NCBI C++ ToolKit
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CBlastFastaInputSource Class Reference

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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...
 
CObjectoperator= (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< CBlastSearchQueryGetNextSequence (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< ILineReaderm_LineReader
 interface to read lines More...
 
AutoPtr< CFastaReaderm_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< Uint8TCounter
 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
infileThe file to read [in]
iconfigInput 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
objmgrObject Manager instance [in]
user_inputUser provided input in a string [in]
iconfigInput 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
scopeCScope object to use in CBlastSearchQuery returned [in]
Exceptions
CObjReaderParseExceptionif 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
scopeCScope object to use in SSeqLoc returned [in]
Exceptions
CObjReaderParseExceptionif 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

◆ x_InitInputReader()

void CBlastFastaInputSource::x_InitInputReader ( )
private

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:
Modified on Wed Feb 21 09:57:05 2024 by modify_doxy.py rev. 669887