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CScoreCache Class Reference

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#include <gui/widgets/aln_score/aln_scoring.hpp>

+ Inheritance diagram for CScoreCache:
+ Collaboration diagram for CScoreCache:

Classes

class  IListener
 

Public Types

typedef IAlnExplorer::TNumrow TNumrow
 
typedef IScoringMethod::TScore TScore
 
typedef IScoringMethod::TScoreVector TScoreVector
 
typedef IScoringMethod::TScoreColl TScoreColl
 
- 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 CEventHandler
enum  EDispatch { eDispatch_SelfOnly , eDispatch_AllHandlers , eDispatch_FirstHandler , eDispatch_Default = eDispatch_AllHandlers }
 enum controlling dispatching strategies More...
 
enum  EPoolName {
  ePool_Default = 0 , ePool_Parent , ePool_Child , ePool_Sibling ,
  ePool_NextAvailable
}
 Identifiers for standard pools. More...
 
typedef vector< CEventHandler * > TListeners
 
typedef map< int, TListenersTPools
 
typedef list< AutoPtr< SPostRequest > > TPostRequests
 
typedef std::map< CEventHandler *, intTHandlerToCount
 
typedef void(* FOnPostCallback) ()
 

Public Member Functions

 CScoreCache ()
 CScoreCache. More...
 
 ~CScoreCache ()
 
void SetListener (IListener *listener)
 
void EnableBackgoundProcessing (bool en)
 
void SetGradNumber (int grad_n)
 Sets the number of score gradations. More...
 
void SetScoringMethod (IScoringMethod *method)
 
IScoringMethodGetScoringMethod ()
 
const IScoringMethodGetScoringMethod () const
 
void SetAlignment (const IScoringAlignment *aln)
 
const IScoringAlignmentGetAlignment () const
 
void ResetScores ()
 
void CalculateScores (const TSeqRange &range=TSeqRange::GetEmpty())
 Recalculate scores using current method; resets scores if no method is selected. More...
 
bool HasScores () const
 returns "true" if CalculateScores() did produce results More...
 
const TScoreCollGetScores (TNumrow row) const
 
const CRgbaColorGetColorForScore (TScore score, IScoringMethod::EColorType type) const
 
const CRgbaColorGetColorForNoScore (IScoringMethod::EColorType type) const
 
void OnAJNotification (CEvent *evt)
 
- 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 CEventHandler
 CEventHandler ()
 CEventHandler. More...
 
virtual ~CEventHandler ()
 
virtual void AddListener (CEventHandler *listener, int pool_name=ePool_Default)
 Add a listener. More...
 
virtual void RemoveListener (CEventHandler *listener)
 Remove a listener. More...
 
virtual void RemoveAllListeners (void)
 
virtual bool HasListener (CEventHandler *listener, int pool_name=ePool_Default) const
 returns "true" if the given listener belongs to the specified pool More...
 
virtual const TListenersGetListeners (int pool_name=ePool_Default) const
 returns a set of listeners fro the specified pool More...
 
virtual bool OnEvent (CEvent *evt)
 Processes en event. Returns "true" if event has been processed. More...
 
virtual bool Dispatch (CEvent *evt, EDispatch disp_how=eDispatch_Default, int pool_name=ePool_Default)
 Dispatches an event to the listeners (but does not handle it). More...
 
virtual bool Send (CEvent *evt, EDispatch disp_how=eDispatch_Default, int pool_name=ePool_Default)
 Sends an event synchronously. More...
 
virtual bool Send (CEvent *evt, int pool_name)
 
void Post (CRef< CEvent > evt, EDispatch disp_how=eDispatch_Default, int pool_name=ePool_Default)
 Handles an event asynchronously (process and/or dispatch). More...
 

Protected Types

typedef vector< TScoreCollTScoreCollVector
 

Protected Member Functions

 DECLARE_EVENT_MAP ()
 
bool x_IsJobRunning ()
 returns true if CScoreCache launched the job and it has not finished yet (it may have finished, but CScoreCache has not yet been notified) More...
 
void x_DeleteJob ()
 stop the job and destriy it More...
 
void x_OnJobCompleted (CAppJobNotification &notn)
 
void x_OnJobFailed (CAppJobNotification &notn)
 
void x_OnJobCanceled (CAppJobNotification &notn)
 
void x_OnJobProgress (CAppJobNotification &notn)
 
bool x_TransferResults (CObject *result)
 
- 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 Member Functions inherited from CEventHandler
virtual const SEvtMapGetEventMap () const
 
void x_DeclareDead ()
 Removes itself unavailable for async event delivery. More...
 
void x_AddListenerToPool (CEventHandler *listener, int pool_name)
 

Protected Attributes

TScoreCollVectorm_ScoreColls
 
IListenerm_Listener
 score storage More...
 
CScoringParams m_Params
 
bool m_EnBgProcessing
 
int m_JobID
 
CRef< CScoringJobm_Job
 
bool m_HasScores
 
CRgbaColor m_NoScoreColor
 
- Protected Attributes inherited from CEventHandler
TPools m_Pools
 

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 Member Functions inherited from CEventHandler
static bool HandlePostRequest ()
 
static void ClearPostQueue ()
 erases all events from the queue More...
 
static void DestroyPostQueue ()
 
- 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...
 
- Static Protected Attributes inherited from CEventHandler
static const SEvtMap sm_EvtMap
 

Detailed Description

Definition at line 153 of file aln_scoring.hpp.

Member Typedef Documentation

◆ TNumrow

Definition at line 156 of file aln_scoring.hpp.

◆ TScore

Definition at line 157 of file aln_scoring.hpp.

◆ TScoreColl

Definition at line 159 of file aln_scoring.hpp.

◆ TScoreCollVector

typedef vector<TScoreColl> CScoreCache::TScoreCollVector
protected

Definition at line 219 of file aln_scoring.hpp.

◆ TScoreVector

Definition at line 158 of file aln_scoring.hpp.

Constructor & Destructor Documentation

◆ CScoreCache()

CScoreCache::CScoreCache ( )

CScoreCache.

Definition at line 63 of file aln_scoring.cpp.

References m_ScoreColls.

◆ ~CScoreCache()

CScoreCache::~CScoreCache ( )

Definition at line 73 of file aln_scoring.cpp.

References m_ScoreColls, x_DeleteJob(), and x_IsJobRunning().

Member Function Documentation

◆ CalculateScores()

void CScoreCache::CalculateScores ( const TSeqRange range = TSeqRange::GetEmpty())

Recalculate scores using current method; resets scores if no method is selected.

Calculates scores for the given CAlnVec object and saves results in form of TScoreColl objects.

Optional range parameter calculates score with the givin range only (WebMSA mode)

Definition at line 141 of file aln_scoring.cpp.

References CAppJobDispatcher::GetInstance(), CRef< C, Locker >::GetPointer(), CScoringJob::GetResult(), m_EnBgProcessing, m_HasScores, m_Job, m_JobID, CScoringParams::m_Method, m_Params, CScoringParams::m_VisibleRange, compile_time_bits::range(), CRef< C, Locker >::Reset(), ResetScores(), CScoringJob::Run(), CAppJobDispatcher::StartJob(), and x_TransferResults().

Referenced by CSGAlnOtherScore::CalculateScores(), CAlnMultiModel::UpdateOnDataChanged(), CAlnMultiModel::UpdateOnScoringChanged(), and CAlnMultiModel::x_UpdateOnCoordsChanged().

◆ DECLARE_EVENT_MAP()

CScoreCache::DECLARE_EVENT_MAP ( )
protected

◆ EnableBackgoundProcessing()

void CScoreCache::EnableBackgoundProcessing ( bool  en)

◆ GetAlignment()

const IScoringAlignment * CScoreCache::GetAlignment ( void  ) const
inline

Definition at line 261 of file aln_scoring.hpp.

References CScoringParams::m_Alignment, and m_Params.

Referenced by CAlnMultiModel::UpdateOnScoringChanged().

◆ GetColorForNoScore()

const CRgbaColor & CScoreCache::GetColorForNoScore ( IScoringMethod::EColorType  type) const

Definition at line 308 of file aln_scoring.cpp.

References CScoringParams::m_Method, and m_Params.

◆ GetColorForScore()

const CRgbaColor & CScoreCache::GetColorForScore ( TScore  score,
IScoringMethod::EColorType  type 
) const
inline

◆ GetScores()

const CScoreCache::TScoreColl & CScoreCache::GetScores ( TNumrow  row) const

◆ GetScoringMethod() [1/2]

IScoringMethod * CScoreCache::GetScoringMethod ( )
inline

◆ GetScoringMethod() [2/2]

const IScoringMethod * CScoreCache::GetScoringMethod ( ) const
inline

Definition at line 249 of file aln_scoring.hpp.

References CScoringParams::m_Method, and m_Params.

◆ HasScores()

bool CScoreCache::HasScores ( ) const

◆ OnAJNotification()

void CScoreCache::OnAJNotification ( CEvent evt)

◆ ResetScores()

void CScoreCache::ResetScores ( )

◆ SetAlignment()

void CScoreCache::SetAlignment ( const IScoringAlignment aln)
inline

◆ SetGradNumber()

void CScoreCache::SetGradNumber ( int  grad_n)

Sets the number of score gradations.

Definition at line 103 of file aln_scoring.cpp.

References _ASSERT, CScoringParams::m_GradNumber, and m_Params.

Referenced by CAlnMultiModel::CAlnMultiModel(), and CSGAlignmentDS::InitAlignScoreCache().

◆ SetListener()

&CScoreCache::OnAJNotification void CScoreCache::SetListener ( IListener listener)

◆ SetScoringMethod()

void CScoreCache::SetScoringMethod ( IScoringMethod method)

◆ x_DeleteJob()

void CScoreCache::x_DeleteJob ( )
protected

◆ x_IsJobRunning()

bool CScoreCache::x_IsJobRunning ( )
protected

returns true if CScoreCache launched the job and it has not finished yet (it may have finished, but CScoreCache has not yet been notified)

Definition at line 197 of file aln_scoring.cpp.

References CRef< C, Locker >::GetPointer(), m_Job, and NULL.

Referenced by SetScoringMethod(), and ~CScoreCache().

◆ x_OnJobCanceled()

void CScoreCache::x_OnJobCanceled ( CAppJobNotification notn)
protected

◆ x_OnJobCompleted()

void CScoreCache::x_OnJobCompleted ( CAppJobNotification notn)
protected

◆ x_OnJobFailed()

void CScoreCache::x_OnJobFailed ( CAppJobNotification notn)
protected

◆ x_OnJobProgress()

void CScoreCache::x_OnJobProgress ( CAppJobNotification notn)
protected

◆ x_TransferResults()

bool CScoreCache::x_TransferResults ( CObject result)
protected

Member Data Documentation

◆ m_EnBgProcessing

bool CScoreCache::m_EnBgProcessing
protected

◆ m_HasScores

bool CScoreCache::m_HasScores
protected

Definition at line 229 of file aln_scoring.hpp.

Referenced by CalculateScores(), HasScores(), ResetScores(), and x_TransferResults().

◆ m_Job

CRef<CScoringJob> CScoreCache::m_Job
protected

◆ m_JobID

int CScoreCache::m_JobID
protected

◆ m_Listener

IListener* CScoreCache::m_Listener
protected

score storage

Definition at line 222 of file aln_scoring.hpp.

Referenced by x_DeleteJob(), x_OnJobCanceled(), x_OnJobCompleted(), x_OnJobFailed(), and x_OnJobProgress().

◆ m_NoScoreColor

CRgbaColor CScoreCache::m_NoScoreColor
protected

Definition at line 230 of file aln_scoring.hpp.

◆ m_Params

CScoringParams CScoreCache::m_Params
protected

◆ m_ScoreColls

TScoreCollVector* CScoreCache::m_ScoreColls
protected

Definition at line 220 of file aln_scoring.hpp.

Referenced by CScoreCache(), GetScores(), ResetScores(), x_TransferResults(), and ~CScoreCache().


The documentation for this class was generated from the following files:
Modified on Fri Mar 01 10:05:57 2024 by modify_doxy.py rev. 669887