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NCBI C++ ToolKit: src/objtools/readers/fasta_reader_utils.cpp Source File

& idString,

& errMessage,

(pMessageListener) {

unique_ptr<CObjReaderLineException> pLineExpt(

idString,

,

,

,

(pMessageListener->

(*pLineExpt)) {

& idString,

& errMessage,

unique_ptr<CObjReaderLineException> pLineExpt(

idString,

,

,

,

(!pMessageListener) {

(!pMessageListener->

(*pLineExpt)) {

has_range =

.has_range;

range_start =

.range_start;

range_end =

.range_end;

titles = std::move(

.titles);

range_len = 0;

.has_range =

;

(defline[0] !=

) {

, 0);

(start = 1 ; start <

; ++start ) {

( !

(defline[start]) ) {

title_start =

;

(pos <

&& defline[pos] >

) {

.range_start,

.range_end, pMessageListener);

id_string = defline.

(start, pos - start - range_len);

, 0);

.has_range = (range_len>0);

(title_start <

&&

((

)defline[title_start])) {

(title_start <

) {

(pos = title_start + 1; pos <

; ++pos) {

((

)defline[pos] <

) {

.titles.push_back(

defline.

(title_start, pos - title_start), lineNumber));

on_start =

;

(pos = s.

() - 1; pos > 0; --pos) {

c = s[pos];

(c >=

&& c <=

) {

start += (c -

) * mult;

end += (c -

) * mult;

}

(c ==

&& !on_start && mult > 1) {

}

(c ==

&& on_start && mult > 1) {

}

(c ==

&& pos > 0 && s[--pos] ==

&& on_start && mult > 1) {

((

? (end > start) : (start > end)) || s[pos] !=

) {

& idString,

&

);

= pair<CObjReaderLineException::EProblem, CObjReaderParseException::EErrCode>;

m_pMessageListener(pMessageListener), m_IgnoreGeneralParsingError(ignoreGeneralParsingError) {}

& idString,

cit = s_CodeMap.

(errCode);

& problem = cit->second.first;

& parseExceptionCode = cit->second.second;

ids.push_back(pSeqId);

f_id_check(ids,

, pMessageListener);

to_parse = id_string;

(id_string.

(

) !=

&&

err_message =

+

+

;

local_copy = id_string;

(

& rit : local_copy)

to_parse = local_copy;

+ id_string +

,

f_id_check(ids,

, pMessageListener);

(

: ids) {

gi =

->GetGi();

(

.maxIdLength) {

advance =

;

static void x_ConvertNumericToLocal(TIds &ids)

vector< ILineError::EProblem > TIgnoredProblems

static TSeqPos ParseRange(const CTempString &s, TSeqPos &start, TSeqPos &end, ILineErrorListener *pMessageListener)

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

static size_t s_MaxGeneralTagLength

static void x_ProcessIDs(const CTempString &id_string, const SDeflineParseInfo &info, TIds &ids, ILineErrorListener *pMessageListener, FIdCheck fn_id_check)

static size_t s_MaxAccessionLength

list< CRef< CSeq_id > > TIds

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

static size_t s_MaxLocalIDLength

vector< SLineTextAndLoc > TSeqTitles

virtual CRef< CSeq_id > GenerateID(bool unique_id)

bool x_IsUniqueIdHandle(CSeq_id_Handle idh)

CRef< CSeqIdGenerator > mp_IdGenerator

void SetMaxLocalIDLength(size_t length)

void SetMaxAccessionLength(size_t length)

void SetMaxGeneralTagLength(size_t length)

void operator()(EDiagSev severity, int lineNum, const string &idString, CFastaIdValidate::EErrCode errCode, const string &msg)

ILineErrorListener * m_pMessageListener

pair< CObjReaderLineException::EProblem, CObjReaderParseException::EErrCode > TCodePair

bool m_IgnoreGeneralParsingError

CIdErrorReporter(ILineErrorListener *pMessageListener, bool ignoreGeneralParsingError=false)

static CObjReaderLineException * Create(EDiagSev eSeverity, unsigned int uLine, const std::string &strMessage, EProblem eProblem=eProblem_GeneralParsingError, const std::string &strSeqId=string(""), const std::string &strFeatureName=string(""), const std::string &strQualifierName=string(""), const std::string &strQualifierValue=string(""), CObjReaderLineException::EErrCode eErrCode=eFormat, const TVecOfLines &vecOfOtherLines=TVecOfLines())

Please use this instead of the constructor because the ctor is protected.

@ eFormat

Some of these are pretty specialized.

@ fNumericIdsAsLocal

numeric identifiers are local IDs

@ fAllIdsAsLocal

all identifiers are local IDs

void operator()(const TIds &ids, const TInfo &info, ILineErrorListener *listener)

CFastaDeflineReader::TIds TIds

std::atomic< TCount > m_Counter

CRef< CSeq_id > GenerateID(const string &defline, bool advance)

CRef< CSeq_id > GenerateID(void) const

Equivalent to GenerateID(false)

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

virtual bool PutError(const ILineError &)=0

Store error in the container, and return true if error was stored fine, and return false if the calle...

@ eProblem_UnexpectedAminoAcids

@ eProblem_UnexpectedNucResidues

@ eProblem_GeneralParsingError

const_iterator end() const

const_iterator find(const key_type &key) const

Operators to edit gaps in sequences.

static void s_PostError(ILineErrorListener *pMessageListener, const TSeqPos lineNumber, const string &idString, const string &errMessage, const CObjReaderLineException::EProblem problem, const CObjReaderParseException::EErrCode errCode)

static void s_PostWarning(ILineErrorListener *pMessageListener, const TSeqPos lineNumber, const string &idString, const string &errMessage, const CObjReaderLineException::EProblem problem, const CObjReaderParseException::EErrCode errCode)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define LOG_POST_X(err_subcode, message)

#define DIAG_COMPILE_INFO

Make compile time diagnostic information object to use in CNcbiDiag and CException.

EDiagSev

Severity level for the posted diagnostics.

@ eDiag_Error

Error message.

@ eDiag_Warning

Warning message.

void Warning(CExceptionArgs_Base &args)

#define NCBI_THROW2(exception_class, err_code, message, extra)

Throw exception with extra parameter.

@ fNoParseID

Generate an ID (whole defline -> title)

@ fParseRawID

Try to identify raw accessions.

@ fDisableParseRange

No ranges in seq-ids. Ranges part of seq-id instead.

static const size_t kMaxAccessionLength

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

static const size_t kMaxLocalIDLength

ID length restrictions.

static SIZE_TYPE ParseIDs(CBioseq::TId &ids, const CTempString &s, TParseFlags flags=fParse_Default)

Parse a string representing one or more Seq-ids, appending the results to IDS.

static const size_t kMaxGeneralTagLength

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

@ fParse_RawText

Try to ID raw non-numeric accessions.

@ fParse_PartialOK

Warn rather than throwing an exception when a FASTA-style ID set contains unparsable portions,...

@ fParse_AnyLocal

Treat otherwise unidentified strings as local accessions as long as they don't resemble FASTA-style I...

CRef< C > Ref(C *object)

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

#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.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

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

Convert int to string.

bool empty(void) const

Return true if the represented string is empty (i.e., the length is zero)

size_type length(void) const

Return the length of the represented array.

CTempString substr(size_type pos) const

Obtain a substring from this string, beginning at a given offset.

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.

size_type find(const CTempString match, size_type pos=0) const

Find the first instance of the entire matching string within the current string, beginning at an opti...

TStr & SetStr(void)

Select the variant.

TId & SetId(void)

Select the variant.

TLocal & SetLocal(void)

Select the variant.

Defines NCBI C++ diagnostic APIs, classes, and macros.

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

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