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NCBI C++ ToolKit: CAlnVecMultiDataSource Class Reference
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CAlnVecMultiDataSource - implementation of IAlnMultiDataSource for CAlnVec-based alignments. More...
#include <gui/widgets/aln_multiple/alnvec_multi_ds.hpp>
CAlnVecMultiDataSource (objects::CScope &scope) ~CAlnVecMultiDataSource () virtual void Init (const objects::CSeq_annot &annot, bool sync=false, bool select_anchor=false) virtual void Init (const objects::CBioseq_Handle &handle, bool sync=false, bool select_anchor=false) virtual void Init (const vector< CConstRef< objects::CSeq_align > > &aligns, bool sync=false, bool select_anchor=false) void OnAppJobNotification (CEvent *evt) virtual bool IsEmpty () const virtual void SetGapChar (TResidue gap_char) virtual IAlnExplorer::EAlignType GetAlignType () const virtual int GetConsensusRow () const returns index of the Consensus row or -1 if it doesn't exist More...
virtual bool CanCreateConsensus () void CreateConsensus (vector< string > &consens) const virtual void CreateConsensus () virtual void SetCreateConsensus (bool b) virtual TNumrow GetNumRows (void) const number of rows in alignment More...
virtual TSeqPos GetAlnStart (void) const virtual TSeqPos GetAlnStop (void) const virtual TSeqPos GetSeqStart (TNumrow row) const virtual TSeqPos GetSeqStop (TNumrow row) const virtual bool IsSetAnchor (void) const Anchoring methods. More...
virtual TNumrow GetAnchor (void) const virtual bool CanChangeAnchor (void) const virtual bool SetAnchor (TNumrow anchor) virtual bool UnsetAnchor (void) virtual bool CanGetId (TNumrow row) const virtual const objects::CSeq_id & GetSeqId (TNumrow row) const virtual const objects::CBioseq_Handle & GetBioseqHandle (TNumrow row) const virtual TSeqPos GetBaseWidth (TNumrow row) const virtual int GetGenCode (IAlnExplorer::TNumrow row) const virtual bool IsPositiveStrand (TNumrow row) const virtual bool IsNegativeStrand (TNumrow row) const virtual TSignedSeqPos GetSeqPosFromAlnPos (TNumrow for_row, TSeqPos aln_pos, TSearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const virtual TSignedSeqPos GetAlnPosFromSeqPos (TNumrow row, TSeqPos seq_pos, TSearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const virtual string & GetAlnSeqString (TNumrow row, string &buffer, const IAlnExplorer::TSignedRange &aln_range) const virtual const IAlignRowHandle * GetRowHandle (TNumrow row) const virtual IAlnSegmentIterator * CreateSegmentIterator (TNumrow row, const IAlnExplorer::TSignedRange &range, IAlnSegmentIterator::EFlags flags) const virtual void GetAlnFromSeq (TNumrow row, const TRangeColl &seq_coll, TRangeColl &aln_coll) const virtual void GetSeqFromAln (TNumrow row, const TRangeColl &aln_coll, TRangeColl &seq_coll) const virtual bool IsDataReadSync () const void CollectAlignStats (const TSignedSeqRange &range, TStatGraphs &graphs, bool translate_sequence=false) const CDataChangeNotifier () CUIDataSource. More...
virtual ~CDataChangeNotifier () virtual void SetListener (IListener *pListener) Subscribe a new listener. More...
virtual IListener * GetListener () virtual void NotifyListener (CUpdate &update) CObjectEx (void) virtual ~CObjectEx (void) CObject (void) Constructor. More...
CObject (const CObject &src) Copy constructor. More...
virtual ~CObject (void) Destructor. More...
CObject & operator= (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...
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 CWeakObject (void) virtual ~CWeakObject (void) CPtrToObjectProxy * GetPtrProxy (void) const Get pointer to proxy object containing pointer to this object. More...
virtual ~IScoringAlignment () virtual bool IsMixedAlign () const New interfaces to handle alignemnt with mixed type (protein-to-genomic) To make them backward compatible, they have default implementation. 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 TListeners * GetListeners (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...
typedef IAlnExplorer::TNumrow TNumrow typedef IAlnExplorer::TResidue TResidue typedef IAlnExplorer::ESearchDirection TSearchDirection typedef CRangeCollection< TSeqPos > TRangeColl using TStatGraphs = map< char, vector< unsigned > > enum EUpdateType { eChanged , eProgressReport , eError } enum EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern } Control filling of newly allocated memory. More...
typedef CObjectCounterLocker TLockerType Default locker type for CRef. More...
typedef atomic< Uint8 > TCounter 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, TListeners > TPools typedef list< AutoPtr< SPostRequest > > TPostRequests typedef std::map< CEventHandler *, int > THandlerToCount typedef void(* FOnPostCallback) () 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
CAlnVecMultiDataSource - implementation of IAlnMultiDataSource for CAlnVec-based alignments.
Definition at line 51 of file alnvec_multi_ds.hpp.
◆ THandleVector ◆ CAlnVecMultiDataSource() [1/2] CAlnVecMultiDataSource::CAlnVecMultiDataSource ( objects::CScope & scope ) ◆ ~CAlnVecMultiDataSource() CAlnVecMultiDataSource::~CAlnVecMultiDataSource ( ) ◆ CAlnVecMultiDataSource() [2/2] ◆ CanChangeAnchor() bool CAlnVecMultiDataSource::CanChangeAnchor ( void ) const virtual ◆ CanCreateConsensus() bool CAlnVecMultiDataSource::CanCreateConsensus ( ) virtual ◆ CanGetId() bool CAlnVecMultiDataSource::CanGetId ( TNumrow row ) const virtual ◆ CreateConsensus() [1/2] void CAlnVecMultiDataSource::CreateConsensus ( void ) virtual ◆ CreateConsensus() [2/2] void CAlnVecMultiDataSource::CreateConsensus ( vector< string > & consens ) const ◆ CreateSegmentIterator() ◆ DECLARE_EVENT_MAP() CAlnVecMultiDataSource::DECLARE_EVENT_MAP ( ) protected ◆ GetAlignType()
Implements IAlnMultiDataSource.
Definition at line 427 of file alnvec_multi_ds.cpp.
References CSeq_inst_Base::eMol_aa, ERR_POST, Error(), IAlnExplorer::fDNA, IAlnExplorer::fInvalid, IAlnExplorer::fMixed, IAlnExplorer::fProtein, GetBioseqHandle(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetMol(), and m_AlnVec.
◆ GetAlnFromSeq() ◆ GetAlnPosFromSeqPos() ◆ GetAlnSeqString() ◆ GetAlnStart() TSeqPos CAlnVecMultiDataSource::GetAlnStart ( void ) const virtual ◆ GetAlnStop() TSeqPos CAlnVecMultiDataSource::GetAlnStop ( void ) const virtual ◆ GetAnchor() ◆ GetBaseWidth() ◆ GetBioseqHandle() ◆ GetConsensusRow() ◆ GetGenCode() ◆ GetNumRows() ◆ GetRowHandle() ◆ GetSeqFromAln() ◆ GetSeqId() ◆ GetSeqPosFromAlnPos() ◆ GetSeqStart() ◆ GetSeqStop() ◆ Init() [1/3] void CAlnVecMultiDataSource::Init ( const objects::CBioseq_Handle & handle, bool sync = false, bool select_anchor = false ) virtual ◆ Init() [2/3] void CAlnVecMultiDataSource::Init ( const objects::CSeq_annot & annot, bool sync = false, bool select_anchor = false ) virtual ◆ Init() [3/3] ◆ IsDataReadSync() virtual bool CAlnVecMultiDataSource::IsDataReadSync ( ) const inlinevirtual ◆ IsEmpty() bool CAlnVecMultiDataSource::IsEmpty ( void ) const virtual ◆ IsNegativeStrand() bool CAlnVecMultiDataSource::IsNegativeStrand ( TNumrow row ) const virtual ◆ IsPositiveStrand() bool CAlnVecMultiDataSource::IsPositiveStrand ( TNumrow row ) const virtual ◆ IsSetAnchor() bool CAlnVecMultiDataSource::IsSetAnchor ( void ) const virtual ◆ OnAppJobNotification() void CAlnVecMultiDataSource::OnAppJobNotification ( CEvent * evt )
Definition at line 317 of file alnvec_multi_ds.cpp.
References _ASSERT, IAppJob::eCanceled, CDataChangeNotifier::eChanged, IAppJob::eCompleted, CDataChangeNotifier::eError, IAppJob::eFailed, CDataChangeNotifier::eProgressReport, ERR_POST, IAppJob::eRunning, CAppJobNotification::GetError(), CAppJobNotification::GetJobID(), CRef< C, Locker >::GetPointer(), CAppJobNotification::GetProgress(), CAppJobNotification::GetResult(), CAppJobNotification::GetState(), CBuildAlnVecResult::m_AlnVec, m_Job, m_JobID, CDataChangeNotifier::NotifyListener(), CRef< C, Locker >::Reset(), and x_Assign().
◆ operator=() ◆ s_CleanScope() void CAlnVecMultiDataSource::s_CleanScope ( ) static ◆ SetAnchor() bool CAlnVecMultiDataSource::SetAnchor ( TNumrow anchor ) virtual ◆ SetCreateConsensus() virtual void CAlnVecMultiDataSource::SetCreateConsensus ( bool b ) inlinevirtual ◆ SetGapChar() void CAlnVecMultiDataSource::SetGapChar ( TResidue gap_char ) virtual ◆ UnsetAnchor() bool CAlnVecMultiDataSource::UnsetAnchor ( void ) virtual ◆ x_Assign() void CAlnVecMultiDataSource::x_Assign ( objects::CAlnVec & aln_vec ) protectedvirtual
Definition at line 365 of file alnvec_multi_ds.cpp.
References CreateConsensus(), m_AlnVec, m_ConsRowIndex, m_CreateConsensus, m_Handles, CRef< C, Locker >::Reset(), row, SetGapChar(), x_ClearHandles(), and x_CreateHandles().
Referenced by OnAppJobNotification().
◆ x_ClearHandles() void CAlnVecMultiDataSource::x_ClearHandles ( ) protectedvirtual ◆ x_CreateHandles() void CAlnVecMultiDataSource::x_CreateHandles ( ) protectedvirtual ◆ x_DeleteJob() void CAlnVecMultiDataSource::x_DeleteJob ( ) protectedvirtual ◆ x_IsJobRunning() bool CAlnVecMultiDataSource::x_IsJobRunning ( ) protectedvirtual ◆ x_OnJobProgress() ◆ m_AlnVec CRef<objects::CAlnVec> CAlnVecMultiDataSource::m_AlnVec protected
Definition at line 158 of file alnvec_multi_ds.hpp.
Referenced by CreateConsensus(), GetAlignType(), GetAlnFromSeq(), GetAlnPosFromSeqPos(), GetAlnSeqString(), GetAlnStart(), GetAlnStop(), GetAnchor(), GetBaseWidth(), GetBioseqHandle(), GetNumRows(), GetSeqFromAln(), GetSeqId(), GetSeqPosFromAlnPos(), GetSeqStart(), GetSeqStop(), IsEmpty(), IsNegativeStrand(), IsPositiveStrand(), IsSetAnchor(), SetAnchor(), SetGapChar(), UnsetAnchor(), x_Assign(), and x_CreateHandles().
◆ m_ConsRowIndex int CAlnVecMultiDataSource::m_ConsRowIndex protected ◆ m_CreateConsensus bool CAlnVecMultiDataSource::m_CreateConsensus protected ◆ m_Handles ◆ m_isDataReadSync bool CAlnVecMultiDataSource::m_isDataReadSync private ◆ m_Job ◆ m_JobID int CAlnVecMultiDataSource::m_JobID protected ◆ m_Scope
The documentation for this class was generated from the following files:
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