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

range_start = 0, range_end = 0;

has_range =

;

parse_info.fBaseFlags = 0;

parse_info.fFastaFlags = fasta_flags | objects::CFastaReader::fParseRawID;

parse_info.lineNumber = line_number;

list<CRef<CSeq_id>> ids;

(

exception&) {}

unique_id = (fasta_flags & objects::CFastaReader::fUniqueIDs);

(ids.empty() || unique_id) {

objects::CFastaDeflineReader::TIgnoredProblems TIgnoredProblems

objects::CFastaDeflineReader::SDeflineParseInfo SDeflineParseInfo

objects::CFastaDeflineReader::TFastaFlags TFastaFlags

objects::CFastaDeflineReader::TSeqTitles TSeqTitles

virtual CRef< objects::CSeq_id > GenerateID(const string &fasta_defline, const TSeqPos &line_number, TFastaFlags fasta_flags)

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

static void ParseDefline(const CTempString &defline, const SDeflineParseInfo &info, const TIgnoredProblems &ignoredErrors, TIds &ids, bool &hasRange, TSeqPos &rangeStart, TSeqPos &rangeEnd, TSeqTitles &seqTitles, ILineErrorListener *pMessageListener)

CRef< objects::CSeq_entry > GetFilteredSeqEntry(TFastaFlags fasta_flags=0)

virtual CRef< objects::CSeq_id > GenerateID(const string &fasta_defline, const TSeqPos &line_number, TFastaFlags fasta_flags) override

fasta_utils::TSeq_idMap m_LocalIds

objects::CScope & m_Scope

Operators to edit gaps in sequences.

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.

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)

CRef< C > Ref(C *object)

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

bool NotEmpty(void) const THROWS_NONE

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

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

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.

static wxAcceleratorEntry entries[3]

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