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CSGAlignmentDS Class Reference

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#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< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 
- Public Types inherited from ISGDataSource
typedef map< string, stringTAnnotNameTitleMap
 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 stringGetDataLoader () 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 TMethodsGetScoringMethods (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 stringGetDNAScoringMethod () const
 
void SetProteinScoringMethod (const string &method)
 
const stringGetProteinScoringMethod () 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 stringGetAnnotName () const
 
void SetHasCoverageGraph (bool flag)
 
bool HasCoverageGraph () const
 
bool HasQualityMap () const
 
void SetSortBy (const string &sortby)
 
const stringGetSortBy () 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...
 
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
 
- Public Member Functions inherited from CWeakObject
 CWeakObject (void)
 
virtual ~CWeakObject (void)
 
CPtrToObjectProxyGetPtrProxy (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< TAlnAnchorPairm_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< CSGAlignScoringJobm_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< ILayoutPolicym_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< intTGraphLevels
 
- 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
 
CEventHandlerm_JobListener
 our listener to JobDispatcher events More...
 
vector< TJobIDm_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< ICoordMapperm_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

Definition at line 54 of file seqgraphic_alignment_ds.hpp.

◆ TAlnMgrVec

Definition at line 55 of file seqgraphic_alignment_ds.hpp.

◆ TAlnScoreMap

Definition at line 191 of file seqgraphic_alignment_ds.hpp.

◆ TMethods

keep instances of score methods here.

Definition at line 68 of file seqgraphic_alignment_ds.hpp.

Member Enumeration Documentation

◆ 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 
)

◆ CalculateAlignmentScore()

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

◆ CanShowRange()

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

◆ ClearCache()

void CSGAlignmentDS::ClearCache ( )

◆ ClearJobID()

void CSGAlignmentDS::ClearJobID ( TJobID  job_id)
virtual

◆ 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 
)

◆ GetAlignmentCost()

double CSGAlignmentDS::GetAlignmentCost ( const TSeqRange range) const

◆ 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

◆ 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

◆ GetDataLoader()

const string & CSGAlignmentDS::GetDataLoader ( ) const

◆ GetDNAScoringMethod()

const string & CSGAlignmentDS::GetDNAScoringMethod ( ) const
inline

◆ GetEnableColoration()

bool CSGAlignmentDS::GetEnableColoration ( ) const
inline

◆ GetGraphCost()

double CSGAlignmentDS::GetGraphCost ( const TSeqRange range) const

◆ GetLinkMatePairs()

bool CSGAlignmentDS::GetLinkMatePairs ( ) const
inline

◆ GetProteinScoringMethod()

const string & CSGAlignmentDS::GetProteinScoringMethod ( ) const
inline

◆ 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

◆ HasCoverageGraph()

bool CSGAlignmentDS::HasCoverageGraph ( ) const
inline

◆ 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 
)

◆ InitAlignScore()

void CSGAlignmentDS::InitAlignScore ( CAlignGlyph aln)

◆ InitAlignScoreCache()

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

◆ 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

◆ IsCSRALoader()

bool CSGAlignmentDS::IsCSRALoader ( ) const
inline

◆ IsGraphCached()

bool CSGAlignmentDS::IsGraphCached ( const TSeqRange range) const

◆ IsRangeCached()

bool CSGAlignmentDS::IsRangeCached ( const TSeqRange range) const

◆ IsValidDNAScoringMethod()

bool CSGAlignmentDS::IsValidDNAScoringMethod ( const string name)

◆ IsValidProteinScoringMethod()

bool CSGAlignmentDS::IsValidProteinScoringMethod ( const string name)

◆ LoadAlignFeats()

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

◆ LoadAlignments()

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

◆ LoadCoverageGraph()

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

◆ NeedReleaseMemory()

bool CSGAlignmentDS::NeedReleaseMemory ( ) const

◆ RecalculateScore()

void CSGAlignmentDS::RecalculateScore ( CConstRef< CSeqGlyph obj)

◆ ReleaseMemory()

void CSGAlignmentDS::ReleaseMemory ( )

◆ ResetAlnScoringJob()

void CSGAlignmentDS::ResetAlnScoringJob ( )

◆ 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

◆ SetEnableColoration()

void CSGAlignmentDS::SetEnableColoration ( bool  f)
inline

◆ 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

◆ 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

◆ 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

◆ SetUnalignedTailsMode()

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

◆ x_DeleteScoringJob()

void CSGAlignmentDS::x_DeleteScoringJob ( )
private

◆ x_GetGraphCacheKey()

void CSGAlignmentDS::x_GetGraphCacheKey ( string data_key) const
private

◆ x_InitScoringMethods()

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

◆ x_IsScoringJobRunning()

bool CSGAlignmentDS::x_IsScoringJobRunning ( ) const
private

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

◆ 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

◆ 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

◆ 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

◆ 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

◆ m_ScoringJobID

TJobID CSGAlignmentDS::m_ScoringJobID
private

◆ m_ShowSecondPass

bool CSGAlignmentDS::m_ShowSecondPass = true
private

◆ 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:
Modified on Fri Sep 20 14:58:03 2024 by modify_doxy.py rev. 669887