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NCBI C++ ToolKit: CAsnvalThreadState Class Reference

Search Toolkit Book for CAsnvalThreadState

#include "thread_state.hpp"
(Private to src/app/asnval.)

Definition at line 86 of file thread_state.hpp.

◆ CAsnvalThreadState() [1/2] ◆ CAsnvalThreadState() [2/2] ◆ ~CAsnvalThreadState() ◆ BuildScope() CRef< CScope > CAsnvalThreadState::BuildScope ( ) const protected ◆ OpenFile()

Definition at line 243 of file thread_state.cpp.

References CFormatGuess::eBinaryASN, CCompressStream::eBZip2, CFormatGuess::eBZip2, CFormatGuess::eGZip, CCompressStream::eGZipFile, CCompressStream::eLZO, CFormatGuess::eLzo, CCompressStream::eNone, eNoOwnership, eSerial_AsnBinary, eSerial_AsnText, eTakeOwnership, CFormatGuess::eTextASN, CCompressStream::fDefault, format, CFormatGuessEx::GuessFormatAndContent(), CFileContentInfo::mInfoGenbank, CFileContentInfoGenbank::mTypeInfo, NcbiCin, CObjectIStream::Open(), s_known_types, and CFormatGuessEx::SetRecognizedGenbankTypes().

◆ ProcessBioseq() ◆ ProcessBioseqset() ◆ ProcessBioSource() ◆ ProcessBSSReleaseFile() void CAsnvalThreadState::ProcessBSSReleaseFile ( IMessageHandler & msgHandler ) protected ◆ ProcessPubdesc() ◆ ProcessSeqAnnot() ◆ ProcessSeqDesc() ◆ ProcessSeqEntry() [1/2] ◆ ProcessSeqEntry() [2/2]

Definition at line 381 of file thread_state.cpp.

References CScope::AddTopLevelSeqEntry(), BuildScope(), CBioseq_Handle::GetId(), LOG_POST_XX, m_CurrentId, m_NumRecords, m_ObjMgr, m_Options, m_pContext, mAppConfig, CAppConfig::mOnlyAnnots, CAppConfig::mQuiet, CValidErrorSuppress::SetSuppressedCodes(), and CValidator::Validate().

Referenced by ProcessBioseq(), ProcessBioseqset(), ProcessSeqEntry(), and ValidateInput().

◆ ProcessSeqFeat() ◆ ProcessSeqSubmit()

Definition at line 472 of file thread_state.cpp.

References CScope::AddTopLevelSeqEntry(), BuildScope(), CSeq_submit_Base::GetData(), CBioseq_Handle::GetId(), CSeq_submit_Base::C_Data::IsEntrys(), LOG_POST_XX, m_CurrentId, m_NumRecords, m_ObjMgr, m_Options, m_pContext, mAppConfig, CAppConfig::mQuiet, CSeq_submit_Base::SetData(), CValidErrorSuppress::SetSuppressedCodes(), and CValidator::Validate().

Referenced by ValidateInput().

◆ ProcessSSMReleaseFile() void CAsnvalThreadState::ProcessSSMReleaseFile ( IMessageHandler & msgHandler ) protected ◆ ReadClassMember()

Definition at line 168 of file thread_state.cpp.

References CScope::AddTopLevelSeqEntry(), BuildScope(), CStopWatch::Elapsed(), CStopWatch::eStart, CBioseq_Handle::GetId(), i, in(), LOG_POST_XX, m_CurrentId, m_Level, m_Longest, m_LongestId, m_NumRecords, m_ObjMgr, m_Options, m_pContext, mAppConfig, CAppConfig::mContinue, CAppConfig::mOnlyAnnots, CAppConfig::mQuiet, CScope::RemoveTopLevelSeqEntry(), CScope::ResetHistory(), sw, and CValidator::Validate().

Referenced by ProcessBSSReleaseFile(), and ProcessSSMReleaseFile().

◆ ReportReadFailure()

Definition at line 304 of file thread_state.cpp.

References IMessageHandler::AddValidErrItem(), eDiag_Critical, CSerialException::eEOF, eErr_GENERIC_InvalidAsn, CAppConfig::eVerbosity_XML, CException::GetErrCode(), m_ReadFailure, mAppConfig, mpIstr, CAppConfig::mVerbosity, NStr::Replace(), CException::ReportAll(), and s_StartWrite().

Referenced by ValidateInput(), and ValidateOneHugeFile().

◆ ValidateAsync()

Definition at line 610 of file thread_state.cpp.

References CScope::AddDataLoader(), BuildScope(), CScope::Exists(), CScope::GetBioseqHandle(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_id_Handle::GetHandle(), CConstRef< C, Locker >::GetPointer(), CSeq_entry_Handle::GetTopLevelEntry(), m_ObjMgr, m_Options, m_pContext, mAppConfig, CAppConfig::mOnlyAnnots, Ref(), CValidErrorSuppress::SetSuppressedCodes(), and CValidator::Validate().

Referenced by ValidateBlobSequential(), and ValidateWorker().

◆ ValidateBatchMode() ◆ ValidateBlobAsync() void CAsnvalThreadState::ValidateBlobAsync ( const string & loader_name, edit::CHugeFileProcess & process, IMessageHandler & msgHandler ) protected ◆ ValidateBlobSequential() void CAsnvalThreadState::ValidateBlobSequential ( const string & loader_name, edit::CHugeFileProcess & process, IMessageHandler & msgHandler ) protected ◆ ValidateInput()

Definition at line 538 of file thread_state.cpp.

References IMessageHandler::AddValidErrItem(), eDiag_Critical, eErr_GENERIC_DuplicateIDs, NStr::eNocase, ERR_POST, Error(), eUnknown, CAppConfig::eVerbosity_XML, CException::GetMsg(), CTypeInfo::GetName(), mAppConfig, mpIstr, CAppConfig::mVerbosity, NCBI_THROW, ProcessBioseq(), ProcessBioseqset(), ProcessBioSource(), ProcessPubdesc(), ProcessSeqAnnot(), ProcessSeqDesc(), ProcessSeqEntry(), ProcessSeqFeat(), ProcessSeqSubmit(), NStr::Replace(), ReportReadFailure(), CRef< C, Locker >::Reset(), s_known_types, and NStr::StartsWith().

Referenced by ValidateTraditionally().

◆ ValidateOneFile() [1/2] ◆ ValidateOneFile() [2/2] ◆ ValidateOneHugeBlob() void CAsnvalThreadState::ValidateOneHugeBlob ( edit::CHugeFileProcess & process, IMessageHandler & msgHandler ) protected

Definition at line 658 of file thread_state.cpp.

References CDirEntry::CreateAbsolutePath(), CObjectManager::eNonDefault, info, LOG_POST_XX, m_CurrentId, m_GlobalInfo, m_ObjMgr, m_Options, m_pContext, mAppConfig, CAppConfig::mOnlyAnnots, CAppConfig::mQuiet, CHugeFileValidator::ReportGlobalErrors(), CHugeFileValidator::ReportPostErrors(), s_StartWrite(), CHugeFileValidator::UpdateValidatorContext(), ValidateBlobAsync(), and ValidateBlobSequential().

Referenced by ValidateOneHugeFile().

◆ ValidateOneHugeFile() void CAsnvalThreadState::ValidateOneHugeFile ( edit::CHugeFileProcess & process, IMessageHandler & msgHandler ) protected

Definition at line 704 of file thread_state.cpp.

References IMessageHandler::AddValidErrItem(), CHugeFileValidator::SGlobalInfo::Clear(), eDiag_Critical, eDiag_Error, eErr_GENERIC_DuplicateIDs, eErr_SEQ_PKG_NoBioseqFound, LOG_POST_XX, m_GlobalInfo, m_NumRecords, m_Reported, ReportReadFailure(), s_StartWrite(), and ValidateOneHugeBlob().

◆ ValidateTraditionally() ◆ ValidateWorker()

Definition at line 748 of file thread_state.cpp.

References IMessageHandler::AddValidErrItem(), eDiag_Fatal, eErr_INTERNAL_Exception, CStopWatch::Elapsed(), ERR_POST, CStopWatch::eStart, CException::GetMsg(), CThreadExitData::mLongest, NStr::Replace(), sw, and ValidateAsync().

◆ m_Cleanup ◆ m_CurrentId string CAsnvalThreadState::m_CurrentId protected ◆ m_eval ◆ m_GlobalInfo ◆ m_Level size_t CAsnvalThreadState::m_Level = 0 protected ◆ m_Longest double CAsnvalThreadState::m_Longest = 0 protected ◆ m_LongestId string CAsnvalThreadState::m_LongestId protected ◆ m_NumRecords size_t CAsnvalThreadState::m_NumRecords = 0 protected ◆ m_ObjMgr

Definition at line 149 of file thread_state.hpp.

Referenced by BuildScope(), CAsnvalThreadState(), ProcessBioSource(), ProcessPubdesc(), ProcessSeqAnnot(), ProcessSeqDesc(), ProcessSeqEntry(), ProcessSeqFeat(), ProcessSeqSubmit(), ReadClassMember(), ValidateAsync(), and ValidateOneHugeBlob().

◆ m_Options unsigned int CAsnvalThreadState::m_Options = 0 protected

Definition at line 150 of file thread_state.hpp.

Referenced by CAsnvalThreadState(), ProcessBioSource(), ProcessPubdesc(), ProcessSeqAnnot(), ProcessSeqEntry(), ProcessSeqFeat(), ProcessSeqSubmit(), ReadClassMember(), ValidateAsync(), ValidateBatchMode(), and ValidateOneHugeBlob().

◆ m_pContext

Definition at line 164 of file thread_state.hpp.

Referenced by CAsnvalThreadState(), ProcessBioSource(), ProcessPubdesc(), ProcessSeqAnnot(), ProcessSeqDesc(), ProcessSeqEntry(), ProcessSeqFeat(), ProcessSeqSubmit(), ReadClassMember(), ValidateAsync(), and ValidateOneHugeBlob().

◆ m_ReadFailure bool CAsnvalThreadState::m_ReadFailure {false} protected ◆ m_Reported std::atomic<size_t> CAsnvalThreadState::m_Reported {0} protected ◆ mAppConfig ◆ mpIstr

The documentation for this class was generated from the following files:

src/app/asnval/thread_state.hpp
src/app/asnval/thread_state.cpp

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