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NCBI C++ ToolKit: src/app/pubseq_gateway/server/snp_client.cpp Source File

(!seq_id)

ret;

(!text_id)

ret;

(text_id->CanGetAccession() && text_id->CanGetVersion() &&

!text_id->GetAccession().empty() && text_id->GetVersion() > 0) {

= s.size();

(pos &&

(s[pos - 1])) {

num_len =

- pos;

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

<

Container>

Container::value_type::TObjectType&

(Container& container)

container.push_back(obj);

id2info =

;

pos = id2info.find_last_of(

);

(pos ==

|| pos + 1 >= id2info.size())

;

= NStr::StringToNumeric<int>(id2info.substr(pos + 1));

pos = id2info.find_last_of(

);

(pos ==

)

;

NStr::StringToNumeric<int>(id2info.substr(pos + 1));

m_IsPrimaryTrack(

),

m_IsPrimaryTrackGraph(

),

m_FilterIndex(

(filter_index)),

m_IsPrimaryTrack(

),

m_IsPrimaryTrackGraph(

),

m_SeqIndex(

(seq_index)),

m_FilterIndex(

(filter_index))

(

.IsValidNA()) {

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);

dot1 =

.find(

);

dot2 =

.find(

, dot1 + 1);

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_SeqIndex(it.GetVDBSeqIndex()),

m_IsPrimaryTrack(

),

m_IsPrimaryTrackGraph(

)

(!

->IsValidNA()) {

: m_IsValidNA(

),

m_RemainingOpenRetries(

.m_Config.m_FileOpenRetry)

(!request.

.empty() || !request.

.empty()))

;

(!request.

.empty()) {

(exception& e) {}

(

&

: request.

) {

(exception& e) {}

(!idh)

;

(

.

() )

;

( text_id->IsSetVersion() ||

> 0 ) {

(

<< acc <<

);

slot->SetObject(

);

( !

->m_SNPDb &&

->m_RemainingOpenRetries > 0 ) {

--

->m_RemainingOpenRetries;

->m_RemainingOpenRetries = 0;

(

<< acc <<

<< exc);

(

->m_RemainingOpenRetries > 0 ) {

(

<< acc <<

);

(

<< acc <<

<< exc);

(

->m_RemainingOpenRetries > 0 ) {

(

<< acc <<

);

( exception& exc ) {

(

<< acc <<

<< exc.what());

(

->m_RemainingOpenRetries > 0 ) {

(

<< acc <<

);

( !

->m_SNPDb ) {

vector<string> can_process;

(

& name : (priority==-1?

can_process.push_back(name);

(filter_index == 0 && acc.size() == name.size()) {

can_process.push_back(name);

(chunk_request.

< 0)

;

parsed_info.

.get();

vector<SSNPData> ret;

(!

.IsAllowedSNPScaleLimit(scale_limit))

ret;

(acc_ver.empty()) {

na_acc =

->GetPrimarySnpTrackForAccVer(acc_ver);

(na_acc.empty()) {

ret.push_back(

);

ret.push_back(

);

(filter_index == 0 && acc.size() == name.size()) {

.m_BlobId = blob_id.ToString();

overview_name =

coverage_name =

ret.push_back(

);

( exception& exc ) {

.m_Error =

+

(exc.what());

ret.push_back(

);

(!parsed_info.

)

ret;

annot_info->SetName(name);

& feat_type =

(annot_info->SetFeat());

annot_info->SetSeq_loc().SetWhole_seq_id().Assign(*

.

());

annot_info->SetName(name);

annot_info->SetGraph();

annot_info->SetSeq_loc().SetWhole_seq_id().Assign(*

.

());

GetTiming().Register(

,

, status, start, 0);

User-defined methods of the data storage class.

CID2S_Seq_annot_Info –.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

EPSGS_Type GetRequestType(void) const

@ ePSGS_AnnotationRequest

@ ePSGS_BlobBySatSatKeyRequest

TRequest & GetRequest(void)

static CPubseqGatewayApp * GetInstance(void)

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

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

static bool IsValidFilterIndex(size_t filter_index)

string GetAccession(void) const

string GetSatNA(void) const

size_t GetSeqIndex(void) const

void SetPrimaryTrackGraph()

SSNPProcessor_Config m_Config

bool CanProcessRequest(CPSGS_Request &request, TProcessorPriority priority) const

SSNPData GetChunk(const string &id2info, int chunk_id)

void x_RegisterTiming(psg_time_point_t start, EPSGOperation operation, EPSGOperationStatus status)

bool IsValidSeqId(const objects::CSeq_id_Handle &idh) const

friend class CSNPFileInfo

vector< SSNPData > GetAnnotInfo(const objects::CSeq_id_Handle &id, const string &name, objects::CSeq_id::ESNPScaleLimit scale_limit)

CRef< objects::CSnpPtisClient > m_PTISClient

CRef< objects::CID2S_Seq_annot_Info > x_GetGraphInfo(const string &name, const objects::CSeq_id_Handle &id)

CSNPClient(const SSNPProcessor_Config &config)

CRef< CSNPSeqInfo > GetSeqInfo(const CSNPBlobId &blob_id)

CRef< CSNPFileInfo > GetFileInfo(const string &acc)

vector< string > WhatNACanProcess(SPSGS_AnnotRequest &annot_request, TProcessorPriority priority=0) const

shared_ptr< objects::CVDBMgr > m_Mgr

bool HaveValidSeq_id(const SPSGS_AnnotRequest &request) const

SSNPData GetBlobByBlobId(const string &blob_id)

CRef< objects::CID2S_Seq_annot_Info > x_GetFeatInfo(const string &name, const objects::CSeq_id_Handle &id)

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

CRef< CSNPSeqInfo > GetSeqInfo(const CSeq_id_Handle &seq_id)

const string & GetBaseAnnotName(void) const

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

CSNPFileInfo(CSNPDataLoader_Impl &impl, const string &file_name)

string GetSNPAnnotName(size_t filter_index) const

CSNPSeqInfo(CSNPFileInfo *file, const CSNPDbSeqIterator &it)

bool m_IsPrimaryTrackGraph

CSNPDbSeqIterator GetSeqIterator(void) const

void SetFromBlobId(const CSNPBlobId &blob_id)

void SetFilterIndex(size_t filter_index)

void LoadBlob(SSNPData &data, bool split_enabled)

string GetAnnotName(void) const

CRef< CSNPBlobId > GetBlobId(void) const

void LoadChunk(SSNPData &data, int chunk_id)

static string CombineWithZoomLevel(const string &acc, int zoom_level)

Combine accession string and zoom level into a string with separator.

static CRef< CSnpPtisClient > CreateClient()

@ eProtectedDb

DB is protected.

@ eNotFoundDb

DB main file not found.

virtual TErrCode GetErrCode(void) const

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

CRef< CSlot > GetSlot(const string &acc_or_path)

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

main entry point for tests

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

#define NCBI_THROW_FMT(exception_class, err_code, message)

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

static EAccessionInfo IdentifyAccession(const CTempString &accession, TParseFlags flags=fParse_AnyRaw)

Deduces information from a bare accession a la WHICH_db_accession; may report false negatives on prop...

void Reset(void)

Reset the handle (remove seq-id reference)

CSeq_id::EAccessionInfo IdentifyAccession(void) const

bool IsAccVer(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

ESNPScaleLimit

SNP annotation scale limits.

void Swap(TThisType &ref)

Swaps the pointer with another reference.

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

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.

CGuard< CRWLock, SSimpleWriteLock< CRWLock > > TWriteLockGuard

operation

Bit operations.

@ e_Other

for historical reasons, 'other' = 'refseq'

constexpr bool empty(list< Ts... >) noexcept

const string version

version string

double value_type

The numeric datatype used by the parser.

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

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)

#define PSG_ERROR(message)

#define PSG_INFO(message)

psg_clock_t::time_point psg_time_point_t

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

static CNamedPipeClient * client

static const char kFileEnd[]

static size_t s_ExtractFilterIndex(string &s)

const int kFilterIndexCount

Container::value_type::TObjectType & s_AddObject(Container &container)

const int kSNPSubSatGraph

const int kFilterIndexMaxLength

static const char kFilterPrefixChar

const unsigned int kRefSeqAccFlags

static string s_GetAccVer(const CSeq_id_Handle &id)

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

vector< string > GetNotProcessedName(TProcessorPriority priority)

vector< string > m_SeqIds

SParsedId2Info(const string &str)

unique_ptr< CSNPBlobId > blob_id

objects::CSeq_id::ESNPScaleLimit m_SNPScaleLimit

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