#include <ncbi_pch.hpp>
#include <common/ncbi_source_ver.h>
#include <corelib/ncbistd.hpp>
#include <corelib/ncbistre.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbienv.hpp>
#include <corelib/ncbiargs.hpp>
#include <corelib/error_codes.hpp>
#include <serial/serial.hpp>
#include <serial/objistr.hpp>
#include <serial/objectio.hpp>
#include <connect/ncbi_core_cxx.hpp>
#include <connect/ncbi_util.h>
#include <objects/taxon3/taxon3.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seq/Seq_inst.hpp>
#include <objects/seq/Pubdesc.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/submit/Seq_submit.hpp>
#include <objects/submit/Submit_block.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/seqfeat/BioSource.hpp>
#include <objtools/validator/validator.hpp>
#include <objtools/validator/valid_cmdargs.hpp>
#include <objtools/validator/validator_context.hpp>
#include <objtools/cleanup/cleanup.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/seq_descr_ci.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/align_ci.hpp>
#include <objmgr/graph_ci.hpp>
#include <objmgr/seq_annot_ci.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <misc/data_loaders_util/data_loaders_util.hpp>
#include <util/compress/stream_util.hpp>
#include <objtools/readers/format_guess_ex.hpp>
#include <objtools/edit/huge_file_process.hpp>
#include <objtools/edit/huge_asn_reader.hpp>
#include <objtools/edit/huge_asn_loader.hpp>
#include <objtools/readers/reader_exception.hpp>
#include <objtools/edit/remote_updater.hpp>
#include <future>
#include <util/message_queue.hpp>
#include "app_config.hpp"
#include "thread_state.hpp"
#include <objtools/validator/huge_file_validator.hpp>
#include <objtools/readers/objhook_lambdas.hpp>
#include <objects/valerr/ValidErrItem.hpp>
#include <objtools/validator/validerror_suppress.hpp>
#include "message_handler.hpp"

Include dependency graph for thread_state.cpp:

Go to the SVN repository for this file.

Functions
	USING_SCOPE (objects)

	USING_SCOPE (validator)

	USING_SCOPE (edit)

static CRef< objects::CSeq_entry >	s_BuildGoodSeq ()

static void	s_StartWrite (IMessageHandler &msgHandler, bool ignoreInferences=false)

Variables
const set< TTypeInfo >	s_known_types

Function Documentation

◆ s_BuildGoodSeq()

static CRef<objects::CSeq_entry> s_BuildGoodSeq ( )

static

Definition at line 133 of file thread_state.cpp.

Referenced by CAsnvalThreadState::ProcessSeqDesc().

◆ s_StartWrite()

static void s_StartWrite	(	IMessageHandler &	msgHandler,
		bool	ignoreInferences = `false`
	)

static

Definition at line 303 of file thread_state.cpp.

References IMessageHandler::InvokeWrite(), IMessageHandler::RequestStop(), and IMessageHandler::Write().

Referenced by CAsnvalThreadState::ReportReadFailure(), CAsnvalThreadState::ValidateBatchMode(), CAsnvalThreadState::ValidateBlobSequential(), CAsnvalThreadState::ValidateOneHugeBlob(), CAsnvalThreadState::ValidateOneHugeFile(), and CAsnvalThreadState::ValidateTraditionally().

◆ USING_SCOPE() [1/3]

USING_SCOPE ( edit )

◆ USING_SCOPE() [2/3]

USING_SCOPE ( objects )

◆ USING_SCOPE() [3/3]

USING_SCOPE ( validator )

Variable Documentation

◆ s_known_types

const set<TTypeInfo> s_known_types

Initial value:

{
    CSeq_submit::GetTypeInfo(), CSeq_entry::GetTypeInfo(), CSeq_annot::GetTypeInfo(),
    CSeq_feat::GetTypeInfo(),   CBioSource::GetTypeInfo(), CPubdesc::GetTypeInfo(),
    CBioseq_set::GetTypeInfo(), CBioseq::GetTypeInfo(),    CSeqdesc::GetTypeInfo(),
}

Definition at line 126 of file thread_state.cpp.

Referenced by CAsnvalThreadState::OpenFile(), and CAsnvalThreadState::ValidateInput().

Functions

Variables