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NCBI C++ ToolKit: src/app/pubseq_gateway/server/async_resolve_base.hpp Source File

1 #ifndef PSGS_ASYNCRESOLVEBASE__HPP 2 #define PSGS_ASYNCRESOLVEBASE__HPP 59  const string

& message,

62  function

<void(

void

)>;

65  function

<void(

void

)>;

92

shared_ptr<CPSGS_Reply> reply,

104

list<string> && secondary_id_list,

105  string

&& primary_seq_id,

151  int16_t

effective_seq_id_type)

const

;

166  bool

with_seq_id_type);

170  int16_t

effective_seq_id_type);

176  EDiagSev

severity,

const string

& message);

179  EDiagSev

severity,

const string

& message);

function< void(SBioseqResolution &&async_bioseq_resolution)> TSeqIdResolutionFinishedCB

function< void(void)> TSeqIdResolutionStartProcessingCB

function< void(void)> TContinueResolveCB

function< void(CRequestStatus::ECode status, int code, EDiagSev severity, const string &message, EPSGS_LoggingFlag logging_flag)> TSeqIdResolutionErrorCB

CRequestStatus::ECode GetCombinedErrorCode(void) const

bool HasErrors(void) const

vector< SResolveInputSeqIdError > m_Errors

void AppendError(const string &msg, CRequestStatus::ECode code)

string GetCombinedErrorMessage(const list< SPSGSeqId > &seq_id_to_resolve) const

string GetCouldNotResolveMessage(void) const

bool MoveToNextSeqId(void)

SPSGS_RequestBase::EPSGS_AccSubstitutioOption GetAccessionSubstitutionOption(void)

string x_GetSeqIdsToResolveList(void) const

psg_time_point_t m_BioseqInfoStart

void x_OnBioseqInfoWithoutSeqIdType(vector< CBioseqInfoRecord > &&records)

list< SPSGSeqId > m_SeqIdsToResolve

psg_time_point_t GetAsyncResolutionStartTimestamp(void) const

psg_time_point_t m_AsyncCassResolutionStart

void x_SignalStartProcessing(void)

int16_t x_GetRequestSeqIdType(void)

void SetAsyncResolutionStartTimestamp(const psg_time_point_t &ts)

void x_OnSi2csiError(CRequestStatus::ECode status, int code, EDiagSev severity, const string &message)

TSeqIdResolutionErrorCB m_ErrorCB

psg_time_point_t m_Si2csiStart

int16_t m_EffectiveSeqIdType

CBioseqInfoRecord::TSeqIdType m_BioseqInfoRequestedSeqIdType

list< string > m_SecondaryIdList

void x_PreparePrimaryBioseqInfoQuery(const CBioseqInfoRecord::TAccession &seq_id, CBioseqInfoRecord::TVersion version, CBioseqInfoRecord::TSeqIdType seq_id_type, CBioseqInfoRecord::TGI gi, bool with_seq_id_type)

virtual ~CPSGS_AsyncResolveBase()

CBioseqInfoRecord::TGI m_BioseqInfoRequestedGI

bool GetSeqIdResolve(void)

SBioseqResolution m_BioseqResolution

SPSGS_ResolveRequest::TPSGS_BioseqIncludeData GetBioseqInfoFields(void)

void SetupSeqIdToResolve(void)

void x_OnBioseqInfoError(CRequestStatus::ECode status, int code, EDiagSev severity, const string &message)

bool CanSkipBioseqInfoRetrieval(const CBioseqInfoRecord &bioseq_info_record)

int16_t m_EffectiveVersion

CPSGSResolveErrors m_ResolveErrors

bool OptimizationPrecondition(const string &primary_id, int16_t effective_seq_id_type) const

list< SPSGSeqId >::const_iterator m_CurrentSeqIdToResolve

bool NonKeyBioseqInfoFieldsRequested(void)

void x_OnBioseqInfo(vector< CBioseqInfoRecord > &&records)

void x_PrepareSecondaryAsIsSi2csiQuery(void)

TContinueResolveCB m_ContinueResolveCB

bool m_StartProcessingCalled

CCassFetch * m_NoSeqIdTypeFetch

EPSGS_AccessionAdjustmentResult AdjustBioseqAccession(SBioseqResolution &bioseq_resolution)

string x_GetRequestSeqId(void)

CCassFetch * m_CurrentFetch

TSeqIdResolutionStartProcessingCB m_StartProcessingCB

CBioseqInfoRecord::TVersion m_BioseqInfoRequestedVersion

TSeqIdResolutionFinishedCB m_FinishedCB

int16_t GetEffectiveVersion(const CTextseq_id *text_seq_id)

EPSGS_ResolveStage m_ResolveStage

void x_OnSi2csiRecord(vector< CSI2CSIRecord > &&records)

void x_OnSeqIdAsyncResolutionFinished(SBioseqResolution &&async_bioseq_resolution)

CBioseqInfoRecord::TAccession m_BioseqInfoRequestedAccession

void x_PrepareSecondarySi2csiQuery(void)

void x_PrepareSi2csiQuery(const string &secondary_id, int16_t effective_seq_id_type)

virtual void Process(void)=0

Main processing function.

EDiagSev

Severity level for the posted diagnostics.

const string version

version string

Defines NCBI C++ diagnostic APIs, classes, and macros.

psg_clock_t::time_point psg_time_point_t

EPSGS_AccessionAdjustmentResult

Defines CRequestStatus class for NCBI C++ diagnostic API.

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

EPSGS_AccSubstitutioOption

int TPSGS_BioseqIncludeData

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