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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/vdbgraphloader__impl_8cpp_source.html below:

NCBI C++ ToolKit: src/sra/data_loaders/vdbgraph/vdbgraphloader_impl.cpp Source File

lookup_type =

(VDBGRAPH_LOADER, LOOKUP_TYPE)::GetDefault();

(1,

<<*it);

<

Call>

retry_count)

( retry_count == 0 ) {

(

= 1;

< retry_count; ++

) {

(

<<

<<name<<

<<

<<

<<exc);

( exception& exc ) {

(

<<

<<name<<

<<

<<

<<exc.

());

(

<<

<<name<<

<<

<<

);

(

<<

<<wait_sec<<

);

);

->m_VDBFile = name;

m_BaseAnnotName;

ds, cref(

), sel, processed_nas),

);

( it.second->ContainsAnnotsFor(

) ) {

(

->ContainsAnnotsFor(

) ) {

<<blob_id.

);

.GetMainAnnotName(),

.GetMainAnnotName(),

.GetMainAnnotName(),

<<blob_id.

);

kSize[3] = {

.GetOverviewAnnotName(),

.GetMidZoomAnnotName(),

.GetMainAnnotName()

(

k = 0; k < 3; ++k ) {

(

= 0;

*kSize[k] < length; ++

) {

from =

*kSize[k], to_open =

(length, from+kSize[k]);

id_add = kIdAdd[k];

*

kTypeName[

] = {

name =

.GetMainAnnotName();

from =

*kSize[k], to_open =

(length, from+kSize[k]);

<<kTypeName[k]<<

<<blob_id.

<<

<<from<<

<<(to_open-1));

<<kTypeName[k]<<

<<blob_id.

<<

( s.size() < 13 ) {

( s[0] !=

|| s[1] !=

|| s[11] !=

) {

(

= 0;

< 9; ++

) {

->m_VDBFile = na_acc;

->m_BaseAnnotName = na_acc;

(2,

<<na_acc);

(3,

<<na_acc);

static const NStr::TNumToStringFlags kFlags

Blob state exceptions, used by GenBank loader.

CTSE_LoadLock GetTSE_LoadLock(const TBlobId &blob_id)

CTSE_LoadLock GetTSE_LoadLockIfLoaded(const TBlobId &blob_id)

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

@ eNotFoundDb

DB main file not found.

virtual TErrCode GetErrCode(void) const

pair< TBioseqId, TBioseq_setId > TPlace

void x_AddAnnotPlace(const TBioseqId &id)

TBlobId GetBlobId(void) const

void x_LoadAnnot(const TPlace &place, const CSeq_annot &annot)

void SetLoaded(CObject *obj=0)

TChunkId GetChunkId(void) const

void x_AddAnnotType(const CAnnotName &annot_name, const SAnnotTypeSelector &annot_type, const TLocationId &location_id)

CTSE_Split_Info & GetSplitInfo(void)

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

bool IsLoaded(void) const

void AddChunk(CTSE_Chunk_Info &chunk_info)

string ToString(void) const

Get string representation of blob id.

bool operator==(const CBlobId &id) const

CRef< CVDBGraphDataLoader_Impl::SVDBFileInfo > m_FileInfo

bool operator<(const CBlobId &id) const

CVDBGraphBlobId(const string &file, const CSeq_id_Handle &id)

CRef< SVDBFileInfo > OpenVDBGraphFileOnce(const string &name)

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

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

void GetChunkOnce(CTSE_Chunk_Info &chunk)

void GetChunk(CTSE_Chunk_Info &chunk)

~CVDBGraphDataLoader_Impl(void)

TTSE_Lock GetBlobById(CDataSource *ds, const TBlobId &blob_id)

CRef< SVDBFileInfo > x_GetFileInfo(const string &name)

TFixedFileMap m_FixedFileMap

CRef< CSeq_entry > LoadFullEntry(const CVDBGraphBlobId &blob_id)

CDataLoader::TTSE_LockSet TTSE_LockSet

TAnnotNames GetPossibleAnnotNames(void) const

TTSE_Lock GetBlobByIdOnce(CDataSource *ds, const TBlobId &blob_id)

CVDBGraphDataLoader_Impl(const TVDBFiles &vdb_files)

vector< string > TVDBFiles

TAutoFileMap m_AutoFileMap

TBlobId GetBlobId(const CSeq_id_Handle &idh)

TBlobId GetBlobIdFromString(const string &str) const

CRef< SVDBFileInfo > OpenVDBGraphFile(const string &name)

TMissingFileSet m_MissingFileSet

CObjectManager::TPriority GetDefaultPriority(void) const

CRef< SVDBFileInfo > x_GetNAFileInfo(const string &na_acc)

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

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

vector< CAnnotName > TAnnotNames

void LoadSplitEntry(CTSE_Info &tse, const CVDBGraphBlobId &blob_id)

bool SeqTableIsSmaller(COpenRange< TSeqPos > range) const

TSeqPos GetSeqLength(void) const

CRef< CSeq_annot > GetAnnot(COpenRange< TSeqPos > range, const string &annot_name=kEmptyStr, TContentFlags content=fDefaultContent) const

const CSeq_id_Handle & GetSeq_id_Handle(void) const

container_type::iterator iterator

const_iterator end() const

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)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

iterator find(const key_type &key)

size_t get_size_limit(void) const

void set_size_limit(size_t size_limit)

#define LOG_POST_X(err_subcode, message)

#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)

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

string GetName(void) const

Get the base entry name with extension (if any).

#define MSerial_AsnText

I/O stream manipulators –.

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

static bool IsRequestedAnyNA(const SAnnotSelector *sel)

static bool IsRequestedNA(const string &na, const SAnnotSelector *sel)

@ kPriority_Extra

Default priority for extra annot loaders.

@ eAll

all blobs (main and external)

@ eOrphanAnnot

all external annotations if no Bioseq exists

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.

uint32_t Uint4

4-byte (32-bit) unsigned integer

static TThisType GetWhole(void)

#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

static int StringToNonNegativeInt(const CTempString str, TStringToNumFlags flags=0)

Convert string to non-negative integer value.

TSet & SetSet(void)

Select the variant.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

void SetId(TId &value)

Assign a value to Id data member.

list< CRef< CSeq_annot > > TAnnot

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

E_Choice

Choice variants.

unsigned int

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

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

constexpr auto sort(_Init &&init)

string s_Value(TValue value)

const GenericPointer< typename T::ValueType > T2 value

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

Helper classes and templates to implement plugins.

string GetMidZoomAnnotName(void) const

string GetMainAnnotName(void) const

bool ContainsAnnotsFor(const CSeq_id_Handle &id) const

string GetOverviewAnnotName(void) const

static const size_t kMainTableChunkIdAdd

static const size_t kMainGraphChunkIdAdd

static unsigned GetRetryCountParam(void)

#define MID_ZOOM_NAME_SUFFIX

static const TSeqPos kMainChunkSize

NCBI_PARAM_DEF(unsigned, VDBGRAPH_LOADER, RETRY_COUNT, 3)

static CVDBGraphDb_Impl::ELookupType GetLookupType(void)

static bool GetEnabledOverview(void)

static const size_t kOverviewChunkIdAdd

static size_t GetGCSize(void)

static const size_t kChunkIdMul

static bool GetEnabledMidZoom(void)

static const size_t kMidZoomChunkIdAdd

static int GetUseTable(void)

static int GetDebugLevel(void)

static size_t GetMissingGCSize(void)

static const TSeqPos kOverviewChunkSize

NCBI_PARAM_DEF_EX(int, VDBGRAPH_LOADER, DEBUG, 0, eParam_NoThread, VDBGRAPH_LOADER_DEBUG)

static bool sx_IsNA(const string &s)

static const TSeqPos kMidZoomChunkSize

NCBI_DEFINE_ERR_SUBCODE_X(8)

static bool GetDisabledZoom(void)

NCBI_PARAM_DECL(int, VDBGRAPH_LOADER, DEBUG)

#define OVERVIEW_NAME_SUFFIX

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