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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/fasta__reader__utils_8hpp_source.html below:

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

1 #ifndef FASTA_READER_UTILS_HPP 2 #define FASTA_READER_UTILS_HPP 58  using TIds

= list<CRef<CSeq_id>>;

66  const string

& sLineText,

68

: m_sLineText(sLineText),

69

m_iLineNum(iLineNum) {}

94  static void

ParseDefline(

const CTempString

& defline,

112  static void

ParseDefline(

const CTempString

& defline,

117  static void

ParseDefline(

const CTempString

& defline,

129  static void

x_ProcessIDs(

136  static void

x_ConvertNumericToLocal(

147  void

operator()(

const TIds

& ids,

152  function

<void (

const string

&

msg

,

EDiagSev

severity)>;

168  CRef<CSeq_id>

GenerateID(

const string

& defline,

bool

advance);

173  const string

&

GetPrefix

(

void

)

const

{

return

m_Prefix; }

175  const string

&

GetSuffix

(

void

)

const

{

return

m_Suffix; }

177  void SetPrefix

(

const string

& prefix) { m_Prefix = prefix; }

179  void SetSuffix

(

const string

& suffix) { m_Suffix = suffix; }

194

mp_IdGenerator.Reset(&generator);

198  return

*mp_IdGenerator;

202  return

*mp_IdGenerator;

207  virtual CRef<CSeq_id>

GenerateID(

const string

& defline,

bool

unique_id=

true

);

211

m_PreviousIdHandles.clear();

215  return

m_PreviousIdHandles.insert(idh).second;

221  return

(m_PreviousIdHandles.find(idh) == m_PreviousIdHandles.end());

vector< ILineError::EProblem > TIgnoredProblems

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

static size_t s_MaxGeneralTagLength

static size_t s_MaxAccessionLength

list< CRef< CSeq_id > > TIds

CReaderBase::TReaderFlags TBaseFlags

static size_t s_MaxLocalIDLength

vector< SLineTextAndLoc > TSeqTitles

function< void(const TIds &id, int lineNum, CFastaIdValidate::FReportError *fReportError)> FIdValidate

bool CacheIdHandle(CSeq_id_Handle idh)

const CSeqIdGenerator & GetGenerator(void) const

void SetGenerator(CSeqIdGenerator &generator)

bool x_IsUniqueIdHandle(CSeq_id_Handle idh)

TIdHandleCache m_PreviousIdHandles

CRef< CSeqIdGenerator > mp_IdGenerator

CSeqIdGenerator & SetGenerator(void)

function< void(EDiagSev severity, int lineNum, const string &idString, EErrCode errCode, const string &msg)> FReportError

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

function< void(const string &msg, EDiagSev severity)> FReportError

CFastaDeflineReader::TIds TIds

std::atomic< TCount > m_Counter

void SetCounter(TCount count)

CSeqIdGenerator(TCount count=1, const string &prefix=kEmptyStr, const string &suffix=kEmptyStr)

void SetPrefix(const string &prefix)

TCount GetCounter(void) const

void SetSuffix(const string &suffix)

const string & GetPrefix(void) const

const string & GetSuffix(void) const

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

unsigned int TSeqPos

Type for sequence locations and lengths.

EDiagSev

Severity level for the posted diagnostics.

Uint8 TCount

Alias for value type of counter.

#define NCBI_STD_DEPRECATED(message)

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.

#define NCBI_XOBJREAD_EXPORT

unsigned int

A callback function used to compare two keys in a database.

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

SLineTextAndLoc(const string &sLineText, TSeqPos iLineNum)

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