NCBI C++ ToolKit
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Search Toolkit Book for CMMAligner
#include <algo/align/nw/mm_aligner.hpp>
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 SNCBIFullScoreMatrix & | GetScoreMatrix (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... | |
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... | |
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< ETranscriptSymbol > | m_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< ETranscriptSymbol > | TTranscript |
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< Uint8 > | TCounter |
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... | |
Definition at line 60 of file mm_aligner.hpp.