Search Toolkit Book for CBlastFastaInputSource

Class representing a text file containing sequences in fasta format. More...

#include <algo/blast/blastinput/blast_fasta_input.hpp>

Inheritance diagram for CBlastFastaInputSource:

Collaboration diagram for CBlastFastaInputSource:

Public Member Functions
	CBlastFastaInputSource (CNcbiIstream &infile, const CBlastInputSourceConfig &iconfig)
	Constructor. More...

	CBlastFastaInputSource (const string &user_input, const CBlastInputSourceConfig &iconfig)
	Constructor. More...

virtual	~CBlastFastaInputSource ()
	Destructor. More...

Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...

	CObject (const CObject &src)
	Copy constructor. More...

virtual	~CObject (void)
	Destructor. More...

CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...

bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...

bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...

bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...

bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...

void	AddReference (void) const
	Add reference to object. More...

void	RemoveReference (void) const
	Remove reference to object. More...

void	ReleaseReference (void) const
	Remove reference without deleting object. More...

virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...

virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...

void *	operator new (size_t size)
	Define new operator for memory allocation. More...

void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...

void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...

void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...

void *	operator new (size_t size, void *place)
	Define new operator. More...

void	operator delete (void ptr, void place)
	Define delete operator. More...

void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...

void	operator delete (void ptr, CObjectMemoryPool place)
	Define delete operator. More...

virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...

Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)

virtual	~CDebugDumpable (void)

void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const

void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const

void	DumpToConsole (void) const

Protected Member Functions
virtual SSeqLoc	GetNextSSeqLoc (CScope &scope)
	Retrieve a single sequence (in an SSeqLoc container) More...

virtual CRef< CBlastSearchQuery >	GetNextSequence (CScope &scope)
	Retrieve a single sequence (in a CBlastSearchQuery container) More...

virtual bool	End ()
	Signal whether there are any unread sequences left. More...

Protected Member Functions inherited from CBlastInputSource
virtual	~CBlastInputSource ()
	Destructor. More...

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Private Member Functions
CRef< objects::CSeq_loc >	x_FastaToSeqLoc (CRef< objects::CSeq_loc > &lcase_mask, CScope &scope)
	Read a single sequence from file and convert to a Seq_loc. More...

void	x_InitInputReader ()
	Initialization method for the input reader. More...

Private Attributes
CBlastInputSourceConfig	m_Config
	Configuration for the sequences to be read. More...

CRef< ILineReader >	m_LineReader
	interface to read lines More...

AutoPtr< CFastaReader >	m_InputReader
	Reader of FASTA sequences or identifiers. More...

bool	m_ReadProteins
	read protein sequences? More...

Additional Inherited Members
Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...

typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...

typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...

typedef Uint8	TCount
	Alias for value type of counter. More...

Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...

static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)

static EAllocFillMode	GetAllocFillMode (void)

static void	SetAllocFillMode (EAllocFillMode mode)

static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...

Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)

Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...

static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...

static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...

static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...

static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...

static const TCount	eCounterStateMask
	Valid object, and object in heap. More...

Detailed Description

Class representing a text file containing sequences in fasta format.

Definition at line 48 of file blast_fasta_input.hpp.

Constructor & Destructor Documentation

◆ CBlastFastaInputSource() [1/2]

CBlastFastaInputSource::CBlastFastaInputSource	(	CNcbiIstream &	infile,
		const CBlastInputSourceConfig &	iconfig
	)

Constructor.

Parameters

infile	The file to read [in]
iconfig	Input configuration object, this options apply to all input read [in]

Definition at line 263 of file blast_fasta_input.cpp.

References x_InitInputReader().

◆ CBlastFastaInputSource() [2/2]

CBlastFastaInputSource::CBlastFastaInputSource	(	const string &	user_input,
		const CBlastInputSourceConfig &	iconfig
	)

Constructor.

Parameters

objmgr	Object Manager instance [in]
user_input	User provided input in a string [in]
iconfig	Input configuration object, this options apply to all input read [in]

Definition at line 274 of file blast_fasta_input.cpp.

References m_LineReader, NCBI_THROW, CRef< C, Locker >::Reset(), and x_InitInputReader().

◆ ~CBlastFastaInputSource()

virtual CBlastFastaInputSource::~CBlastFastaInputSource ( )

inlinevirtual

Destructor.

Definition at line 68 of file blast_fasta_input.hpp.

Member Function Documentation

◆ End()

bool CBlastFastaInputSource::End ( void )

protectedvirtual

Signal whether there are any unread sequences left.

Returns: true if no unread sequences remaining

Implements CBlastInputSource.

Definition at line 343 of file blast_fasta_input.cpp.

References ILineReader::AtEOF(), and m_LineReader.

◆ GetNextSequence()

CRef< CBlastSearchQuery > CBlastFastaInputSource::GetNextSequence ( CScope & scope )

protectedvirtual

Retrieve a single sequence (in a CBlastSearchQuery container)

Parameters

scope CScope object to use in CBlastSearchQuery returned [in]

Exceptions

CObjReaderParseException if input file is empty of the end of file is reached unexpectedly

Note: all masks are returned in either both strands (for nucleotides) or unknown (for proteins)

Implements CBlastInputSource.

Definition at line 456 of file blast_fasta_input.cpp.

References eBlastTypeBlastn, eBlastTypeBlastp, CBlastInputSourceConfig::GetLowercaseMask(), m_Config, m_ReadProteins, PackedSeqLocToMaskedQueryRegions(), and x_FastaToSeqLoc().

◆ GetNextSSeqLoc()

SSeqLoc CBlastFastaInputSource::GetNextSSeqLoc ( CScope & scope )

protectedvirtual

Retrieve a single sequence (in an SSeqLoc container)

Parameters

scope CScope object to use in SSeqLoc returned [in]

Exceptions

CObjReaderParseException if input file is empty or the end of file is reached unexpectedly

Note: all masks are returned in either the plus strand (for nucleotides) or unknown (for proteins)

Implements CBlastInputSource.

Definition at line 442 of file blast_fasta_input.cpp.

References CBlastInputSourceConfig::GetLowercaseMask(), m_Config, SSeqLoc::mask, and x_FastaToSeqLoc().

◆ x_FastaToSeqLoc()

CRef< CSeq_loc > CBlastFastaInputSource::x_FastaToSeqLoc	(	CRef< objects::CSeq_loc > &	lcase_mask,
		CScope &	scope
	)

private

Read a single sequence from file and convert to a Seq_loc.

Parameters

lcase_mask	A Seq_loc that describes the lowercase-masked regions in the query that was read in. If there are no such locations, the Seq_loc is of type 'null', otherwise it is of type 'packed_seqint' [out]
scope	CScope object to which the read sequence is added [in]

Returns: The sequence in Seq_loc format

Definition at line 349 of file blast_fasta_input.cpp.

References _ASSERT, CBlastScopeSource::AddDataLoaders(), CScope::AddTopLevelSeqEntry(), CSeq_id::BestRank(), ConstBegin(), CSeq_loc_Base::e_not_set, eNa_strand_both, eNa_strand_other, eNa_strand_plus, eNa_strand_unknown, FindBestChoice(), AutoPtr< X, Del >::get(), COpenRange< TSeqPos >::GetEmpty(), CRange_Base::GetFrom(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetLength(), CBlastInputSourceConfig::GetLowercaseMask(), CBlastInputReader::GetQueryScopeSource(), CBlastInputSourceConfig::GetRange(), CSeq_entry_Base::GetSeq(), CBlastInputSourceConfig::GetStrand(), CRange_Base::GetTo(), HasRawSequenceData(), m_Config, m_InputReader, m_ReadProteins, max(), NCBI_THROW, CRef< C, Locker >::NotEmpty(), CFastaReader::ReadOneSeq(), CFastaReader::SaveMask(), and CSeq_loc::SetInt().

Referenced by GetNextSequence(), and GetNextSSeqLoc().

◆ x_InitInputReader()

void CBlastFastaInputSource::x_InitInputReader ( )

private

Initialization method for the input reader.

Definition at line 289 of file blast_fasta_input.cpp.

References ILineError::eProblem_ModifierFoundButNoneExpected, ILineError::eProblem_TooLong, ILineError::eProblem_TooManyAmbiguousResidues, CFastaReader::fAssumeNuc, CFastaReader::fAssumeProt, CFastaReader::fDisableNoResidues, CFastaReader::fDLOptional, CFastaReader::fHyphensIgnoreAndWarn, flags, CFastaReader::fNoParseID, CFastaReader::fNoSplit, CFastaReader::fParseRawID, CFastaReader::fQuickIDCheck, CFastaReader::fSkipCheck, CBlastInputSourceConfig::GetBelieveDeflines(), CBlastInputSourceConfig::GetDataLoaderConfig(), CBlastInputSourceConfig::GetLocalIdCounterInitValue(), CBlastInputSourceConfig::GetLocalIdPrefix(), CBlastInputSourceConfig::GetSeqLenThreshold2Guess(), CBlastInputSourceConfig::GetSkipSeqCheck(), CFastaReader::IgnoreProblem(), kEmptyStr, m_Config, m_InputReader, m_LineReader, m_ReadProteins, NULL, AutoPtr< X, Del >::reset(), CBlastInputSourceConfig::RetrieveSeqData(), CFastaReader::SetIDGenerator(), and SDataLoaderConfig::UseDataLoaders().

Referenced by CBlastFastaInputSource().

Member Data Documentation

◆ m_Config

CBlastInputSourceConfig CBlastFastaInputSource::m_Config

private

Configuration for the sequences to be read.

Definition at line 92 of file blast_fasta_input.hpp.

Referenced by GetNextSequence(), GetNextSSeqLoc(), x_FastaToSeqLoc(), and x_InitInputReader().

◆ m_InputReader

AutoPtr<CFastaReader> CBlastFastaInputSource::m_InputReader

private

Reader of FASTA sequences or identifiers.

Definition at line 95 of file blast_fasta_input.hpp.

Referenced by x_FastaToSeqLoc(), and x_InitInputReader().

◆ m_LineReader

CRef<ILineReader> CBlastFastaInputSource::m_LineReader

private

interface to read lines

Definition at line 93 of file blast_fasta_input.hpp.

Referenced by CBlastFastaInputSource(), End(), and x_InitInputReader().

◆ m_ReadProteins

bool CBlastFastaInputSource::m_ReadProteins

private

read protein sequences?

Definition at line 96 of file blast_fasta_input.hpp.

Referenced by GetNextSequence(), x_FastaToSeqLoc(), and x_InitInputReader().

The documentation for this class was generated from the following files:

include/algo/blast/blastinput/blast_fasta_input.hpp
src/algo/blast/blastinput/blast_fasta_input.cpp

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CBlastFastaInputSource() [1/2]

◆ CBlastFastaInputSource() [2/2]

◆ ~CBlastFastaInputSource()

Member Function Documentation

◆ End()

◆ GetNextSequence()

◆ GetNextSSeqLoc()

◆ x_FastaToSeqLoc()

◆ x_InitInputReader()

Member Data Documentation

◆ m_Config

◆ m_InputReader

◆ m_LineReader

◆ m_ReadProteins