CSGAlignmentDS Class Reference

Search Toolkit Book for CSGAlignmentDS

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

Inheritance diagram for CSGAlignmentDS:

Collaboration diagram for CSGAlignmentDS:

Public Types
enum	EDataLoader { eLoader_Unknown , eLoader_BAM , eLoader_CSRA }
typedef CAlignGlyph::TAlnAnchorPair	TAlnAnchorPair
typedef vector< CConstRef< IAlnGraphicDataSource > >	TAlnMgrVec
typedef list< CIRef< IScoringMethod > >	TMethods
	keep instances of score methods here. 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
	CSGAlignmentDS (objects::CScope &scope, const objects::CSeq_id &id)
virtual	~CSGAlignmentDS ()
void	LoadCoverageGraph (const TSeqRange &range, TModelUnit window, TJobToken token)
void	LoadAlignments (const TSeqRange &range, TModelUnit window, int align_limit, bool smear_if_overlimit, TJobToken token)
void	CalcAlnStat (const TAlnMgrVec &aligns, const TSeqRange &range, TModelUnit window, TJobToken token)
void	LoadAlignFeats (const TSeqRange &range, TModelUnit window, vector< CRef< CAlignGlyph > > aligns, const vector< int > &projected_feats, TJobToken token)
IAlnExplorer::EAlignType	GetAlignType (const CSeqGlyph *obj) const
IAlnExplorer::EAlignType	GetAlignType () const
	CSGAlignmentDS inline methods. More...
const string &	GetDataLoader () const
bool	IsBamLoader () const
bool	IsCSRALoader () const
IAlnExplorer::EAlignType	InitAlignType (bool isFastConfig=false)
	This method might need object manager to connect to ID, and it is a block call. More...
void	InitAlignScore (CAlignGlyph *aln)
	Alignment scoring. More...
void	InitAlignQualityScore (CAlignGlyph *aln, const TAlnAnchorPair &align_pair, IAlnExplorer::EAlignType sc_type)
void	InitAlignScoreCache (CAlignGlyph *aln, const TAlnAnchorPair &align_pair, IAlnExplorer::EAlignType sc_type)
void	CalculateAlignmentScore (CSeqGlyph::TObjects &objs, TJobToken token)
void	ResetAlnScoringJob ()
void	SetDefaultScoringMethods (string dna_method, string protein_method)
const TMethods &	GetScoringMethods (IAlnExplorer::EAlignType aln_type)
	get all the existing align scoring methods. More...
void	RecalculateScore (CConstRef< CSeqGlyph > obj)
void	GetAnnotNames (objects::SAnnotSelector &sel, const TSeqRange &range, TAnnotNameTitleMap &names) const
void	SetDNAScoringMethod (const string &method)
const string &	GetDNAScoringMethod () const
void	SetProteinScoringMethod (const string &method)
const string &	GetProteinScoringMethod () const
bool	IsValidProteinScoringMethod (const string &name)
bool	IsValidDNAScoringMethod (const string &name)
void	SetEnableColoration (bool f)
bool	GetEnableColoration () const
void	SetLinkMatePairs (bool f)
bool	GetLinkMatePairs () const
virtual void	ClearJobID (TJobID job_id)
virtual void	DeleteAllJobs ()
	Remove waiting jobs from queue or cancel the unfinished jobs. More...
void	SetAnnotName (const string &name)
const string &	GetAnnotName () const
void	SetHasCoverageGraph (bool flag)
bool	HasCoverageGraph () const
bool	HasQualityMap () const
void	SetSortBy (const string &sortby)
const string &	GetSortBy () const
void	SetHideSra (CAlignmentConfig::EHideSraAlignments hideSra)
void	SetUnalignedTailsMode (CAlignmentConfig::EUnalignedTailsMode tailsMode)
void	SetShowSecondPassAlignments (bool value=true)
double	GetGraphCost (const TSeqRange &range) const
bool	IsGraphCached (const TSeqRange &range) const
double	GetAlignmentCost (const TSeqRange &range) const
void	SetLayoutPolicy (ILayoutPolicy *layout_policy)
void	SetRemotePath (const string &remote_path)
void	EnablePileUpCache (bool enable, bool enable_icache)
void	ClearCache ()
bool	CanShowRange (const TSeqRange &range, int align_limit)
bool	IsRangeCached (const TSeqRange &range) const
void	SetDataHandle (const objects::CTSE_Handle &tse)
bool	NeedReleaseMemory () const
void	ReleaseMemory ()
void	SetMemoryLimit (Uint8 memory_limit)
void	SetCgiMode (bool cgi_mode)
void	SetAlnDataLoader (EDataLoader data_loader)
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...
bool	IsJobNeeded (TJobID job_id) const
virtual bool	AllJobsFinished () const
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 Types
typedef map< TAlnAnchorPair, CIRef< ISGAlnScore > >	TAlnScoreMap

Private Member Functions
bool	x_IsScoringJobRunning () const
void	x_DeleteScoringJob ()
void	x_InitScoringMethods (IAlnExplorer::EAlignType aln_type)
void	x_GetGraphCacheKey (string &data_key) const

Private Attributes
string	m_AnnotName
TMethods	m_DNAMethods
	registered DNA scoring methods More...
TMethods	m_ProteinMethods
	registered Protein scoring methods More...
TAlnScoreMap	m_AlnScoreMap
set< TAlnAnchorPair >	m_PartialAlnSet
string	m_DNAMethod
	default scoring method for DNA alignments More...
string	m_ProtMethod
	default scoring method for protein alignments More...
IAlnExplorer::EAlignType	m_AlnType
string	m_SortBy
bool	m_Enabled
	is alignment score coloration enabled More...
bool	m_LinkMatePairs
	link mate pair alignments More...
bool	m_HasCoverageGraph
	High level coverage graph? More...
bool	m_HasQualityMap
	Has quality map? (e.g. cSRA alignments) More...
TJobToken	m_ScoreToken
	the scoring job token More...
TJobID	m_ScoringJobID
	alignment scoring job id More...
CRef< CSGAlignScoringJob >	m_ScoringJob
CAlignmentConfig::EHideSraAlignments	m_HideSra
	Flag, indicating whether to hide duplicates and/or bad reads. More...
CAlignmentConfig::EUnalignedTailsMode	m_UnalignedTailsMode
	Flag, indicating whether and how to display unaligned tails. More...
bool	m_ShowSecondPass = true
TSignedSeqPos	m_MaxStartTail
	> Flag to show second-pass alignments (relevant to assembly to assembly alignments) More...
TSignedSeqPos	m_MaxEndTail
	Max length of unaligned tail at the end of the sequence. More...
string	m_DataLoader = "none"
CIRef< ILayoutPolicy >	m_LayoutPolicy
string	m_RemotePath
	url to the remote data More...
objects::CTSE_Handle	m_DataHandle
	The last loaded data. More...
Uint8	m_MemoryLimit = 2 * (Uint8)1073741824
	NeedReleaseMemory's default limit 2GB. More...
bool	m_HasPileUpCache = false
bool	m_CgiMode = false
	sviewer context More...
EDataLoader	m_AlnDataLoader = eLoader_Unknown

Additional Inherited Members
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

Detailed Description

Definition at line 50 of file seqgraphic_alignment_ds.hpp.

Member Typedef Documentation

TAlnAnchorPair

typedef CAlignGlyph::TAlnAnchorPair CSGAlignmentDS::TAlnAnchorPair

Definition at line 54 of file seqgraphic_alignment_ds.hpp.

TAlnMgrVec

typedef vector< CConstRef<IAlnGraphicDataSource> > CSGAlignmentDS::TAlnMgrVec

Definition at line 55 of file seqgraphic_alignment_ds.hpp.

TAlnScoreMap

typedef map< TAlnAnchorPair, CIRef<ISGAlnScore> > CSGAlignmentDS::TAlnScoreMap

private

Definition at line 191 of file seqgraphic_alignment_ds.hpp.

TMethods

typedef list<CIRef<IScoringMethod> > CSGAlignmentDS::TMethods

keep instances of score methods here.

Definition at line 68 of file seqgraphic_alignment_ds.hpp.

Member Enumeration Documentation

EDataLoader

enum CSGAlignmentDS::EDataLoader

Enumerator
eLoader_Unknown
eLoader_BAM
eLoader_CSRA

Definition at line 57 of file seqgraphic_alignment_ds.hpp.

Constructor & Destructor Documentation

CSGAlignmentDS()

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

Definition at line 61 of file seqgraphic_alignment_ds.cpp.

~CSGAlignmentDS()

CSGAlignmentDS::~CSGAlignmentDS ( )

virtual

Definition at line 77 of file seqgraphic_alignment_ds.cpp.

References m_CgiMode, NeedReleaseMemory(), and ReleaseMemory().

Member Function Documentation

CalcAlnStat()

void CSGAlignmentDS::CalcAlnStat	(	const TAlnMgrVec &	aligns,
		const TSeqRange &	range,
		TModelUnit	window,
		TJobToken	token
	)

Definition at line 331 of file seqgraphic_alignment_ds.cpp.

References CSeq_annot_Base::C_Data::e_Align, CSeq_annot_Base::C_Data::e_Graph, CSeqUtils::GetAnnotSelector(), CSGGenBankDS::m_Adaptive, m_AnnotName, CSGGenBankDS::m_Depth, CSGGenBankDS::m_Handle, m_HasPileUpCache, compile_time_bits::range(), CSeqUtils::SetAnnot(), CSeqUtils::SetResolveDepth(), x_GetGraphCacheKey(), and CSGGenBankDS::x_LaunchJob().

Referenced by CAlignmentTrack::x_AddAlignmentLayout(), and CAlignmentTrack::x_UpdateData().

CalculateAlignmentScore()

void CSGAlignmentDS::CalculateAlignmentScore	(	CSeqGlyph::TObjects &	objs,
		TJobToken	token
	)

Definition at line 608 of file seqgraphic_alignment_ds.cpp.

References map_checker< Container >::begin(), map_checker< Container >::clear(), set< Key, Compare >::clear(), map_checker< Container >::empty(), set< Key, Compare >::empty(), map_checker< Container >::end(), set< Key, Compare >::end(), map_checker< Container >::erase(), set< Key, Compare >::find(), CAlignGlyph::GetAlignMgr(), GetDNAScoringMethod(), CSGAlnQualityScore::GetScoreName(), InitAlignScore(), IAlnGraphicDataSource::IsCigarUnambiguous(), m_AlnScoreMap, m_PartialAlnSet, m_ScoringJob, m_ScoringJobID, NON_CONST_ITERATE, ResetAlnScoringJob(), CAlignGlyph::SetScore(), CMatePairGlyph::SetSeqAligns(), CSeqGraphicJob::SetToken(), map_checker< Container >::swap(), x_DeleteScoringJob(), x_IsScoringJobRunning(), and CSGGenBankDS::x_LaunchJob().

Referenced by CAlignmentTrack::x_AddAlignmentLayout().

CanShowRange()

bool CSGAlignmentDS::CanShowRange	(	const TSeqRange &	range,
		int	align_limit
	)

Definition at line 295 of file seqgraphic_alignment_ds.cpp.

References data, CGraphCache< TData >::GetData(), CGraphCache< TData >::GetInstance(), m_HasPileUpCache, compile_time_bits::range(), and x_GetGraphCacheKey().

Referenced by CAlignmentTrack::x_UpdateData().

ClearCache()

void CSGAlignmentDS::ClearCache

(

)

Definition at line 793 of file seqgraphic_alignment_ds.cpp.

References ERR_POST, Error(), CGraphCache< TData >::GetInstance(), m_HasPileUpCache, CGraphCache< TData >::RemoveData(), and x_GetGraphCacheKey().

Referenced by CAlignmentTrack::~CAlignmentTrack().

ClearJobID()

void CSGAlignmentDS::ClearJobID ( TJobID  job_id )

virtual

Reimplemented from CSGGenBankDS.

Definition at line 709 of file seqgraphic_alignment_ds.cpp.

References CSGGenBankDS::ClearJobID(), m_ScoringJobID, and ResetAlnScoringJob().

Referenced by CAlignmentTrack::x_OnJobCompleted().

DeleteAllJobs()

void CSGAlignmentDS::DeleteAllJobs ( )

virtual

Remove waiting jobs from queue or cancel the unfinished jobs.

Reimplemented from CSGGenBankDS.

Definition at line 718 of file seqgraphic_alignment_ds.cpp.

References CSGGenBankDS::DeleteAllJobs(), m_ScoringJob, m_ScoringJobID, and x_DeleteScoringJob().

Referenced by ReleaseMemory(), CAlignmentTrack::x_UpdateData(), and CAlignmentTrack::~CAlignmentTrack().

EnablePileUpCache()

void CSGAlignmentDS::EnablePileUpCache	(	bool	enable,
		bool	enable_icache
	)

Definition at line 786 of file seqgraphic_alignment_ds.cpp.

References CGraphCache< TData >::EnableICache(), CGraphCache< TData >::GetInstance(), and m_HasPileUpCache.

Referenced by CAlignmentTrack::x_AddAlignmentLayout(), and CAlignmentTrack::x_LoadSettings().

GetAlignmentCost()

double CSGAlignmentDS::GetAlignmentCost

(

const TSeqRange &

range

)

const

Definition at line 158 of file seqgraphic_alignment_ds.cpp.

References CSeq_annot_Base::C_Data::e_Align, CSeqUtils::GetAnnotSelector(), CAnnotTypes_CI::GetCostOfLoadingInSeconds(), CSGGenBankDS::m_Adaptive, m_AnnotName, CSGGenBankDS::m_Depth, CSGGenBankDS::m_Handle, compile_time_bits::range(), CSeqUtils::SetAnnot(), SAnnotSelector::SetCollectCostOfLoading(), and CSeqUtils::SetResolveDepth().

Referenced by CAlignmentTrack::x_UpdateData().

GetAlignType() [1/2]

IAlnExplorer::EAlignType CSGAlignmentDS::GetAlignType ( void  ) const

inline

CSGAlignmentDS inline methods.

Definition at line 251 of file seqgraphic_alignment_ds.hpp.

References m_AlnType.

Referenced by InitAlignScore().

GetAlignType() [2/2]

IAlnExplorer::EAlignType CSGAlignmentDS::GetAlignType

(

const CSeqGlyph *

obj

)

const

Definition at line 382 of file seqgraphic_alignment_ds.cpp.

References IAlnExplorer::fInvalid, CAlignGlyph::GetAlignMgr(), IAlnGraphicDataSource::GetAlignType(), CException::GetMsg(), LOG_POST, and Warning().

Referenced by CAlignmentTrack::x_AddAlignmentLayout().

GetAnnotName()

const string & CSGAlignmentDS::GetAnnotName ( ) const

inline

Definition at line 320 of file seqgraphic_alignment_ds.hpp.

References m_AnnotName.

GetAnnotNames()

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

inline

Definition at line 257 of file seqgraphic_alignment_ds.hpp.

References CSGAlignmentJob::GetAnnotNames(), CSGGenBankDS::m_Adaptive, CSGGenBankDS::m_Depth, CSGGenBankDS::m_Handle, names, compile_time_bits::range(), and CSeqUtils::SetResolveDepth().

Referenced by CAlignmentTrackFactory::CreateTracks().

GetDataLoader()

const string & CSGAlignmentDS::GetDataLoader

(

)

const

Definition at line 416 of file seqgraphic_alignment_ds.cpp.

References CAnnotTypes_CI::GetAnnot(), CSeqUtils::GetAnnotSelector(), CTSE_Handle::GetDataLoader(), CDataLoader::GetName(), CAnnotTypes_CI::GetSize(), CSeq_annot_Handle::GetTSE_Handle(), COpenRange< TSeqPos >::GetWhole(), kBamDataLoader, kCSRADataLoader, CSGGenBankDS::m_Adaptive, m_AnnotName, m_DataLoader, CSGGenBankDS::m_Depth, CSGGenBankDS::m_Handle, SAnnotSelector::SetCollectNames(), and SAnnotSelector::SetMaxSize().

Referenced by IsBamLoader(), and IsCSRALoader().

GetDNAScoringMethod()

const string & CSGAlignmentDS::GetDNAScoringMethod ( ) const

inline

Definition at line 272 of file seqgraphic_alignment_ds.hpp.

References m_DNAMethod.

Referenced by CalculateAlignmentScore(), CAlignmentTrack::x_OnScoreIconClicked(), CAlignmentTrack::x_SaveConfiguration(), and CAlignmentTrack::x_SaveSettings().

GetEnableColoration()

bool CSGAlignmentDS::GetEnableColoration ( ) const

inline

Definition at line 296 of file seqgraphic_alignment_ds.hpp.

References m_Enabled.

Referenced by CAlignmentTrack::x_AddAlignmentLayout(), CAlignmentTrack::x_OnScoreIconClicked(), CAlignmentTrack::x_SaveConfiguration(), and CAlignmentTrack::x_SaveSettings().

GetGraphCost()

double CSGAlignmentDS::GetGraphCost

(

const TSeqRange &

range

)

const

Definition at line 100 of file seqgraphic_alignment_ds.cpp.

References data, CSeq_annot_Base::C_Data::e_Graph, CSeqUtils::GetAnnotSelector(), CAnnotTypes_CI::GetCostOfLoadingInSeconds(), CGraphCache< TData >::GetData(), CGraphCache< TData >::GetInstance(), CSGGenBankDS::m_Adaptive, m_AnnotName, CSGGenBankDS::m_Depth, CSGGenBankDS::m_Handle, m_HasPileUpCache, max(), r(), compile_time_bits::range(), CSeqUtils::SetAnnot(), SAnnotSelector::SetCollectCostOfLoading(), CSeqUtils::SetResolveDepth(), and x_GetGraphCacheKey().

Referenced by CAlignmentTrack::x_UpdateData().

GetLinkMatePairs()

bool CSGAlignmentDS::GetLinkMatePairs ( ) const

inline

Definition at line 308 of file seqgraphic_alignment_ds.hpp.

References m_LinkMatePairs.

Referenced by CAlignmentTrack::OnToggleContent(), CAlignmentTrack::x_OnContentIconClicked(), CAlignmentTrack::x_SaveConfiguration(), and CAlignmentTrack::x_SaveSettings().

GetProteinScoringMethod()

const string & CSGAlignmentDS::GetProteinScoringMethod ( ) const

inline

Definition at line 284 of file seqgraphic_alignment_ds.hpp.

References m_ProtMethod.

Referenced by CAlignmentTrack::x_OnScoreIconClicked(), CAlignmentTrack::x_SaveConfiguration(), and CAlignmentTrack::x_SaveSettings().

GetScoringMethods()

const CSGAlignmentDS::TMethods & CSGAlignmentDS::GetScoringMethods

(

IAlnExplorer::EAlignType

aln_type

)

get all the existing align scoring methods.

Definition at line 452 of file seqgraphic_alignment_ds.cpp.

References IAlnExplorer::fMixed, IAlnExplorer::fProtein, m_DNAMethods, m_ProteinMethods, and x_InitScoringMethods().

Referenced by CAlignmentTrack::x_OnScoreIconClicked().

GetSortBy()

const string & CSGAlignmentDS::GetSortBy ( ) const

inline

Definition at line 350 of file seqgraphic_alignment_ds.hpp.

References m_SortBy.

Referenced by CAlignmentTrack::OnToggleContent(), CAlignmentTrack::x_OnContentIconClicked(), and CAlignmentTrack::x_SaveSettings().

HasCoverageGraph()

bool CSGAlignmentDS::HasCoverageGraph ( ) const

inline

Definition at line 332 of file seqgraphic_alignment_ds.hpp.

References m_HasCoverageGraph.

Referenced by CAlignmentTrack::x_AddAlignmentLayout(), CAlignmentTrack::x_LoadSettings(), and CAlignmentTrack::x_UpdateData().

HasQualityMap()

bool CSGAlignmentDS::HasQualityMap ( ) const

inline

Definition at line 338 of file seqgraphic_alignment_ds.hpp.

References m_HasQualityMap.

Referenced by CAlignmentTrack::x_OnScoreIconClicked().

InitAlignQualityScore()

void CSGAlignmentDS::InitAlignQualityScore	(	CAlignGlyph *	aln,
		const TAlnAnchorPair &	align_pair,
		IAlnExplorer::EAlignType	sc_type
	)

Definition at line 518 of file seqgraphic_alignment_ds.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), CAlignGlyph::GetAlignment(), CAlignGlyph::GetAlignMgr(), IScoringAlignment::GetAnchor(), CSGGenBankDS::GetScope(), set< Key, Compare >::insert(), IAlnGraphicDataSource::IsPartial(), m_AlnScoreMap, m_PartialAlnSet, and CAlignGlyph::SetScore().

Referenced by InitAlignScore().

InitAlignScore()

void CSGAlignmentDS::InitAlignScore

(

CAlignGlyph *

aln

)

Alignment scoring.

Definition at line 502 of file seqgraphic_alignment_ds.cpp.

References IAlnExplorer::fDNA, CAlignGlyph::GetAlignMgr(), GetAlignType(), CAlignGlyph::GetAlnAnchorPair(), IScoringAlignment::GetBaseWidth(), IScoringAlignment::GetNumRows(), CSGAlnQualityScore::GetScoreName(), InitAlignQualityScore(), InitAlignScoreCache(), and m_DNAMethod.

Referenced by CalculateAlignmentScore().

InitAlignScoreCache()

void CSGAlignmentDS::InitAlignScoreCache	(	CAlignGlyph *	aln,
		const TAlnAnchorPair &	align_pair,
		IAlnExplorer::EAlignType	sc_type
	)

Definition at line 542 of file seqgraphic_alignment_ds.cpp.

References _ASSERT, CScoreCache::EnableBackgoundProcessing(), map_checker< Container >::end(), IAlnExplorer::fDNA, map_checker< Container >::find(), IAlnExplorer::fMixed, IAlnExplorer::fProtein, CAlignGlyph::GetAlignMgr(), CRef< C, Locker >::GetPointer(), CSGAlnOtherScore::GetScoreCache(), CScoreCache::GetScoringMethod(), CScoreCache::HasScores(), set< Key, Compare >::insert(), IAlnGraphicDataSource::IsPartial(), ITERATE, kColorGradNumber, kEmptyStr, m_AlnScoreMap, m_DNAMethod, m_DNAMethods, m_PartialAlnSet, m_ProteinMethods, m_ProtMethod, NULL, CRef< C, Locker >::Reset(), CScoreCache::ResetScores(), CScoreCache::SetAlignment(), CScoreCache::SetGradNumber(), CScoreCache::SetListener(), CAlignGlyph::SetScore(), CScoreCache::SetScoringMethod(), and x_InitScoringMethods().

Referenced by InitAlignScore().

InitAlignType()

IAlnExplorer::EAlignType CSGAlignmentDS::InitAlignType

(

bool

isFastConfig = false

)

This method might need object manager to connect to ID, and it is a block call.

Please make sure it is called in a background thread to avoid blocking the main application. when isFastConfig set to true, it indicates that that the call is used by seqconfig this means that setting m_HasCoverageGraph and getting the actual type that are taking a long time and not needed by seqconfig will be skipped (IAlnExplorer::fHomogenous will be returned)

Definition at line 403 of file seqgraphic_alignment_ds.cpp.

References IAlnExplorer::fInvalid, CSGAlignmentJob::GetAlignType(), CSeqUtils::GetAnnotSelector(), CSGGenBankDS::m_Adaptive, m_AlnType, m_AnnotName, CSGGenBankDS::m_Depth, CSGGenBankDS::m_Handle, m_HasQualityMap, and x_InitScoringMethods().

Referenced by CAlignmentTrackFactory::CreateTracks().

IsBamLoader()

bool CSGAlignmentDS::IsBamLoader ( ) const

inline

Definition at line 356 of file seqgraphic_alignment_ds.hpp.

References eLoader_BAM, eLoader_Unknown, GetDataLoader(), kBamDataLoader, and m_AlnDataLoader.

Referenced by CAlignmentTrackFactory::CreateTracks().

IsCSRALoader()

bool CSGAlignmentDS::IsCSRALoader ( ) const

inline

Definition at line 366 of file seqgraphic_alignment_ds.hpp.

References eLoader_CSRA, eLoader_Unknown, GetDataLoader(), kCSRADataLoader, and m_AlnDataLoader.

Referenced by CAlignmentTrackFactory::CreateTracks().

IsGraphCached()

bool CSGAlignmentDS::IsGraphCached

(

const TSeqRange &

range

)

const

Definition at line 134 of file seqgraphic_alignment_ds.cpp.

References data, CGraphCache< TData >::GetCachedData(), CGraphCache< TData >::GetInstance(), len, m_HasPileUpCache, r(), compile_time_bits::range(), and x_GetGraphCacheKey().

IsRangeCached()

bool CSGAlignmentDS::IsRangeCached

(

const TSeqRange &

range

)

const

Definition at line 312 of file seqgraphic_alignment_ds.cpp.

References data, CGraphCache< TData >::GetData(), CGraphCache< TData >::GetInstance(), m_HasPileUpCache, compile_time_bits::range(), and x_GetGraphCacheKey().

Referenced by CAlignmentTrack::x_UpdateData().

IsValidDNAScoringMethod()

bool CSGAlignmentDS::IsValidDNAScoringMethod

(

const string &

name

)

Definition at line 481 of file seqgraphic_alignment_ds.cpp.

References IAlnExplorer::fDNA, CSGAlnQualityScore::GetScoreName(), ITERATE, m_DNAMethods, m_HasQualityMap, and x_InitScoringMethods().

Referenced by CAlignmentTrack::x_LoadSettings().

IsValidProteinScoringMethod()

bool CSGAlignmentDS::IsValidProteinScoringMethod

(

const string &

name

)

Definition at line 465 of file seqgraphic_alignment_ds.cpp.

References IAlnExplorer::fProtein, ITERATE, m_ProteinMethods, and x_InitScoringMethods().

Referenced by CAlignmentTrack::x_LoadSettings().

LoadAlignFeats()

void CSGAlignmentDS::LoadAlignFeats	(	const TSeqRange &	range,
		TModelUnit	window,
		vector< CRef< CAlignGlyph > >	aligns,
		const vector< int > &	projected_feats,
		TJobToken	token
	)

Definition at line 359 of file seqgraphic_alignment_ds.cpp.

References CSeqFeatData::eSubtype_bad, CSeqFeatData::eSubtype_max, CSeqUtils::GetAnnotSelector(), SAnnotSelector::IncludeFeatSubtype(), ITERATE, CSGGenBankDS::m_Handle, m_HideSra, m_MaxEndTail, m_MaxStartTail, m_ShowSecondPass, m_UnalignedTailsMode, compile_time_bits::range(), and CSGGenBankDS::x_LaunchJob().

Referenced by CAlignmentTrack::x_AddAlignmentLayout().

LoadAlignments()

void CSGAlignmentDS::LoadAlignments	(	const TSeqRange &	range,
		TModelUnit	window,
		int	align_limit,
		bool	smear_if_overlimit,
		TJobToken	token
	)

Definition at line 234 of file seqgraphic_alignment_ds.cpp.

References CSeq_annot_Base::C_Data::e_Align, CSeqUtils::GetAnnotSelector(), CSGGenBankDS::m_Adaptive, m_AnnotName, CSGGenBankDS::m_Depth, CSGGenBankDS::m_Handle, m_HideSra, m_LayoutPolicy, m_LinkMatePairs, m_MaxEndTail, m_MaxStartTail, m_ShowSecondPass, m_SortBy, m_UnalignedTailsMode, compile_time_bits::range(), CRef< C, Locker >::Reset(), CSeqUtils::SetAnnot(), CSeqUtils::SetResolveDepth(), CSGAlignmentJob::SetSortBy(), and CSGGenBankDS::x_LaunchJob().

Referenced by CAlignmentTrack::x_UpdateData().

LoadCoverageGraph()

void CSGAlignmentDS::LoadCoverageGraph	(	const TSeqRange &	range,
		TModelUnit	window,
		TJobToken	token
	)

Parameters

smear_align	smear the alignments also depending on flag 'adpative'
adaptive_smear	if true, the alignments will be smeared adaptively

Definition at line 209 of file seqgraphic_alignment_ds.cpp.

References _ASSERT, CSeq_annot_Base::C_Data::e_Graph, CSeqUtils::GetAnnotSelector(), m_AnnotName, CSGGenBankDS::m_Depth, CSGGenBankDS::m_Handle, m_HasCoverageGraph, m_HideSra, m_MaxEndTail, m_MaxStartTail, m_ShowSecondPass, m_UnalignedTailsMode, compile_time_bits::range(), CRef< C, Locker >::Reset(), CSeqUtils::SetAnnot(), CSeqUtils::SetResolveDepth(), and CSGGenBankDS::x_LaunchJob().

Referenced by CAlignmentTrack::x_UpdateData().

NeedReleaseMemory()

bool CSGAlignmentDS::NeedReleaseMemory

(

)

const

Definition at line 182 of file seqgraphic_alignment_ds.cpp.

References m_DataHandle, m_HasCoverageGraph, and m_MemoryLimit.

Referenced by CAlignmentTrack::x_UpdateData(), CAlignmentTrack::~CAlignmentTrack(), and ~CSGAlignmentDS().

RecalculateScore()

void CSGAlignmentDS::RecalculateScore

(

CConstRef< CSeqGlyph >

obj

)

ReleaseMemory()

void CSGAlignmentDS::ReleaseMemory

(

)

Definition at line 191 of file seqgraphic_alignment_ds.cpp.

References map_checker< Container >::clear(), DeleteAllJobs(), ERR_POST, CScope::eThrowIfLocked, CSGGenBankDS::GetScope(), Info(), m_AlnScoreMap, m_DataHandle, m_HasCoverageGraph, m_MemoryLimit, and s_fromatstr().

Referenced by CAlignmentTrack::x_UpdateData(), CAlignmentTrack::~CAlignmentTrack(), and ~CSGAlignmentDS().

ResetAlnScoringJob()

void CSGAlignmentDS::ResetAlnScoringJob

(

)

Definition at line 699 of file seqgraphic_alignment_ds.cpp.

References CSGGenBankDS::ClearJobID(), m_ScoringJob, m_ScoringJobID, and CRef< C, Locker >::Reset().

Referenced by CalculateAlignmentScore(), ClearJobID(), x_DeleteScoringJob(), and CAlignmentTrack::x_OnJobCompleted().

SetAlnDataLoader()

void CSGAlignmentDS::SetAlnDataLoader ( EDataLoader  data_loader )

inline

Definition at line 406 of file seqgraphic_alignment_ds.hpp.

References m_AlnDataLoader.

Referenced by CAlignmentTrackFactory::CreateTracks().

SetAnnotName()

void CSGAlignmentDS::SetAnnotName ( const string &  name )

inline

Definition at line 314 of file seqgraphic_alignment_ds.hpp.

References m_AnnotName.

Referenced by CAlignmentTrackFactory::CreateTracks().

SetCgiMode()

void CSGAlignmentDS::SetCgiMode ( bool  cgi_mode )

inline

Definition at line 399 of file seqgraphic_alignment_ds.hpp.

References m_CgiMode.

Referenced by CAlignmentTrack::x_LoadSettings().

SetDataHandle()

void CSGAlignmentDS::SetDataHandle ( const objects::CTSE_Handle &  tse )

inline

Definition at line 387 of file seqgraphic_alignment_ds.hpp.

References m_DataHandle.

Referenced by CAlignmentTrack::x_OnJobCompleted().

SetDefaultScoringMethods()

void CSGAlignmentDS::SetDefaultScoringMethods	(	string	dna_method,
		string	protein_method
	)

Definition at line 85 of file seqgraphic_alignment_ds.cpp.

References m_DNAMethod, and m_ProtMethod.

SetDNAScoringMethod()

void CSGAlignmentDS::SetDNAScoringMethod ( const string &  method )

inline

Definition at line 266 of file seqgraphic_alignment_ds.hpp.

References m_DNAMethod.

Referenced by CAlignmentTrack::x_LoadSettings(), and CAlignmentTrack::x_OnScoreIconClicked().

SetEnableColoration()

void CSGAlignmentDS::SetEnableColoration ( bool  f )

inline

Definition at line 290 of file seqgraphic_alignment_ds.hpp.

References f, and m_Enabled.

Referenced by CAlignmentTrack::x_LoadSettings(), and CAlignmentTrack::x_OnScoreIconClicked().

SetHasCoverageGraph()

void CSGAlignmentDS::SetHasCoverageGraph ( bool  flag )

inline

Definition at line 326 of file seqgraphic_alignment_ds.hpp.

References m_HasCoverageGraph.

Referenced by CAlignmentTrackFactory::CreateTracks().

SetHideSra()

void CSGAlignmentDS::SetHideSra ( CAlignmentConfig::EHideSraAlignments  hideSra )

inline

Definition at line 153 of file seqgraphic_alignment_ds.hpp.

References m_HideSra.

Referenced by CAlignmentTrack::x_LoadSettings().

SetLayoutPolicy()

void CSGAlignmentDS::SetLayoutPolicy ( ILayoutPolicy *  layout_policy )

inline

Definition at line 375 of file seqgraphic_alignment_ds.hpp.

References m_LayoutPolicy.

Referenced by CAlignmentTrack::x_OnLayoutPolicyChanged().

SetLinkMatePairs()

void CSGAlignmentDS::SetLinkMatePairs ( bool  f )

inline

Definition at line 302 of file seqgraphic_alignment_ds.hpp.

References f, and m_LinkMatePairs.

Referenced by CAlignmentTrack::OnToggleContent(), and CAlignmentTrack::x_LoadSettings().

SetMemoryLimit()

void CSGAlignmentDS::SetMemoryLimit ( Uint8  memory_limit )

inline

Definition at line 393 of file seqgraphic_alignment_ds.hpp.

References m_MemoryLimit.

Referenced by CAlignmentTrack::x_LoadSettings().

SetProteinScoringMethod()

void CSGAlignmentDS::SetProteinScoringMethod ( const string &  method )

inline

Definition at line 278 of file seqgraphic_alignment_ds.hpp.

References m_ProtMethod.

Referenced by CAlignmentTrack::x_LoadSettings(), and CAlignmentTrack::x_OnScoreIconClicked().

SetRemotePath()

void CSGAlignmentDS::SetRemotePath ( const string &  remote_path )

inline

Definition at line 381 of file seqgraphic_alignment_ds.hpp.

References m_RemotePath.

Referenced by CAlignmentTrackFactory::CreateTracks().

SetShowSecondPassAlignments()

void CSGAlignmentDS::SetShowSecondPassAlignments ( bool  value = true )

inline

Definition at line 155 of file seqgraphic_alignment_ds.hpp.

References m_ShowSecondPass, and rapidjson::value.

Referenced by CAlignmentTrack::x_LoadSettings().

SetSortBy()

void CSGAlignmentDS::SetSortBy ( const string &  sortby )

inline

Definition at line 344 of file seqgraphic_alignment_ds.hpp.

References m_SortBy.

Referenced by CAlignmentTrackFactory::CreateTracks(), CAlignmentTrack::OnToggleContent(), and CAlignmentTrack::x_LoadSettings().

SetUnalignedTailsMode()

void CSGAlignmentDS::SetUnalignedTailsMode ( CAlignmentConfig::EUnalignedTailsMode  tailsMode )

inline

Definition at line 154 of file seqgraphic_alignment_ds.hpp.

References m_UnalignedTailsMode.

Referenced by CAlignmentTrack::x_LoadSettings(), and CAlignmentTrack::x_OnTailsIconClicked().

x_DeleteScoringJob()

void CSGAlignmentDS::x_DeleteScoringJob ( )

private

Definition at line 735 of file seqgraphic_alignment_ds.cpp.

References _ASSERT, CAppJobDispatcher::DeleteJob(), CAppJobDispatcher::GetInstance(), m_ScoringJob, m_ScoringJobID, and ResetAlnScoringJob().

Referenced by CalculateAlignmentScore(), and DeleteAllJobs().

x_GetGraphCacheKey()

void CSGAlignmentDS::x_GetGraphCacheKey ( string &  data_key ) const

private

Definition at line 93 of file seqgraphic_alignment_ds.cpp.

References CPileUpGraph::CreateCacheKey(), m_AnnotName, CSGGenBankDS::m_Handle, and m_RemotePath.

Referenced by CalcAlnStat(), CanShowRange(), ClearCache(), GetGraphCost(), IsGraphCached(), and IsRangeCached().

x_InitScoringMethods()

void CSGAlignmentDS::x_InitScoringMethods ( IAlnExplorer::EAlignType  aln_type )

private

Definition at line 745 of file seqgraphic_alignment_ds.cpp.

References _ASSERT, CUIToolRegistry::CreateToolInstance(), IAlnExplorer::fDNA, IAlnExplorer::fInvalid, IAlnExplorer::fMixed, IAlnExplorer::fProtein, CUIToolRegistry::GetInstance(), IUITool::GetName(), CRef< C, Locker >::GetPointer(), CUIToolRegistry::GetTools(), IScoringMethod::GetType(), i, m_DNAMethods, and m_ProteinMethods.

Referenced by GetScoringMethods(), InitAlignScoreCache(), InitAlignType(), IsValidDNAScoringMethod(), and IsValidProteinScoringMethod().

x_IsScoringJobRunning()

bool CSGAlignmentDS::x_IsScoringJobRunning ( ) const

private

Definition at line 727 of file seqgraphic_alignment_ds.cpp.

References CRef< C, Locker >::GetPointer(), CSGGenBankDS::IsJobNeeded(), m_ScoringJob, m_ScoringJobID, and NULL.

Referenced by CalculateAlignmentScore().

Member Data Documentation

m_AlnDataLoader

EDataLoader CSGAlignmentDS::m_AlnDataLoader = eLoader_Unknown

private

Definition at line 225 of file seqgraphic_alignment_ds.hpp.

Referenced by IsBamLoader(), IsCSRALoader(), and SetAlnDataLoader().

m_AlnScoreMap

TAlnScoreMap CSGAlignmentDS::m_AlnScoreMap

mutableprivate

Definition at line 192 of file seqgraphic_alignment_ds.hpp.

Referenced by CalculateAlignmentScore(), InitAlignQualityScore(), InitAlignScoreCache(), and ReleaseMemory().

m_AlnType

IAlnExplorer::EAlignType CSGAlignmentDS::m_AlnType

private

Definition at line 197 of file seqgraphic_alignment_ds.hpp.

Referenced by GetAlignType(), and InitAlignType().

m_AnnotName

string CSGAlignmentDS::m_AnnotName

private

Definition at line 186 of file seqgraphic_alignment_ds.hpp.

Referenced by CalcAlnStat(), GetAlignmentCost(), GetAnnotName(), GetDataLoader(), GetGraphCost(), InitAlignType(), LoadAlignments(), LoadCoverageGraph(), SetAnnotName(), and x_GetGraphCacheKey().

m_CgiMode

bool CSGAlignmentDS::m_CgiMode = false

private

sviewer context

Definition at line 224 of file seqgraphic_alignment_ds.hpp.

Referenced by SetCgiMode(), and ~CSGAlignmentDS().

m_DataHandle

objects::CTSE_Handle CSGAlignmentDS::m_DataHandle

private

The last loaded data.

Definition at line 220 of file seqgraphic_alignment_ds.hpp.

Referenced by NeedReleaseMemory(), ReleaseMemory(), and SetDataHandle().

m_DataLoader

string CSGAlignmentDS::m_DataLoader = "none"

mutableprivate

Definition at line 215 of file seqgraphic_alignment_ds.hpp.

Referenced by GetDataLoader().

m_DNAMethod

string CSGAlignmentDS::m_DNAMethod

private

default scoring method for DNA alignments

Definition at line 195 of file seqgraphic_alignment_ds.hpp.

Referenced by GetDNAScoringMethod(), InitAlignScore(), InitAlignScoreCache(), SetDefaultScoringMethods(), and SetDNAScoringMethod().

m_DNAMethods

TMethods CSGAlignmentDS::m_DNAMethods

private

registered DNA scoring methods

Definition at line 188 of file seqgraphic_alignment_ds.hpp.

Referenced by GetScoringMethods(), InitAlignScoreCache(), IsValidDNAScoringMethod(), and x_InitScoringMethods().

m_Enabled

bool CSGAlignmentDS::m_Enabled

private

is alignment score coloration enabled

Definition at line 201 of file seqgraphic_alignment_ds.hpp.

Referenced by GetEnableColoration(), and SetEnableColoration().

m_HasCoverageGraph

bool CSGAlignmentDS::m_HasCoverageGraph

private

High level coverage graph?

Definition at line 203 of file seqgraphic_alignment_ds.hpp.

Referenced by HasCoverageGraph(), LoadCoverageGraph(), NeedReleaseMemory(), ReleaseMemory(), and SetHasCoverageGraph().

m_HasPileUpCache

bool CSGAlignmentDS::m_HasPileUpCache = false

private

Definition at line 223 of file seqgraphic_alignment_ds.hpp.

Referenced by CalcAlnStat(), CanShowRange(), ClearCache(), EnablePileUpCache(), GetGraphCost(), IsGraphCached(), and IsRangeCached().

m_HasQualityMap

bool CSGAlignmentDS::m_HasQualityMap

private

Has quality map? (e.g. cSRA alignments)

Definition at line 204 of file seqgraphic_alignment_ds.hpp.

Referenced by HasQualityMap(), InitAlignType(), and IsValidDNAScoringMethod().

m_HideSra

CAlignmentConfig::EHideSraAlignments CSGAlignmentDS::m_HideSra

private

Flag, indicating whether to hide duplicates and/or bad reads.

Definition at line 209 of file seqgraphic_alignment_ds.hpp.

Referenced by LoadAlignFeats(), LoadAlignments(), LoadCoverageGraph(), and SetHideSra().

m_LayoutPolicy

CIRef<ILayoutPolicy> CSGAlignmentDS::m_LayoutPolicy

private

Definition at line 217 of file seqgraphic_alignment_ds.hpp.

Referenced by LoadAlignments(), and SetLayoutPolicy().

m_LinkMatePairs

bool CSGAlignmentDS::m_LinkMatePairs

private

link mate pair alignments

Definition at line 202 of file seqgraphic_alignment_ds.hpp.

Referenced by GetLinkMatePairs(), LoadAlignments(), and SetLinkMatePairs().

m_MaxEndTail

TSignedSeqPos CSGAlignmentDS::m_MaxEndTail

private

Max length of unaligned tail at the end of the sequence.

Definition at line 213 of file seqgraphic_alignment_ds.hpp.

Referenced by LoadAlignFeats(), LoadAlignments(), and LoadCoverageGraph().

m_MaxStartTail

TSignedSeqPos CSGAlignmentDS::m_MaxStartTail

private

> Flag to show second-pass alignments (relevant to assembly to assembly alignments)

Max length of unaligned tail at the start of the sequence

Definition at line 212 of file seqgraphic_alignment_ds.hpp.

Referenced by LoadAlignFeats(), LoadAlignments(), and LoadCoverageGraph().

m_MemoryLimit

Uint8 CSGAlignmentDS::m_MemoryLimit = 2 * (Uint8)1073741824

private

NeedReleaseMemory's default limit 2GB.

Definition at line 221 of file seqgraphic_alignment_ds.hpp.

Referenced by NeedReleaseMemory(), ReleaseMemory(), and SetMemoryLimit().

m_PartialAlnSet

set<TAlnAnchorPair> CSGAlignmentDS::m_PartialAlnSet

mutableprivate

Definition at line 193 of file seqgraphic_alignment_ds.hpp.

Referenced by CalculateAlignmentScore(), InitAlignQualityScore(), and InitAlignScoreCache().

m_ProteinMethods

TMethods CSGAlignmentDS::m_ProteinMethods

private

registered Protein scoring methods

Definition at line 189 of file seqgraphic_alignment_ds.hpp.

Referenced by GetScoringMethods(), InitAlignScoreCache(), IsValidProteinScoringMethod(), and x_InitScoringMethods().

m_ProtMethod

string CSGAlignmentDS::m_ProtMethod

private

default scoring method for protein alignments

Definition at line 196 of file seqgraphic_alignment_ds.hpp.

Referenced by GetProteinScoringMethod(), InitAlignScoreCache(), SetDefaultScoringMethods(), and SetProteinScoringMethod().

m_RemotePath

string CSGAlignmentDS::m_RemotePath

private

url to the remote data

Definition at line 218 of file seqgraphic_alignment_ds.hpp.

Referenced by SetRemotePath(), and x_GetGraphCacheKey().

m_ScoreToken

TJobToken CSGAlignmentDS::m_ScoreToken

private

the scoring job token

Definition at line 206 of file seqgraphic_alignment_ds.hpp.

m_ScoringJob

CRef<CSGAlignScoringJob> CSGAlignmentDS::m_ScoringJob

private

Definition at line 208 of file seqgraphic_alignment_ds.hpp.

Referenced by CalculateAlignmentScore(), DeleteAllJobs(), ResetAlnScoringJob(), x_DeleteScoringJob(), and x_IsScoringJobRunning().

m_ScoringJobID

TJobID CSGAlignmentDS::m_ScoringJobID

private

alignment scoring job id

Definition at line 207 of file seqgraphic_alignment_ds.hpp.

Referenced by CalculateAlignmentScore(), ClearJobID(), DeleteAllJobs(), ResetAlnScoringJob(), x_DeleteScoringJob(), and x_IsScoringJobRunning().

m_ShowSecondPass

bool CSGAlignmentDS::m_ShowSecondPass = true

private

Definition at line 211 of file seqgraphic_alignment_ds.hpp.

Referenced by LoadAlignFeats(), LoadAlignments(), LoadCoverageGraph(), and SetShowSecondPassAlignments().

m_SortBy

string CSGAlignmentDS::m_SortBy

private

Definition at line 199 of file seqgraphic_alignment_ds.hpp.

Referenced by GetSortBy(), LoadAlignments(), and SetSortBy().

m_UnalignedTailsMode

CAlignmentConfig::EUnalignedTailsMode CSGAlignmentDS::m_UnalignedTailsMode

private

Flag, indicating whether and how to display unaligned tails.

Definition at line 210 of file seqgraphic_alignment_ds.hpp.

Referenced by LoadAlignFeats(), LoadAlignments(), LoadCoverageGraph(), and SetUnalignedTailsMode().

---

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

• include/gui/widgets/seq_graphic/seqgraphic_alignment_ds.hpp
• src/gui/widgets/seq_graphic/seqgraphic_alignment_ds.cpp