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CMMAligner Class Reference

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#include <algo/align/nw/mm_aligner.hpp>

+ Inheritance diagram for CMMAligner:
+ Collaboration diagram for CMMAligner:

Public Member Functions

 CMMAligner ()
 
 CMMAligner (const char *seq1, size_t len1, const char *seq2, size_t len2, const SNCBIPackedScoreMatrix *scoremat=0)
 
 CMMAligner (const string &seq1, const string &seq2, const SNCBIPackedScoreMatrix *scoremat=0)
 
virtual ~CMMAligner ()
 
- Public Member Functions inherited from CNWAligner
 CNWAligner (void)
 
 CNWAligner (const char *seq1, size_t len1, const char *seq2, size_t len2, const SNCBIPackedScoreMatrix *scoremat=0)
 
 CNWAligner (const string &seq1, const string &seq2, const SNCBIPackedScoreMatrix *scoremat=0)
 
virtual ~CNWAligner (void)
 
virtual TScore Run (void)
 
CRef< objects::CSeq_align > Run (objects::CScope &scope, const objects::CSeq_loc &loc1, const objects::CSeq_loc &loc2, bool trim_end_gaps=true)
 
CRef< objects::CSeq_align > Run (objects::CScope &scope, const objects::CSeq_id &id1, const objects::CSeq_id &id2, bool trim_end_gaps=true)
 
virtual void SetSequences (const char *seq1, size_t len1, const char *seq2, size_t len2, bool verify=true)
 
void SetSequences (const string &seq1, const string &seq2, bool verify=true)
 
void SetScoreMatrix (const SNCBIPackedScoreMatrix *scoremat)
 
const SNCBIFullScoreMatrixGetScoreMatrix (void) const
 
void SetWm (TScore value)
 
void SetWms (TScore value)
 
void SetWg (TScore value)
 
void SetWs (TScore value)
 
void SetEndSpaceFree (bool Left1, bool Right1, bool Left2, bool Right2)
 
void SetSmithWaterman (bool SW)
 
void SetGapPreference (EGapPreference p)
 Control preference for where to place a gap if there is a choice; default is eLater, placing the gap as late as possible. More...
 
void SetPattern (const vector< size_t > &pattern)
 
void SetSpaceLimit (const size_t &maxmem)
 
void SetProgressCallback (FProgressCallback prg_callback, void *data)
 
TScore GetWm (void) const
 
TScore GetWms (void) const
 
TScore GetWg (void) const
 
TScore GetWs (void) const
 
const char * GetSeq1 (void) const
 
size_t GetSeqLen1 (void) const
 
const char * GetSeq2 (void) const
 
size_t GetSeqLen2 (void) const
 
void GetEndSpaceFree (bool *L1, bool *R1, bool *L2, bool *R2) const
 
bool IsSmithWaterman () const
 
EGapPreference GetGapPreference () const
 
TScore GetScore (void) const
 
size_t GetSpaceLimit (void) const
 
TTranscript GetTranscript (bool reversed=true) const
 
void SetTranscript (const TTranscript &transcript)
 
string GetTranscriptString (void) const
 
void SetPositivesAsMatches (bool positives_as_matches=true)
 
bool GetPositivesAsMatches (void) const
 
size_t GetLeftSeg (size_t *q0, size_t *q1, size_t *s0, size_t *s1, size_t min_size) const
 
size_t GetRightSeg (size_t *q0, size_t *q1, size_t *s0, size_t *s1, size_t min_size) const
 
size_t GetLongestSeg (size_t *q0, size_t *q1, size_t *s0, size_t *s1) const
 
virtual size_t GetElemSize (void) const
 
virtual TScore ScoreFromTranscript (const TTranscript &transcript, size_t start1=kMax_UInt, size_t start2=kMax_UInt) const
 
void EnableMultipleThreads (bool enable=true)
 
size_t MakePattern (const size_t hit_size=100, const size_t core_size=28)
 
CRef< objects::CDense_seg > GetDense_seg (TSeqPos query_start, objects::ENa_strand query_strand, TSeqPos subj_start, objects::ENa_strand subj_strand, bool trim_end_gaps=false) const
 
CRef< objects::CDense_seg > GetDense_seg (TSeqPos query_start, objects::ENa_strand query_strand, const objects::CSeq_id &query_id, TSeqPos subj_start, objects::ENa_strand subj_strand, const objects::CSeq_id &subj_id, bool trim_end_gaps=false) const
 
- 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
 

Protected Types

enum  ETransitionType {
  eII = 0 , eDI , eGI , eID ,
  eDD , eGD , eIG , eDG ,
  eGG
}
 

Protected Member Functions

virtual TScore x_Run ()
 
void x_DoSubmatrix (const SCoordRect &submatr, list< ETranscriptSymbol >::iterator translist_pos, bool left_top, bool right_bottom)
 
void x_RunTop (const SCoordRect &rect, vector< TScore > &vE, vector< TScore > &vF, vector< TScore > &vG, vector< unsigned char > &trace, bool lt) const
 
void x_RunBtm (const SCoordRect &rect, vector< TScore > &vE, vector< TScore > &vF, vector< TScore > &vG, vector< unsigned char > &trace, bool rb) const
 
TScore x_RunTerm (const SCoordRect &rect, bool left_top, bool right_bottom, list< ETranscriptSymbol > &subpath)
 
TScore x_FindBestJ (const vector< TScore > &vEtop, const vector< TScore > &vFtop, const vector< TScore > &vGtop, const vector< TScore > &vEbtm, const vector< TScore > &vFbtm, const vector< TScore > &vGbtm, size_t &pos, ETransitionType &trans_type) const
 
size_t x_ExtendSubpath (vector< unsigned char >::const_iterator trace_it, bool direction, list< ETranscriptSymbol > &subpath) const
 
virtual bool x_CheckMemoryLimit ()
 
- Protected Member Functions inherited from CNWAligner
size_t x_CheckSequence (const char *seq, size_t len) const
 
unsigned char x_CalcFingerPrint64 (const char *beg, const char *end, size_t &err_index)
 
const char * x_FindFingerPrint64 (const char *beg, const char *end, unsigned char fingerprint, size_t size, size_t &err_index)
 
virtual TScore x_Align (SAlignInOut *data)
 
void x_DoBackTrace (const CBacktraceMatrix4 &backtrace, SAlignInOut *data)
 
virtual ETranscriptSymbol x_GetDiagTS (size_t i1, size_t i2) const
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Protected Attributes

list< ETranscriptSymbolm_TransList
 
- Protected Attributes inherited from CNWAligner
TScore m_Wm
 
TScore m_Wms
 
TScore m_Wg
 
TScore m_Ws
 
bool m_esf_L1
 
bool m_esf_R1
 
bool m_esf_L2
 
bool m_esf_R2
 
bool m_SmithWaterman
 
EGapPreference m_GapPreference
 
const char * m_abc
 
SNCBIFullScoreMatrix m_ScoreMatrix
 
bool m_ScoreMatrixInvalid
 
FProgressCallback m_prg_callback
 
SProgressInfo m_prg_info
 
bool m_terminate
 
vector< char > m_Seq1Vec
 
const char * m_Seq1
 
size_t m_SeqLen1
 
vector< char > m_Seq2Vec
 
const char * m_Seq2
 
size_t m_SeqLen2
 
TTranscript m_Transcript
 
bool m_PositivesAsMatches
 
TScore m_score
 
vector< size_t > m_guides
 
bool m_mt
 
size_t m_maxthreads
 
size_t m_MaxMem
 

Friends

class CThreadRunOnTop
 
class CThreadDoSM
 

Additional Inherited Members

- Public Types inherited from CNWAligner
enum  EGapPreference { eEarlier , eLater }
 
enum  ETranscriptSymbol {
  eTS_None = 0 , eTS_Delete = 'D' , eTS_Insert = 'I' , eTS_Match = 'M' ,
  eTS_Replace = 'R' , eTS_Intron = 'Z' , eTS_SlackDelete , eTS_SlackInsert
}
 
typedef int TScore
 
typedef bool(* FProgressCallback) (SProgressInfo *)
 
typedef vector< ETranscriptSymbolTTranscript
 
- 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...
 
- Static Public Member Functions inherited from CNWAligner
static TScore GetDefaultWm (void)
 
static TScore GetDefaultWms (void)
 
static TScore GetDefaultWg (void)
 
static TScore GetDefaultWs (void)
 
static size_t GetDefaultSpaceLimit (void)
 
- 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 60 of file mm_aligner.hpp.


The documentation for this class was generated from the following files:
Modified on Fri Jun 14 16:53:05 2024 by modify_doxy.py rev. 669887