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

CSeq_loc& loc = *visitor;

& bioseqAnnots = bioseq.

();

it = find_if(bioseqAnnots.begin(),

return (pAnnot && pAnnot->IsFtable());

(it != bioseqAnnots.end()) {

s_AddAnnotsToBioseq(

(

pAnnot : annots) {

objects::edit::CFeatTableEdit featEdit(*pBioseqAnnot);

featEdit.MergeFeatures(pAnnot->SetData().SetFtable());

pBioseqAnnot = s_GetBioseqAnnot(bioseq);

pBioseqAnnot = annots.front();

bioseq.

().push_back(pBioseqAnnot);

it =

(annots.begin());

(it != annots.end()) {

objects::edit::CFeatTableEdit featEdit(*pBioseqAnnot);

featEdit.MergeFeatures((*it)->SetData().SetFtable());

(

pAnnot : annots) {

objects::edit::CFeatTableEdit featEdit(*pBioseqAnnot);

featEdit.MergeFeatures(pAnnot->SetData().SetFtable());

CBioseq_set::GetTypeInfo(),

CBioseq::GetTypeInfo(),

CSeq_entry::GetTypeInfo(),

CSeq_submit::GetTypeInfo(),

CSeq_annot::GetTypeInfo(),

(content_type ==

) {

& bioseq_set = obj->SetSet();

(content_type ==

) {

(content_type ==

) {

(content_type ==

) {

(sType == CBioseq_set::GetTypeInfo()->GetName()) {

}

(sType == CSeq_submit::GetTypeInfo()->GetName()) {

entry = *submit->

().SetEntrys().begin();

}

(sType == CSeq_entry::GetTypeInfo()->GetName()) {

}

(sType == CSeq_annot::GetTypeInfo()->GetName()) {

}

(sType == CSeq_annot::GetTypeInfo()->GetName());

(submit.

())

reader.

(args[

].AsString());

reader.

(args[

].AsString());

(args[

].AsString() ==

) {

(pSeqEntry && args[

]) {

it = s_StringToClass.

(args[

].AsString());

(it != s_StringToClass.

()) {

pSeqEntry->SetSet().SetClass(it->second);

, 0);

pReader->SetGapLinkageEvidence(

(

.NotEmpty()) {

(! content_info) {

*

=

.m_stream.get();

(

.m_format)

mAtSequenceData(

)

sType = pObjIstrm->ReadFileHeader();

(sType == CSeq_descr::GetTypeInfo()->GetName()) {

out_desc->

().insert(out_desc->

().end(), descr->

().begin(), descr->

().end());

}

(sType == CSeqdesc::GetTypeInfo()->GetName()) {

out_desc->

().push_back(desc);

}

(sType == CPubdesc::GetTypeInfo()->GetName()) {

out_desc->

().push_back(desc);

runtime_error(

);

runtime_error(

+ ex.

());

sType = pObjIstrm->ReadFileHeader();

(sType == CSeq_entry::GetTypeInfo()->GetName()) {

}

(sType == CBioseq::GetTypeInfo()->GetName()) {

}

(sType == CSeq_submit::GetTypeInfo()->GetName()) {

runtime_error(

);

}

(sType == CSubmit_block::GetTypeInfo()->GetName()) {

}

(sType == CSeqdesc::GetTypeInfo()->GetName()) {

<< sType);

(ent_iter->IsSetDescr()) {

descr = &ent_iter->GetDescr();

->SetSeq().SetInst();

((*desc_iter)->Which()) {

desc->

(**desc_iter);

->SetSeq().SetDescr().Set().push_back(desc);

(

->IsSetDescr() && !

->GetDescr().Get().empty())

(!pObjIstrm->EndOfData()) {

(sType != CSeqdesc::GetTypeInfo()->GetName())

sType = pObjIstrm->ReadFileHeader();

(sType == CSeqdesc::GetTypeInfo()->GetName()) {

(pObjIstrm->EndOfData())

sType = pObjIstrm->ReadFileHeader();

runtime_error(

);

(args[

].AsString() ==

) {

AllowedDuplicates :

<CSeqdesc_Base::E_Choice>

AllowedDuplicates m_allowed_duplicates;

<

_which>

_which::E_Choice compare_to;

operator()(_which

)

.Which() == compare_to;

->Which() == compare_to;

duplicates = (m_allowed_duplicates.find(

.Which()) != m_allowed_duplicates.end());

desc.Set(duplicates).Assign(

);

post_process =

;

, 0);

& objectType,

unique_ptr<istream>& pIstr,

(! pInputObject) {

, 0);

istream.

().open(filename);

(input_sequence.

())

, 0);

input_sequence =

(input_sequence, merge_template_descriptors);

entry = submit->

().SetEntrys().front();

(submit.

())

(entry->

() &&

CopyDescr(*seq, *entry);

CopyAnnot(*seq, *entry);

(merge_template_descriptors) {

);

*unique_ptr<CLineError>(

(submit.

())

(

&

: readerListener) {

(

pFeat :

) {

(pFeat->IsSetDbxref()) {

& dbxrefs = pFeat->SetDbxref();

it =

(dbxrefs.begin(), dbxrefs.end(),

return(pDbtag && pDbtag->IsSetDb() &&

NStr::EqualNocase(pDbtag->GetDb(),

));

dbxrefs.erase(it, dbxrefs.end());

(dbxrefs.empty()) {

pFeat->ResetDbxref();

(

orig_protein_id = seqfeat.

(

);

!orig_protein_id.empty()) {

(

orig_transcript_id = seqfeat.

(

);

!orig_transcript_id.empty()) {

(

pFeat :

) {

startingLocusTagNumber = 1;

startingFeatureId = 1;

(

it = annots.begin(); it != annots.end(); ++it) {

(!

.IsFtable() ||

.GetFtable().empty()) {

edit::CFeatTableEdit fte(

);

fte.GenerateLocusTags();

fte.GenerateProteinAndTranscriptIds();

fte.ProcessCodonRecognized();

fte.EliminateBadQualifiers();

fte.SubmitFixProducts();

startingLocusTagNumber = fte.PendingLocusTagNumber();

startingFeatureId = fte.PendingFeatureId();

unique_ptr<istream> instream(

(filename));

unique_ptr<CObjectIStream> pObjIstrm(

unique_ptr<IIndexedFeatureReader> reader;

hugefile = std::make_unique<objects::edit::CHugeFile>();

hugefile->OpenPlain(filename);

(ext ==

|| ext ==

)

(ext ==

)

(ext ==

)

(ext ==

|| ext ==

|| ext ==

)

*

= hugefile->m_stream.get();

hasAnnots{

};

reader5col = std::make_unique<CFast5colReader>();

reader5col->Open(std::move(hugefile));

hasAnnots = (reader5col->size()>0);

reader = std::move(reader5col);

obj_stream = hugefile->MakeObjStream(0);

(pEntry && pEntry->IsSetAnnot()) {

annots = pEntry->GetAnnot();

, 1);

(!reader.get() && !annots.empty()) {

whole_file = std::make_unique<CWholeFileAnnotation>();

whole_file->AddAnnots(annots);

reader = std::move(whole_file);

+ filename, 0);

std::vector<CRef<CSeq_id>> ids(bioseq.

().begin(), bioseq.

().end());

return CSeq_id::Score(l) < CSeq_id::Score(r);

(

pSeqId : ids) {

(annots.empty()) {

(

pAnnot : annots) {

s_ModifySeqIds(*pAnnot, *pAnnotId, matching_id);

s_AddAnnotsToBioseq(annots, bioseq, pBioseqAnnot);

unique_ptr<Parser> pp(

);

+ filename, 0);

obj = ffparser.

(*pp, instream);

(obj.NotEmpty()) {

(obj->GetThisTypeInfo() == CBioseq_set::GetTypeInfo()) {

& annot = entry->SetAnnot();

(

& bioseq : bioseq_set->SetSeq_set()) {

annot.splice(annot.end(), bioseq->

());

(entry->IsSetAnnot())

indexed_annots = std::make_unique<CWholeFileAnnotation>();

indexed_annots->AddAnnots(annots);

reader = std::move(indexed_annots);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

void g_LogGeneralParsingError(EDiagSev sev, const string &idString, const string &msg, objects::ILineErrorListener &listener)

void remove_if(Container &c, Predicate *__pred)

class CAlnReader supports importing a large variety of text-based alignment formats into standard dat...

void Read(bool guess, bool generate_local_ids=false, objects::ILineErrorListener *pErrorListener=nullptr)

void SetAlphabet(const string &value)

CRef< objects::CSeq_entry > GetSeqEntry(TFastaFlags fasta_flags=objects::CFastaReader::fAddMods, objects::ILineErrorListener *pErrorListener=nullptr)

void SetMissing(const string &value)

void SetAllGap(const string &value)

Convenience function for setting beginning, middle, and end gap to the same thing.

Modification of the CFastaReader class that allows for reading a single sequence as a degenarate mult...

@ fAllIdsAsLocal

= 0x100 (Do not attempt to parse accessions)

@ fLeaveProteinIds

= 0x80 (Leave all protein_id as a qualifiers)

@ fCreateGenesFromCDSs

= 0x10 (If a CDS has a gene xref, create a gene with the same intervals if one doesn't already exist....

@ fPreferGenbankId

= 0x200 (Prefer Genbank accession ids)

CRef< CSerialObject > Parse(Parser &parseInfo)

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

CFormatGuess::EFormat GuessFormatAndContent(CFileContentInfo &contentInfo)

CFormatGuess::CFormatHints & GetFormatHints(void)

Get format hints.

void SetRecognizedGenbankTypes(const set< TTypeInfo > &recognizedGenbankTypes)

CFormatGuess::EFormat GuessFormat()

CFormatHints & AddPreferredFormat(TFormat fmt)

Mark the format as preferred.

CFormatHints & DisableAllNonpreferred(void)

Disable all formats not marked as preferred.

Class implements different ad-hoc unreliable file format identifications.

CFormatHints & GetFormatHints(void)

Get format hints.

EFormat

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

@ eFiveColFeatureTable

Five-column feature table.

@ eBinaryASN

Binary ASN.1.

@ eGtf

New GTF, CGtfReader.

@ eGff3

GFF3, CGff3Reader.

@ eFasta

FASTA format sequence record, CFastaReader.

@ eUnknown

unknown format

@ eGffAugustus

GFFish output of Augustus Gene Prediction.

EFormat GuessFormat(EMode)

static const char * GetFormatName(EFormat format)

void ConvertNs2Gaps(CSeq_entry &entry)

bool AtSequenceData() const

void ReadSeqAnnots(TAnnotList &, CNcbiIstream &, ILineErrorListener *=nullptr) override

Read all objects from given insput stream, returning them as a vector of Seq-annots.

shared_ptr< CGff3LocationMerger > GetLocationMerger()

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.

CFormatGuess::EFormat OpenFile(const string &filename, CRef< CSerialObject > &input_sequence, TAnnots &annots)

void LoadGFF3Fasta(istream &in, TAnnots &annots)

static void GetSeqEntry(CRef< objects::CSeq_entry > &entry, CRef< objects::CSeq_submit > &submit, CRef< CSerialObject > obj)

TAnnots xReadGFF3(CNcbiIstream &instream, bool post_process)

void MergeDescriptors(objects::CSeq_descr &dest, const objects::CSeq_descr &source) const

CMultiReader(CTable2AsnContext &context)

list< CRef< objects::CSeq_annot > > TAnnots

unique_ptr< CObjectIStream > xCreateASNStream(const string &filename) const

void AddAnnots(IIndexedFeatureReader *reader, CBioseq &bioseq) const

CTable2AsnContext & m_context

CRef< CSerialObject > ReadNextEntry()

void xAnnotGetFormat(objects::edit::CHugeFile &file) const

static const set< TTypeInfo > kSupportedTypes

TAnnots xReadGTF(CNcbiIstream &instream) const

shared_ptr< objects::CGff3LocationMerger > m_gff3_merger

CRef< CSerialObject > xReadASN1Binary(CObjectIStream &pObjIstrm, const string &content_type) const

bool AtSeqenceData() const

std::unique_ptr< IIndexedFeatureReader > LoadIndexedAnnot(const string &filename)

void x_PostProcessAnnots(TAnnots &annots, CFormatGuess::EFormat format=CFormatGuess::eUnknown) const

void WriteObject(const CSerialObject &, ostream &)

void LoadDescriptors(const string &ifname, CRef< objects::CSeq_descr > &out_desc) const

void ApplyDescriptors(objects::CSeq_entry &obj, const objects::CSeq_descr &source) const

CRef< CSerialObject > xApplyTemplate(CRef< CSerialObject > obj, bool merge_template_descriptors) const

CRef< objects::CSeq_entry > xReadFasta(CNcbiIstream &instream)

CRef< CSerialObject > FetchEntry(const CFormatGuess::EFormat &format, const string &objectType, unique_ptr< CNcbiIstream > &pIstr, TAnnots &annots)

CRef< objects::CSeq_entry > ReadAlignment(CNcbiIstream &instream, const CArgs &args)

void LoadTemplate(const string &ifname)

void GetIndexedAnnot(std::unique_ptr< IIndexedFeatureReader > &reader, TAnnots &annots)

CFormatGuess::EFormat xInputGetFormat(CNcbiIstream &, CFileContentInfo *=nullptr) const

unique_ptr< CObjectIStream > m_obj_stream

CRef< objects::CSeq_entry > xReadFlatfile(CFormatGuess::EFormat format, const string &filename, CNcbiIstream &instream)

CRef< CSerialObject > xReadASN1Text(CObjectIStream &pObjIstrm) const

static CRef< CSeq_id > AsSeqId(const string &rawId, long flags=0, bool localInts=true)

Convert a raw ID string to a Seq-id, based in given customization flags.

@ fAllIdsAsLocal

all identifiers are local IDs

@Seq_descr.hpp User-defined methods of the data storage class.

const TAnnot & GetAnnot(void) const

const CSeq_descr & GetDescr(void) const

bool IsSetAnnot(void) const

void ResetParentEntry(void)

void SetDescr(CSeq_descr &value)

bool IsSetDescr(void) const

namespace ncbi::objects::

const string & GetNamedQual(const CTempString &qual_name) const

Return a named qualifier.

void AddOrReplaceQualifier(const string &qual_name, const string &qual_val)

Add a qualifier to this feature, or replace the value for the first one if it already exists.

void RemoveQualifier(const string &qual_name)

Remove all qualifiers with the given name; do nothing if no such qualifier exists.

Base class for all serializable objects.

Simple implementation of ILineReader for i(o)streams.

string m_genome_center_id

bool m_binary_asn1_output

objects::ILineErrorListener * m_logger

TSeqPos m_gap_Unknown_length

objects::CGapsEditor::TEvidenceSet m_DefaultEvidence

CRef< objects::CSeq_entry > m_entry_template

CRef< objects::CSeq_submit > m_submit_template

void MergeWithTemplate(objects::CSeq_entry &entry) const

string m_locus_tag_prefix

objects::CGapsEditor::TCountToEvidenceMap m_GapsizeToEvidence

objects::CBioseq_set::TClass m_ClassValue

void MakeGenomeCenterId(objects::CSeq_entry &entry) const

Template class for iteration on objects of class C.

virtual std::list< CRef< objects::CSeq_annot > > GetAndUseAnnot(CRef< objects::CSeq_id > seqid)=0

static CRef< objects::CSeq_id > GetAnnotId(const objects::CSeq_annot &annot)

const_iterator end() const

const_iterator find(const key_type &key) const

static DLIST_TYPE *DLIST_NAME() next(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

@ eTakeOwnership

An object can take ownership of another.

@ eDiag_Info

Informational message.

@ eDiag_Warning

Warning message.

#define NCBI_USER_THROW_FMT(message)

Throw a "user exception" with message processed as output to ostream.

#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.

#define NCBI_THROW2(exception_class, err_code, message, extra)

Throw exception with extra parameter.

static void SplitPath(const string &path, string *dir=0, string *base=0, string *ext=0)

Split a path string into its basic components.

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

Set object to copy of another one.

virtual const CTypeInfo * GetThisTypeInfo(void) const =0

ESerialDataFormat

Data file format.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

@ fHyphensIgnoreAndWarn

When a hyphen is encountered in seq data, ignore it but warn.

@ fLetterGaps

Parse runs of Ns when splitting data.

@ fIgnoreMods

Ignore mods entirely. Incompatible with fAddMods.

@ fNoUserObjs

Don't save raw deflines in User-objects.

@ fForceType

Force specified type regardless of accession.

@ fParseRawID

Try to identify raw accessions.

@ fNoSplit

Don't split out ambiguous sequence regions.

@ fAssumeNuc

Assume nucs unless accns indicate otherwise.

@ fParseGaps

Make a delta sequence if gaps found.

@ fValidate

Check (alphabetic) residue validity.

@ fDisableParseRange

No ranges in seq-ids. Ranges part of seq-id instead.

@ e_YES

SeqIds compared, but are different.

void Read(const CObjectInfo &object)

Read object of know type.

pair< TObjectPtr, TTypeInfo > ObjectInfo(C &obj)

virtual string ReadFileHeader(void)

Read file header.

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

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

CRef< C > Ref(C *object)

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

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

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::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static string & ToLower(string &str)

Convert string to lower case – string& version.

@ eCurrent

Use current time. See also CCurrentTime.

TData & SetData(void)

Assign a value to Data data member.

TSub & SetSub(void)

Select the variant.

bool IsSetQual(void) const

qualifiers Check if a value has been assigned to Qual data member.

const TQual & GetQual(void) const

Get the Qual member data.

TSet & SetSet(void)

Select the variant.

const TSet & GetSet(void) const

Get the variant data.

bool IsSet(void) const

Check if variant Set is selected.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

@ eClass_pop_set

population study

@ eClass_phy_set

phylogenetic study

@ eClass_mut_set

set of mutations

@ eClass_eco_set

ecological sample study

@ eClass_genbank

converted genbank

@ eClass_small_genome_set

viral segments or mitochondrial minicircles

void SetData(TData &value)

Assign a value to Data data member.

list< CRef< CSeqdesc > > Tdata

TId & SetId(void)

Assign a value to Id data member.

const TUser & GetUser(void) const

Get the variant data.

void SetPub(TPub &value)

Assign a value to Pub data member.

TPub & SetPub(void)

Select the variant.

bool IsSetAnnot(void) const

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

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

const TId & GetId(void) const

Get the Id member data.

const Tdata & Get(void) const

Get the member data.

void SetInst(TInst &value)

Assign a value to Inst data member.

TUser & SetUser(void)

Select the variant.

Tdata & Set(void)

Assign a value to data member.

bool IsUser(void) const

Check if variant User is selected.

@ eRepr_raw

continuous sequence

@ e_User

user defined object

@ e_Pub

a reference to the publication

@ e_Source

source of materials, includes Org-ref

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.

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

static const CS_INT unused

constexpr auto sort(_Init &&init)

const CharType(& source)[N]

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

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

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

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

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

static SLJIT_INLINE sljit_ins lr(sljit_gpr dst, sljit_gpr src)

static void s_RemoveGenBankDbxrefs(list< CRef< CSeq_feat >> &ftable)

static void s_UpdateProteinAndTranscriptIds(CSeq_feat &seqfeat)

void g_LogDiagMessage(ILineErrorListener *logger, EDiagSev sev, const string &msg)

CFileContentInfoGenbank mInfoGenbank

static CS_CONTEXT * context

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