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NCBI C++ ToolKit: src/app/table2asn/table2asn_huge.cpp Source File

(

parentClass = rec.m_parent_set->m_class;

(

descr : rec.m_descr->Get()) {

THugeFileWriteContext {

is_fasta =

;

atomic_bool m_PubLookupDone{

};

std::mutex m_cleanup_mutex;

std::function<CRef<CSeq_entry>()> next_entry;

(

->IsMultiSequence() || (is_fasta && handle_as_set)) {

(!

->IsMultiSequence()) {

m_topentry = next_entry();

temp_submit->

(*m_submit);

temp_top = temp_submit->

().SetEntrys().front();

temp_submit->

().SetEntrys().clear();

temp_submit->

().SetEntrys().push_back(entry);

}

(m_topentry->

()) {

temp_top->

(*m_topentry);

<

_token>

CFlatFileAsyncWriter

CFlatFileAsyncWriter()

m_multi_writer.SetMaxWriters(20);

~CFlatFileAsyncWriter() {}

TFFFunction = std::function<void(

&, std::ostream&)>;

Post(

& iotoken, TFFFunction ff_func)

= m_multi_writer.NewStream();

ff_func(token, ostr);

}

(

std::exception& e) {

std::cerr << e.what();

std::cerr <<

;

(std::ostream& o_stream)

m_multi_writer.Open(o_stream);

(

sev = 0; sev < current.size(); ++sev) {

total[sev].total += current[sev].total;

& individual = current[sev].individual;

(

it = begin(individual); it != end(individual); ++it) {

= it->first;

= it->second;

THugeFileWriteContext

;

.source = &fasta_reader;

.source = &fasta_reader;

);

*unique_ptr<CLineError>(

firstEntryInBlob =

;

entry =

.source->GetNextSeqEntry();

(firstEntryInBlob) {

(entry->

()) {

firstEntryInBlob =

;

(

.source->GetNextBlob()) {

firstEntryInBlob =

;

.asn_reader.FlattenGenbankSet();

->m_feature_table_reader->m_local_id_counter =

.asn_reader.GetMaxLocalId() + 1;

future<void> validator_writetask;

(

.is_fasta && descrs) {

(

.m_topentry->IsSet() &&

.m_topentry->GetSet().IsSetSeq_set() &&

!

.m_topentry->GetSet().GetSeq_set().empty()) {

top_set =

.m_topentry->SetSet().SetSeq_set().front();

process_async = [&hugeFile,

](

& token) {

make_ff_async = [

, &ff_mutex](

& token, std::ostream& ostr) {

(

.m_topentry->IsSet())

(

.source->GetSubmitBlock()) {

.m_submit->SetSub().Assign(*

.source->GetSubmitBlock());

.m_submit->SetData().SetEntrys().clear();

.m_submit->SetData().SetEntrys().push_back(

.m_topentry);

unique_ptr<CObjectOStream> ostr{

TWriter async_writer(ostr.get());

async_writer.SetDepth(10);

TWriter::TProcessFunction ff_chain_func;

need_update_date = !

.is_fasta && s_AddUpdateDescriptor(

.asn_reader);

(numThreads >= 3) {

std::ofstream ff_file;

ff_file.exceptions(ios::failbit | ios::badbit);

CFlatFileAsyncWriter<TAsyncToken> ff_writer;

ff_chain_func = [&ff_writer, make_ff_async](

& token) {

ff_writer.Post(token, make_ff_async);

ff_writer.Write(ff_file);

async_writer.WriteAsyncMT(topobject, make_next_token, process_async, ff_chain_func);

}

(numThreads == 2) {

async_writer.WriteAsync2T(topobject, make_next_token, process_async, ff_chain_func);

async_writer.WriteAsyncST(topobject, make_next_token, process_async, ff_chain_func);

process_async(token);

async_writer.Write(topobject);

ff_chain_func(token);

validator_writetask.wait();

(

& pErrItem : postponed) {

sev = pErrItem->GetSev();

valStats[sev].total++;

valStats[sev].individual[pErrItem->GetErrIndex()]++;

(

& pErrItem : postponed) {

s_AppendValStats(

, valStats);

totalErrors{ 0 };

(

statsEntry : valStats) {

totalErrors += statsEntry.total;

(totalErrors > 0) {

statsStream.exceptions(ios::failbit | ios::badbit);

& submit = token.

;

& scope = token.

;

& seh = token.

;

scope->AddDefaults();

readModsFromTitle =

->m_feature_table_reader->MergeCDSFeatures(*entry, token);

->m_feature_table_reader->MoveProteinSpecificFeats(*entry);

->m_feature_table_reader->MakeGapsFromFeatures(*entry);

seh = scope->AddTopLevelSeqEntry(*entry);

->m_feature_table_reader->ChangeDeltaProteinToRawProtein(*entry);

modMergePolicy =

User-defined methods of the data storage class.

User-defined methods of the data storage class.

static bool ConvertPubFeatsToPubDescs(CSeq_entry_Handle seh)

Convert full-length publication features to publication descriptors.

EFormat

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

@ eBinaryASN

Binary ASN.1.

@ eGff3

GFF3, CGff3Reader.

@ eFasta

FASTA format sequence record, CFastaReader.

@ eAlignment

Text alignment.

void ConvertNs2Gaps(CSeq_entry &entry)

auto & GetTopEntry() const

auto & GetBioseqs() const

void Open(objects::edit::CHugeFile *file, objects::ILineErrorListener *pMessageListener) override

std::unique_ptr< std::istream > m_stream

CFormatGuess::EFormat m_format

static CLineError * Create(EProblem eProblem, EDiagSev eSeverity, const std::string &strSeqId, unsigned int uLine, const std::string &strFeatureName=string(""), const std::string &strQualifierName=string(""), const std::string &strQualifierValue=string(""), const std::string &strErrorMessage=string(""), const TVecOfLines &vecOfOtherLines=TVecOfLines())

Use this because the constructor is protected.

namespace ncbi::objects::

CRef< objects::CObjectManager > m_ObjMgr

void SetSeqId(objects::CSeq_entry &entry) const

void ApplyFileTracks(objects::CSeq_entry &entry) const

bool m_RemoteTaxonomyLookup

bool m_binary_asn1_output

unique_ptr< objects::edit::CRemoteUpdater > m_remote_updater

void ApplyAccession(objects::CSeq_entry &entry) const

objects::ILineErrorListener * m_logger

TSeqPos m_gap_Unknown_length

objects::CGapsEditor::TEvidenceSet m_DefaultEvidence

CRef< CSerialObject > CreateSubmitFromTemplate(CRef< objects::CSeq_entry > &object, CRef< objects::CSeq_submit > &submit) const

CRef< objects::CSeq_entry > m_entry_template

void CorrectCollectionDates(objects::CSeq_entry &entry) const

optional< size_t > m_use_threads

string GenerateOutputFilename(eFiles kind, string_view basename=kEmptyStr) const

unique_ptr< CValidMessageHandler > pValMsgHandler

void RenameProteinIdsQuals(objects::CSeq_feat &feature) const

void ApplyComments(objects::CSeq_entry &entry) const

objects::CGapsEditor::TCountToEvidenceMap m_GapsizeToEvidence

std::ostream & GetOstream(eFiles suffix)

bool ApplyCreateUpdateDates(objects::CSeq_entry &entry) const

void RemoveProteinIdsQuals(objects::CSeq_feat &feature) const

static void MergeSeqDescr(objects::CSeq_entry &dest, const objects::CSeq_descr &src, bool only_set)

objects::CBioseq_set::TClass m_ClassValue

static void UpdateTaxonFromTable(objects::CBioseq &bioseq)

const TGlobalInfo & GetGlobalInfo()

void UpdateECNumbers(objects::CSeq_entry &entry)

void Cleanup(CRef< objects::CSeq_submit > submit, objects::CSeq_entry_Handle &entry, const string &flags) const

void CollectDiscrepancies(CRef< objects::CSeq_submit > submit, objects::CSeq_entry_Handle &entry)

void Validate(CRef< objects::CSeq_submit > pSubmit, CRef< objects::CSeq_entry > pEntry, CValidMessageHandler &msgHandler)

shared_ptr< TValidatorContext > GetContextPtr()

CRef< CTable2AsnValidator > m_validator

void ProcessHugeFile(edit::CHugeFile &hugeFile, CNcbiOstream *output)

CTable2AsnContext m_context

void AddAnnots(CSeq_entry &entry)

void ProcessSecretFiles2Phase(CSeq_entry &result) const

TAdditionalFiles m_global_files

void ProcessSecretFiles1Phase(bool readModsFromTitle, TAsyncToken &)

void MakeFlatFile(CSeq_entry_Handle seh, CRef< CSeq_submit > submit, std::ostream &ostream)

void ProcessSingleEntry(CFormatGuess::EFormat inputFormat, TAsyncToken &token)

CMultiReader::TAnnots TAnnots

unique_ptr< CMultiReader > m_reader

CRef< CTable2AsnLogger > m_logger

void ProcessTopEntry(CFormatGuess::EFormat inputFormat, bool need_update_date, CRef< CSeq_submit > &submit, CRef< CSeq_entry > &entry)

unique_ptr< TAdditionalFiles > m_secret_files

static SQLCHAR output[256]

static const char * validate(DSNINFO *di)

Go looking for trouble.

@ eDiag_Warning

Warning message.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

void Write(CObjectOStream &out, TConstObjectPtr object, const CTypeRef &type)

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

static CObjectOStream * Open(ESerialDataFormat format, CNcbiOstream &outStream, bool deleteOutStream)

Create serial object writer and attach it to an output stream.

CRef< C > Ref(C *object)

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

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

const TSeq & GetSeq(void) const

Get the variant data.

TSet & SetSet(void)

Select the variant.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSet(void) const

Check if variant Set is selected.

void SetClass(TClass value)

Assign a value to Class data member.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

@ eClass_genbank

converted genbank

@ e_Create_date

date entry first created/released

bool IsSetData(void) const

Check if a value has been assigned to Data data member.

const TEntrys & GetEntrys(void) const

Get the variant data.

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.

void g_PostprocessErrors(const CHugeFileValidator::TGlobalInfo &globalInfo, const string &genbankSetId, CRef< CValidError > &pErrors)

void VisitAllFeatures(objects::CSeq_entry_EditHandle &entry_h, _M m)

void VisitAllBioseqs(objects::CSeq_entry &entry, _M &&m)

const CharType(& source)[N]

void SortSeqDescr(CSeq_entry &entry)

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

void g_ApplyMods(CMemorySrcFileMap *pNamedSrcFileMap, CMemorySrcFileMap *pDefaultSrcFileMap, const string &commandLineStr, bool readModsFromTitle, bool isVerbose, CModHandler::EHandleExisting mergePolicy, ILineErrorListener *pEC, CSeq_entry &entry)

CRef< CSeq_descr > m_descriptors

unique_ptr< IIndexedFeatureReader > m_indexed_annots

unique_ptr< CMemorySrcFileMap > mp_src_qual_map

CRef< CSeq_submit > submit

atomic_bool * pPubLookupDone

CRef< CSeq_entry > top_entry

std::mutex * cleanup_mutex

void g_FormatErrItem(const CValidErrItem &item, CNcbiOstream &ostr)

void g_FormatValStats(const TValStats &stats, size_t total, CNcbiOstream &ostr)

int g(Seg_Gsm *spe, Seq_Mtf *psm, Thd_Gsm *tdg)

static CS_CONTEXT * context

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