Search Toolkit Book for CAlnMixSequences

#include <objtools/alnmgr/alnseq.hpp>

Inheritance diagram for CAlnMixSequences:

Collaboration diagram for CAlnMixSequences:

Classes
struct	SSeqIds

Public Types
enum	EAddFlags { fCalcScore = 0x01 , fForceTranslation = 0x02 , fPreserveRows = 0x04 }

typedef vector< CRef< CAlnMixSeq > >	TSeqs

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< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...

typedef Uint8	TCount
	Alias for value type of counter. More...

Public Member Functions
	CAlnMixSequences (void)

	CAlnMixSequences (CScope &scope)

const TSeqs &	Get () const

TSeqs &	Set ()

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

void	SortByScore ()

void	SortByChainScore ()

void	BuildRows ()

void	InitRowsStartIts ()

void	InitExtraRowsStartIts ()

void	RowsStartItsContsistencyCheck (size_t match_idx)

Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...

	CObject (const CObject &src)
	Copy constructor. More...

virtual	~CObject (void)
	Destructor. More...

CObject &	operator= (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 Types
typedef map< CBioseq_Handle, CRef< CAlnMixSeq > >	TBioseqHandleMap

typedef map< CRef< CSeq_id >, CRef< CAlnMixSeq >, SSeqIds >	TSeqIdMap

Private Member Functions
void	x_IdentifyAlnMixSeq (CRef< CAlnMixSeq > &aln_seq, const CSeq_id &seq_id)

Static Private Member Functions
static bool	x_CompareScores (const CRef< CAlnMixSeq > &seq1, const CRef< CAlnMixSeq > &seq2)

static bool	x_CompareChainScores (const CRef< CAlnMixSeq > &seq1, const CRef< CAlnMixSeq > &seq2)

Private Attributes
size_t	m_DsCnt

map< const CDense_seg *, vector< CRef< CAlnMixSeq > > >	m_DsSeq

CRef< CScope >	m_Scope

TSeqs	m_Seqs

TSeqIdMap	m_SeqIds

TBioseqHandleMap	m_BioseqHandles

bool	m_ContainsAA

bool	m_ContainsNA

vector< CRef< CAlnMixSeq > >	m_Rows

list< CRef< CAlnMixSeq > >	m_ExtraRows

Friends
class	CAlnMix

class	CAlnMixMatches

class	CAlnMixSegments

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...