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

;

(

<<

<< (

)Guess);

(

loop = 0; loop < checkCount; loop++ ) {

CheckFormat = CheckOrder[loop];

streamsize Total = 0;

In.read(buff,

(buff));

streamsize

= In.gcount();

(Total >= (1024*1024))

Bioseqs.swap( agp_reader.

() );

(!Bioseqs.empty());

Annot =

.ReadSeqAnnot(LineReader);

(WiggleCount > 0);

list<CRef<CSeq_annot> > LocalAnnots;

.ReadSeqAnnots(LocalAnnots, LineReader);

(!AnnotIter->IsNull() && (*AnnotIter)->CanGetData() &&

(*AnnotIter)->GetData().IsFtable())

(BedCount > 0);

Annot =

.ReadSeqAnnot(LineReader);

(Bed15Count > 0);

Result =

.ReadSet(1);

.ReadSeqAnnots(LocalAnnots, LineReader);

(!AnnotIter->IsNull() && (**AnnotIter).CanGetData() &&

(**AnnotIter).GetData().IsFtable())

(GtfCount > 0);

.ReadSeqAnnots(LocalAnnots, LineReader);

(!AnnotIter->IsNull() && (**AnnotIter).CanGetData() &&

(**AnnotIter).GetData().IsFtable())

(Gff3Count > 0);

.ReadSeqAnnots(LocalAnnots, LineReader);

(!AnnotIter->IsNull() && (**AnnotIter).CanGetData() &&

(**AnnotIter).IsFtable())

(Gff2Count > 0);

unique_ptr<CObjectIStream> pObjStream;

(baseFormat) {

( !pObjStream.get() ) {

(

.size() != 1 ) {

*

.begin();

set<TTypeInfo>& recognizedGenbankTypes)

(baseFormat) {

User-defined methods of the data storage class.

virtual int ReadStream(CNcbiIstream &is, EFinalize eFinalize=eFinalize_Yes)

Read an AGP file from the given input stream.

This class is used to turn an AGP file into a vector of Seq-entry's.

vector< CRef< objects::CSeq_entry > > TSeqEntryRefVec

This is the way the results will be returned Each Seq-entry contains just one Bioseq,...

TSeqEntryRefVec & GetResult(void)

This gets the results found, but don't call before finalizing.

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

CFormatGuess::EFormat GuessFormatAndContent(CFileContentInfo &contentInfo)

const set< TTypeInfo > * m_pEffectiveRecognizedGenbankObjectTypes

static set< TTypeInfo > sDefaultRecognizedGenbankObjectTypes

bool x_TryFormat(CFormatGuess::EFormat Format)

unique_ptr< CFormatGuess > m_Guesser

std::stringstream m_LocalBuffer

bool TestFormat(CFormatGuess::EFormat)

void SetRecognizedGenbankTypes(const set< TTypeInfo > &recognizedGenbankTypes)

CFormatGuess::EFormat GuessFormat()

bool x_FillLocalBuffer(CNcbiIstream &In)

TTypeInfo xGuessGenbankObjectType(CFormatGuess::EFormat baseFormat)

Class implements different ad-hoc unreliable file format identifications.

EFormat

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

@ eBinaryASN

Binary ASN.1.

@ eGff2

GFF2, CGff2Reader, any GFF-like that doesn't fit the others.

@ eBed

UCSC BED file format, CBedReader.

@ eGtf

New GTF, CGtfReader.

@ eAgp

AGP format assembly, AgpRead.

@ eGff3

GFF3, CGff3Reader.

@ eFasta

FASTA format sequence record, CFastaReader.

@ eUnknown

unknown format

@ eRmo

RepeatMasker Output.

@ eAlignment

Text alignment.

@ eBed15

UCSC BED15 or microarray format.

@ eWiggle

UCSC WIGGLE file format.

CObjectIStreamAsnBinary –.

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

Simple implementation of ILineReader for i(o)streams.

CTypeInfo class contains all information about C++ types (both basic and classes): members and layout...

@ fIncludeRepeatClass

Same as fIncludeRepeatFamily.

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

Operators to edit gaps in sequences.

set< TTypeInfo > sDefaultRecognizedGenbankObjectTypes

static void TestResult(SQLRETURN result0, int level, const char *func)

static const struct type types[]

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

@ eNoOwnership

No ownership is assumed.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

void Info(CExceptionArgs_Base &args)

static TTypeInfo GetTypeInfo(void)

bool NotEmpty(void) const THROWS_NONE

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

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static void Pushback(CNcbiIstream &is, CT_CHAR_TYPE *buf, streamsize buf_size, void *del_ptr)

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

const string & GetName(void) const

Get name of this type.

const TSet & GetSet(void) const

Get the variant data.

bool IsSet(void) const

Check if variant Set is selected.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

bool IsFtable(void) const

Check if variant Ftable is selected.

const TData & GetData(void) const

Get the Data member data.

bool CanGetData(void) const

Check if it is safe to call GetData method.

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

Magic spell ;-) needed for some weird compilers... very empiric.

GenericReader< UTF8< char >, UTF8< char >, CrtAllocator > Reader

Reader with UTF8 encoding and default allocator.

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.

CFileContentInfoGff3 mInfoGff3

CFileContentInfoNone mInfoNone

CFileContentInfoAlign mInfoAlign

CFileContentInfoGenbank mInfoGenbank

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