NCBI C++ ToolKit
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CSGFeatureDS Class Reference

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CSGFeatureDS. More...

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

+ Inheritance diagram for CSGFeatureDS:
+ Collaboration diagram for CSGFeatureDS:

Public Member Functions

 CSGFeatureDS (objects::CScope &scope, const objects::CSeq_id &id)
 CSGFeatureDS. More...
 
virtual void LoadFeatures (objects::SAnnotSelector &sel, const TSeqRange &range, TModelUnit window, TJobToken token=-1, int max_feat=-1, ELinkedFeatDisplay LinkedFeatDisplay=ELinkedFeatDisplay::eLFD_Default, const string &extra_filter="")
 
virtual void LoadFeatures (const TSeqRange &range, TModelUnit window, TJobToken token, const TFeatBatchJobRequests &requests)
 
void CalcFeatHistogram (const CSeqGlyph::TObjects &objs, const TSeqRange &range, TModelUnit window, TJobToken token=-1)
 
void LoadGeneModelFeatures (objects::SAnnotSelector &lm_feat_sel, objects::SAnnotSelector &m_feat_sel, TJobToken lm_token, TJobToken main_token, bool landmark_feat, const TSeqRange &range, TModelUnit window, const CRef< CGeneModelConfig > &conf)
 load features for gene model. More...
 
void GetAnnotNames (objects::SAnnotSelector &sel, const TSeqRange &range, TAnnotNameTitleMap &names) const
 
void GetAnnotNames_var (objects::SAnnotSelector &sel, const TSeqRange &range, TAnnotNameTitleMap &names) const
 
vector< stringGetFilters (const string &annot_name, const TSeqRange &range) const
 
void SetFilter (const string &filter)
 CSGFeatureDS inline method. More...
 
const stringGetFilter () const
 
void SetSortBy (const string &sortby)
 
const stringGetSortBy () const
 
void SetGraphCacheKey (const string &graph_cache_key)
 
void SetRemoteDataType (const string &data_type)
 
bool IsBigBed () const
 
bool IsVcfTabix () const
 
- Public Member Functions inherited from CSGGenBankDS
 CSGGenBankDS (objects::CScope &scope, const objects::CSeq_id &id)
 
virtual ~CSGGenBankDS ()
 
bool IsRefSeq () const
 
void SetDepth (int depth)
 Set the annotation selector resolving depth. More...
 
int GetDepth () const
 
void SetAdaptive (bool flag)
 
bool GetAdaptive () const
 
objects::CBioseq_Handle & GetBioseqHandle (void)
 Get the underlying bioseq handle. More...
 
const objects::CBioseq_Handle & GetBioseqHandle (void) const
 
objects::CScope & GetScope (void) const
 Get the scope from the handle. More...
 
void SetJobListener (CEventHandler *listener)
 Set JobDispatcher listener. More...
 
virtual void ClearJobID (TJobID job_id)
 
bool IsJobNeeded (TJobID job_id) const
 
virtual bool AllJobsFinished () const
 
virtual void DeleteAllJobs ()
 Remove waiting jobs from queue or cancel the unfinished jobs. More...
 
void SetCoordMapper (ICoordMapper *mapper)
 
void SetGraphLevels (const string &annot)
 
- Public Member Functions inherited from CObjectEx
 CObjectEx (void)
 
virtual ~CObjectEx (void)
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
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 Attributes

string m_Filter
 
string m_SortBy
 
string m_GraphCacheKey
 
string m_RmtDataType
 

Additional Inherited Members

- Public Types inherited from CSGGenBankDS
typedef CAppJobDispatcher::TJobID TJobID
 
typedef int TJobToken
 
- Public Types inherited from CObject
enum  EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
 Control filling of newly allocated memory. More...
 
typedef CObjectCounterLocker TLockerType
 Default locker type for CRef. More...
 
typedef atomic< 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...
 
- 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

CSGFeatureDS.

Definition at line 48 of file feature_ds.hpp.

Constructor & Destructor Documentation

◆ CSGFeatureDS()

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

CSGFeatureDS.

Definition at line 432 of file feature_ds.cpp.

Member Function Documentation

◆ CalcFeatHistogram()

void CSGFeatureDS::CalcFeatHistogram ( const CSeqGlyph::TObjects objs,
const TSeqRange range,
TModelUnit  window,
TJobToken  token = -1 
)

Definition at line 502 of file feature_ds.cpp.

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

◆ GetAnnotNames()

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

◆ GetAnnotNames_var()

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

◆ GetFilter()

const string & CSGFeatureDS::GetFilter ( void  ) const
inline

Definition at line 180 of file feature_ds.hpp.

References m_Filter.

Referenced by CFeatureTrack::GenerateAsn1().

◆ GetFilters()

vector< string > CSGFeatureDS::GetFilters ( const string annot_name,
const TSeqRange range 
) const

◆ GetSortBy()

const string & CSGFeatureDS::GetSortBy ( ) const
inline

Definition at line 188 of file feature_ds.hpp.

References m_SortBy.

◆ IsBigBed()

bool CSGFeatureDS::IsBigBed ( ) const
inline

Definition at line 204 of file feature_ds.hpp.

References NStr::EqualNocase(), and m_RmtDataType.

Referenced by LoadFeatures(), and CFeatureTrack::x_AddFeaturesLayout().

◆ IsVcfTabix()

bool CSGFeatureDS::IsVcfTabix ( ) const
inline

Definition at line 210 of file feature_ds.hpp.

References NStr::EqualNocase(), and m_RmtDataType.

Referenced by LoadFeatures().

◆ LoadFeatures() [1/2]

void CSGFeatureDS::LoadFeatures ( const TSeqRange range,
TModelUnit  window,
TJobToken  token,
const TFeatBatchJobRequests requests 
)
virtual

◆ LoadFeatures() [2/2]

virtual void CSGFeatureDS::LoadFeatures ( objects::SAnnotSelector &  sel,
const TSeqRange range,
TModelUnit  window,
TJobToken  token = -1,
int  max_feat = -1,
ELinkedFeatDisplay  LinkedFeatDisplay = ELinkedFeatDisplay::eLFD_Default,
const string extra_filter = "" 
)
virtual

◆ LoadGeneModelFeatures()

void CSGFeatureDS::LoadGeneModelFeatures ( objects::SAnnotSelector &  lm_feat_sel,
objects::SAnnotSelector &  m_feat_sel,
TJobToken  lm_token,
TJobToken  main_token,
bool  landmark_feat,
const TSeqRange range,
TModelUnit  window,
const CRef< CGeneModelConfig > &  conf 
)

load features for gene model.

This method will either load landmark features or all main features based on both overview flag and number of genes presented given the range. The main features include genes, Rnas, CDSs, and exons.

Parameters
lm_feat_selannot selector for loading landmark features (genes)
m_feat_selannot selector for loading main features.
lm_tokentoken for loading landmark features job.
main_tokentoken for loading main features job.
stylethe merging style for RNA and cds features.
landmark_featshow landmark features if suitable.
min_overview_featminimal feature number to be in overview model.
rangethe data range.
windowthe window scale bases per pixel for creating densitymap.
max_featthe maximum features allowed.

Definition at line 482 of file feature_ds.cpp.

References CSGGenBankDS::m_Adaptive, CSGGenBankDS::m_Depth, m_Filter, CSGGenBankDS::m_Handle, CSGGenBankDS::m_Mapper, m_SortBy, compile_time_bits::range(), CSeqUtils::SetResolveDepth(), and CSGGenBankDS::x_LaunchJob().

Referenced by CGeneModelTrack::x_UpdateData().

◆ SetFilter()

void CSGFeatureDS::SetFilter ( const string filter)
inline

◆ SetGraphCacheKey()

void CSGFeatureDS::SetGraphCacheKey ( const string graph_cache_key)
inline

◆ SetRemoteDataType()

void CSGFeatureDS::SetRemoteDataType ( const string data_type)
inline

Definition at line 198 of file feature_ds.hpp.

References m_RmtDataType.

Referenced by CVarTrackFactory::CreateTracks(), and CFeatureTrackFactory::CreateTracks().

◆ SetSortBy()

void CSGFeatureDS::SetSortBy ( const string sortby)
inline

Member Data Documentation

◆ m_Filter

string CSGFeatureDS::m_Filter
private

Definition at line 110 of file feature_ds.hpp.

Referenced by GetFilter(), GetFilters(), LoadGeneModelFeatures(), and SetFilter().

◆ m_GraphCacheKey

string CSGFeatureDS::m_GraphCacheKey
private

Definition at line 112 of file feature_ds.hpp.

Referenced by LoadFeatures(), and SetGraphCacheKey().

◆ m_RmtDataType

string CSGFeatureDS::m_RmtDataType
private

Definition at line 113 of file feature_ds.hpp.

Referenced by IsBigBed(), IsVcfTabix(), and SetRemoteDataType().

◆ m_SortBy

string CSGFeatureDS::m_SortBy
private

Definition at line 111 of file feature_ds.hpp.

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


The documentation for this class was generated from the following files:
Modified on Sat Feb 24 07:48:38 2024 by modify_doxy.py rev. 669887