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NCBI C++ ToolKit: src/gui/objutils/seq_fasta_reader.cpp Source File

defline = m_LineReader->GetCurrentLine();

range_start = 0, range_end = 0;

has_range =

;

SDefLineParseInfo parseInfo;

parseInfo.fBaseFlags = m_iFlags;

parseInfo.maxIdLength = m_MaxIDLength;

parseInfo.lineNumber = LineNumber();

list<CRef<CSeq_id> > ids;

(

exception&) {}

(

it = ids.begin(); it != ids.end();) {

(

.Which()) {

seq_id_text =

;

seq_id_text +=

;

SetIDs().push_back(seq_id);

(defline_ids.empty())

(non_local_id.

())

CRef< objects::CSeq_entry > ReadSequences(vector< CConstRef< objects::CSeq_id >> *wellknown_ids=nullptr, int max_seqs=kMax_Int, objects::ILineErrorListener *pMessageListener=0)

Read multiple sequences and remove the well-known sequences from the entry.

fasta_utils::TSeq_idMap m_LocalIds

objects::CScope & m_Scope

virtual void GenerateID() override

virtual void PostProcessIDs(const objects::CBioseq::TId &defline_ids, const string &defline, bool has_range=false, TSeqPos range_start=kInvalidSeqPos, TSeqPos range_end=kInvalidSeqPos) override

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

CRef< objects::CSeq_id > IdentifyLocalId(const string &fasta_id)

Tries to identify the specified local id (works for ids, prefixed with rng_ or mod_,...

CRef< objects::CSeq_entry > ReplaceWellknownSeqs(objects::CSeq_entry &entry, objects::CScope &scope, vector< CConstRef< objects::CSeq_id >> *wellknown_ids=nullptr, TSeq_idMap *local_ids=nullptr)

Removes the well-known sequences from the set and returns their ids (optional)

void UpdateOrgInformation(objects::CSeq_entry &entry, objects::CScope &scope, const TSeq_idMap &local_ids)

Updates the organism information for the Seq-entry object by copying the information from a well-know...

unsigned int TSeqPos

Type for sequence locations and lengths.

CRef< CSeq_entry > ReadSet(int max_seqs=kMax_Int, ILineErrorListener *pMessageListener=nullptr)

Read multiple sequences (by default, as many as are available.)

virtual void PostProcessIDs(const CBioseq::TId &defline_ids, const string &defline, bool has_range=false, TSeqPos range_start=kInvalidSeqPos, TSeqPos range_end=kInvalidSeqPos)

virtual void GenerateID(void)

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

static int BestRank(const CRef< CSeq_id > &id)

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.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

bool IsLocal(void) const

Check if variant Local is selected.

@ e_not_set

No variant selected.

list< CRef< CSeq_id > > TId

Useful/utility classes and methods.

static wxAcceleratorEntry entries[3]

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