NCBI C++ ToolKit
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CQueryOptionsArgs Class Reference

Search Toolkit Book for CQueryOptionsArgs

Argument class to collect query options. More...

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

+ Inheritance diagram for CQueryOptionsArgs:
+ Collaboration diagram for CQueryOptionsArgs:

Public Member Functions

 CQueryOptionsArgs (bool query_cannot_be_nucl=false)
 Constructor. More...
 
virtual void SetArgumentDescriptions (CArgDescriptions &arg_desc)
 Interface method,. More...
 
virtual void ExtractAlgorithmOptions (const CArgs &cmd_line_args, CBlastOptions &options)
 Interface method,. More...
 
TSeqRange GetRange () const
 Get query sequence range restriction. More...
 
void SetRange (const TSeqRange &range)
 Set query sequence range restriction. More...
 
objects::ENa_strand GetStrand () const
 Get strand to search in query sequence(s) More...
 
bool UseLowercaseMasks () const
 Use lowercase masking in FASTA input? More...
 
bool GetParseDeflines () const
 Should the defline be parsed? More...
 
bool QueryIsProtein () const
 Is the query sequence protein? More...
 
- Public Member Functions inherited from IBlastCmdLineArgs
virtual ~IBlastCmdLineArgs ()
 Our virtual 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
 

Private Attributes

objects::ENa_strand m_Strand
 Strand(s) to search. More...
 
TSeqRange m_Range
 range to restrict the query sequence(s) More...
 
bool m_UseLCaseMask
 use lowercase masking in FASTA input More...
 
bool m_ParseDeflines
 Should the deflines be parsed? More...
 
bool m_QueryCannotBeNucl
 only false for blast[xn], and tblastx true in case of PSI-BLAST 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...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

Argument class to collect query options.

Definition at line 774 of file blast_args.hpp.

Constructor & Destructor Documentation

◆ CQueryOptionsArgs()

CQueryOptionsArgs::CQueryOptionsArgs ( bool  query_cannot_be_nucl = false)
inline

Constructor.

Parameters
query_cannot_be_nuclcan the query not be nucleotide?

Definition at line 782 of file blast_args.hpp.

Member Function Documentation

◆ ExtractAlgorithmOptions()

void CQueryOptionsArgs::ExtractAlgorithmOptions ( const CArgs cmd_line_args,
CBlastOptions options 
)
virtual

◆ GetParseDeflines()

bool CQueryOptionsArgs::GetParseDeflines ( ) const
inline

◆ GetRange()

TSeqRange CQueryOptionsArgs::GetRange ( ) const
inline

◆ GetStrand()

objects::ENa_strand CQueryOptionsArgs::GetStrand ( void  ) const
inline

◆ QueryIsProtein()

bool CQueryOptionsArgs::QueryIsProtein ( ) const
inline

◆ SetArgumentDescriptions()

void CQueryOptionsArgs::SetArgumentDescriptions ( CArgDescriptions arg_desc)
virtual

◆ SetRange()

void CQueryOptionsArgs::SetRange ( const TSeqRange range)
inline

Set query sequence range restriction.

Definition at line 798 of file blast_args.hpp.

References m_Range, and compile_time_bits::range().

◆ UseLowercaseMasks()

bool CQueryOptionsArgs::UseLowercaseMasks ( ) const
inline

Member Data Documentation

◆ m_ParseDeflines

bool CQueryOptionsArgs::m_ParseDeflines
private

Should the deflines be parsed?

Definition at line 817 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), and GetParseDeflines().

◆ m_QueryCannotBeNucl

bool CQueryOptionsArgs::m_QueryCannotBeNucl
private

only false for blast[xn], and tblastx true in case of PSI-BLAST

Definition at line 821 of file blast_args.hpp.

Referenced by QueryIsProtein(), and SetArgumentDescriptions().

◆ m_Range

TSeqRange CQueryOptionsArgs::m_Range
private

range to restrict the query sequence(s)

Definition at line 813 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), GetRange(), and SetRange().

◆ m_Strand

objects::ENa_strand CQueryOptionsArgs::m_Strand
private

Strand(s) to search.

Definition at line 811 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), and GetStrand().

◆ m_UseLCaseMask

bool CQueryOptionsArgs::m_UseLCaseMask
private

use lowercase masking in FASTA input

Definition at line 815 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), and UseLowercaseMasks().


The documentation for this class was generated from the following files:
Modified on Sat Feb 24 07:45:57 2024 by modify_doxy.py rev. 669887