NCBI C++ ToolKit
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CMapperQueryOptionsArgs Class Reference

Search Toolkit Book for CMapperQueryOptionsArgs

Argument class to collect query options for BLAST Mapper. More...

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

+ Inheritance diagram for CMapperQueryOptionsArgs:
+ Collaboration diagram for CMapperQueryOptionsArgs:

Public Types

enum  EInputFormat {
  eFasta = 0 , eFastc , eFastq , eASN1text ,
  eASN1bin , eSra
}
 Input formats. More...
 
- 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...
 

Public Member Functions

 CMapperQueryOptionsArgs (void)
 
virtual void SetArgumentDescriptions (CArgDescriptions &arg_desc)
 Interface method,. More...
 
virtual void ExtractAlgorithmOptions (const CArgs &args, CBlastOptions &opt)
 Interface method,. More...
 
bool IsPaired (void) const
 Are query sequences paired. More...
 
EInputFormat GetInputFormat (void) const
 Are queries provided in Fastc format. More...
 
bool HasMateInputStream (void) const
 Does the mate input stream exits. More...
 
CNcbiIstreamGetMateInputStream (void) const
 Get input stream for query mates. More...
 
const vector< string > & GetSraAccessions (void) const
 Get a list of SRA accessions. More...
 
bool IsSraCacheEnabled (void) const
 Is SRA caching in local files enabled (see File Caching at https://github.com/ncbi/sra-tools/wiki/Toolkit-Configuration) More...
 
- Public Member Functions inherited from CQueryOptionsArgs
 CQueryOptionsArgs (bool query_cannot_be_nucl=false)
 Constructor. 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

bool m_IsPaired
 
EInputFormat m_InputFormat
 
vector< stringm_SraAccessions
 
CNcbiIstreamm_MateInputStream
 
unique_ptr< CDecompressIStreamm_DecompressIStream
 
bool m_EnableSraCache
 

Additional Inherited Members

- 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 for BLAST Mapper.

Definition at line 825 of file blast_args.hpp.

Member Enumeration Documentation

◆ EInputFormat

Input formats.

Enumerator
eFasta 
eFastc 
eFastq 
eASN1text 
eASN1bin 
eSra 

Definition at line 830 of file blast_args.hpp.

Constructor & Destructor Documentation

◆ CMapperQueryOptionsArgs()

CMapperQueryOptionsArgs::CMapperQueryOptionsArgs ( void  )
inline

Definition at line 840 of file blast_args.hpp.

Member Function Documentation

◆ ExtractAlgorithmOptions()

void CMapperQueryOptionsArgs::ExtractAlgorithmOptions ( const CArgs args,
CBlastOptions opt 
)
virtual

◆ GetInputFormat()

EInputFormat CMapperQueryOptionsArgs::GetInputFormat ( void  ) const
inline

Are queries provided in Fastc format.

Definition at line 857 of file blast_args.hpp.

References m_InputFormat.

Referenced by CMagicBlastApp::Run(), and s_CreateInputSource().

◆ GetMateInputStream()

CNcbiIstream* CMapperQueryOptionsArgs::GetMateInputStream ( void  ) const
inline

Get input stream for query mates.

Definition at line 864 of file blast_args.hpp.

References m_MateInputStream.

Referenced by s_CreateInputSource().

◆ GetSraAccessions()

const vector<string>& CMapperQueryOptionsArgs::GetSraAccessions ( void  ) const
inline

Get a list of SRA accessions.

Definition at line 867 of file blast_args.hpp.

References m_SraAccessions.

Referenced by s_CreateInputSource().

◆ HasMateInputStream()

bool CMapperQueryOptionsArgs::HasMateInputStream ( void  ) const
inline

Does the mate input stream exits.

Definition at line 861 of file blast_args.hpp.

References m_MateInputStream.

Referenced by s_CreateInputSource().

◆ IsPaired()

bool CMapperQueryOptionsArgs::IsPaired ( void  ) const
inline

Are query sequences paired.

Definition at line 854 of file blast_args.hpp.

References m_IsPaired.

Referenced by CMagicBlastThread::Main(), and s_CreateInputSource().

◆ IsSraCacheEnabled()

bool CMapperQueryOptionsArgs::IsSraCacheEnabled ( void  ) const
inline

Is SRA caching in local files enabled (see File Caching at https://github.com/ncbi/sra-tools/wiki/Toolkit-Configuration)

Definition at line 873 of file blast_args.hpp.

References m_EnableSraCache.

Referenced by s_CreateInputSource().

◆ SetArgumentDescriptions()

void CMapperQueryOptionsArgs::SetArgumentDescriptions ( CArgDescriptions arg_desc)
virtual

Member Data Documentation

◆ m_DecompressIStream

unique_ptr<CDecompressIStream> CMapperQueryOptionsArgs::m_DecompressIStream
private

Definition at line 881 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions().

◆ m_EnableSraCache

bool CMapperQueryOptionsArgs::m_EnableSraCache
private

Definition at line 883 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), and IsSraCacheEnabled().

◆ m_InputFormat

EInputFormat CMapperQueryOptionsArgs::m_InputFormat
private

Definition at line 877 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), and GetInputFormat().

◆ m_IsPaired

bool CMapperQueryOptionsArgs::m_IsPaired
private

Definition at line 876 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), and IsPaired().

◆ m_MateInputStream

CNcbiIstream* CMapperQueryOptionsArgs::m_MateInputStream
private

Definition at line 880 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), GetMateInputStream(), and HasMateInputStream().

◆ m_SraAccessions

vector<string> CMapperQueryOptionsArgs::m_SraAccessions
private

Definition at line 878 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), and GetSraAccessions().


The documentation for this class was generated from the following files:
Modified on Fri Jan 05 07:26:10 2024 by modify_doxy.py rev. 669887