NCBI C++ ToolKit
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CTreeBuilderJob Class Reference

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CTreeBuilderJob. More...

+ Inheritance diagram for CTreeBuilderJob:
+ Collaboration diagram for CTreeBuilderJob:

Public Member Functions

 CTreeBuilderJob (const CTreeBuilderParams &params)
 CTreeBuilderJob. More...
- Public Member Functions inherited from CDataLoadingAppJob
 CDataLoadingAppJob ()
 constructor for derived classes More...
virtual ~CDataLoadingAppJob ()
const CSelectProjectOptions::TDataGetData () const
const objects::CScope & GetScope () const
virtual void GetHTMLResults (wxString &, wxString &)
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...

Protected Member Functions

virtual void x_CreateProjectItems ()
 override this function in derived classes and populate m_Items. 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...

Static Protected Member Functions

static void x_Divergence (CSparseAln &spaln, CDistMethods::TMatrix &result)

Protected Attributes

CTreeBuilderParams m_Params
- 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

Additional Inherited Members

- 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...
- 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...

Detailed Description


Definition at line 162 of file tree_builder_tool.cpp.

Constructor & Destructor Documentation

◆ CTreeBuilderJob()

CTreeBuilderJob::CTreeBuilderJob ( const CTreeBuilderParams params)


Definition at line 185 of file tree_builder_tool.cpp.

References CAppJob::m_Descr.

Member Function Documentation

◆ x_CreateProjectItems()

void CTreeBuilderJob::x_CreateProjectItems ( )

override this function in derived classes and populate m_Items.

If data loaders are needed, they should be created here too.

Implements CDataLoadingAppJob.

Definition at line 209 of file tree_builder_tool.cpp.

References CDataLoadingAppJob::AddProjectItem(), CDistMethods::AllFinite(), BuildAln(), COrgName_Base::CanGetMod(), CreateAnchoredAlnVec(), CDistMethods::Divergence(), CLabel::eDefault, eGetId_Best, eGetId_ForceGi, ctll::empty(), CAlnUserOptions::ePreserveRows, ERR_POST, CSubSource_Base::eSubtype_collection_date, CSubSource_Base::eSubtype_country, CSubSource_Base::eSubtype_isolation_source, COrgMod_Base::eSubtype_nat_host, CDistMethods::FastMeTree(), CAlnVec::GetBioseqHandle(), CSparseAln::GetBioseqHandle(), GetBioSource(), CNcbiMatrix< T >::GetCols(), CTreeBuilderParams::GetConstructMethod(), CSeq_align_Base::C_Segs::GetDenseg(), CAnchoredAln::GetDim(), CTreeBuilderParams::GetDistanceMethod(), CSeq_id_Handle::GetGi(), CSeq_id_Base::GetGi(), GetId(), CLabel::GetLabel(), CTaxon1::GetLastError(), CTreeBuilderParams::GetLeafLabels(), COrgName_Base::GetMod(), CBioseq_Handle::GetNonLocalIdOrNull(), CAlnMap::GetNumRows(), CSparseAln::GetNumRows(), CTreeBuilderParams::GetObject(), GetOrg_ref(), CTaxon1::GetOrgRef(), CSeq_align_Base::GetSegs(), CSeq_id_Handle::GetSeqId(), CSeq_id::GetSeqIdString(), CTaxon1::GetTaxId4GI(), i, CTaxon1::Init(), CAlnContainer::insert(), set< Key, Compare >::insert(), NStr::IntToString(), CTaxon1::IsAlive(), CSeq_align_Base::C_Segs::IsDenseg(), CSeq_id_Base::IsGi(), CDistMethods::JukesCantorDist(), CDistMethods::KimuraDist(), kTaxId, CAlnUserOptions::m_MergeAlgo, m_Params, MakeBioTreeContainer(), CDistMethods::NjTree(), NON_CONST_ITERATE, SConstScopedObject::object, CDistMethods::PoissonDist(), CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::push_back(), CConstRef< C, Locker >::Reset(), s_AddFeature(), s_AddFeatureDescr(), sc_FastMe(), sc_JukesCantor(), sc_Kimura(), sc_Nj(), sc_Poisson(), sc_SeqTitle(), sc_TaxName(), SConstScopedObject::scope, CAlnVec::SetEndChar(), CAlnVec::SetGapChar(), CSparseAln::SetGapChar(), CLabel::SetLabelByData(), CBioTreeContainer_Base::SetNodes(), CProjectItem::SetObject(), CBioTreeContainer_Base::SetTreetype(), CAlnContainer::size(), NStr::SizetToString(), NStr::StringToUInt(), ToStdString(), x_Divergence(), and ZERO_GI.

◆ x_Divergence()

void CTreeBuilderJob::x_Divergence ( CSparseAln spaln,
CDistMethods::TMatrix result 

Member Data Documentation

◆ m_Params

CTreeBuilderParams CTreeBuilderJob::m_Params

Definition at line 173 of file tree_builder_tool.cpp.

Referenced by x_CreateProjectItems().

The documentation for this class was generated from the following file:
Modified on Wed Apr 17 13:09:48 2024 by rev. 669887