NCBI C++ ToolKit
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CStdCmdLineArgs Class Reference

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Argument class to retrieve input and output streams for a command line program. More...

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

+ Inheritance diagram for CStdCmdLineArgs:
+ Collaboration diagram for CStdCmdLineArgs:

Public Member Functions

 CStdCmdLineArgs ()
 Default constructor. More...
 
virtual void SetArgumentDescriptions (CArgDescriptions &arg_desc)
 Interface method,. More...
 
virtual void ExtractAlgorithmOptions (const CArgs &cmd_line_args, CBlastOptions &options)
 Interface method,. More...
 
CNcbiIstreamGetInputStream () const
 Get the input stream for a command line application. More...
 
CNcbiOstreamGetOutputStream () const
 Get the output stream for a command line application. More...
 
void SetInputStream (CRef< CTmpFile > input_file)
 Set the input stream if read from a saved search strategy. More...
 
void SetGzipEnabled (bool g)
 Set automatic decompression of the input file is file name is recognized. More...
 
void SetSRAaccessionEnabled (bool g)
 enables sra accession flag More...
 
bool HasUnalignedOutputStream (void) const
 Is there a separate output stream for unaligned sequences/reads (for magicblast) More...
 
CNcbiOstreamGetUnalignedOutputStream () const
 Get output stream for unaligned sequences/reads (for magicblast) 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

CNcbiIstreamm_InputStream
 Application's input stream. More...
 
CNcbiOstreamm_OutputStream
 Application's output stream. More...
 
unique_ptr< CDecompressIStreamm_DecompressIStream
 
unique_ptr< CCompressOStreamm_CompressOStream
 
CRef< CTmpFilem_QueryTmpInputFile
 ASN.1 specification of query sequences when read from a saved search strategy. More...
 
bool m_GzipEnabled
 If true input file will be decompressed with gzip if filename ends with ".gz". More...
 
bool m_SRAaccessionEnabled
 If true, option to specify SRA runs will be presented as possible query input. More...
 
CNcbiOstreamm_UnalignedOutputStream
 Output stream to report unaligned sequences/reads. More...
 
unique_ptr< CCompressOStreamm_UnalignedCompressOStream
 

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 retrieve input and output streams for a command line program.

Definition at line 109 of file blast_args.hpp.

Constructor & Destructor Documentation

◆ CStdCmdLineArgs()

CStdCmdLineArgs::CStdCmdLineArgs ( )
inline

Default constructor.

Definition at line 113 of file blast_args.hpp.

Member Function Documentation

◆ ExtractAlgorithmOptions()

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

◆ GetInputStream()

CNcbiIstream & CStdCmdLineArgs::GetInputStream ( ) const

Get the input stream for a command line application.

Definition at line 3476 of file blast_args.cpp.

References abort(), and m_InputStream.

Referenced by CBlastAppArgs::GetInputStream().

◆ GetOutputStream()

CNcbiOstream & CStdCmdLineArgs::GetOutputStream ( ) const

Get the output stream for a command line application.

Definition at line 3487 of file blast_args.cpp.

References _ASSERT, and m_OutputStream.

Referenced by CBlastAppArgs::GetOutputStream().

◆ GetUnalignedOutputStream()

CNcbiOstream* CStdCmdLineArgs::GetUnalignedOutputStream ( ) const
inline

Get output stream for unaligned sequences/reads (for magicblast)

Returns
Output stream for unaligned reads or NULL

Definition at line 150 of file blast_args.hpp.

References m_UnalignedOutputStream.

◆ HasUnalignedOutputStream()

bool CStdCmdLineArgs::HasUnalignedOutputStream ( void  ) const
inline

Is there a separate output stream for unaligned sequences/reads (for magicblast)

Returns
True if separate output stream has been set up, otherwise false

Definition at line 145 of file blast_args.hpp.

References m_UnalignedOutputStream.

◆ SetArgumentDescriptions()

void CStdCmdLineArgs::SetArgumentDescriptions ( CArgDescriptions arg_desc)
virtual

◆ SetGzipEnabled()

void CStdCmdLineArgs::SetGzipEnabled ( bool  g)
inline

Set automatic decompression of the input file is file name is recognized.

Parameters
gIf true input file will be unzgipped if the file name ends with ".gz" [in]

Definition at line 134 of file blast_args.hpp.

References g(), and m_GzipEnabled.

Referenced by CMagicBlastAppArgs::CMagicBlastAppArgs().

◆ SetInputStream()

void CStdCmdLineArgs::SetInputStream ( CRef< CTmpFile input_file)

Set the input stream if read from a saved search strategy.

Definition at line 3496 of file blast_args.cpp.

References CTmpFile::eIfExists_Throw, input_file, m_InputStream, and m_QueryTmpInputFile.

Referenced by CBlastAppArgs::SetInputStream().

◆ SetSRAaccessionEnabled()

void CStdCmdLineArgs::SetSRAaccessionEnabled ( bool  g)
inline

enables sra accession flag

Parameters
gIf true "-sra" will be added (not compatible with "-query")

Definition at line 139 of file blast_args.hpp.

References g(), and m_SRAaccessionEnabled.

Referenced by CIgBlastnAppArgs::CIgBlastnAppArgs().

Member Data Documentation

◆ m_CompressOStream

unique_ptr<CCompressOStream> CStdCmdLineArgs::m_CompressOStream
private

Definition at line 157 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions().

◆ m_DecompressIStream

unique_ptr<CDecompressIStream> CStdCmdLineArgs::m_DecompressIStream
private

Definition at line 156 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions().

◆ m_GzipEnabled

bool CStdCmdLineArgs::m_GzipEnabled
private

If true input file will be decompressed with gzip if filename ends with ".gz".

Definition at line 165 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), SetArgumentDescriptions(), and SetGzipEnabled().

◆ m_InputStream

CNcbiIstream* CStdCmdLineArgs::m_InputStream
private

Application's input stream.

Definition at line 154 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), GetInputStream(), and SetInputStream().

◆ m_OutputStream

CNcbiOstream* CStdCmdLineArgs::m_OutputStream
private

Application's output stream.

Definition at line 155 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), and GetOutputStream().

◆ m_QueryTmpInputFile

CRef<CTmpFile> CStdCmdLineArgs::m_QueryTmpInputFile
private

ASN.1 specification of query sequences when read from a saved search strategy.

Definition at line 161 of file blast_args.hpp.

Referenced by SetInputStream().

◆ m_SRAaccessionEnabled

bool CStdCmdLineArgs::m_SRAaccessionEnabled
private

If true, option to specify SRA runs will be presented as possible query input.

Definition at line 169 of file blast_args.hpp.

Referenced by SetArgumentDescriptions(), and SetSRAaccessionEnabled().

◆ m_UnalignedCompressOStream

unique_ptr<CCompressOStream> CStdCmdLineArgs::m_UnalignedCompressOStream
private

Definition at line 173 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions().

◆ m_UnalignedOutputStream

CNcbiOstream* CStdCmdLineArgs::m_UnalignedOutputStream
private

Output stream to report unaligned sequences/reads.

Definition at line 172 of file blast_args.hpp.

Referenced by ExtractAlgorithmOptions(), GetUnalignedOutputStream(), and HasUnalignedOutputStream().


The documentation for this class was generated from the following files:
Modified on Tue Feb 27 05:50:27 2024 by modify_doxy.py rev. 669887