CSFTransDS - Six-frames translation data source. More...

#include <gui/widgets/seq_graphic/six_frames_trans_track.hpp>

Inheritance diagram for CSFTransDS:

Collaboration diagram for CSFTransDS:

Public Member Functions
	CSFTransDS (objects::CScope &scope, const objects::CSeq_id &id)
	CSFTransDS. More...

void	DoTranslation (const TSeqRange &range, objects::ENa_strand strand=objects::eNa_strand_both)
	do Six-frames translation. More...

void	SetGeneticCode (int id)
	CSFTransDS inline methods. More...

int	GetGeneticCode () const

void	SetAltStart (bool f)

bool	GetAltStart () const

void	SetSubsetAltStart (bool value)

bool	GetSubsetAltStart () const

Public Member Functions inherited from CSGGenBankDS
	CSGGenBankDS (objects::CScope &scope, const objects::CSeq_id &id)

virtual	~CSGGenBankDS ()

bool	IsRefSeq () const

void	SetDepth (int depth)
	Set the annotation selector resolving depth. More...

int	GetDepth () const

void	SetAdaptive (bool flag)

bool	GetAdaptive () const

objects::CBioseq_Handle &	GetBioseqHandle (void)
	Get the underlying bioseq handle. More...

const objects::CBioseq_Handle &	GetBioseqHandle (void) const

objects::CScope &	GetScope (void) const
	Get the scope from the handle. More...

void	SetJobListener (CEventHandler *listener)
	Set JobDispatcher listener. More...

virtual void	ClearJobID (TJobID job_id)

bool	IsJobNeeded (TJobID job_id) const

virtual bool	AllJobsFinished () const

virtual void	DeleteAllJobs ()
	Remove waiting jobs from queue or cancel the unfinished jobs. More...

void	SetCoordMapper (ICoordMapper *mapper)

void	SetGraphLevels (const string &annot)

Public Member Functions inherited from CObjectEx
	CObjectEx (void)

virtual	~CObjectEx (void)

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

Public Member Functions inherited from CWeakObject
	CWeakObject (void)

virtual	~CWeakObject (void)

CPtrToObjectProxy *	GetPtrProxy (void) const
	Get pointer to proxy object containing pointer to this object. More...

Public Member Functions inherited from ISGDataSource
virtual	~ISGDataSource ()

Private Attributes
int	m_GeneticCode

bool	m_AltStart
	allow alternative start codon More...

bool	m_SubsetAltStart
	allow ATG (Met) and two alternative start codons: GTG (Val), TTG (Leu) for gcode = 11 More...

Additional Inherited Members
Public Types inherited from CSGGenBankDS
typedef CAppJobDispatcher::TJobID	TJobID

typedef int	TJobToken

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 Types inherited from ISGDataSource
typedef map< string, string >	TAnnotNameTitleMap
	List of annotations with the corresponding titles. More...

Static Public Member Functions inherited from CSGDataSource
static void	SetBackgroundJob (bool flag)

static bool	IsBackgroundJob ()

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 Types inherited from CSGGenBankDS
typedef set< int >	TGraphLevels

Protected Member Functions inherited from CSGGenBankDS
void	x_ForegroundJob (IAppJob &job)

TJobID	x_BackgroundJob (IAppJob &job, int report_period, const string &pool)
	Jobs on thread pool. More...

TJobID	x_LaunchJob (IAppJob &job, int report_period=1, const string &pool="ObjManagerEngine")
	Launch either a background or foreground job. More...

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Protected Member Functions inherited from CWeakObject
void	CleanWeakRefs (void) const
	Method cleaning all CWeakRefs referencing at this moment to the object After calling to this method all existing CWeakRefs referencing to the object will return NULL, so it effectively will be equal to deleting the object. More...

Protected Attributes inherited from CSGGenBankDS
objects::CBioseq_Handle	m_Handle

CEventHandler *	m_JobListener
	our listener to JobDispatcher events More...

vector< TJobID >	m_ActiveJobs
	all currently active jobs for this DS More...

int	m_Depth
	annotation resolving depth More...

bool	m_Adaptive
	adaptive/exact annot selector More...

CIRef< ICoordMapper >	m_Mapper
	coordinate mapper between mapped features coord. and sequence coord. More...

TGraphLevels	m_GraphLevels
	Existing coverage graph levels. More...

Static Protected Attributes inherited from CSGDataSource
static bool	m_Background = true