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NCBI C++ ToolKit: src/app/asnval/thread_state.cpp Source File

;

<

TLoader>

: m_loader{

.GetLoader() } {}

CSeq_submit::GetTypeInfo(), CSeq_entry::GetTypeInfo(), CSeq_annot::GetTypeInfo(),

CSeq_feat::GetTypeInfo(), CBioSource::GetTypeInfo(), CPubdesc::GetTypeInfo(),

CBioseq_set::GetTypeInfo(), CBioseq::GetTypeInfo(), CSeqdesc::GetTypeInfo(),

entry->SetSeq().SetInst().SetMol(objects::CSeq_inst::eMol_dna);

entry->SetSeq().SetInst().SetRepr(objects::CSeq_inst::eRepr_raw);

entry->SetSeq().SetInst().SetSeq_data().SetIupacna().Set(

);

entry->SetSeq().SetInst().SetLength(60);

->SetLocal().SetStr(

);

entry->SetSeq().SetId().push_back(

);

mdesc->SetMolinfo().SetBiomol(objects::CMolInfo::eBiomol_genomic);

entry->SetSeq().SetDescr().Set().push_back(mdesc);

mAppConfig(appConfig)

.ReadClassMember(member);

unique_ptr<CNcbiIstream> hold_stream;

(!fname.empty()) {

hold_stream = make_unique<CNcbiIfstream>(fname, ios::binary);

InputStream = hold_stream.get();

hold_stream.release();

hold_stream.reset(decompress);

InputStream = hold_stream.get();

=

.GuessFormatAndContent(contentInfo);

unique_ptr<CObjectIStream> objectStream;

hold_stream.release();

msgHandler.

();

os <<

;

os <<

<<

->GetPosition();

os <<

;

os <<

+ p_exception->

(0);

errstr = os.str();

(Corelib_App, 1,

);

(Corelib_App, 1,

);

se->SetSet(*bioseqset);

(

& se: ss->

().SetEntrys() ) {

(asninfo==

) {

(content.size() == 1) {

asninfo = *content.begin();

(asninfo==

) {

obj_info =

->Read(asninfo);

serial.

(

CSerialObject*

(obj_info.GetObjectPtr()));

asn_type = asninfo->

();

unhandledType{

};

(asn_type ==

) {

}

(asn_type ==

) {

}

(asn_type ==

) {

}

(asn_type ==

) {

}

(asn_type ==

) {

}

(asn_type ==

) {

}

(asn_type ==

) {

}

(asn_type ==

) {

}

(asn_type ==

) {

unhandledType =

;

errstr = e.

();

& loader_name,

(!loader_name.empty())

(scope->

(seq_id_h)) {

pSubmit->SetSub().Assign(*pSubmitBlock);

pSubmit->SetData().SetEntrys().push_back(pEntry);

& reader = process.GetReader();

= edit::CHugeAsnDataLoader::RegisterInObjectManager(

CAutoRevoker autorevoker(

);

(

& topIds = reader.GetTopIds(); !topIds.empty()) {

(!process.ReadNextBlob())

(process.GetReader().GetBioseqs().size() == 0) {

(

edit::CHugeFileException& e) {

(e.GetErrCode() == edit::CHugeFileException::eDuplicateSeqIds)

(Corelib_App, 1,

+ process.GetConstFile().m_filename);

& loader_name,

_this->

(loader_name, pSubmitBlock, seqid, msgHandler);

errstr = e.

();

& reader = process.GetReader();

pSubmitBlock = reader.GetSubmitBlock();

(

seqid : reader.GetTopIds())

auto fut = mAppConfig.m_thread_pool2->launch(ValidateWorker, this, loader_name, pSubmitBlock, seqid, std::ref(msgHandler));

val_queue.push_back(std::move(fut));

val_queue.push_back({});

= val_queue.pop_front();

exit_data =

.get();

& loader_name,

edit::CHugeFileProcess& process,

& reader = process.GetReader();

(

seqid : reader.GetTopIds())

pSubmitBlock = reader.GetSubmitBlock();

(loader_name, pSubmitBlock, seqid, msgHandler);

(asninfo == CBioseq_set::GetTypeInfo()) {

(asninfo == CSeq_submit::GetTypeInfo()) {

commandLineOptions =

;

(Corelib_App, 1,

);

unique_ptr<IMessageHandler> pMsgHandler;

.mReported += pMsgHandler->GetNumReported();

unique_ptr<edit::CHugeFileProcess> mpHugeFileProcess;

(filename.empty())

huge_reader =

(

edit::CHugeAsnReader());

mpHugeFileProcess.reset(

edit::CHugeFileProcess(huge_reader.GetPointer()));

asninfo = mpHugeFileProcess->GetFile().m_content;

mpHugeFileProcess.reset();

= mpHugeFileProcess->GetReader().MakeObjStream(0);

proceed =

;

(Corelib_App, 1,

+ filename);

(

->EndOfData())

errstr = e.

();

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eErr_SEQ_PKG_NoBioseqFound

@ eErr_GENERIC_InvalidAsn

@ eErr_GENERIC_DuplicateIDs

@ eErr_INTERNAL_Exception

CValidatorThreadPool * m_thread_pool1

unsigned int mNumInstances

void ProcessPubdesc(CRef< CSerialObject > serial, IMessageHandler &msgHandler)

void ValidateBlobAsync(const string &loader_name, edit::CHugeFileProcess &process, IMessageHandler &msgHandler)

bool ValidateTraditionally(TTypeInfo asninfo, IMessageHandler &msgHandler)

void ValidateBlobSequential(const string &loader_name, edit::CHugeFileProcess &process, IMessageHandler &msgHandler)

void ReportReadFailure(const CException *p_exception, IMessageHandler &msgHandler)

void ProcessSeqAnnot(CRef< CSerialObject > serial, IMessageHandler &msgHandler)

shared_ptr< SValidatorContext > m_pContext

static CThreadExitData ValidateWorker(CAsnvalThreadState *_this, const string &loader_name, CConstRef< CSubmit_block > pSubmitBlock, CConstRef< CSeq_id > seqid, IMessageHandler &msgHandler)

void ProcessBioSource(CRef< CSerialObject > serial, IMessageHandler &msgHandler)

void ReadClassMember(CObjectIStream &in, const CObjectInfo::CMemberIterator &member, IMessageHandler &msgHandler)

std::list< CConstRef< CValidError > > m_eval

void ProcessSeqEntry(CSeq_entry &se, IMessageHandler &msgHandler)

CHugeFileValidator::TGlobalInfo m_GlobalInfo

void ProcessBioseq(CRef< CSerialObject > serial, IMessageHandler &msgHandler)

CRef< CScope > BuildScope() const

bool ValidateBatchMode(TTypeInfo asninfo, IMessageHandler &msgHandler)

CAsnvalThreadState(const CAppConfig &, SValidatorContext::taxupdate_func_t taxon)

void ProcessBioseqset(CRef< CSerialObject > serial, IMessageHandler &msgHandler)

void ProcessSeqSubmit(CRef< CSerialObject > serial, IMessageHandler &msgHandler)

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

CThreadExitData ValidateOneFile(const string &infilename, CNcbiOstream &ostr)

void ProcessSSMReleaseFile(IMessageHandler &msgHandler)

const CAppConfig & mAppConfig

void ProcessSeqFeat(CRef< CSerialObject > serial, IMessageHandler &msgHandler)

unique_ptr< CObjectIStream > OpenFile(TTypeInfo &asn_info, const string &filename) const

void ProcessBSSReleaseFile(IMessageHandler &msgHandler)

std::atomic< size_t > m_Reported

void ValidateInput(TTypeInfo asninfo, IMessageHandler &msgHandler)

void ValidateAsync(const string &loader_name, CConstRef< CSubmit_block > pSubmitBlock, CConstRef< CSeq_id > seqid, IMessageHandler &msgHandler) const

void ProcessSeqDesc(CRef< CSerialObject > serial, IMessageHandler &msgHandler)

void ValidateOneHugeBlob(edit::CHugeFileProcess &process, IMessageHandler &msgHandler)

CRef< CObjectManager > m_ObjMgr

unique_ptr< CObjectIStream > mpIstr

Wraps CFormatGuess, and if CFormatGuess's result is Unknown, it tries every file reader until one wor...

CFormatGuess::EFormat GuessFormatAndContent(CFileContentInfo &contentInfo)

void SetRecognizedGenbankTypes(const set< TTypeInfo > &recognizedGenbankTypes)

EFormat

The formats are checked in the same order as declared here.

@ eBZip2

bzip2 compressed file

@ eBinaryASN

Binary ASN.1.

@ eLzo

lzo compressed file

@ eGZip

GNU zip compressed file.

void ReportGlobalErrors(const TGlobalInfo &globalInfo, IValidError &errors) const

void UpdateValidatorContext(TGlobalInfo &globalInfo, SValidatorContext &context) const

static void RegisterReaderHooks(CObjectIStream &objStream, SGlobalInfo &m_GlobalInfo)

void ReportPostErrors(const SValidatorContext &context, IValidError &errors) const

Reading (iterating through) elements of containers (SET OF, SEQUENCE OF).

Root class for all serialization exceptions.

CTypeInfo class contains all information about C++ types (both basic and classes): members and layout...

static void SetSuppressedCodes(const CUser_object &user, TCodes &errCodes)

CRef< CValidError > Validate(const CSeq_entry &se, CScope *scope=nullptr, Uint4 options=0)

virtual bool InvokeWrite() const =0

void AddValidErrItem(EDiagSev sev, unsigned int ec, const string &msg, const string &desc, const CSerialObject &obj, const string &acc, const int ver, const string &location=kEmptyStr, const int seq_offset=0) override

virtual void RequestStop()=0

auto launch(_Function &&f, TArgs &&...args)

Include a standard set of the NCBI C++ Toolkit most basic headers.

static const struct type types[]

@ eTakeOwnership

An object can take ownership of another.

@ eNoOwnership

No ownership is assumed.

EMethod

Compression/decompression methods.

@ eNone

no compression method (copy "as is")

@ eGZipFile

.gz file (including concatenated files)

@ fDefault

Use algorithm-specific defaults.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define LOG_POST_XX(error_name, err_subcode, message)

@ eDiag_Error

Error message.

@ eDiag_Fatal

Fatal error – guarantees exit(or abort)

@ eDiag_Critical

Critical error message.

void Error(CExceptionArgs_Base &args)

TErrCode GetErrCode(void) const

Get error code.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string & GetMsg(void) const

Get message string.

string ReportAll(TDiagPostFlags flags=eDPF_Exception) const

Report all exceptions.

static string CreateAbsolutePath(const string &path, ERelativeToWhat rtw=eRelativeToCwd)

Get an absolute path from some, possibly relative, path.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

@ eEOF

Unexpected end-of-file.

void ResetHistory(EActionIfLocked action=eKeepIfLocked)

Clean all unused TSEs from the scope's cache and release the memory.

void AddDataLoader(const string &loader_name, TPriority pri=kPriority_Default)

Add data loader by name.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

CSeq_annot_Handle AddSeq_annot(CSeq_annot &annot, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add Seq-annot, return its CSeq_annot_Handle.

void RemoveTopLevelSeqEntry(const CTSE_Handle &entry)

Revoke TSE previously added using AddTopLevelSeqEntry() or AddBioseq().

bool RevokeDataLoader(CDataLoader &loader)

Revoke previously registered data loader.

bool Exists(const CSeq_id &id)

Check existence of sequence with this id.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

const TId & GetId(void) const

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Reset(void)

Reset reference object.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

static string & Replace(const string &src, const string &search, const string &replace, string &dst, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

@ eNocase

Case insensitive compare.

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

@ eStart

Start timer immediately after creating.

const string & GetName(void) const

Get name of this type.

ENcbiOwnership

Ownership relations between objects.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

bool IsEntrys(void) const

Check if variant Entrys is selected.

Definition of all error codes used in corelib (xncbi.lib).

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

Magic spell ;-) needed for some weird compilers... very empiric.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

std::istream & in(std::istream &in_, double &x_)

void SetLocalReadHook(const CObjectTypeInfo &obj_type_info, CObjectIStream &ostr, _Func _func)

C++ I/O stream wrappers to compress/decompress data on-the-fly.

function< CRef< CTaxon3_reply >(const vector< CRef< COrg_ref > > &list)> taxupdate_func_t

const set< TTypeInfo > s_known_types

static CRef< objects::CSeq_entry > s_BuildGoodSeq()

static void s_StartWrite(IMessageHandler &msgHandler)

CFileContentInfoGenbank mInfoGenbank

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