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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/multireader_8hpp_source.html below:

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

= list<CRef<objects::CSeq_annot>>;

std::unique_ptr<IIndexedFeatureReader>

(

& filename);

unique_ptr<CNcbiIstream>& pIstr,

& annots);

unique_ptr<CObjectIStream>

(

& filename)

;

EFormat

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

@ eUnknown

unknown format

IdMapper base class implementation.

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

void MergeDescriptors(objects::CSeq_descr &dest, const objects::CSeqdesc &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

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

Base class for all serializable objects.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

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

void g_ModifySeqIds(CSeq_annot &annot, const CSeq_id &match, CRef< CSeq_id > new_id)

const CharType(& source)[N]

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

Useful/utility classes and methods.

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

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 CS_CONTEXT * context

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