t>(

.substr(dot2+1),

<<

);

m_FileReopenTime, m_FileRecheckTime)

(

);

<

Call>

retry_count)

( retry_count == 0 ) {

(

= 1;

< retry_count; ++

) {

(

<<

<<name<<

<<

<<

<<exc);

( exception& exc ) {

(

<<

<<name<<

<<

<<

<<exc.

());

(

<<

<<name<<

<<

<<

);

(

<<

<<wait_sec<<

);

=

->GetBaseAnnotName();

<<

info_slot->SetObject(

);

->InitializeDb(*

);

<<

);

info_slot->ResetObject();

info_slot->SetObject(

);

->InitializeDb(*

);

data_source, cref(blob_id)),

(

seq_id =

.

() ) {

(

* text_id = seq_id->GetTextseq_Id() ) {

( text_id->IsSetAccession() && !text_id->GetAccession().empty() &&

text_id->IsSetVersion() && text_id->GetVersion() > 0 ) {

ds, cref(

), sel, processed_nas),

);

accs_size = accs.

();

(!

.IsAllowedSNPScaleLimit(scale_limit))

;

( !acc_ver.empty() ) {

(13,

<<

<<acc_ver);

(13,

<<

<<acc_ver<<

<<na_acc);

( !na_acc.empty() ) {

seq->SetFilterIndex(filter_index);

blob_id = seq->GetBlobId();

blob_id = seq->GetBlobId();

acc = it->first;

( filter_index == 0 && acc.size() == it->first.size() ) {

seq->SetFilterIndex(filter_index);

(5,

<<

<<blob_id<<

);

(6,

<<

<<blob_id<<

cref(blob_id), ref(chunk)),

<<blob_id<<

<<chunk_info.

()<<

);

<<blob_id<<

<<chunk_info.

()<<

& csra)

( sep !=

) {

m_SeqIndex(it.GetVDBSeqIndex()),

m_IsPrimaryTrack(

),

m_IsPrimaryTrackGraph(

)

( !

->IsValidNA() ) {

blob_id->SetPrimaryTrackGraph();

blob_id->SetPrimaryTrackFeat();

<<

<<

.second

<<

<< split_version

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Blob state exceptions, used by GenBank loader.

CTSE_LoadLock GetTSE_LoadLock(const TBlobId &blob_id)

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

Int4 GetSubSat(void) const

void SetPrimaryTrackFeat()

bool IsValidSatKey(void) const

static bool IsValidSeqIndex(size_t seq_index)

bool m_IsPrimaryTrackGraph

int GetSubSatBase(void) const

bool IsValidSat(void) const

size_t GetFilterIndex(void) const

string ToString(void) const

Get string representation of blob id.

CSNPBlobId(const CTempString &str)

static bool IsValidNAIndex(size_t index)

static bool IsValidNAVersion(size_t version)

void FromString(CTempString str)

void SetSatNA(CTempString acc)

void SetSeqAndFilterIndex(size_t seq_index, size_t filter_index)

size_t GetNAVersion(void) const

bool operator<(const CSNPBlobId &id) const

static pair< size_t, size_t > ParseNA(CTempString acc)

void SetNAIndex(size_t na_index)

static bool IsValidNA(pair< size_t, size_t > na)

Int4 GetSatKey(void) const

void SetNAVersion(size_t na_version)

size_t GetNAIndex(void) const

bool FromSatString(CTempString str)

bool IsPrimaryTrackGraph() const

int GetSatBase(void) const

bool IsValidSubSat(void) const

bool IsPrimaryTrack() const

CSeq_id_Handle GetSeqId(void) const

bool operator==(const CSNPBlobId &id) const

static bool IsValidFilterIndex(size_t filter_index)

string GetAccession(void) const

string GetSatNA(void) const

size_t GetSeqIndex(void) const

void SetPrimaryTrackGraph()

CRef< CSNPFileInfo > FindFile(const string &acc)

CRef< CSNPFileInfo > GetFixedFile(const string &acc)

std::invoke_result< Call >::type CallWithRetry(Call &&call, const char *name, unsigned retry_count=0)

CRef< CSNPFileInfo > x_GetFileInfo(const string &file)

CRef< CSNPSeqInfo > GetSeqInfo(const CSNPBlobId &blob_id)

void GetChunkOnce(const CSNPBlobId &blob_id, CTSE_Chunk_Info &chunk_info)

CDataLoader::TTSE_LockSet GetRecords(CDataSource *data_source, const CSeq_id_Handle &idh, CDataLoader::EChoice choice)

void LoadBlob(const CSNPBlobId &blob_id, CTSE_LoadLock &load_lock)

CObjectManager::TPriority GetDefaultPriority(void) const

CSNPDataLoader_Impl(const CSNPDataLoader::SLoaderParams &params)

CTSE_LoadLock GetBlobById(CDataSource *data_source, const CSNPBlobId &blob_id)

friend class CSNPFileInfo

CRef< CSnpPtisClient > m_PTISClient

CTSE_LoadLock GetBlobByIdOnce(CDataSource *data_source, const CSNPBlobId &blob_id)

CRef< CSNPFileInfo > GetFileInfo(const string &acc)

CDataLoader::TTSE_LockSet GetOrphanAnnotRecords(CDataSource *ds, const CSeq_id_Handle &idh, const SAnnotSelector *sel, CDataLoader::TProcessedNAs *processed_nas)

CSNPDataLoader::TAnnotNames TAnnotNames

TAnnotNames GetPossibleAnnotNames(void) const

void GetChunk(const CSNPBlobId &blob_id, CTSE_Chunk_Info &chunk)

CDataLoader::TTSE_LockSet GetOrphanAnnotRecordsOnce(CDataSource *ds, const CSeq_id_Handle &id, const SAnnotSelector *sel, CDataLoader::TProcessedNAs *processed_nas)

void AddFixedFileOnce(const string &file_name)

void AddFixedFile(const string &file_name)

~CSNPDataLoader_Impl(void)

vector< CAnnotName > TAnnotNames

static CSeq_id::ESNPScaleLimit GetSNP_Scale_Limit(void)

pair< CRef< CID2S_Split_Info >, TSplitVersion > GetSplitInfoAndVersion(const string &base_name, TFlags flags=fDefaultFlags) const

void SetTrack(const CSNPDbTrackIterator &track)

CSNPDb_Impl & GetDb(void) const

const CSeq_id_Handle & GetSeqIdHandle(void) const

CRef< CSeq_entry > GetEntry(const string &base_name, TFlags flags=fDefaultFlags) const

CRef< CID2S_Chunk > GetChunkForVersion(const string &base_name, TChunkId chunk_id, TSplitVersion split_version) const

size_t GetVDBSeqIndex(void) const

const string & GetDbPath(void) const

unsigned m_RemainingOpenRetries

CSNPDataLoader::TAnnotNames TAnnotNames

CRef< CSNPSeqInfo > GetSeqInfo(const CSeq_id_Handle &seq_id)

const string & GetBaseAnnotName(void) const

void InitializeDb(CSNPDataLoader_Impl &impl)

void x_Initialize(CSNPDataLoader_Impl &impl, const string &file_name)

CSNPFileInfo(CSNPDataLoader_Impl &impl, const string &file_name)

void GetPossibleAnnotNames(TAnnotNames &names) const

string GetSNPAnnotName(size_t filter_index) const

void LoadAnnotChunk(CTSE_Chunk_Info &chunk_info)

CSNPSeqInfo(CSNPFileInfo *file, const CSNPDbSeqIterator &it)

bool m_IsPrimaryTrackGraph

CSNPDbSeqIterator GetSeqIterator(void) const

void LoadAnnotBlob(CTSE_LoadLock &load_lock)

void SetFromBlobId(const CSNPBlobId &blob_id)

void SetFilterIndex(size_t filter_index)

string GetAnnotName(void) const

CRef< CSNPBlobId > GetBlobId(void) const

static CRef< CSnpPtisClient > CreateClient()

virtual string GetPrimarySnpTrackForAccVer(const string &acc_ver)=0

static void Attach(CTSE_Info &tse, const CID2S_Split_Info &split)

static void Load(CTSE_Chunk_Info &chunk, const CID2S_Chunk &data)

@ eProtectedDb

DB is protected.

@ eNotFoundDb

DB main file not found.

virtual TErrCode GetErrCode(void) const

void SetLoaded(CObject *obj=0)

TChunkId GetChunkId(void) const

const CTSE_Split_Info & GetSplitInfo(void) const

CTSE_Split_Info & GetSplitInfo(void)

void SetSeq_entry(CSeq_entry &entry, CTSE_SetObjectInfo *set_info=0)

bool IsLoaded(void) const

void SetSplitVersion(TSplitVersion version)

TSplitVersion GetSplitVersion(void) const

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

size_t get_size_limit() const

void set_size_limit(size_t limit)

CRef< CSlot > GetSlot(const string &acc_or_path)

container_type::iterator iterator

const_iterator end() const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

Include a standard set of the NCBI C++ Toolkit most basic headers.

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

main entry point for tests

static const struct name_t names[]

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define LOG_POST_X(err_subcode, message)

#define ERR_POST_ONCE(message)

Error posting only once during program execution.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

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.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

void Info(CExceptionArgs_Base &args)

#define MSerial_AsnText

I/O stream manipulators –.

void Reset(void)

Reset the handle (remove seq-id reference)

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

static void SetProcessedNA(const string &na, TProcessedNAs *processed_nas)

EChoice

main blob is blob with sequence all other blobs are external and contain external annotations

@ kPriority_Replace

Default priority for replacement loaders.

bool IsIncludedAnyNamedAnnotAccession(void) const

check if any named annot accession is included in the search

TSNPScaleLimit GetSNPScaleLimit(void) const

const TNamedAnnotAccessions & GetNamedAnnotAccessions(void) const

void Swap(TThisType &ref)

Swaps the pointer with another reference.

TObjectType & GetObject(void)

Get object.

#define NCBI_PARAM_TYPE(section, name)

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

@ eParam_NoThread

Do not use per-thread values.

int32_t Int4

4-byte (32-bit) signed integer

unsigned char Uchar

Alias for unsigned char.

uint32_t Uint4

4-byte (32-bit) unsigned integer

uint16_t Uint2

2-byte (16-bit) unsigned 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.

NCBI_NS_STD::string::size_type SIZE_TYPE

CTempString substr(size_type pos) const

Obtain a substring from this string, beginning at a given offset.

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.

size_type size(void) const

Return the length of the represented array.

@ fConvErr_NoThrow

Do not throw an exception on error.

CMutexGuard TWriteLockGuard

Define Write Lock Guard.

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

void Start(void)

Start the timer.

@ eStart

Start timer immediately after creating.

Definition of all error codes used in SRA C++ support libraries.

const struct ncbi::grid::netcache::search::fields::SIZE size

const struct ncbi::grid::netcache::search::fields::KEY key

string s_Value(TValue value)

const GenericPointer< typename T::ValueType > T2 value

void SleepMilliSec(unsigned long ml_sec, EInterruptOnSignal onsignal=eRestartOnSignal)

void split(std::vector< std::string > *strVec, const std::string &str_, const std::string &split_)

const CConstRef< CSeq_id > GetAccession(const CSeq_id_Handle &id_handle)

Helper classes and templates to implement plugins.

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

static const char kFileEnd[]

static size_t sx_ExtractFilterIndex(string &s)

static unsigned GetRetryCountParam(void)

NCBI_PARAM_DEF(unsigned, SNP_LOADER, RETRY_COUNT, 3)

static bool IsSplitEnabled(void)

const int kFilterIndexCount

static size_t GetGCSize(void)

const int kSNPSubSatGraph

const int kFilterIndexMaxLength

static int GetDebugLevel(void)

static unsigned GetFileRecheckTimeParam(void)

static string sx_AddFilterIndex(const string &s, size_t filter_index)

NCBI_PARAM_DECL(int, SNP_LOADER, DEBUG)

NCBI_PARAM_DEF_EX(int, SNP_LOADER, DEBUG, 0, eParam_NoThread, SNP_LOADER_DEBUG)

static const char kFilterPrefixChar

static unsigned GetFileReopenTimeParam(void)

NCBI_DEFINE_ERR_SUBCODE_X(16)

static string s_GetAccVer(const CSeq_id_Handle &id)

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4