Search Toolkit Book for CSGSegmentMapDS

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

Inheritance diagram for CSGSegmentMapDS:

Collaboration diagram for CSGSegmentMapDS:

Public Types
enum	ESegmentLevel { eInvalid = -2 , eAdaptive = -1 , eContig = 0 , eComponent = 1 }
	It is not technically correct to name a specific segment level as config/scaffold and component because segment map is just a representation of sequence relationship at different level of sequence assembly. More...

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...

Public Member Functions
	CSGSegmentMapDS (objects::CScope &scope, const objects::CSeq_id &id)

void	LoadSegmentMap (const TSeqRange &range, int cutoff, TJobToken token)

void	LoadSegmentSmear (const TSeqRange &range, TModelUnit scale, const objects::CSeqVector *seq_vec=nullptr)
	Used in sequence track for showing segment color. More...

void	LoadSegmentMapSeqIDs (CSeqGlyph::TObjects &objs, TJobToken token)

void	LoadSwitchPoints ()

int	GetSegmentMapLevels (const TSeqRange &range) const
	Get total number of segment map levels. More...

bool	HasSegmentMap (int level, const TSeqRange &range) const
	Query if there is segment maps for given level. More...

bool	HasComponent (const TSeqRange &range) const

bool	HasScaffold (const TSeqRange &range) const

void	GetAnnotNames (objects::SAnnotSelector &sel, const TSeqRange &range, TAnnotNameTitleMap &names) const

void	SetAnnot (const string &annot)
	CSGFeatureDS inline methods. More...

const string &	GetAnnot () const

void	SetChromosome (bool flag)

bool	IsChromosome () const

void	SetSegmentLevel (ESegmentLevel level)
	Set which segment level to show. More...

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 ()

Static Public Member Functions
static void	SetICacheClient (ICache *pCache)
	Set cache client to use. More...

static void	SetEnabled (bool enabled=true)
	Enables/disables the segment map. More...

static bool	GetEnabled ()
	Indicates if the segment map is enabled. 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)

Private Member Functions
int	x_ConceptualToRealDepth (ESegmentLevel level) const
	Convert conceptual segment level to real segment depth. More...

Private Attributes
bool	m_IsChromosome
	Flag to indicate if the sequence is a chromosome sequence. More...

string	m_Annot
	The named annotation storing segment map data. More...

Static Private Attributes
static ICache *	m_Cache = 0
	Cache, used to store segment smear. More...

static bool	m_Enabled = true
	Indicates if the segment map is enabled. More...

Additional Inherited Members
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

Detailed Description

CSGSegmentMapDS.

Definition at line 48 of file segment_map_ds.hpp.

Member Enumeration Documentation

◆ ESegmentLevel

enum CSGSegmentMapDS::ESegmentLevel

It is not technically correct to name a specific segment level as config/scaffold and component because segment map is just a representation of sequence relationship at different level of sequence assembly.

Assumption: For all chromosome sequences, contigs/scaffolds are at level 0, and components are at level 1. For any other sequences, there will be only one level of segments which are components. And the components are at level 0.

Enumerator
eInvalid
eAdaptive	show either contigs or components based on range
eContig
eComponent

Definition at line 59 of file segment_map_ds.hpp.

Constructor & Destructor Documentation

◆ CSGSegmentMapDS()

CSGSegmentMapDS::CSGSegmentMapDS	(	objects::CScope &	scope,
		const objects::CSeq_id &	id
	)

Definition at line 182 of file segment_map_ds.cpp.

Member Function Documentation

◆ GetAnnot()

const string & CSGSegmentMapDS::GetAnnot ( void ) const

inline

Definition at line 164 of file segment_map_ds.hpp.

References m_Annot.

Referenced by CSequenceTrackFactory::GetSettings().

◆ GetAnnotNames()

void CSGSegmentMapDS::GetAnnotNames	(	objects::SAnnotSelector &	sel,
		const TSeqRange &	range,
		TAnnotNameTitleMap &	names
	)		const

Definition at line 255 of file segment_map_ds.cpp.

References CSGSegmentSmearJob::GetAnnotNames(), CSGGenBankDS::m_Handle, names, compile_time_bits::range(), and CSeqUtils::SetResolveDepth().

Referenced by CSequenceTrackFactory::CreateTracks().

◆ GetEnabled()

bool CSGSegmentMapDS::GetEnabled ( void )

static

Indicates if the segment map is enabled.

Definition at line 280 of file segment_map_ds.cpp.

References m_Enabled.

Referenced by CSequenceTrackFactory::CreateTracks().

◆ GetSegmentMapLevels()

int CSGSegmentMapDS::GetSegmentMapLevels ( const TSeqRange & range ) const

Get total number of segment map levels.

Definition at line 226 of file segment_map_ds.cpp.

References CSGSegmentMapJob::GetSegmentMapLevels(), CSGGenBankDS::m_Handle, and compile_time_bits::range().

Referenced by CSegmentMapTrackFactory::x_IsChromosome().

◆ HasComponent()

bool CSGSegmentMapDS::HasComponent ( const TSeqRange & range ) const

Definition at line 238 of file segment_map_ds.cpp.

References HasSegmentMap(), IsChromosome(), and compile_time_bits::range().

Referenced by CComponentTrackFactory::CreateTracks().

◆ HasScaffold()

bool CSGSegmentMapDS::HasScaffold ( const TSeqRange & range ) const

Definition at line 245 of file segment_map_ds.cpp.

References HasSegmentMap(), IsChromosome(), and compile_time_bits::range().

Referenced by CScaffoldTrackFactory::CreateTracks().

◆ HasSegmentMap()

bool CSGSegmentMapDS::HasSegmentMap	(	int	level,
		const TSeqRange &	range
	)		const

Query if there is segment maps for given level.

Parameters

level if it is -1, it checks all the way down until either finding one or reaching the bottom.

Definition at line 232 of file segment_map_ds.cpp.

References CSGSegmentMapJob::HasSegmentMap(), CSGGenBankDS::m_Handle, and compile_time_bits::range().

Referenced by CSegmentMapTrackFactory::CreateTracks(), CSequenceTrackFactory::CreateTracks(), HasComponent(), and HasScaffold().

◆ IsChromosome()

bool CSGSegmentMapDS::IsChromosome ( ) const

inline

Definition at line 172 of file segment_map_ds.hpp.

References m_IsChromosome.

Referenced by HasComponent(), and HasScaffold().

◆ LoadSegmentMap()

void CSGSegmentMapDS::LoadSegmentMap	(	const TSeqRange &	range,
		int	cutoff,
		TJobToken	token
	)

Definition at line 188 of file segment_map_ds.cpp.

References CSGGenBankDS::m_Depth, CSGGenBankDS::m_Handle, compile_time_bits::range(), and CSGGenBankDS::x_LaunchJob().

Referenced by CSegmentMapTrack::x_UpdateData().

◆ LoadSegmentMapSeqIDs()

void CSGSegmentMapDS::LoadSegmentMapSeqIDs	(	CSeqGlyph::TObjects &	objs,
		TJobToken	token
	)

Definition at line 208 of file segment_map_ds.cpp.

References CSGGenBankDS::GetScope(), and CSGGenBankDS::x_LaunchJob().

Referenced by CSegmentMapTrack::x_AddSegmentMapLayout().

◆ LoadSegmentSmear()

void CSGSegmentMapDS::LoadSegmentSmear	(	const TSeqRange &	range,
		TModelUnit	scale,
		const objects::CSeqVector *	seq_vec = `nullptr`
	)

Used in sequence track for showing segment color.

Definition at line 198 of file segment_map_ds.cpp.

References m_Annot, m_Cache, CSGGenBankDS::m_Handle, compile_time_bits::range(), and CSGGenBankDS::x_LaunchJob().

Referenced by CSequenceTrack::x_UpdateData().

◆ LoadSwitchPoints()

void CSGSegmentMapDS::LoadSwitchPoints ( )

Definition at line 218 of file segment_map_ds.cpp.

References CSGGenBankDS::m_Handle, and CSGGenBankDS::x_LaunchJob().

◆ SetAnnot()

void CSGSegmentMapDS::SetAnnot ( const string & annot )

inline

CSGFeatureDS inline methods.

Definition at line 159 of file segment_map_ds.hpp.

References m_Annot.

Referenced by CSequenceTrackFactory::CreateTracks().

◆ SetChromosome()

void CSGSegmentMapDS::SetChromosome ( bool flag )

inline

Definition at line 168 of file segment_map_ds.hpp.

References m_IsChromosome.

Referenced by CComponentTrackFactory::CreateTracks(), CScaffoldTrackFactory::CreateTracks(), and CSegmentMapTrackFactory::CreateTracks().

◆ SetEnabled()

void CSGSegmentMapDS::SetEnabled ( bool enabled = true )

static

Enables/disables the segment map.

Definition at line 275 of file segment_map_ds.cpp.

References m_Enabled.

◆ SetICacheClient()

void CSGSegmentMapDS::SetICacheClient ( ICache * pCache )

static

Set cache client to use.

Definition at line 270 of file segment_map_ds.cpp.

References m_Cache.

◆ SetSegmentLevel()

void CSGSegmentMapDS::SetSegmentLevel ( ESegmentLevel level )

Set which segment level to show.

Parameters

level is the conceptual segment level. It needs to be converted to the real segment level. If the level is the actual segment level, call SetDepth() directly.

Definition at line 264 of file segment_map_ds.cpp.

References depth, CSGGenBankDS::SetDepth(), and x_ConceptualToRealDepth().

Referenced by CComponentTrackFactory::CreateTracks(), CScaffoldTrackFactory::CreateTracks(), and CSegmentMapTrack::x_LoadSettings().

◆ x_ConceptualToRealDepth()

int CSGSegmentMapDS::x_ConceptualToRealDepth ( ESegmentLevel level ) const

private

Convert conceptual segment level to real segment depth.

For all chromosome sequences, contigs/scaffolds are at level 0, and components are at level 1. For any other sequences, there will be only one level of segments (components) which are at level 0. -1 means 'Adaptive'.

Definition at line 285 of file segment_map_ds.cpp.

References depth, eComponent, eContig, and m_IsChromosome.

Referenced by SetSegmentLevel().

Member Data Documentation

◆ m_Annot

string CSGSegmentMapDS::m_Annot

private

The named annotation storing segment map data.

Used in sequence track (not segment map tracks, such as components or scaffolds)

Definition at line 124 of file segment_map_ds.hpp.

Referenced by GetAnnot(), LoadSegmentSmear(), and SetAnnot().

◆ m_Cache

ICache * CSGSegmentMapDS::m_Cache = 0

staticprivate

Cache, used to store segment smear.

CSGSegmentMapDS implementation.

Definition at line 127 of file segment_map_ds.hpp.

Referenced by LoadSegmentSmear(), and SetICacheClient().

◆ m_Enabled

bool CSGSegmentMapDS::m_Enabled = true

staticprivate

Indicates if the segment map is enabled.

Definition at line 129 of file segment_map_ds.hpp.

Referenced by GetEnabled(), and SetEnabled().

◆ m_IsChromosome

bool CSGSegmentMapDS::m_IsChromosome

private

Flag to indicate if the sequence is a chromosome sequence.

Definition at line 119 of file segment_map_ds.hpp.

Referenced by IsChromosome(), SetChromosome(), and x_ConceptualToRealDepth().

The documentation for this class was generated from the following files:

include/gui/widgets/seq_graphic/segment_map_ds.hpp
src/gui/widgets/seq_graphic/segment_map_ds.cpp

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ ESegmentLevel

Constructor & Destructor Documentation

◆ CSGSegmentMapDS()

Member Function Documentation

◆ GetAnnot()

◆ GetAnnotNames()

◆ GetEnabled()

◆ GetSegmentMapLevels()

◆ HasComponent()

◆ HasScaffold()

◆ HasSegmentMap()

◆ IsChromosome()

◆ LoadSegmentMap()

◆ LoadSegmentMapSeqIDs()

◆ LoadSegmentSmear()

◆ LoadSwitchPoints()

◆ SetAnnot()

◆ SetChromosome()

◆ SetEnabled()

◆ SetICacheClient()

◆ SetSegmentLevel()

◆ x_ConceptualToRealDepth()

Member Data Documentation

◆ m_Annot

◆ m_Cache

◆ m_Enabled

◆ m_IsChromosome