NCBI C++ ToolKit
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CVcfLoadingJob Class Reference

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CVcfLoadingJob. More...

+ Inheritance diagram for CVcfLoadingJob:
+ Collaboration diagram for CVcfLoadingJob:

Public Types

using TSeqIdsVector = vector< CConstRef< CSeq_id > >
 
- 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 IAppJob
enum  EJobState {
  eInvalid , eRunning , eCompleted , eFailed ,
  eCanceled , eSuspended
}
 Job states (describe FSM) More...
 

Public Member Functions

 CVcfLoadingJob ()
 
void SetVcfFiles (const vector< wxString > &files)
 
TSeqIdsVectorSetChromosomes ()
 
TSeqIdsVectorSetSeqIdsToLoad ()
 
void SetReadAllChrms (bool value)
 
void SetGenCollAssembly (const CRef< CGC_Assembly > &assm)
 
set< string > & SetInfoFields ()
 
void SetReadAllInfoFields (bool value)
 
map< unsigned, string > & SetSamples ()
 
void SetReadAllSamples (bool value)
 
- Public Member Functions inherited from CDataLoadingAppJob
 CDataLoadingAppJob ()
 constructor for derived classes More...
 
virtual ~CDataLoadingAppJob ()
 
const CSelectProjectOptions::TDataGetData () const
 
const objects::CScope & GetScope () const
 
void AddProjectItem (objects::CProjectItem &item)
 
void AddProjectItem (objects::CProjectItem &item, objects::CLoaderDescriptor &loader)
 
void AddDataLoader (objects::CLoaderDescriptor &loader)
 
void ClearItems ()
 
virtual EJobState Run ()
 Function that does all the useful work, called by the Engine. More...
 
virtual CRef< CObjectGetResult ()
 Returns the Job Result. More...
 
virtual CConstIRef< IAppJobProgressGetProgress ()
 implement Run() in derived classes, make sure that exceptions are handled and m_StopRequested flag is respected. More...
 
- Public Member Functions inherited from CAppJob
 CAppJob (const string &descr="AppJob")
 CAppJob. More...
 
virtual CConstIRef< IAppJobErrorGetError () override
 Returns IAppJobError object describing internal error that caused the Job to fail. More...
 
virtual string GetDescr () const override
 Returns a human readable description of the Job (optional) More...
 
- Public Member Functions inherited from CJobCancelable
 CJobCancelable ()
 
void SetDataLocker (ILocker *locker)
 
virtual void RequestCancel () override
 RequestCancel() is called to notify the Job that it shall exit Run() function ASAP. More...
 
virtual bool IsCanceled () const override
 
- 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 IAppJob
virtual ~IAppJob ()
 
virtual bool BeforeRun ()
 Function will be called on the main thread before execution of Run Should not do any lengthy work returns true to continue job execution on worker thread false to quit execution with status - failed. More...
 
- Public Member Functions inherited from CReportLoaderErrors
 CReportLoaderErrors ()
 
void SetWorkDir (const wxString &workDir)
 

Private Member Functions

void x_OnVCFVariantListReady (CVCFVariantList &vars)
 
void x_CreateColumnarVCFProjectItem (const CSeq_id &seq_id, CVCFVariantList &vars)
 
void x_CreateSeqIdProjectItem (const CSeq_id &seq_id)
 
vector< stringx_FindSynonyms (const CSeq_id &seq_id, const CGC_Assembly::TSequenceList &chromosomes)
 

Private Attributes

vector< wxString > m_VcfFiles
 
TSeqIdsVector m_ChromIds
 
TSeqIdsVector m_SeqIdsToLoad
 
bool m_ReadAllChrms { true }
 
CRef< CGC_Assemblym_GenCollAssm
 
unique_ptr< IIdMapperm_IdMapper
 
wxFileName m_CurrentFile
 
set< stringm_LoadInfoFields
 
bool m_ReadAllInfoFields
 
map< unsigned, stringm_Samples
 
bool m_ReadAllSamples
 

CDataLoadingAppJob implementation

void GetHTMLResults (wxString &title, wxString &html)
 
virtual void x_CreateProjectItems ()
 override this function in derived classes and populate m_Items. More...
 

Additional Inherited Members

- 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 Member Functions inherited from CDataLoadingAppJob
virtual void x_ResetState ()
 prepares job for execution by clearing state variables More...
 
virtual void x_Run ()
 
void x_SetTextResult (const string &result)
 
- Protected Member Functions inherited from CAppJob
virtual void x_SetStatusText (const string &text)
 
- Protected Member Functions inherited from CJobCancelable
CLockerGuard x_GetGuard ()
 
ICanceledx_GetICanceled ()
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 
- Protected Member Functions inherited from CReportLoaderErrors
void x_UpdateHTMLResults (const wxString &object, objects::ILineErrorListener *errCont, const string &exception="", const string &error_msg="", const wxString &objectName=wxT("File:"))
 
void x_ShowErrorsDlg (const wxString &title)
 
wxString x_GetHTMLResults () const
 
- Protected Attributes inherited from CDataLoadingAppJob
string m_TextResult
 
CRef< objects::CScope > m_Scope
 
- Protected Attributes inherited from CAppJob
CFastMutex m_Mutex
 
string m_Descr
 mutex to sync our internals More...
 
string m_Status
 Current status of the Job. More...
 
CRef< CAppJobErrorm_Error
 

Detailed Description

CVcfLoadingJob.

Definition at line 73 of file columnar_vcf_load_manager.cpp.

Member Typedef Documentation

◆ TSeqIdsVector

Definition at line 78 of file columnar_vcf_load_manager.cpp.

Constructor & Destructor Documentation

◆ CVcfLoadingJob()

CVcfLoadingJob::CVcfLoadingJob ( )

Definition at line 505 of file columnar_vcf_load_manager.cpp.

References CAppJob::m_Descr.

Member Function Documentation

◆ GetHTMLResults()

void CVcfLoadingJob::GetHTMLResults ( wxString &  title,
wxString &  html 
)
virtual

Reimplemented from CDataLoadingAppJob.

Definition at line 510 of file columnar_vcf_load_manager.cpp.

References CReportLoaderErrors::x_GetHTMLResults().

◆ SetChromosomes()

TSeqIdsVector& CVcfLoadingJob::SetChromosomes ( )
inline

Definition at line 88 of file columnar_vcf_load_manager.cpp.

References m_ChromIds.

◆ SetGenCollAssembly()

void CVcfLoadingJob::SetGenCollAssembly ( const CRef< CGC_Assembly > &  assm)
inline

Definition at line 91 of file columnar_vcf_load_manager.cpp.

References m_GenCollAssm.

◆ SetInfoFields()

set<string>& CVcfLoadingJob::SetInfoFields ( )
inline

Definition at line 93 of file columnar_vcf_load_manager.cpp.

References m_LoadInfoFields.

◆ SetReadAllChrms()

void CVcfLoadingJob::SetReadAllChrms ( bool  value)
inline

Definition at line 90 of file columnar_vcf_load_manager.cpp.

References m_ReadAllChrms, and rapidjson::value.

◆ SetReadAllInfoFields()

void CVcfLoadingJob::SetReadAllInfoFields ( bool  value)
inline

Definition at line 94 of file columnar_vcf_load_manager.cpp.

References m_ReadAllInfoFields, and rapidjson::value.

◆ SetReadAllSamples()

void CVcfLoadingJob::SetReadAllSamples ( bool  value)
inline

Definition at line 97 of file columnar_vcf_load_manager.cpp.

References m_ReadAllSamples, and rapidjson::value.

◆ SetSamples()

map<unsigned, string>& CVcfLoadingJob::SetSamples ( )
inline

Definition at line 96 of file columnar_vcf_load_manager.cpp.

References m_Samples.

◆ SetSeqIdsToLoad()

TSeqIdsVector& CVcfLoadingJob::SetSeqIdsToLoad ( )
inline

Definition at line 89 of file columnar_vcf_load_manager.cpp.

References m_SeqIdsToLoad.

◆ SetVcfFiles()

void CVcfLoadingJob::SetVcfFiles ( const vector< wxString > &  files)
inline

Definition at line 87 of file columnar_vcf_load_manager.cpp.

References m_VcfFiles.

◆ x_CreateColumnarVCFProjectItem()

void CVcfLoadingJob::x_CreateColumnarVCFProjectItem ( const CSeq_id seq_id,
CVCFVariantList vars 
)
inlineprivate

◆ x_CreateProjectItems()

void CVcfLoadingJob::x_CreateProjectItems ( )
protectedvirtual

◆ x_CreateSeqIdProjectItem()

void CVcfLoadingJob::x_CreateSeqIdProjectItem ( const CSeq_id seq_id)
inlineprivate

◆ x_FindSynonyms()

vector< string > CVcfLoadingJob::x_FindSynonyms ( const CSeq_id seq_id,
const CGC_Assembly::TSequenceList chromosomes 
)
private

◆ x_OnVCFVariantListReady()

void CVcfLoadingJob::x_OnVCFVariantListReady ( CVCFVariantList vars)
private

Member Data Documentation

◆ m_ChromIds

TSeqIdsVector CVcfLoadingJob::m_ChromIds
private

Definition at line 112 of file columnar_vcf_load_manager.cpp.

Referenced by SetChromosomes().

◆ m_CurrentFile

wxFileName CVcfLoadingJob::m_CurrentFile
private

◆ m_GenCollAssm

CRef<CGC_Assembly> CVcfLoadingJob::m_GenCollAssm
private

◆ m_IdMapper

unique_ptr<IIdMapper> CVcfLoadingJob::m_IdMapper
private

Definition at line 116 of file columnar_vcf_load_manager.cpp.

Referenced by x_CreateProjectItems(), and x_OnVCFVariantListReady().

◆ m_LoadInfoFields

set<string> CVcfLoadingJob::m_LoadInfoFields
private

Definition at line 119 of file columnar_vcf_load_manager.cpp.

Referenced by SetInfoFields(), and x_CreateProjectItems().

◆ m_ReadAllChrms

bool CVcfLoadingJob::m_ReadAllChrms { true }
private

Definition at line 114 of file columnar_vcf_load_manager.cpp.

Referenced by SetReadAllChrms(), and x_CreateProjectItems().

◆ m_ReadAllInfoFields

bool CVcfLoadingJob::m_ReadAllInfoFields
private

Definition at line 120 of file columnar_vcf_load_manager.cpp.

Referenced by SetReadAllInfoFields(), and x_CreateProjectItems().

◆ m_ReadAllSamples

bool CVcfLoadingJob::m_ReadAllSamples
private

Definition at line 123 of file columnar_vcf_load_manager.cpp.

Referenced by SetReadAllSamples(), and x_CreateProjectItems().

◆ m_Samples

map<unsigned, string> CVcfLoadingJob::m_Samples
private

Definition at line 122 of file columnar_vcf_load_manager.cpp.

Referenced by SetSamples(), and x_CreateProjectItems().

◆ m_SeqIdsToLoad

TSeqIdsVector CVcfLoadingJob::m_SeqIdsToLoad
private

Definition at line 113 of file columnar_vcf_load_manager.cpp.

Referenced by SetSeqIdsToLoad(), and x_CreateProjectItems().

◆ m_VcfFiles

vector<wxString> CVcfLoadingJob::m_VcfFiles
private

Definition at line 111 of file columnar_vcf_load_manager.cpp.

Referenced by SetVcfFiles(), and x_CreateProjectItems().


The documentation for this class was generated from the following file:
Modified on Tue May 28 05:52:20 2024 by modify_doxy.py rev. 669887