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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/fasta_8hpp_source.html below:

NCBI C++ ToolKit: include/objtools/readers/fasta.hpp Source File

fStrictGuess = 1<<15,

fBadModThrow

(

) = 1<<20,

fUnknModThrow

(

) = 1<<21,

fLeaveAsText = 1<<22,

fQuickIDCheck = 1<<23,

fHyphensIgnoreAndWarn = 1<<25,

fDisableNoResidues = 1<<26,

fDisableParseRange = 1<<27,

AddStringFlags(

list<string>& stringFlags,

(

)

{

m_LineReader->AtEOF(); }

SetExcludedMods(

vector<string>& excluded_mods);

SetIgnoredMods(

list<string>& ignored_mods);

SetPostponedMods(

list<string>& postponed_mods);

SetMaxIDLength(

max_len);

CanonicalizeString(

& sValue);

SetGapLinkageEvidence(

SetGapLinkageEvidences(

ParseDefLine(

& defLine,

fAligning = 0x40000000,

fInSegSet = 0x20000000

PostProcessIDs(

& defline_ids,

& defline,

has_range=

,

ParseTitle (

SLineTextAndLoc & lineInfo,

* pMessageListener);

IsValidLocalID(

TStr& s)

;

IsValidLocalID(

TStr& idString, TFlags fFastaFlags);

GenerateID (

);

x_OpenMask (

);

x_CloseMask (

);

CreateWarningsForSeqDataInTitle(

TStr& sLineText,

vector<CRef<CSeq_id> >

;

x_AddPairwiseAlignments(

& annot,

& ids,

x_AddMultiwayAlignment(

& annot,

& ids);

(m_CurrentGapLength > 0) {

x_CloseGap(m_CurrentGapLength, atStartOfLine, pMessageListener);

m_CurrentGapLength = 0;

OpenMask(

);

{

m_LineReader->GetLineNumber(); }

{

(GetFlags() & flag) != 0; }

{

(GetFlags() & flag) != 0; }

x_ApplyMods(

& title,

x_AddMods(

line_number,

& processed_title,

x_CheckForPostponedMods(

& idString,

m_bModifiedMaxIdLength=

;

* counter =

,

User-defined methods of the data storage class.

User-defined methods of the data storage class.

function< void(const TIds &id, const TInfo &info, ILineErrorListener *listener)> FIdCheck

Base class for reading FASTA sequences.

list< CModData > TModList

Defines and provides stubs for a general interface to a variety of file readers.

virtual CRef< CSerialObject > ReadObject(CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr)

Read an object from a given input stream, render it as the most appropriate Genbank object.

virtual CRef< CSeq_entry > ReadSeqEntry(CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr)

Read an object from a given input stream, render it as a single Seq-entry, if possible.

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

Callback interface to scan fasta file for entries.

Abstract base class for lightweight line-by-line reading.

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

EDiagSev

Severity level for the posted diagnostics.

TFastaSeqIds all_seq_ids

List of all seq.ids.

TSeqTitles m_CurrentSeqTitles

function< bool(const CTempString &mod_name)> FModFilter

bool TestFlag(EFlags flag) const

TSeqPos m_CurrentGapLength

CConstRef< TGapTypeObj > TNullableGapType

const CSeqIdGenerator & GetIDGenerator(void) const

Uint4 GetMaxIDLength(void) const

Get the maximum ID allowed, which will be kMax_UI4 unless someone has manually lowered it.

SGap::TNullableGapType m_gap_type

TFlags GetFlags(void) const

CSeqIdGenerator & SetIDGenerator(void)

void SaveMasks(TMasks *masks)

const TNullableGapType m_pGapType

long TFlags

binary OR of EFlags

const Uint8 m_uLineNumber

SGap::TLinkEvidSet m_DefaultLinkageEvidence

CBioseq & SetCurrentSeq(void)

const EKnownSize m_eKnownSize

void ResetIDTracker(void)

Re-allow previously seen IDs even if fUniqueIds is on.

CRef< CFastaIdHandler > m_IDHandler

TSeqPos m_gap_Unknown_length

CRef< ILineReader > m_LineReader

map< TSeqPos, TSubMap > TStartsMap

const CSeq_id & GetBestID(void) const

CBioseq::TId & SetIDs(void)

TSeqPos GetCurrentPos(EPosType pos_type)

EFlags

Note on fAllSeqIds: some databases (notably nr) have merged identical sequences, joining their deflin...

TPostponedModMap m_PostponedModMap

CRef< CBioseq > m_CurrentSeq

virtual void EntryFound(CRef< CSeq_entry > se, CNcbiStreampos stream_position)=0

Callback function, called after reading the fasta entry.

vector< CRef< CSeq_id > > TIds

virtual void x_OpenMask(void)

CObjectFor< CSeq_gap::EType > TGapTypeObj

CSourceModParser::TMods m_BadMods

list< string > TFastaSeqIds

List of qll sequence ids.

map< TRowNum, TSignedSeqPos > TSubMap

std::vector< ILineError::EProblem > m_ignorable

CNcbiStreampos stream_offset

Molecule offset in file.

vector< ILineError::EProblem > TIgnoredProblems

set< CSeq_id_Handle > TIDTracker

bool AtEOF(void) const

Indicates (negatively) whether there is any more input.

set< CLinkage_evidence::EType > TLinkEvidSet

void ScanFastaFile(IFastaEntryScan *scanner, CNcbiIfstream &input, CFastaReader::TFlags fread_flags)

Scan FASTA files, call IFastaEntryScan::EntryFound (payload function)

Uint8 LineNumber(void) const

Int8 StreamPosition(void) const

string seq_id

Primary sequence Id.

CFastaReader::TFlags TReadFastaFlags

CFastaDeflineReader::FIdCheck FIdCheck

void ReadFastaFileMap(SFastaFileMap *fasta_map, CNcbiIfstream &input)

Function reads input stream (assumed that it is FASTA format) one molecule entry after another fillin...

string description

Molecule description.

void CloseGap(bool atStartOfLine=false, ILineErrorListener *pMessageListener=nullptr)

unordered_set< string > m_PostponedMods

CSourceModParser::TMods m_UnusedMods

bool TestFlag(EInternalFlags flag) const

const TLinkEvidSet m_setOfLinkageEvidence

ILineReader & GetLineReader(void)

const CBioseq::TId & GetIDs(void) const

vector< SLineTextAndLoc > TSeqTitles

TCountToLinkEvidMap m_GapsizeToLinkageEvidence

vector< SFastaEntry > TMapVector

CRef< CSeq_entry > ReadFasta(CNcbiIstream &in, CFastaReader::TFlags flags=0, int *counter=nullptr, CFastaReader::TMasks *lcv=nullptr, ILineErrorListener *pMessageListener=nullptr)

A const-correct replacement for the deprecated ReadFasta function.

bool NotEmpty(void) const THROWS_NONE

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

#define NCBI_STD_DEPRECATED(message)

uint32_t Uint4

4-byte (32-bit) unsigned integer

int64_t Int8

8-byte (64-bit) signed integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

Int8 NcbiStreamposToInt8(NCBI_NS_STD::char_traits< char >::pos_type stream_pos)

Convert stream position to 64-bit int.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

IO_PREFIX::streampos CNcbiStreampos

Portable alias for streampos.

#define NCBI_XOBJREAD_EXPORT

list< CRef< CSeq_id > > TId

EMol

molecule class in living organism

Lightweight interface for getting lines of data with minimal memory copying.

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

static SLJIT_INLINE sljit_ins lr(sljit_gpr dst, sljit_gpr src)

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