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CProSplignOptions_Base Class Reference

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Scoring parameters object. More...

#include <algo/align/prosplign/prosplign.hpp>

+ Inheritance diagram for CProSplignOptions_Base:
+ Collaboration diagram for CProSplignOptions_Base:

Public Member Functions

 CProSplignOptions_Base ()
 creates scoring parameter object with default values More...
 
 CProSplignOptions_Base (const CArgs &args)
 
CProSplignOptions_BaseSetScoreMatrix (const string &matrix_name)
 
const stringGetScoreMatrix () const
 
CProSplignOptions_BaseSetAltStarts (bool allow_alt_start)
 
bool GetAltStarts () const
 
- 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
 

Static Public Member Functions

static void SetupArgDescriptions (CArgDescriptions *argdescr)
 
- Static Public Member Functions inherited from CObject
static NCBI_NORETURN void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_NORETURN 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

static const char * default_score_matrix_name = "BLOSUM62"
 
static const bool default_allow_alt_starts = false
 
- 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...
 

Private Attributes

string score_matrix_name
 
bool allow_alt_starts
 

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 CAtomicCounter TCounter
 Counter type is CAtomiCounter. More...
 
typedef TCounter::TValue TCount
 Alias for value type of counter. More...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

Scoring parameters object.

Definition at line 53 of file prosplign.hpp.

Constructor & Destructor Documentation

CProSplignOptions_Base::CProSplignOptions_Base ( )

creates scoring parameter object with default values

Definition at line 76 of file prosplign.cpp.

References default_allow_alt_starts, default_score_matrix_name, SetAltStarts(), and SetScoreMatrix().

CProSplignOptions_Base::CProSplignOptions_Base ( const CArgs args)

Definition at line 82 of file prosplign.cpp.

References SetAltStarts(), and SetScoreMatrix().

Member Function Documentation

bool CProSplignOptions_Base::GetAltStarts ( ) const

Definition at line 104 of file prosplign.cpp.

References allow_alt_starts.

Referenced by CProSplign::CImplementation::FindGlobalAlignment_stage1().

const string & CProSplignOptions_Base::GetScoreMatrix ( void  ) const

Definition at line 93 of file prosplign.cpp.

References score_matrix_name.

Referenced by CProSplign::RefineAlignment().

CProSplignOptions_Base & CProSplignOptions_Base::SetAltStarts ( bool  allow_alt_start)

Definition at line 98 of file prosplign.cpp.

References allow_alt_starts.

Referenced by CProSplignOptions_Base().

CProSplignOptions_Base & CProSplignOptions_Base::SetScoreMatrix ( const string matrix_name)

Definition at line 88 of file prosplign.cpp.

References score_matrix_name.

Referenced by CProSplignOptions_Base().

void CProSplignOptions_Base::SetupArgDescriptions ( CArgDescriptions argdescr)
static

Member Data Documentation

bool CProSplignOptions_Base::allow_alt_starts
private

Definition at line 73 of file prosplign.hpp.

Referenced by GetAltStarts(), and SetAltStarts().

const bool CProSplignOptions_Base::default_allow_alt_starts = false
static

Definition at line 69 of file prosplign.hpp.

Referenced by CProSplignOptions_Base().

const char * CProSplignOptions_Base::default_score_matrix_name = "BLOSUM62"
static

Definition at line 68 of file prosplign.hpp.

Referenced by CProSplignOptions_Base(), and SetupArgDescriptions().

string CProSplignOptions_Base::score_matrix_name
private

Definition at line 72 of file prosplign.hpp.

Referenced by GetScoreMatrix(), and SetScoreMatrix().


The documentation for this class was generated from the following files:
Modified on Tue May 22 12:44:23 2018 by modify_doxy.py rev. 546573