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

& annotName,

& annotTitle,

m_uProgressReportInterval(0),

m_uNextProgressReport(0),

m_AnnotName(annotName),

m_AnnotTitle(annotTitle),

mSeqIdResolve(seqidresolver),

(readerData.empty()) {

(!readerData.empty()) {

);

annots.push_back(annot);

,

(!pContainer || !pContainer->

(err)) {

list<string>& stringFlags,

(

stringFlag: stringFlags) {

flagEntry = flagMap.

(stringFlag);

(flagEntry == flagMap.

()) {

message =

+ stringFlag;

baseFlags |= flagEntry->second;

);

interval.

(n_to-1);

desc.

().push_back( region );

);

vector<string> fields;

( vector<string>::iterator it = fields.begin(); it != fields.end(); ++it ) {

( *it ==

) {

( it == fields.end() ) {

vector<string> parts;

(countInfos + countWarnings + countErrors + countCritical == 0) {

conversioninfo->

().SetStr(

);

conversioninfo->

(

,

(countCritical));

conversioninfo->

(

,

(countErrors));

conversioninfo->

(

,

(countWarnings));

conversioninfo->

(

,

(countInfos));

user->

(*conversioninfo);

annot.

().Set().push_back(user);

uCurrentTime = (

)time(0);

(strLine.

()) {

(strLine[0] ==

&& strLine[1] !=

);

(strLine.

() == 5 || strLine[5] ==

|| strLine[5] ==

)

(line ==

);

(!

.AtEOF()) {

+

.GetMsg());

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

CReaderBase implementation that reads BED data files, either a single object or all objects found.

Base class for reading FASTA sequences.

EFormat

The formats are checked in the same order as declared here.

@ eFiveColFeatureTable

Five-column feature table.

@ eBed

UCSC BED file format, CBedReader.

@ eGtf

New GTF, CGtfReader.

@ eGff3

GFF3, CGff3Reader.

@ eGtf_POISENED

Old and Dead GFF/GTF style annotations.

@ eFasta

FASTA format sequence record, CFastaReader.

@ eRmo

RepeatMasker Output.

@ eUCSCRegion

USCS Region file format.

@ ePsl

PSL alignment format.

@ eBed15

UCSC BED15 or microarray format.

@ eWiggle

UCSC WIGGLE file format.

void Throw(void) const

copy constructor is protected so please use this function to throw the object.

void SetLineNumber(unsigned int uLineNumber)

void Throw(void) const

this function to throw this object.

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.

std::string Message() const

static void Tokenize(const string &instr, const string &delim, vector< string > &tokens)

Tokenize a given string, respecting quoted substrings an atomic units.

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

virtual bool xParseBrowserLine(const CTempString &, CSeq_annot &)

unique_ptr< CReaderMessageHandler > m_pMessageHandler

void xProcessLineError(const ILineError &, ILineErrorListener *)

void xGuardedGetData(ILineReader &, TReaderData &, ILineErrorListener *)

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 void xSetBrowserRegion(const CTempString &, CAnnot_descr &)

virtual void xValidateAnnot(const CSeq_annot &)

virtual void xProcessData(const TReaderData &, CSeq_annot &)

bool xIsReportingProgress() const

void SetProgressReportInterval(unsigned int intv)

virtual void ReadSeqAnnots(TAnnots &annots, CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr)

Read all objects from given insput stream, returning them as a vector of Seq-annots.

virtual bool xUngetLine(ILineReader &)

virtual bool xIsCommentLine(const CTempString &)

virtual CRef< CSeq_annot > xCreateSeqAnnot()

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.

unsigned int m_uLineNumber

void xProcessReaderMessage(CReaderMessage &, ILineErrorListener *)

static CReaderBase * GetReader(CFormatGuess::EFormat format, TReaderFlags flags=0, CReaderListener *=nullptr)

Allocate a CReaderBase derived reader object based on the given file format.

unique_ptr< CTrackData > m_pTrackDefaults

CReaderBase(TReaderFlags flags=0, const string &name="", const string &title="", SeqIdResolver seqresolver=CReadUtil::AsSeqId, CReaderListener *pListener=nullptr)

Protected constructor. Use GetReader() to get an actual reader object.

bool xIsOperationCanceled() const

unsigned int m_uProgressReportInterval

unsigned int m_uNextProgressReport

virtual void xPostProcessAnnot(CSeq_annot &)

virtual bool xProgressInit(ILineReader &istr)

void ProcessError(CObjReaderLineException &, ILineErrorListener *)

vector< TReaderLine > TReaderData

virtual bool xGetLine(ILineReader &, string &)

virtual void xAddConversionInfo(CSeq_annot &, ILineErrorListener *)

virtual void xGuardedProcessData(const TReaderData &, CSeq_annot &, ILineErrorListener *)

virtual bool xParseTrackLine(const CTempString &)

bool xParseComment(const CTempString &, CRef< CSeq_annot > &)

virtual bool xIsBrowserLine(const CTempString &)

void xReportProgress(ILineErrorListener *=nullptr)

virtual void xAssignTrackData(CSeq_annot &)

void SetCanceler(ICanceled *=nullptr)

void xProcessUnknownException(const CException &)

virtual void xGetData(ILineReader &, TReaderData &)

virtual CRef< CSeq_annot > ReadSeqAnnot(CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr)

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

std::atomic< unsigned int > m_uDataCount

static void xAddStringFlagsWithMap(const list< string > &stringFlags, const map< string, TReaderFlags > flagMap, TReaderFlags &baseFlags)

void ProcessWarning(CObjReaderLineException &, ILineErrorListener *)

virtual bool xIsTrackTerminator(const CTempString &)

virtual bool xIsTrackLine(const CTempString &)

void SetLineNumber(int lineNumber)

virtual EDiagSev Severity() const

Implements a concrete class for reading RepeatMasker output from tabular form and rendering it as ASN...

void SetNameDesc(const string &name)

void SetTitleDesc(const string &title)

Simple implementation of ILineReader for i(o)streams.

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

static bool IsTrackData(const LineData &)

CUser_object & AddField(const string &label, const string &value, EParseField parse=eParse_String)

add a data field to the user object that holds a given value

Interface for testing cancellation request in a long lasting operation.

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...

virtual size_t LevelCount(EDiagSev)=0

Returns the number of errors seen so far at the given severity.

bool PutMessage(const IObjtoolsMessage &message) override

virtual string Message() const

@ eProblem_GeneralParsingError

string SeverityStr() const

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

const_iterator end() const

const_iterator find(const key_type &key) const

Include a standard set of the NCBI C++ Toolkit most basic headers.

Operators to edit gaps in sequences.

static const char location[]

@ eDiag_Info

Informational message.

@ eDiag_Error

Error message.

@ eDiag_Warning

Warning message.

@ eDiag_Fatal

Fatal error – guarantees exit(or abort)

@ eDiag_Critical

Critical error message.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

virtual CT_POS_TYPE GetPosition(void) const =0

Return the current (absolute) position.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

virtual bool IsCanceled(void) const =0

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

static CTempString TruncateSpaces_Unsafe(const CTempString str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

bool empty(void) const

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

static int Compare(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Compare of a substring with another string.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

size_type size(void) const

Return the length of the represented array.

@ fAllowCommas

Allow commas. See 'ENumToStringFlags::fWithCommas'.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

void SetType(TType &value)

Assign a value to Type data member.

void SetTo(TTo value)

Assign a value to To data member.

void SetFrom(TFrom value)

Assign a value to From data member.

void SetStrand(TStrand value)

Assign a value to Strand data member.

Tdata & Set(void)

Assign a value to data member.

void SetDesc(TDesc &value)

Assign a value to Desc data member.

TUser & SetUser(void)

Select the variant.

TRegion & SetRegion(void)

Select the variant.

unsigned int

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

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

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

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines NCBI C++ exception handling.

Multi-threading – classes, functions, and features.

Useful/utility classes and methods.

static SLJIT_INLINE sljit_ins lr(sljit_gpr dst, sljit_gpr src)

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