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CAlnMixMatches Class Reference

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#include <objtools/alnmgr/alnmatch.hpp>

+ Inheritance diagram for CAlnMixMatches:
+ Collaboration diagram for CAlnMixMatches:

Public Types

enum  EAddFlags { fCalcScore = 0x01 , fForceTranslation = 0x02 , fPreserveRows = 0x04 }
 
typedef int(* TCalcScoreMethod) (const string &s1, const string &s2, bool s1_is_prot, bool s2_is_prot, int gene_code1, int gene_code2)
 Typedefs. More...
 
typedef vector< CRef< CAlnMixMatch > > TMatches
 
typedef int TAddFlags
 
- 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

 CAlnMixMatches (CRef< CAlnMixSequences > &sequences, TCalcScoreMethod calc_score=0)
 Constructor. More...
 
const TMatchesGet () const
 Container accessors. More...
 
TMatchesSet ()
 
void Add (const CDense_seg &ds, TAddFlags flags=0)
 "Add" a Dense-seg to the existing matches. More...
 
void SortByScore ()
 Modifying algorithms. More...
 
void SortByChainScore ()
 
- 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 Private Member Functions

static bool x_CompareScores (const CRef< CAlnMixMatch > &match1, const CRef< CAlnMixMatch > &match2)
 
static bool x_CompareChainScores (const CRef< CAlnMixMatch > &match1, const CRef< CAlnMixMatch > &match2)
 

Private Attributes

size_t m_DsCnt
 
CRef< CScopem_Scope
 
TMatches m_Matches
 
CRef< CAlnMixSequencesm_AlnMixSequences
 
CAlnMixSequences::TSeqsm_Seqs
 
TCalcScoreMethod x_CalculateScore
 
TAddFlags m_AddFlags
 
boolm_ContainsAA
 
boolm_ContainsNA
 

Friends

class CAlnMixMerger
 

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

Definition at line 48 of file alnmatch.hpp.

Member Typedef Documentation

◆ TAddFlags

Definition at line 75 of file alnmatch.hpp.

◆ TCalcScoreMethod

typedef int(* CAlnMixMatches::TCalcScoreMethod) (const string &s1, const string &s2, bool s1_is_prot, bool s2_is_prot, int gene_code1, int gene_code2)

Typedefs.

Definition at line 53 of file alnmatch.hpp.

◆ TMatches

Definition at line 60 of file alnmatch.hpp.

Member Enumeration Documentation

◆ EAddFlags

Enumerator
fCalcScore 
fForceTranslation 
fPreserveRows 

Definition at line 62 of file alnmatch.hpp.

Constructor & Destructor Documentation

◆ CAlnMixMatches()

CAlnMixMatches::CAlnMixMatches ( CRef< CAlnMixSequences > &  sequences,
TCalcScoreMethod  calc_score = 0 
)

Constructor.

Definition at line 49 of file alnmatch.cpp.

Member Function Documentation

◆ Add()

void CAlnMixMatches::Add ( const CDense_seg ds,
TAddFlags  flags = 0 
)

◆ Get()

const TMatches& CAlnMixMatches::Get ( void  ) const
inline

Container accessors.

Definition at line 84 of file alnmatch.hpp.

References m_Matches.

◆ Set()

TMatches& CAlnMixMatches::Set ( void  )
inline

Definition at line 85 of file alnmatch.hpp.

References m_Matches.

◆ SortByChainScore()

void CAlnMixMatches::SortByChainScore ( )

Definition at line 90 of file alnmatch.cpp.

References m_Matches, and x_CompareChainScores().

Referenced by CAlnMix::Merge().

◆ SortByScore()

void CAlnMixMatches::SortByScore ( )

Modifying algorithms.

Definition at line 83 of file alnmatch.cpp.

References m_Matches, and x_CompareScores().

Referenced by CAlnMix::Merge().

◆ x_CompareChainScores()

bool CAlnMixMatches::x_CompareChainScores ( const CRef< CAlnMixMatch > &  match1,
const CRef< CAlnMixMatch > &  match2 
)
inlinestaticprivate

Definition at line 72 of file alnmatch.cpp.

Referenced by SortByChainScore().

◆ x_CompareScores()

bool CAlnMixMatches::x_CompareScores ( const CRef< CAlnMixMatch > &  match1,
const CRef< CAlnMixMatch > &  match2 
)
inlinestaticprivate

Definition at line 63 of file alnmatch.cpp.

Referenced by SortByScore().

Friends And Related Function Documentation

◆ CAlnMixMerger

friend class CAlnMixMerger
friend

Definition at line 101 of file alnmatch.hpp.

Member Data Documentation

◆ m_AddFlags

TAddFlags CAlnMixMatches::m_AddFlags
private

Definition at line 115 of file alnmatch.hpp.

Referenced by Add(), CAlnMixMerger::x_CreateDenseg(), and CAlnMixMerger::x_Merge().

◆ m_AlnMixSequences

CRef<CAlnMixSequences> CAlnMixMatches::m_AlnMixSequences
private

Definition at line 112 of file alnmatch.hpp.

Referenced by Add().

◆ m_ContainsAA

bool& CAlnMixMatches::m_ContainsAA
private

Definition at line 116 of file alnmatch.hpp.

Referenced by CAlnMixMerger::x_CreateDenseg(), and CAlnMixMerger::x_Merge().

◆ m_ContainsNA

bool& CAlnMixMatches::m_ContainsNA
private

Definition at line 117 of file alnmatch.hpp.

Referenced by CAlnMixMerger::x_CreateDenseg(), and CAlnMixMerger::x_Merge().

◆ m_DsCnt

size_t CAlnMixMatches::m_DsCnt
private

Definition at line 109 of file alnmatch.hpp.

Referenced by Add().

◆ m_Matches

TMatches CAlnMixMatches::m_Matches
private

Definition at line 111 of file alnmatch.hpp.

Referenced by Add(), Get(), Set(), SortByChainScore(), and SortByScore().

◆ m_Scope

CRef<CScope> CAlnMixMatches::m_Scope
private

Definition at line 110 of file alnmatch.hpp.

◆ m_Seqs

CAlnMixSequences::TSeqs& CAlnMixMatches::m_Seqs
private

Definition at line 113 of file alnmatch.hpp.

◆ x_CalculateScore

TCalcScoreMethod CAlnMixMatches::x_CalculateScore
private

Definition at line 114 of file alnmatch.hpp.

Referenced by Add().


The documentation for this class was generated from the following files:
Modified on Wed Jul 24 17:19:38 2024 by modify_doxy.py rev. 669887