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NCBI C++ ToolKit: CAlnVecGraphicDataSource Class Reference
CAlnVecGraphicDataSource (const objects::CAlnVec &aln_mgr) ~CAlnVecGraphicDataSource () virtual IAlnExplorer::EAlignType GetAlignType () const virtual TNumrow GetNumRows (void) const virtual TSeqPos GetAlnStart (void) const virtual TSeqPos GetAlnStop (void) const virtual TSeqPos GetSeqStart (TNumrow row) const virtual TSeqPos GetSeqStop (TNumrow row) const virtual TSignedRange GetAlnRange (void) const virtual TSignedRange GetSeqAlnRange (TNumrow row) const virtual TSeqPos GetSeqLength (TNumrow row) const virtual TSeqPos GetBaseWidth (TNumrow row) const virtual TNumrow GetAnchor (void) const virtual const objects::CSeq_id & GetSeqId (TNumrow row) const virtual const objects::CBioseq_Handle & GetBioseqHandle (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, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const virtual string & GetAlnSeqString (TNumrow row, string &buffer, const TSignedRange &aln_range) const virtual IAlnSegmentIterator * CreateSegmentIterator (TNumrow row, const TSignedRange &range, IAlnSegmentIterator::EFlags flags) const virtual TSignedSeqPos GetSeqPosFromSeqPos (TNumrow for_row, TNumrow row, TSeqPos seq_pos) const virtual EPolyATail HasPolyATail () const Check if there is any unaligned polyA tail. More...
virtual bool HasCigar () const Check if there is a CIGAR string. More...
virtual const TCigar * GetCigar () const Get CIGAR vector. More...
virtual string & GetSeqString (string &buffer, TNumrow row, const TSignedRange &seq_rng, const TSignedRange &aln_rng, bool anchor_direct) const Get sequence string for a given row in sequence range. More...
virtual TSignedSeqPos AlnPosToNativeSeqPos (TNumrow row, TSignedSeqPos aln_pos) const Convert alignment (genomic) coordinate on the selected row to real sequence position. More...
virtual TSignedSeqPos NativeSeqPosToAlnPos (TNumrow row, TSignedSeqPos seq_pos, int frame=0) const Convert sequence position to alignment (genomic) coordinate. More...
virtual IAlnExplorer::TNumrow GetQuery () const virtual void GetUnalignedTails (TSignedSeqPos &start_tail, TSignedSeqPos &end_tail, bool clipped=true) const const TSignedSeqPos GetUnalignedTailLimit () const virtual TSeqRange GetAlnRangeWithTails () const virtual bool IsCigarUnambiguous () const Check if cigar doesn't have ambiguous M's. More...
virtual bool IsSimplified () const virtual bool IsRegular () const bool IsPartial () const int GetPartialFlags () const void SetPartialFlags (int partial_flags) virtual bool IsColoringAvailable () const virtual const TCigarPair * GetCigarAtAlnPos (int row, TSignedSeqPos pos) const int GetGenCode (IAlnExplorer::TNumrow row) const void SetCrossOrigin (bool value) bool IsCrossOrigin () const void SetCrossOriginRange (const string &ranges) const string & GetCrossOriginRanges () const 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...
enum EPolyATail { ePolyA_Yes , ePolyA_No , ePolyA_Unknown } Cetantiy of having unaligned polyA tail. More...
enum ECigarOp {
eCigar_M = 'M' , eCigar_I = 'I' , eCigar_D = 'D' , eCigar_N = 'N' ,
eCigar_S = 'S' , eCigar_H = 'H' , eCigar_P = 'P' , eCigar_Eq = '=' ,
eCigar_X = 'X'
} enum EPartialAlignment { ePartial_None = 0 , ePartial_5prime = 1 << 0 , ePartial_3prime = 1 << 1 } datasource may point to an alignment that was modified from the original actual alignment it's done to optimize rendering. More...
typedef pair< ECigarOp, size_t > TCigarPair typedef vector< TCigarPair > TCigar typedef IAlnExplorer::TSignedRange TSignedRange typedef IAlnExplorer::TNumrow TNumrow typedef IAlnExplorer::TResidue TResidue typedef IAlnExplorer::ESearchDirection TSearchDirection typedef CRangeCollection< TSeqPos > TRangeColl 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 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 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 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...
virtual void DeleteThis (void) Virtual method "deleting" this object. More...
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 SEvtMap * GetEventMap () const void x_DeclareDead () Removes itself unavailable for async event delivery. More...
void x_AddListenerToPool (CEventHandler *listener, int pool_name) Static Protected Attributes inherited from CEventHandler static const SEvtMap sm_EvtMap
CAlnVecGraphicDataSource - implementation of CAlnGraphicDataSource for CAlnVec-based alignments.
Definition at line 48 of file alnvec_graphic_ds.hpp.
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