Generic Global(Needleman-Wunsch) Alignment

Collaboration diagram for Generic Global(Needleman-Wunsch) Alignment:

Classes
class	CNWAligner
struct	CNWAligner::SProgressInfo
class	CNWAligner::CBacktraceMatrix4
struct	CNWAligner::SAlignInOut
class	CBandAligner
class	CPSSMAligner
class	CHitCoverageAccumulator< THit >
class	CHitFilter< THit >
struct	CHitFilter< THit >::SHitEnd

Typedefs
typedef int	CNWAligner::TScore
typedef bool(*	CNWAligner::FProgressCallback) (SProgressInfo *)
typedef vector< ETranscriptSymbol >	CNWAligner::TTranscript
typedef CRef< THit >	CHitCoverageAccumulator< THit >::THitRef
typedef THit::TCoord	CHitCoverageAccumulator< THit >::TCoord
typedef CRef< THit >	CHitFilter< THit >::THitRef
typedef vector< THitRef >	CHitFilter< THit >::THitRefs
typedef THit::TCoord	CHitFilter< THit >::TCoord
typedef SHitEnd	CHitFilter< THit >::THitEnd
typedef multiset< THitEnd >	CHitFilter< THit >::THitEnds
typedef THitEnds::iterator	CHitFilter< THit >::THitEndsIter

Enumerations
enum	CNWAligner::EGapPreference { CNWAligner::eEarlier , CNWAligner::eLater }
enum	CNWAligner::ETranscriptSymbol {   CNWAligner::eTS_None = 0 , CNWAligner::eTS_Delete = 'D' , CNWAligner::eTS_Insert = 'I' , CNWAligner::eTS_Match = 'M' ,   CNWAligner::eTS_Replace = 'R' , CNWAligner::eTS_Intron = 'Z' , CNWAligner::eTS_SlackDelete , CNWAligner::eTS_SlackInsert }
enum	CHitFilter< THit >::EUnique_type { CHitFilter< THit >::e_Strict , CHitFilter< THit >::e_Query , CHitFilter< THit >::e_Subject }
	Multiple-sequences greedy alignment uniquification algorithm. More...

Functions
	CNWAligner::CNWAligner (void)
	CNWAligner::CNWAligner (const char *seq1, size_t len1, const char *seq2, size_t len2, const SNCBIPackedScoreMatrix *scoremat=0)
	CNWAligner::CNWAligner (const string &seq1, const string &seq2, const SNCBIPackedScoreMatrix *scoremat=0)
virtual	CNWAligner::~CNWAligner (void)
virtual TScore	CNWAligner::Run (void)
CRef< objects::CSeq_align >	CNWAligner::Run (objects::CScope &scope, const objects::CSeq_loc &loc1, const objects::CSeq_loc &loc2, bool trim_end_gaps=true)
CRef< objects::CSeq_align >	CNWAligner::Run (objects::CScope &scope, const objects::CSeq_id &id1, const objects::CSeq_id &id2, bool trim_end_gaps=true)
virtual void	CNWAligner::SetSequences (const char *seq1, size_t len1, const char *seq2, size_t len2, bool verify=true)
void	CNWAligner::SetSequences (const string &seq1, const string &seq2, bool verify=true)
void	CNWAligner::SetScoreMatrix (const SNCBIPackedScoreMatrix *scoremat)
const SNCBIFullScoreMatrix &	CNWAligner::GetScoreMatrix (void) const
void	CNWAligner::SetWm (TScore value)
void	CNWAligner::SetWms (TScore value)
void	CNWAligner::SetWg (TScore value)
void	CNWAligner::SetWs (TScore value)
void	CNWAligner::SetEndSpaceFree (bool Left1, bool Right1, bool Left2, bool Right2)
void	CNWAligner::SetSmithWaterman (bool SW)
void	CNWAligner::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	CNWAligner::SetPattern (const vector< size_t > &pattern)
void	CNWAligner::SetSpaceLimit (const size_t &maxmem)
	CNWAligner::SProgressInfo::SProgressInfo (void)
void	CNWAligner::SetProgressCallback (FProgressCallback prg_callback, void *data)
static TScore	CNWAligner::GetDefaultWm (void)
static TScore	CNWAligner::GetDefaultWms (void)
static TScore	CNWAligner::GetDefaultWg (void)
static TScore	CNWAligner::GetDefaultWs (void)
TScore	CNWAligner::GetWm (void) const
TScore	CNWAligner::GetWms (void) const
TScore	CNWAligner::GetWg (void) const
TScore	CNWAligner::GetWs (void) const
const char *	CNWAligner::GetSeq1 (void) const
size_t	CNWAligner::GetSeqLen1 (void) const
const char *	CNWAligner::GetSeq2 (void) const
size_t	CNWAligner::GetSeqLen2 (void) const
void	CNWAligner::GetEndSpaceFree (bool *L1, bool *R1, bool *L2, bool *R2) const
bool	CNWAligner::IsSmithWaterman () const
EGapPreference	CNWAligner::GetGapPreference () const
TScore	CNWAligner::GetScore (void) const
size_t	CNWAligner::GetSpaceLimit (void) const
static size_t	CNWAligner::GetDefaultSpaceLimit (void)
TTranscript	CNWAligner::GetTranscript (bool reversed=true) const
void	CNWAligner::SetTranscript (const TTranscript &transcript)
string	CNWAligner::GetTranscriptString (void) const
void	CNWAligner::SetPositivesAsMatches (bool positives_as_matches=true)
bool	CNWAligner::GetPositivesAsMatches (void) const
size_t	CNWAligner::GetLeftSeg (size_t *q0, size_t *q1, size_t *s0, size_t *s1, size_t min_size) const
size_t	CNWAligner::GetRightSeg (size_t *q0, size_t *q1, size_t *s0, size_t *s1, size_t min_size) const
size_t	CNWAligner::GetLongestSeg (size_t *q0, size_t *q1, size_t *s0, size_t *s1) const
virtual size_t	CNWAligner::GetElemSize (void) const
virtual TScore	CNWAligner::ScoreFromTranscript (const TTranscript &transcript, size_t start1=kMax_UInt, size_t start2=kMax_UInt) const
void	CNWAligner::EnableMultipleThreads (bool enable=true)
size_t	CNWAligner::MakePattern (const size_t hit_size=100, const size_t core_size=28)
CRef< objects::CDense_seg >	CNWAligner::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 >	CNWAligner::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
size_t	CNWAligner::x_CheckSequence (const char *seq, size_t len) const
virtual bool	CNWAligner::x_CheckMemoryLimit (void)
unsigned char	CNWAligner::x_CalcFingerPrint64 (const char *beg, const char *end, size_t &err_index)
const char *	CNWAligner::x_FindFingerPrint64 (const char *beg, const char *end, unsigned char fingerprint, size_t size, size_t &err_index)
virtual TScore	CNWAligner::x_Run (void)
virtual TScore	CNWAligner::x_Align (SAlignInOut *data)
	CNWAligner::CBacktraceMatrix4::CBacktraceMatrix4 (size_t dim)
	CNWAligner::CBacktraceMatrix4::~CBacktraceMatrix4 ()
void	CNWAligner::CBacktraceMatrix4::SetAt (size_t i, Uint1 v)
void	CNWAligner::CBacktraceMatrix4::SetBestPos (size_t k)
size_t	CNWAligner::CBacktraceMatrix4::BestPos () const
void	CNWAligner::CBacktraceMatrix4::SetBestScore (TNCBIScore score)
TNCBIScore	CNWAligner::CBacktraceMatrix4::BestScore () const
void	CNWAligner::CBacktraceMatrix4::Purge (size_t i)
Uint1	CNWAligner::CBacktraceMatrix4::operator[] (size_t i) const
void	CNWAligner::x_DoBackTrace (const CBacktraceMatrix4 &backtrace, SAlignInOut *data)
virtual ETranscriptSymbol	CNWAligner::x_GetDiagTS (size_t i1, size_t i2) const
void	CNWAligner::x_SWDoBackTrace (const CBacktraceMatrix4 &backtrace, SAlignInOut *data)
	CNWAligner::SAlignInOut::SAlignInOut ()
	CNWAligner::SAlignInOut::SAlignInOut (size_t offset1, size_t len1, bool esfL1, bool esfR1, size_t offset2, size_t len2, bool esfL2, bool esfR2)
size_t	CNWAligner::SAlignInOut::GetSpace (void) const
void	CNWAligner::SAlignInOut::FillEdgeGaps (size_t len, bool seq1_gap_fist)
static bool	CNWAligner::SAlignInOut::PSpace (const SAlignInOut *p1, const SAlignInOut *p2)
	CBandAligner::CBandAligner (size_t band=0)
	CBandAligner::CBandAligner (const char *seq1, size_t len1, const char *seq2, size_t len2, const SNCBIPackedScoreMatrix *scoremat=0, size_t band=0)
	CBandAligner::CBandAligner (const string &seq1, const string &seq2, const SNCBIPackedScoreMatrix *scoremat=0, size_t band=0)
virtual	CBandAligner::~CBandAligner (void)
void	CBandAligner::SetBand (size_t band)
void	CBandAligner::SetShift (Uint1 where, size_t offset)
size_t	CBandAligner::GetBand (void) const
pair< Uint1, size_t >	CBandAligner::GetShift (void) const
virtual TScore	CBandAligner::x_Align (CNWAligner::SAlignInOut *data)
void	CBandAligner::x_DoBackTrace (const CBacktraceMatrix4 &backtrace, CNWAligner::SAlignInOut *data)
void	CBandAligner::x_CheckParameters (const SAlignInOut *data) const
virtual bool	CBandAligner::x_CheckMemoryLimit (void)
	CPSSMAligner::CPSSMAligner ()
	CPSSMAligner::CPSSMAligner (const CNWAligner::TScore **pssm1, size_t len1, const char *seq2, size_t len2)
	CPSSMAligner::CPSSMAligner (const double **freq1, size_t len1, const double **freq2, size_t len2, const SNCBIPackedScoreMatrix *scoremat, const int scale=1)
virtual	CPSSMAligner::~CPSSMAligner (void)
virtual CNWAligner::TScore	CPSSMAligner::Run (void)
void	CPSSMAligner::SetSequences (const char *seq1, size_t len1, const char *seq2, size_t len2, bool verify=true)
void	CPSSMAligner::SetSequences (const CNWAligner::TScore **pssm1, size_t len1, const char *seq2, size_t len2, bool verify=true)
void	CPSSMAligner::SetSequences (const double **freq1, size_t len1, const double **freq2, size_t len2, const int scale=1)
void	CPSSMAligner::SetScoreMatrix (const SNCBIPackedScoreMatrix *scoremat)
void	CPSSMAligner::SetFreqScale (const int scale)
void	CPSSMAligner::SetWg (TScore value)
void	CPSSMAligner::SetWs (TScore value)
void	CPSSMAligner::SetStartWg (TScore value)
void	CPSSMAligner::SetStartWs (TScore value)
void	CPSSMAligner::SetEndWg (TScore value)
void	CPSSMAligner::SetEndWs (TScore value)
const CNWAligner::TScore **	CPSSMAligner::GetPssm1 () const
const char *	CPSSMAligner::GetSeq1 () const
const double **	CPSSMAligner::GetFreq1 () const
const double **	CPSSMAligner::GetFreq2 () const
int	CPSSMAligner::GetFreqScale () const
TScore	CPSSMAligner::GetStartWg () const
TScore	CPSSMAligner::GetStartWs () const
TScore	CPSSMAligner::GetEndWg () const
TScore	CPSSMAligner::GetEndWs () const
SNCBIFullScoreMatrix &	CPSSMAligner::GetMatrix ()
virtual TScore	CPSSMAligner::ScoreFromTranscript (const TTranscript &transcript, size_t start1=0, size_t start2=0) const
virtual TScore	CPSSMAligner::x_Align (SAlignInOut *data)
TScore	CPSSMAligner::x_AlignProfile (SAlignInOut *data)
TScore	CPSSMAligner::x_AlignPSSM (SAlignInOut *data)
virtual ETranscriptSymbol	CPSSMAligner::x_GetDiagTS (size_t i1, size_t i2) const
	CHitCoverageAccumulator< THit >::CHitCoverageAccumulator (Uint1 where)
	Create the object; specify the accumulation sequence. More...
TCoord	CHitCoverageAccumulator< THit >::operator() (TCoord iVal, const THitRef &ph)
	Overloaded function call operator to be used with std::accumulate() More...
static TCoord	CHitFilter< THit >::s_GetCoverage (Uint1 where, typename THitRefs::const_iterator from, typename THitRefs::const_iterator to)
	Collect coverage for the range of hits on the specified source sequence. More...
static void	CHitFilter< THit >::s_GetSpan (const THitRefs &hitrefs, TCoord span[4])
	Get sequence span for a set of alignments (hits). More...
static TCoord	CHitFilter< THit >::s_GetOverlap (TCoord L1, TCoord R1, TCoord L2, TCoord R2)
static void	CHitFilter< THit >::s_RunGreedy (typename THitRefs::iterator hri_beg, typename THitRefs::iterator hri_end, THitRefs *phits_new, TCoord min_hit_len=100, double min_hit_idty=.9, TCoord margin=1, TCoord retain_overlap=0, EUnique_type unique_type=e_Strict)
static void	CHitFilter< THit >::s_MergeAbutting (typename THitRefs::iterator hri_beg, typename THitRefs::iterator hri_end, const double &maxlenfr, THitRefs *pout)
static bool	CHitFilter< THit >::s_PNullRef (const THitRef &hr)
bool	CHitFilter< THit >::SHitEnd::operator< (const SHitEnd &rhs) const
static void	CHitFilter< THit >::sx_AddMidIfNeeded (THitRef *hit, const float curscore, THitRef *container_candidate, const Uint1 where, TCoord margin, THitEnds &hit_mids)
static pair< THitEndsIter, THitEndsIter >	CHitFilter< THit >::sx_GetEndsInRange (const THitRef &hc, const TCoord *box, Uint1 where, TCoord margin, THitEnds &hit_ends)
static void	CHitFilter< THit >::sx_AddMidPoints (THitRef &h, const TCoord *outer_box, TCoord margin, THitEnds &hit_ends, vector< bool > &skip, const THitRef *hitref_firstptr)
static pair< int, Uint1 >	CHitFilter< THit >::sx_Cleave (THitRef &h, Uint1 where, TCoord cmin, TCoord cmax, TCoord min_hit_len, double &min_idty, THitRef *pnew_hit, TCoord retain_overlap)
static THitRef	CHitFilter< THit >::sx_Merge (const THitRef &lhs, const THitRef &rhs, Uint1 where)
static bool	CHitFilter< THit >::s_TrackHit (const THit &h)
static void	CHitFilter< THit >::sx_TM (Uint1 where, typename THitRefs::iterator ii_beg, typename THitRefs::iterator ii_end, const THitEnds &hit_ends, const double &maxlenfr, map< typename THitRefs::iterator, THitRef > &m)
static void	CHitFilter< THit >::sx_TestAndMerge (typename THitRefs::iterator ii_beg, typename THitRefs::iterator ii_end, const THitEnds &hit_ends, const double &maxlenfr, THitRefs *pout)

Variables
size_t	CNWAligner::SProgressInfo::m_iter_done
size_t	CNWAligner::SProgressInfo::m_iter_total
void *	CNWAligner::SProgressInfo::m_data
char	CNWAligner::SProgressInfo::m_text_buffer [1024]
TScore	CNWAligner::m_Wm
TScore	CNWAligner::m_Wms
TScore	CNWAligner::m_Wg
TScore	CNWAligner::m_Ws
bool	CNWAligner::m_esf_L1
bool	CNWAligner::m_esf_R1
bool	CNWAligner::m_esf_L2
bool	CNWAligner::m_esf_R2
bool	CNWAligner::m_SmithWaterman
EGapPreference	CNWAligner::m_GapPreference
const char *	CNWAligner::m_abc
SNCBIFullScoreMatrix	CNWAligner::m_ScoreMatrix
bool	CNWAligner::m_ScoreMatrixInvalid
FProgressCallback	CNWAligner::m_prg_callback
SProgressInfo	CNWAligner::m_prg_info
bool	CNWAligner::m_terminate
vector< char >	CNWAligner::m_Seq1Vec
const char *	CNWAligner::m_Seq1
size_t	CNWAligner::m_SeqLen1
vector< char >	CNWAligner::m_Seq2Vec
const char *	CNWAligner::m_Seq2
size_t	CNWAligner::m_SeqLen2
TTranscript	CNWAligner::m_Transcript
bool	CNWAligner::m_PositivesAsMatches
TScore	CNWAligner::m_score
vector< size_t >	CNWAligner::m_guides
bool	CNWAligner::m_mt
size_t	CNWAligner::m_maxthreads
size_t	CNWAligner::m_MaxMem
Uint1 *	CNWAligner::CBacktraceMatrix4::m_Buf
Uint1	CNWAligner::CBacktraceMatrix4::m_Elem
size_t	CNWAligner::CBacktraceMatrix4::m_BestPos
TNCBIScore	CNWAligner::CBacktraceMatrix4::m_BestScore
size_t	CNWAligner::SAlignInOut::m_offset1
size_t	CNWAligner::SAlignInOut::m_len1
bool	CNWAligner::SAlignInOut::m_esf_L1
bool	CNWAligner::SAlignInOut::m_esf_R1
size_t	CNWAligner::SAlignInOut::m_offset2
size_t	CNWAligner::SAlignInOut::m_len2
bool	CNWAligner::SAlignInOut::m_esf_L2
bool	CNWAligner::SAlignInOut::m_esf_R2
TTranscript	CNWAligner::SAlignInOut::m_transcript
size_t	CNWAligner::SAlignInOut::m_space
size_t	CBandAligner::m_band
long	CBandAligner::m_Shift
size_t	CBandAligner::m_TermK
size_t	CBandAligner::m_LastCoordSeq1
size_t	CBandAligner::m_LastCoordSeq2
static const int	CPSSMAligner::kPSSM_ColumnSize = 28
const TScore **	CPSSMAligner::m_Pssm1
const double **	CPSSMAligner::m_Freq1
const char *	CPSSMAligner::m_Seq2
const double **	CPSSMAligner::m_Freq2
int	CPSSMAligner::m_FreqScale
TScore	CPSSMAligner::m_StartWg
TScore	CPSSMAligner::m_StartWs
TScore	CPSSMAligner::m_EndWg
TScore	CPSSMAligner::m_EndWs
double	CPSSMAligner::m_DScoreMatrix [kPSSM_ColumnSize][kPSSM_ColumnSize]
Uint1	CHitCoverageAccumulator< THit >::m_Where
TCoord	CHitCoverageAccumulator< THit >::m_Finish
Uint1	CHitCoverageAccumulator< THit >::m_i1
Uint1	CHitCoverageAccumulator< THit >::m_i2
Uint1	CHitFilter< THit >::SHitEnd::m_Point
THitRef *	CHitFilter< THit >::SHitEnd::m_Ptr
TCoord	CHitFilter< THit >::SHitEnd::m_X

Friends
class	CNWAligner::CNWAlignerThread_Align
ostream &	CHitFilter< THit >::SHitEnd::operator<< (ostream &ostr, const SHitEnd &he)

Detailed Description

Typedef Documentation

FProgressCallback

typedef bool(* CNWAligner::FProgressCallback) (SProgressInfo *)

Definition at line 155 of file nw_aligner.hpp.

TCoord [1/2]

template<class THit >

typedef THit::TCoord CHitCoverageAccumulator< THit >::TCoord

Definition at line 60 of file hit_filter.hpp.

TCoord [2/2]

template<class THit >

typedef THit::TCoord CHitFilter< THit >::TCoord

Definition at line 126 of file hit_filter.hpp.

THitEnd

template<class THit >

typedef SHitEnd CHitFilter< THit >::THitEnd

protected

Definition at line 616 of file hit_filter.hpp.

THitEnds

template<class THit >

typedef multiset<THitEnd> CHitFilter< THit >::THitEnds

protected

Definition at line 617 of file hit_filter.hpp.

THitEndsIter

template<class THit >

typedef THitEnds::iterator CHitFilter< THit >::THitEndsIter

protected

Definition at line 618 of file hit_filter.hpp.

THitRef [1/2]

template<class THit >

typedef CRef<THit> CHitCoverageAccumulator< THit >::THitRef

Definition at line 59 of file hit_filter.hpp.

THitRef [2/2]

template<class THit >

typedef CRef<THit> CHitFilter< THit >::THitRef

Definition at line 124 of file hit_filter.hpp.

THitRefs

template<class THit >

typedef vector<THitRef> CHitFilter< THit >::THitRefs

Definition at line 125 of file hit_filter.hpp.

TScore

typedef int CNWAligner::TScore

Definition at line 72 of file nw_aligner.hpp.

TTranscript

typedef vector<ETranscriptSymbol> CNWAligner::TTranscript

Definition at line 199 of file nw_aligner.hpp.

Enumeration Type Documentation

EGapPreference

enum CNWAligner::EGapPreference

Enumerator
eEarlier
eLater

Definition at line 74 of file nw_aligner.hpp.

ETranscriptSymbol

enum CNWAligner::ETranscriptSymbol

Enumerator
eTS_None
eTS_Delete
eTS_Insert
eTS_Match
eTS_Replace
eTS_Intron
eTS_SlackDelete
eTS_SlackInsert

Definition at line 189 of file nw_aligner.hpp.

EUnique_type

template<class THit >

enum CHitFilter::EUnique_type

Multiple-sequences greedy alignment uniquification algorithm.

Parameters

hri_begin	Input hit range start
hri_end	Input hit range stop
phits_new	An external hit vector to keep any extra hits created during the call
min_hit_len	Minimum alignment length to keep
min_hit_idty	Minimum alignment identity to keep
margin	Speed/memory trade-off (0 will use max memory; >0 will slow down a bit but
retain_overlap	Minimum length of overlaps to keep (0 = no overlaps)

Enumerator
e_Strict
e_Query
e_Subject

Definition at line 228 of file hit_filter.hpp.

Function Documentation

BestPos()

size_t CNWAligner::CBacktraceMatrix4::BestPos ( ) const

inline

Definition at line 358 of file nw_aligner.hpp.

Referenced by CNWAligner::x_SWDoBackTrace().

BestScore()

TNCBIScore CNWAligner::CBacktraceMatrix4::BestScore ( ) const

inline

Definition at line 365 of file nw_aligner.hpp.

Referenced by CNWAligner::x_SWDoBackTrace().

CBacktraceMatrix4()

CNWAligner::CBacktraceMatrix4::CBacktraceMatrix4 ( size_t  dim )

inline

Definition at line 337 of file nw_aligner.hpp.

CBandAligner() [1/3]

CBandAligner::CBandAligner	(	const char *	seq1,
		size_t	len1,
		const char *	seq2,
		size_t	len2,
		const SNCBIPackedScoreMatrix *	scoremat = 0,
		size_t	band = 0
	)

Definition at line 46 of file nw_band_aligner.cpp.

CBandAligner() [2/3]

CBandAligner::CBandAligner	(	const string &	seq1,
		const string &	seq2,
		const SNCBIPackedScoreMatrix *	scoremat = 0,
		size_t	band = 0
	)

Definition at line 57 of file nw_band_aligner.cpp.

CBandAligner() [3/3]

CBandAligner::CBandAligner ( size_t  band = 0 )

inline

Definition at line 55 of file nw_band_aligner.hpp.

CHitCoverageAccumulator()

template<class THit >

CHitCoverageAccumulator< THit >::CHitCoverageAccumulator ( Uint1  where )

inline

Create the object; specify the accumulation sequence.

Parameters

where

Accumulation source sequence (0 = query, 1 = subject)

Definition at line 66 of file hit_filter.hpp.

References CHitCoverageAccumulator< THit >::m_i1, CHitCoverageAccumulator< THit >::m_i2, and CHitCoverageAccumulator< THit >::m_Where.

CNWAligner() [1/3]

CNWAligner::CNWAligner	(	const char *	seq1,
		size_t	len1,
		const char *	seq2,
		size_t	len2,
		const SNCBIPackedScoreMatrix *	scoremat = 0
	)

Definition at line 82 of file nw_aligner.cpp.

References CNWAligner::SetScoreMatrix(), and CNWAligner::SetSequences().

CNWAligner() [2/3]

CNWAligner::CNWAligner	(	const string &	seq1,
		const string &	seq2,
		const SNCBIPackedScoreMatrix *	scoremat = 0
	)

Definition at line 112 of file nw_aligner.cpp.

References CNWAligner::SetScoreMatrix(), and CNWAligner::SetSequences().

CNWAligner() [3/3]

CNWAligner::CNWAligner

(

void

)

Definition at line 56 of file nw_aligner.cpp.

References CNWAligner::SetScoreMatrix().

CPSSMAligner() [1/3]

CPSSMAligner::CPSSMAligner

(

)

Definition at line 44 of file nw_pssm_aligner.cpp.

CPSSMAligner() [2/3]

CPSSMAligner::CPSSMAligner	(	const CNWAligner::TScore **	pssm1,
		size_t	len1,
		const char *	seq2,
		size_t	len2
	)

Definition at line 57 of file nw_pssm_aligner.cpp.

References CPSSMAligner::SetSequences().

CPSSMAligner() [3/3]

CPSSMAligner::CPSSMAligner	(	const double **	freq1,
		size_t	len1,
		const double **	freq2,
		size_t	len2,
		const SNCBIPackedScoreMatrix *	scoremat,
		const int	scale = 1
	)

Definition at line 72 of file nw_pssm_aligner.cpp.

References CPSSMAligner::SetScoreMatrix(), and CPSSMAligner::SetSequences().

EnableMultipleThreads()

void CNWAligner::EnableMultipleThreads

(

bool

enable = true

)

Definition at line 1135 of file nw_aligner.cpp.

References CSystemInfo::GetCpuCount(), CNWAligner::m_maxthreads, and CNWAligner::m_mt.

FillEdgeGaps()

void CNWAligner::SAlignInOut::FillEdgeGaps ( size_t  len, bool  seq1_gap_fist  )

inline

Definition at line 435 of file nw_aligner.hpp.

References CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, len, CNWAligner::SAlignInOut::m_len2, and CNWAligner::SAlignInOut::m_transcript.

GetBand()

size_t CBandAligner::GetBand ( void  ) const

inline

Definition at line 78 of file nw_band_aligner.hpp.

References CBandAligner::m_band.

GetDefaultSpaceLimit()

static size_t CNWAligner::GetDefaultSpaceLimit ( void  )

inlinestatic

Definition at line 184 of file nw_aligner.hpp.

Referenced by CSplignArgUtil::SetupArgDescriptions().

GetDefaultWg()

static TScore CNWAligner::GetDefaultWg ( void  )

inlinestatic

Definition at line 161 of file nw_aligner.hpp.

Referenced by CAppNWA::Init().

GetDefaultWm()

static TScore CNWAligner::GetDefaultWm ( void  )

inlinestatic

Definition at line 159 of file nw_aligner.hpp.

Referenced by CAppNWA::Init().

GetDefaultWms()

static TScore CNWAligner::GetDefaultWms ( void  )

inlinestatic

Definition at line 160 of file nw_aligner.hpp.

Referenced by CAppNWA::Init().

GetDefaultWs()

static TScore CNWAligner::GetDefaultWs ( void  )

inlinestatic

Definition at line 162 of file nw_aligner.hpp.

Referenced by CAppNWA::Init().

GetDense_seg() [1/2]

CRef<objects::CDense_seg> CNWAligner::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

GetDense_seg() [2/2]

CRef<objects::CDense_seg> CNWAligner::GetDense_seg	(	TSeqPos	query_start,
		objects::ENa_strand	query_strand,
		TSeqPos	subj_start,
		objects::ENa_strand	subj_strand,
		bool	trim_end_gaps = false
	)		const

Referenced by CInstancedAligner::x_RunMMGlobal().

GetElemSize()

virtual size_t CNWAligner::GetElemSize ( void  ) const

inlinevirtual

Reimplemented in CSplicedAligner32, and CSplicedAligner16.

Definition at line 229 of file nw_aligner.hpp.

Referenced by CNWAligner::x_CheckMemoryLimit(), and CBandAligner::x_CheckMemoryLimit().

GetEndSpaceFree()

void CNWAligner::GetEndSpaceFree	(	bool *	L1,
		bool *	R1,
		bool *	L2,
		bool *	R2
	)		const

Definition at line 890 of file nw_aligner.cpp.

References CNWAligner::m_esf_L1, CNWAligner::m_esf_L2, CNWAligner::m_esf_R1, and CNWAligner::m_esf_R2.

Referenced by CNWFormatter::MakeSegments().

GetEndWg()

TScore CPSSMAligner::GetEndWg ( ) const

inline

Definition at line 120 of file nw_pssm_aligner.hpp.

References CPSSMAligner::m_EndWg.

Referenced by CMultiAligner::x_RealignBlocks().

GetEndWs()

TScore CPSSMAligner::GetEndWs ( ) const

inline

Definition at line 121 of file nw_pssm_aligner.hpp.

References CPSSMAligner::m_EndWs.

GetFreq1()

const double** CPSSMAligner::GetFreq1 ( ) const

inline

Definition at line 114 of file nw_pssm_aligner.hpp.

References CPSSMAligner::m_Freq1.

GetFreq2()

const double** CPSSMAligner::GetFreq2 ( ) const

inline

Definition at line 115 of file nw_pssm_aligner.hpp.

References CPSSMAligner::m_Freq2.

GetFreqScale()

int CPSSMAligner::GetFreqScale ( ) const

inline

Definition at line 116 of file nw_pssm_aligner.hpp.

References CPSSMAligner::m_FreqScale.

GetGapPreference()

CNWAligner::EGapPreference CNWAligner::GetGapPreference

(

)

const

Definition at line 903 of file nw_aligner.cpp.

References CNWAligner::m_GapPreference.

GetLeftSeg()

size_t CNWAligner::GetLeftSeg	(	size_t *	q0,
		size_t *	q1,
		size_t *	s0,
		size_t *	s1,
		size_t	min_size
	)		const

Definition at line 1296 of file nw_aligner.cpp.

References CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, CNWAligner::eTS_Match, CNWAligner::eTS_Replace, g_msg_InvalidTranscriptSymbol, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CNWAligner::m_Transcript, and NCBI_THROW.

GetLongestSeg()

size_t CNWAligner::GetLongestSeg	(	size_t *	q0,
		size_t *	q1,
		size_t *	s0,
		size_t *	s1
	)		const

Definition at line 1643 of file nw_aligner.cpp.

References CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, CNWAligner::eTS_Match, CNWAligner::eTS_Replace, g_msg_InvalidTranscriptSymbol, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CNWAligner::m_Transcript, and NCBI_THROW.

Referenced by CSplign::x_SetPattern().

GetMatrix()

SNCBIFullScoreMatrix& CPSSMAligner::GetMatrix ( )

inline

Definition at line 122 of file nw_pssm_aligner.hpp.

References CNWAligner::m_ScoreMatrix.

Referenced by CMultiAligner::x_ComputeTree(), and x_ScoreFromTranscriptCore().

GetPositivesAsMatches()

bool CNWAligner::GetPositivesAsMatches ( void  ) const

inline

Definition at line 214 of file nw_aligner.hpp.

GetPssm1()

const CNWAligner::TScore** CPSSMAligner::GetPssm1 ( ) const

inline

Definition at line 112 of file nw_pssm_aligner.hpp.

References CPSSMAligner::m_Pssm1.

GetRightSeg()

size_t CNWAligner::GetRightSeg	(	size_t *	q0,
		size_t *	q1,
		size_t *	s0,
		size_t *	s1,
		size_t	min_size
	)		const

Definition at line 1556 of file nw_aligner.cpp.

References CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, CNWAligner::eTS_Match, CNWAligner::eTS_Replace, g_msg_InvalidTranscriptSymbol, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, CNWAligner::m_Transcript, and NCBI_THROW.

GetScore()

CNWAligner::TScore CNWAligner::GetScore

(

void

)

const

Definition at line 1086 of file nw_aligner.cpp.

References g_msg_NoAlignment, CNWAligner::m_score, CNWAligner::m_Transcript, and NCBI_THROW.

Referenced by CNWFormatter::AsSeqAlign().

GetScoreMatrix()

const SNCBIFullScoreMatrix& CNWAligner::GetScoreMatrix ( void  ) const

inline

Definition at line 117 of file nw_aligner.hpp.

GetSeq1() [1/2]

const char* CPSSMAligner::GetSeq1 ( void  ) const

inline

Definition at line 113 of file nw_pssm_aligner.hpp.

References CNWAligner::m_Seq1.

GetSeq1() [2/2]

const char* CNWAligner::GetSeq1 ( void  ) const

inline

Definition at line 169 of file nw_aligner.hpp.

Referenced by CSplicedAligner::CheckPreferences(), and CNWFormatter::MakeSegments().

GetSeq2()

const char* CNWAligner::GetSeq2 ( void  ) const

inline

Definition at line 171 of file nw_aligner.hpp.

Referenced by CSplicedAligner::CheckPreferences(), and CNWFormatter::MakeSegments().

GetSeqLen1()

size_t CNWAligner::GetSeqLen1 ( void  ) const

inline

Definition at line 170 of file nw_aligner.hpp.

GetSeqLen2()

size_t CNWAligner::GetSeqLen2 ( void  ) const

inline

Definition at line 172 of file nw_aligner.hpp.

Referenced by CNWFormatter::SSegment::ImproveFromRight(), CNWFormatter::SSegment::ImproveFromRight1(), and CNWFormatter::MakeSegments().

GetShift()

pair< Uint1, size_t > CBandAligner::GetShift

(

void

)

const

Definition at line 80 of file nw_band_aligner.cpp.

References CBandAligner::m_Shift, and offset.

GetSpace()

size_t CNWAligner::SAlignInOut::GetSpace ( void  ) const

inline

Definition at line 431 of file nw_aligner.hpp.

References CNWAligner::SAlignInOut::m_space.

GetSpaceLimit()

size_t CNWAligner::GetSpaceLimit ( void  ) const

inline

Definition at line 183 of file nw_aligner.hpp.

GetStartWg()

TScore CPSSMAligner::GetStartWg ( ) const

inline

Definition at line 118 of file nw_pssm_aligner.hpp.

References CPSSMAligner::m_StartWg.

Referenced by x_AlignProfileProfile().

GetStartWs()

TScore CPSSMAligner::GetStartWs ( ) const

inline

Definition at line 119 of file nw_pssm_aligner.hpp.

References CPSSMAligner::m_StartWs.

Referenced by x_AlignProfileProfile().

GetTranscript()

CNWAligner::TTranscript CNWAligner::GetTranscript

(

bool

reversed = true

)

const

Definition at line 909 of file nw_aligner.cpp.

References copy(), and CNWAligner::m_Transcript.

Referenced by CNWFormatter::AsDenseSeg(), CNWFormatter::AsText(), CNWFormatter::MakeSegments(), CMultiAligner::x_AlignInClusters(), CMultiAligner::x_AlignProfileProfile(), CMultiAligner::x_ComputeProfileRangeAlignment(), CMultiAligner::x_RealignBlocks(), CNWAligner::x_Run(), and x_ScoreFromTranscriptCore().

GetTranscriptString()

string CNWAligner::GetTranscriptString

(

void

)

const

Definition at line 931 of file nw_aligner.cpp.

References CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, CNWAligner::eTS_Intron, CNWAligner::eTS_Match, CNWAligner::eTS_Replace, CNWAligner::eTS_SlackDelete, CNWAligner::eTS_SlackInsert, g_msg_InvalidTranscriptSymbol, i, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CNWAligner::m_Transcript, NCBI_THROW, and CNWAligner::x_GetDiagTS().

Referenced by CNWFormatter::AsDenseSeg(), CNWFormatter::AsSeqAlign(), and CContigAssembly::BandedGlobalAlignment().

GetWg()

TScore CNWAligner::GetWg ( void  ) const

inline

Definition at line 166 of file nw_aligner.hpp.

Referenced by CMultiAligner::x_RealignBlocks(), and x_ScoreFromTranscriptCore().

GetWm()

TScore CNWAligner::GetWm ( void  ) const

inline

Definition at line 164 of file nw_aligner.hpp.

Referenced by CNWFormatter::SSegment::Update().

GetWms()

TScore CNWAligner::GetWms ( void  ) const

inline

Definition at line 165 of file nw_aligner.hpp.

GetWs()

TScore CNWAligner::GetWs ( void  ) const

inline

Definition at line 167 of file nw_aligner.hpp.

Referenced by CMultiAligner::x_RealignBlocks(), and x_ScoreFromTranscriptCore().

IsSmithWaterman()

bool CNWAligner::IsSmithWaterman

(

)

const

Definition at line 898 of file nw_aligner.cpp.

References CNWAligner::m_SmithWaterman.

Referenced by CNWFormatter::AsDenseSeg(), CNWFormatter::AsSeqAlign(), and CNWAligner::ScoreFromTranscript().

MakePattern()

size_t CNWAligner::MakePattern	(	const size_t	hit_size = 100,
		const size_t	core_size = 28
	)

Definition at line 1462 of file nw_aligner.cpp.

References fp, g_msg_NullParameter, i, CNWAligner::m_guides, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, NCBI_THROW, CNWAligner::x_CalcFingerPrint64(), and CNWAligner::x_FindFingerPrint64().

operator()()

template<class THit >

TCoord CHitCoverageAccumulator< THit >::operator() ( TCoord  iVal, const THitRef &  ph  )

inline

Overloaded function call operator to be used with std::accumulate()

Parameters

iVal	Accumulation target

Returns

Updated accumulation target

Definition at line 86 of file hit_filter.hpp.

References CHitCoverageAccumulator< THit >::m_Finish, CHitCoverageAccumulator< THit >::m_i1, and CHitCoverageAccumulator< THit >::m_i2.

operator<()

template<class THit >

bool CHitFilter< THit >::SHitEnd::operator< ( const SHitEnd &  rhs ) const

inline

Definition at line 596 of file hit_filter.hpp.

References CAlignShadow::GetId(), CBlastTabular::GetScore(), CHitFilter< THit >::SHitEnd::m_Point, CHitFilter< THit >::SHitEnd::m_Ptr, and CHitFilter< THit >::SHitEnd::m_X.

operator[]()

Uint1 CNWAligner::CBacktraceMatrix4::operator[] ( size_t  i ) const

inline

Definition at line 375 of file nw_aligner.hpp.

References i.

PSpace()

static bool CNWAligner::SAlignInOut::PSpace ( const SAlignInOut *  p1, const SAlignInOut *  p2  )

inlinestatic

Definition at line 445 of file nw_aligner.hpp.

References CNWAligner::SAlignInOut::m_space.

Referenced by CNWAligner::x_Run().

Purge()

void CNWAligner::CBacktraceMatrix4::Purge ( size_t  i )

inline

Definition at line 369 of file nw_aligner.hpp.

References i.

Referenced by CBandAligner::x_Align(), CNWAligner::x_Align(), CPSSMAligner::x_AlignProfile(), and CPSSMAligner::x_AlignPSSM().

Run() [1/4]

CRef<objects::CSeq_align> CNWAligner::Run	(	objects::CScope &	scope,
		const objects::CSeq_id &	id1,
		const objects::CSeq_id &	id2,
		bool	trim_end_gaps = true
	)

Run() [2/4]

CRef<objects::CSeq_align> CNWAligner::Run	(	objects::CScope &	scope,
		const objects::CSeq_loc &	loc1,
		const objects::CSeq_loc &	loc2,
		bool	trim_end_gaps = true
	)

Run() [3/4]

CNWAligner::TScore CNWAligner::Run ( void  )

virtual

Reimplemented in CPSSMAligner.

Definition at line 503 of file nw_aligner.cpp.

References g_msg_DataNotAvailable, g_msg_HitSpaceLimit, CNWAligner::m_guides, CNWAligner::m_score, CNWAligner::m_ScoreMatrixInvalid, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CNWAligner::m_SmithWaterman, NCBI_THROW, CNWAligner::x_CheckMemoryLimit(), and CNWAligner::x_Run().

Referenced by CContigAssembly::BandedGlobalAlignment(), CInstancedAligner::x_RunMMGlobal(), and CSplign::x_SetPattern().

Run() [4/4]

CPSSMAligner::TScore CPSSMAligner::Run ( void  )

virtual

Reimplemented from CNWAligner.

Definition at line 171 of file nw_pssm_aligner.cpp.

References g_msg_HitSpaceLimit, CNWAligner::m_score, NCBI_THROW, CNWAligner::x_CheckMemoryLimit(), and CNWAligner::x_Run().

Referenced by CMultiAligner::x_AlignInClusters(), x_AlignProfileProfile(), CMultiAligner::x_AlignProfileProfile(), CMultiAligner::x_ComputeProfileRangeAlignment(), and CMultiAligner::x_RealignBlocks().

s_GetCoverage()

template<class THit >

static TCoord CHitFilter< THit >::s_GetCoverage ( Uint1  where, typename THitRefs::const_iterator  from, typename THitRefs::const_iterator  to  )

inlinestatic

Collect coverage for the range of hits on the specified source sequence.

Parameters

where	Accumulation source sequence (0 = query, 1 = subject)
from	Hit range start
to	Hit range stop

Returns

The number of residues on the source sequences covered by at least one alignment

Definition at line 139 of file hit_filter.hpp.

s_GetOverlap()

template<class THit >

static TCoord CHitFilter< THit >::s_GetOverlap ( TCoord  L1, TCoord  R1, TCoord  L2, TCoord  R2  )

inlinestatic

Definition at line 202 of file hit_filter.hpp.

References max(), min(), and n.

Referenced by CHitFilter< THit >::sx_Cleave().

s_GetSpan()

template<class THit >

static void CHitFilter< THit >::s_GetSpan ( const THitRefs &  hitrefs, TCoord  span[4]  )

inlinestatic

Get sequence span for a set of alignments (hits).

Parameters

hitrefs	Source hits
span	Destination array (0=query min, 1=query max, 2=subj min, 3=subj max)

Definition at line 175 of file hit_filter.hpp.

References kMax_UInt.

Referenced by CCompactSAMApplication::FindCompactAligns(), and CSplign::x_RunOnCompartment().

s_MergeAbutting()

template<class THit >

static void CHitFilter< THit >::s_MergeAbutting ( typename THitRefs::iterator  hri_beg, typename THitRefs::iterator  hri_end, const double &  maxlenfr, THitRefs *  pout  )

inlinestatic

Definition at line 494 of file hit_filter.hpp.

References all, multiset< Key, Compare >::insert(), CHitFilter< THit >::SHitEnd::m_Point, CHitFilter< THit >::SHitEnd::m_Ptr, CHitFilter< THit >::SHitEnd::m_X, NCBI_THROW, NON_CONST_ITERATE, and CHitFilter< THit >::sx_TestAndMerge().

Referenced by CAppHitFilter::Run().

s_PNullRef()

template<class THit >

static bool CHitFilter< THit >::s_PNullRef ( const THitRef &  hr )

inlinestatic

Definition at line 584 of file hit_filter.hpp.

References CRef< C, Locker >::IsNull().

s_RunGreedy()

template<class THit >

static void CHitFilter< THit >::s_RunGreedy ( typename THitRefs::iterator  hri_beg, typename THitRefs::iterator  hri_end, THitRefs *  phits_new, TCoord  min_hit_len = 100, double  min_hit_idty = .9, TCoord  margin = 1, TCoord  retain_overlap = 0, EUnique_type  unique_type = e_Strict  )

inlinestatic

Definition at line 234 of file hit_filter.hpp.

References all, multiset< Key, Compare >::begin(), copy(), CHitFilter< THit >::e_Query, CHitFilter< THit >::e_Strict, CHitFilter< THit >::e_Subject, multiset< Key, Compare >::end(), i, multiset< Key, Compare >::insert(), ITERATE, CHitFilter< THit >::SHitEnd::m_Point, CHitFilter< THit >::SHitEnd::m_Ptr, CHitFilter< THit >::SHitEnd::m_X, NCBI_THROW, CRef< C, Locker >::NotEmpty(), NULL, CHitFilter< THit >::sx_AddMidIfNeeded(), CHitFilter< THit >::sx_AddMidPoints(), CHitFilter< THit >::sx_Cleave(), and CHitFilter< THit >::sx_GetEndsInRange().

Referenced by RemoveOverlaps(), CCleanupAlignmentsJob::x_CreateProjectItems(), CAppHitFilter::x_DoMultiple(), and CAppHitFilter::x_DoPairwise().

s_TrackHit()

template<class THit >

static bool CHitFilter< THit >::s_TrackHit ( const THit &  h )

inlinestaticprotected

Definition at line 889 of file hit_filter.hpp.

References CAlignShadow::GetQueryStart(), CAlignShadow::GetQueryStop(), CAlignShadow::GetQueryStrand(), CAlignShadow::GetSubjStart(), CAlignShadow::GetSubjStop(), CAlignShadow::GetSubjStrand(), CAlignShadow::GetTranscript(), ITERATE, NCBI_THROW, and CAlignShadow::s_RunLengthDecode().

SAlignInOut() [1/2]

CNWAligner::SAlignInOut::SAlignInOut ( )

inline

Definition at line 406 of file nw_aligner.hpp.

SAlignInOut() [2/2]

CNWAligner::SAlignInOut::SAlignInOut ( size_t  offset1, size_t  len1, bool  esfL1, bool  esfR1, size_t  offset2, size_t  len2, bool  esfL2, bool  esfR2  )

inline

Definition at line 410 of file nw_aligner.hpp.

References CNWAligner::SAlignInOut::m_len1, CNWAligner::SAlignInOut::m_len2, and CNWAligner::SAlignInOut::m_space.

ScoreFromTranscript() [1/2]

CNWAligner::TScore CPSSMAligner::ScoreFromTranscript ( const TTranscript &  transcript, size_t  start1 = 0, size_t  start2 = 0  ) const

virtual

Reimplemented from CNWAligner.

Definition at line 692 of file nw_pssm_aligner.cpp.

References CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, CNWAligner::eTS_Match, CNWAligner::eTS_Replace, g_msg_InvalidTranscriptSymbol, i, CPSSMAligner::kPSSM_ColumnSize, CPSSMAligner::m_EndWg, CPSSMAligner::m_EndWs, CNWAligner::m_esf_L1, CNWAligner::m_esf_L2, CNWAligner::m_esf_R1, CNWAligner::m_esf_R2, CPSSMAligner::m_Freq1, CPSSMAligner::m_Freq2, CPSSMAligner::m_FreqScale, CPSSMAligner::m_Pssm1, CNWAligner::m_ScoreMatrix, CPSSMAligner::m_Seq2, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, CPSSMAligner::m_StartWg, CPSSMAligner::m_StartWs, CNWAligner::m_Wg, CNWAligner::m_Ws, n, NCBI_FSM_DIM, NCBI_THROW, SNCBIFullScoreMatrix::s, and CNWAligner::ScoreFromTranscript().

ScoreFromTranscript() [2/2]

CNWAligner::TScore CNWAligner::ScoreFromTranscript ( const TTranscript &  transcript, size_t  start1 = kMax_UInt, size_t  start2 = kMax_UInt  ) const

virtual

Reimplemented in CSplicedAligner32, CSplicedAligner16, and CPSSMAligner.

Definition at line 1141 of file nw_aligner.cpp.

References CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, CNWAligner::eTS_Match, CNWAligner::eTS_Replace, g(), g_msg_InconsistentArguments, g_msg_InvalidTranscriptSymbol, i, CNWAligner::IsSmithWaterman(), kMax_UInt, CNWAligner::m_esf_L1, CNWAligner::m_esf_L2, CNWAligner::m_esf_R1, CNWAligner::m_esf_R2, CNWAligner::m_ScoreMatrix, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CNWAligner::m_Wg, CNWAligner::m_Wm, CNWAligner::m_Wms, CNWAligner::m_Ws, NCBI_FSM_DIM, NCBI_THROW, and SNCBIFullScoreMatrix::s.

Referenced by CPSSMAligner::ScoreFromTranscript(), CNWAligner::SetTranscript(), CNWAligner::x_Align(), and CNWAligner::x_Run().

SetAt()

void CNWAligner::CBacktraceMatrix4::SetAt ( size_t  i, Uint1  v  )

inline

Definition at line 346 of file nw_aligner.hpp.

References i.

Referenced by CBandAligner::x_Align(), CNWAligner::x_Align(), CPSSMAligner::x_AlignProfile(), and CPSSMAligner::x_AlignPSSM().

SetBand()

void CBandAligner::SetBand ( size_t  band )

inline

Definition at line 74 of file nw_band_aligner.hpp.

References CBandAligner::m_band.

Referenced by CSplicedAligner32::x_Align(), and CSplign::x_SetPattern().

SetBestPos()

void CNWAligner::CBacktraceMatrix4::SetBestPos ( size_t  k )

inline

Definition at line 355 of file nw_aligner.hpp.

Referenced by CNWAligner::x_Align().

SetBestScore()

void CNWAligner::CBacktraceMatrix4::SetBestScore ( TNCBIScore  score )

inline

Definition at line 362 of file nw_aligner.hpp.

Referenced by CNWAligner::x_Align().

SetEndSpaceFree()

void CNWAligner::SetEndSpaceFree	(	bool	Left1,
		bool	Right1,
		bool	Left2,
		bool	Right2
	)

Definition at line 192 of file nw_aligner.cpp.

References CNWAligner::m_esf_L1, CNWAligner::m_esf_L2, CNWAligner::m_esf_R1, and CNWAligner::m_esf_R2.

Referenced by CContigAssembly::BandedGlobalAlignment(), CSplicedAligner::CSplicedAligner(), CMultiAligner::x_AlignInClusters(), CMultiAligner::x_AlignProfileProfile(), CMultiAligner::x_ComputeProfileRangeAlignment(), and CMultiAligner::x_RealignBlocks().

SetEndWg()

void CPSSMAligner::SetEndWg ( TScore  value )

inline

Definition at line 108 of file nw_pssm_aligner.hpp.

References CPSSMAligner::m_EndWg, and rapidjson::value.

Referenced by CMultiAligner::x_AlignInClusters(), CMultiAligner::x_AlignProfileProfile(), CMultiAligner::x_ComputeProfileRangeAlignment(), CMultiAligner::x_InitAligner(), and CMultiAligner::x_RealignBlocks().

SetEndWs()

void CPSSMAligner::SetEndWs ( TScore  value )

inline

Definition at line 109 of file nw_pssm_aligner.hpp.

References CPSSMAligner::m_EndWs, and rapidjson::value.

Referenced by CMultiAligner::x_AlignInClusters(), CMultiAligner::x_AlignProfileProfile(), CMultiAligner::x_ComputeProfileRangeAlignment(), CMultiAligner::x_InitAligner(), and CMultiAligner::x_RealignBlocks().

SetFreqScale()

void CPSSMAligner::SetFreqScale ( const int  scale )

inline

Definition at line 96 of file nw_pssm_aligner.hpp.

References CPSSMAligner::m_FreqScale.

SetGapPreference()

void CNWAligner::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.

Definition at line 210 of file nw_aligner.cpp.

References CNWAligner::m_GapPreference.

SetPattern()

void CNWAligner::SetPattern

(

const vector< size_t > &

pattern

)

Definition at line 845 of file nw_aligner.cpp.

References i, CNWAligner::m_guides, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, and NCBI_THROW.

Referenced by CMultiAligner::x_AlignProfileProfile(), and CMultiAligner::x_ComputeProfileRangeAlignment().

SetPositivesAsMatches()

void CNWAligner::SetPositivesAsMatches ( bool  positives_as_matches = true )

inline

Definition at line 211 of file nw_aligner.hpp.

SetProgressCallback()

void CNWAligner::SetProgressCallback	(	FProgressCallback	prg_callback,
		void *	data
	)

Definition at line 1015 of file nw_aligner.cpp.

References data, CNWAligner::SProgressInfo::m_data, CNWAligner::m_prg_callback, and CNWAligner::m_prg_info.

Referenced by CInstancedAligner::x_RunMMGlobal().

SetScoreMatrix() [1/2]

void CNWAligner::SetScoreMatrix

(

const SNCBIPackedScoreMatrix *

scoremat

)

Definition at line 1036 of file nw_aligner.cpp.

References SNCBIPackedScoreMatrix::defscore, CNWAligner::m_abc, CNWAligner::m_ScoreMatrix, CNWAligner::m_ScoreMatrixInvalid, CNWAligner::m_Wm, CNWAligner::m_Wms, NCBISM_Unpack(), SNCBIPackedScoreMatrix::scores, and SNCBIPackedScoreMatrix::symbols.

Referenced by CNWAligner::CNWAligner(), CSplign::s_CreateDefaultAligner(), CPSSMAligner::SetScoreMatrix(), and CInstancedAligner::x_RunMMGlobal().

SetScoreMatrix() [2/2]

void CPSSMAligner::SetScoreMatrix

(

const SNCBIPackedScoreMatrix *

scoremat

)

Definition at line 149 of file nw_pssm_aligner.cpp.

References g_msg_NullParameter, i, CPSSMAligner::kPSSM_ColumnSize, CPSSMAligner::m_DScoreMatrix, CNWAligner::m_ScoreMatrix, NCBI_THROW, SNCBIFullScoreMatrix::s, and CNWAligner::SetScoreMatrix().

Referenced by CPSSMAligner::CPSSMAligner(), CMultiAligner::x_SetScoreMatrix(), and x_SetScoreMatrix().

SetSequences() [1/5]

void CNWAligner::SetSequences ( const char *  seq1, size_t  len1, const char *  seq2, size_t  len2, bool  verify = true  )

virtual

Reimplemented in CPSSMAligner.

Definition at line 140 of file nw_aligner.cpp.

References g_msg_NullParameter, CNWAligner::m_Seq1, CNWAligner::m_Seq1Vec, CNWAligner::m_Seq2, CNWAligner::m_Seq2Vec, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, CNWAligner::m_Transcript, NCBI_THROW, verify, and CNWAligner::x_CheckSequence().

Referenced by CNWAligner::CNWAligner(), CPSSMAligner::SetSequences(), CNWAligner::SetSequences(), and CSplign::x_SetPattern().

SetSequences() [2/5]

void CPSSMAligner::SetSequences ( const char *  seq1, size_t  len1, const char *  seq2, size_t  len2, bool  verify = true  )

virtual

Reimplemented from CNWAligner.

Definition at line 89 of file nw_pssm_aligner.cpp.

References CPSSMAligner::m_Freq1, CPSSMAligner::m_Freq2, CPSSMAligner::m_Pssm1, CPSSMAligner::m_Seq2, CNWAligner::SetSequences(), and verify.

Referenced by CPSSMAligner::CPSSMAligner(), CMultiAligner::x_AlignInClusters(), x_AlignProfileProfile(), CMultiAligner::x_AlignProfileProfile(), CMultiAligner::x_ComputeProfileRangeAlignment(), and CMultiAligner::x_RealignBlocks().

SetSequences() [3/5]

void CPSSMAligner::SetSequences	(	const CNWAligner::TScore **	pssm1,
		size_t	len1,
		const char *	seq2,
		size_t	len2,
		bool	verify = true
	)

Definition at line 101 of file nw_pssm_aligner.cpp.

References g_msg_InvalidSequenceChars, g_msg_NullParameter, i, CPSSMAligner::kPSSM_ColumnSize, CPSSMAligner::m_Freq1, CPSSMAligner::m_Freq2, CPSSMAligner::m_Pssm1, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CPSSMAligner::m_Seq2, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, NCBI_THROW, and verify.

SetSequences() [4/5]

void CPSSMAligner::SetSequences	(	const double **	freq1,
		size_t	len1,
		const double **	freq2,
		size_t	len2,
		const int	scale = 1
	)

Definition at line 129 of file nw_pssm_aligner.cpp.

References g_msg_NullParameter, CPSSMAligner::m_Freq1, CPSSMAligner::m_Freq2, CPSSMAligner::m_FreqScale, CPSSMAligner::m_Pssm1, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CPSSMAligner::m_Seq2, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, and NCBI_THROW.

SetSequences() [5/5]

void CNWAligner::SetSequences	(	const string &	seq1,
		const string &	seq2,
		bool	verify = true
	)

Definition at line 184 of file nw_aligner.cpp.

References CNWAligner::SetSequences(), and verify.

SetShift()

void CBandAligner::SetShift	(	Uint1	where,
		size_t	offset
	)

Definition at line 68 of file nw_band_aligner.cpp.

References CBandAligner::m_Shift, NCBI_THROW, and offset.

Referenced by CContigAssembly::BandedGlobalAlignment(), CSplicedAligner32::x_Align(), and CAppNWA::x_RunOnPair().

SetSmithWaterman()

void CNWAligner::SetSmithWaterman

(

bool

SW

)

Definition at line 201 of file nw_aligner.cpp.

References CNWAligner::m_esf_L1, CNWAligner::m_esf_L2, CNWAligner::m_esf_R1, CNWAligner::m_esf_R2, and CNWAligner::m_SmithWaterman.

SetSpaceLimit()

void CNWAligner::SetSpaceLimit ( const size_t &  maxmem )

inline

Definition at line 142 of file nw_aligner.hpp.

Referenced by CSplignArgUtil::ArgsToSplign(), CContigAssembly::BandedGlobalAlignment(), and BOOST_AUTO_TEST_CASE().

SetStartWg()

void CPSSMAligner::SetStartWg ( TScore  value )

inline

Definition at line 106 of file nw_pssm_aligner.hpp.

References CPSSMAligner::m_StartWg, and rapidjson::value.

Referenced by CMultiAligner::x_AlignInClusters(), CMultiAligner::x_AlignProfileProfile(), CMultiAligner::x_ComputeProfileRangeAlignment(), CMultiAligner::x_InitAligner(), and CMultiAligner::x_RealignBlocks().

SetStartWs()

void CPSSMAligner::SetStartWs ( TScore  value )

inline

Definition at line 107 of file nw_pssm_aligner.hpp.

References CPSSMAligner::m_StartWs, and rapidjson::value.

Referenced by CMultiAligner::x_AlignInClusters(), CMultiAligner::x_AlignProfileProfile(), CMultiAligner::x_ComputeProfileRangeAlignment(), CMultiAligner::x_InitAligner(), and CMultiAligner::x_RealignBlocks().

SetTranscript()

void CNWAligner::SetTranscript

(

const TTranscript &

transcript

)

Definition at line 923 of file nw_aligner.cpp.

References CNWAligner::m_score, CNWAligner::m_Transcript, and CNWAligner::ScoreFromTranscript().

SetWg() [1/2]

void CNWAligner::SetWg ( TScore  value )

inline

Definition at line 121 of file nw_aligner.hpp.

References rapidjson::value.

Referenced by CSplign::s_CreateDefaultAligner(), and CInstancedAligner::x_RunMMGlobal().

SetWg() [2/2]

void CPSSMAligner::SetWg ( TScore  value )

inline

Definition at line 98 of file nw_pssm_aligner.hpp.

References CPSSMAligner::m_EndWg, CPSSMAligner::m_StartWg, CNWAligner::m_Wg, and rapidjson::value.

Referenced by CMultiAligner::x_AlignInClusters(), CMultiAligner::x_AlignProfileProfile(), CMultiAligner::x_ComputeProfileRangeAlignment(), CMultiAligner::x_InitAligner(), and CMultiAligner::x_RealignBlocks().

SetWm()

void CNWAligner::SetWm

(

TScore

value

)

Definition at line 1029 of file nw_aligner.cpp.

References CNWAligner::m_ScoreMatrixInvalid, CNWAligner::m_Wm, and val.

Referenced by CSplign::s_CreateDefaultAligner(), and CInstancedAligner::x_RunMMGlobal().

SetWms()

void CNWAligner::SetWms

(

TScore

value

)

Definition at line 1022 of file nw_aligner.cpp.

References CNWAligner::m_ScoreMatrixInvalid, CNWAligner::m_Wms, and val.

Referenced by CSplign::s_CreateDefaultAligner(), and CInstancedAligner::x_RunMMGlobal().

SetWs() [1/2]

void CNWAligner::SetWs ( TScore  value )

inline

Definition at line 122 of file nw_aligner.hpp.

References rapidjson::value.

Referenced by CSplign::s_CreateDefaultAligner(), and CInstancedAligner::x_RunMMGlobal().

SetWs() [2/2]

void CPSSMAligner::SetWs ( TScore  value )

inline

Definition at line 102 of file nw_pssm_aligner.hpp.

References CPSSMAligner::m_EndWs, CPSSMAligner::m_StartWs, CNWAligner::m_Ws, and rapidjson::value.

Referenced by CMultiAligner::x_AlignInClusters(), CMultiAligner::x_AlignProfileProfile(), CMultiAligner::x_ComputeProfileRangeAlignment(), CMultiAligner::x_InitAligner(), and CMultiAligner::x_RealignBlocks().

SProgressInfo()

CNWAligner::SProgressInfo::SProgressInfo ( void  )

inline

Definition at line 147 of file nw_aligner.hpp.

sx_AddMidIfNeeded()

template<class THit >

static void CHitFilter< THit >::sx_AddMidIfNeeded ( THitRef *  hit, const float  curscore, THitRef *  container_candidate, const Uint1  where, TCoord  margin, THitEnds &  hit_mids  )

inlinestaticprotected

Definition at line 620 of file hit_filter.hpp.

References multiset< Key, Compare >::insert(), CHitFilter< THit >::SHitEnd::m_Point, CHitFilter< THit >::SHitEnd::m_Ptr, and CHitFilter< THit >::SHitEnd::m_X.

Referenced by CHitFilter< THit >::s_RunGreedy(), and CHitFilter< THit >::sx_AddMidPoints().

sx_AddMidPoints()

template<class THit >

static void CHitFilter< THit >::sx_AddMidPoints ( THitRef &  h, const TCoord *  outer_box, TCoord  margin, THitEnds &  hit_ends, vector< bool > &  skip, const THitRef *  hitref_firstptr  )

inlinestaticprotected

Definition at line 709 of file hit_filter.hpp.

References multiset< Key, Compare >::begin(), multiset< Key, Compare >::end(), multiset< Key, Compare >::insert(), CHitFilter< THit >::sx_AddMidIfNeeded(), and CHitFilter< THit >::sx_GetEndsInRange().

Referenced by CHitFilter< THit >::s_RunGreedy().

sx_Cleave()

template<class THit >

static pair<int, Uint1> CHitFilter< THit >::sx_Cleave ( THitRef &  h, Uint1  where, TCoord  cmin, TCoord  cmax, TCoord  min_hit_len, double &  min_idty, THitRef *  pnew_hit, TCoord  retain_overlap  )

inlinestaticprotected

Definition at line 732 of file hit_filter.hpp.

References NULL, CRef< C, Locker >::Reset(), and CHitFilter< THit >::s_GetOverlap().

Referenced by CHitFilter< THit >::s_RunGreedy().

sx_GetEndsInRange()

template<class THit >

static pair<THitEndsIter, THitEndsIter> CHitFilter< THit >::sx_GetEndsInRange ( const THitRef &  hc, const TCoord *  box, Uint1  where, TCoord  margin, THitEnds &  hit_ends  )

inlinestaticprotected

Definition at line 645 of file hit_filter.hpp.

References a, b, multiset< Key, Compare >::begin(), multiset< Key, Compare >::lower_bound(), CHitFilter< THit >::SHitEnd::m_Point, CHitFilter< THit >::SHitEnd::m_Ptr, CHitFilter< THit >::SHitEnd::m_X, max(), and multiset< Key, Compare >::upper_bound().

Referenced by CHitFilter< THit >::s_RunGreedy(), and CHitFilter< THit >::sx_AddMidPoints().

sx_Merge()

template<class THit >

static THitRef CHitFilter< THit >::sx_Merge ( const THitRef &  lhs, const THitRef &  rhs, Uint1  where  )

inlinestaticprotected

Definition at line 817 of file hit_filter.hpp.

References abs, NCBI_THROW, CRef< C, Locker >::Reset(), and CAlignShadow::s_RunLengthDecode().

Referenced by CHitFilter< THit >::sx_TM().

sx_TestAndMerge()

template<class THit >

static void CHitFilter< THit >::sx_TestAndMerge ( typename THitRefs::iterator  ii_beg, typename THitRefs::iterator  ii_end, const THitEnds &  hit_ends, const double &  maxlenfr, THitRefs *  pout  )

inlinestaticprotected

Definition at line 1032 of file hit_filter.hpp.

References CRef< C, Locker >::NotEmpty(), and CHitFilter< THit >::sx_TM().

Referenced by CHitFilter< THit >::s_MergeAbutting().

sx_TM()

template<class THit >

static void CHitFilter< THit >::sx_TM ( Uint1  where, typename THitRefs::iterator  ii_beg, typename THitRefs::iterator  ii_end, const THitEnds &  hit_ends, const double &  maxlenfr, map< typename THitRefs::iterator, THitRef > &  m  )

inlinestaticprotected

Definition at line 919 of file hit_filter.hpp.

References map_checker< Container >::end(), map_checker< Container >::find(), multiset< Key, Compare >::lower_bound(), CHitFilter< THit >::SHitEnd::m_Point, CHitFilter< THit >::SHitEnd::m_Ptr, CHitFilter< THit >::SHitEnd::m_X, min(), CRef< C, Locker >::NotEmpty(), CRef< C, Locker >::NotNull(), CHitFilter< THit >::sx_Merge(), and multiset< Key, Compare >::upper_bound().

Referenced by CHitFilter< THit >::sx_TestAndMerge().

x_Align() [1/3]

CNWAligner::TScore CBandAligner::x_Align ( CNWAligner::SAlignInOut *  data )

protectedvirtual

Reimplemented from CNWAligner.

Reimplemented in CSplicedAligner32, and CSplicedAligner16.

Definition at line 110 of file nw_band_aligner.cpp.

References data, E, G, g_msg_UnexpectedTermIndex, i, kMaskD(), kMaskE(), kMaskEc(), kMaskFc(), kMax_size_t, CBandAligner::m_band, CNWAligner::SProgressInfo::m_iter_done, CNWAligner::SProgressInfo::m_iter_total, CBandAligner::m_LastCoordSeq1, CBandAligner::m_LastCoordSeq2, CNWAligner::m_prg_callback, CNWAligner::m_prg_info, CNWAligner::m_ScoreMatrix, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CBandAligner::m_Shift, CNWAligner::m_terminate, CBandAligner::m_TermK, CNWAligner::m_Wg, CNWAligner::m_Ws, NCBI_FSM_DIM, NCBI_THROW, CNWAligner::CBacktraceMatrix4::Purge(), SNCBIFullScoreMatrix::s, CNWAligner::CBacktraceMatrix4::SetAt(), CBandAligner::x_CheckParameters(), and CBandAligner::x_DoBackTrace().

Referenced by CSplicedAligner32::x_Align().

x_Align() [2/3]

CNWAligner::TScore CNWAligner::x_Align ( SAlignInOut *  data )

protectedvirtual

Reimplemented in CPSSMAligner, CSplicedAligner32, CSplicedAligner16, and CBandAligner.

Definition at line 229 of file nw_aligner.cpp.

References copy(), data, E, CNWAligner::eLater, F, G, kMaskD, kMaskE, kMaskEc, kMaskFc, CNWAligner::m_GapPreference, CNWAligner::SProgressInfo::m_iter_done, CNWAligner::SProgressInfo::m_iter_total, CNWAligner::m_prg_callback, CNWAligner::m_prg_info, CNWAligner::m_ScoreMatrix, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, CNWAligner::m_SmithWaterman, CNWAligner::m_terminate, CNWAligner::m_Wg, CNWAligner::m_Ws, NCBI_FSM_DIM, NCBI_THROW, CNWAligner::CBacktraceMatrix4::Purge(), SNCBIFullScoreMatrix::s, CNWAligner::ScoreFromTranscript(), CNWAligner::CBacktraceMatrix4::SetAt(), CNWAligner::CBacktraceMatrix4::SetBestPos(), CNWAligner::CBacktraceMatrix4::SetBestScore(), and CNWAligner::x_SWDoBackTrace().

Referenced by CNWAlignerThread_Align::Main(), CPSSMAligner::x_Align(), and CNWAligner::x_Run().

x_Align() [3/3]

CNWAligner::TScore CPSSMAligner::x_Align ( SAlignInOut *  data )

protectedvirtual

Reimplemented from CNWAligner.

Definition at line 195 of file nw_pssm_aligner.cpp.

References data, CPSSMAligner::m_Freq1, CPSSMAligner::m_Pssm1, CNWAligner::x_Align(), CPSSMAligner::x_AlignProfile(), and CPSSMAligner::x_AlignPSSM().

x_AlignProfile()

CNWAligner::TScore CPSSMAligner::x_AlignProfile ( SAlignInOut *  data )

protected

Definition at line 409 of file nw_pssm_aligner.cpp.

References data, E, G, i, kMaskD, kMaskE, kMaskEc, kMaskFc, CPSSMAligner::kPSSM_ColumnSize, CPSSMAligner::m_DScoreMatrix, CPSSMAligner::m_EndWg, CPSSMAligner::m_EndWs, CPSSMAligner::m_Freq1, CPSSMAligner::m_Freq2, CPSSMAligner::m_FreqScale, CNWAligner::SProgressInfo::m_iter_done, CNWAligner::SProgressInfo::m_iter_total, CNWAligner::m_prg_callback, CNWAligner::m_prg_info, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, CPSSMAligner::m_StartWg, CPSSMAligner::m_StartWs, CNWAligner::m_terminate, CNWAligner::m_Wg, CNWAligner::m_Ws, n, CNWAligner::CBacktraceMatrix4::Purge(), CNWAligner::CBacktraceMatrix4::SetAt(), and CNWAligner::x_DoBackTrace().

Referenced by CPSSMAligner::x_Align().

x_AlignPSSM()

CNWAligner::TScore CPSSMAligner::x_AlignPSSM ( SAlignInOut *  data )

protected

Definition at line 220 of file nw_pssm_aligner.cpp.

References data, E, G, i, kMaskD, kMaskE, kMaskEc, kMaskFc, CPSSMAligner::m_EndWg, CPSSMAligner::m_EndWs, CNWAligner::SProgressInfo::m_iter_done, CNWAligner::SProgressInfo::m_iter_total, CNWAligner::m_prg_callback, CNWAligner::m_prg_info, CPSSMAligner::m_Pssm1, CPSSMAligner::m_Seq2, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, CPSSMAligner::m_StartWg, CPSSMAligner::m_StartWs, CNWAligner::m_terminate, CNWAligner::m_Wg, CNWAligner::m_Ws, CNWAligner::CBacktraceMatrix4::Purge(), CNWAligner::CBacktraceMatrix4::SetAt(), and CNWAligner::x_DoBackTrace().

Referenced by CPSSMAligner::x_Align().

x_CalcFingerPrint64()

unsigned char CNWAligner::x_CalcFingerPrint64 ( const char *  beg, const char *  end, size_t &  err_index  )

protected

Definition at line 1396 of file nw_aligner.cpp.

References fp.

Referenced by CNWAligner::MakePattern(), and CNWAligner::x_FindFingerPrint64().

x_CheckMemoryLimit() [1/2]

bool CNWAligner::x_CheckMemoryLimit ( void  )

protectedvirtual

Reimplemented in CSplicedAligner, CBandAligner, and CMMAligner.

Definition at line 1098 of file nw_aligner.cpp.

References CNWAligner::GetElemSize(), i, CNWAligner::m_guides, CNWAligner::m_MaxMem, CNWAligner::m_SeqLen1, and CNWAligner::m_SeqLen2.

Referenced by CNWAligner::Run(), CPSSMAligner::Run(), and CSplicedAligner::x_CheckMemoryLimit().

x_CheckMemoryLimit() [2/2]

bool CBandAligner::x_CheckMemoryLimit ( void  )

protectedvirtual

Reimplemented from CNWAligner.

Reimplemented in CSplicedAligner.

Definition at line 446 of file nw_band_aligner.cpp.

References CNWAligner::GetElemSize(), i, CBandAligner::m_band, CNWAligner::m_guides, CNWAligner::m_MaxMem, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, and max().

x_CheckParameters()

void CBandAligner::x_CheckParameters ( const SAlignInOut *  data ) const

protected

Definition at line 305 of file nw_band_aligner.cpp.

References data, CBandAligner::m_band, CBandAligner::m_Shift, and NCBI_THROW.

Referenced by CBandAligner::x_Align().

x_CheckSequence()

size_t CNWAligner::x_CheckSequence ( const char *  seq, size_t  len  ) const

protected

Definition at line 1064 of file nw_aligner.cpp.

References len, CNWAligner::m_abc, tolower(), and toupper().

Referenced by CNWAligner::SetSequences().

x_DoBackTrace() [1/2]

void CBandAligner::x_DoBackTrace ( const CBacktraceMatrix4 &  backtrace, CNWAligner::SAlignInOut *  data  )

protected

Definition at line 359 of file nw_band_aligner.cpp.

References abs, data, CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, g_msg_InvalidBacktraceData, kMaskD(), kMaskE(), kMaskEc(), kMaskFc(), kMax, kMax_size_t, CBandAligner::m_band, CBandAligner::m_LastCoordSeq1, CBandAligner::m_LastCoordSeq2, CBandAligner::m_Shift, CBandAligner::m_TermK, NCBI_THROW, and CNWAligner::x_GetDiagTS().

Referenced by CBandAligner::x_Align().

x_DoBackTrace() [2/2]

void CNWAligner::x_DoBackTrace ( const CBacktraceMatrix4 &  backtrace, SAlignInOut *  data  )

protected

Definition at line 726 of file nw_aligner.cpp.

References data, CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, kMaskD, kMaskE, kMaskEc, kMaskFc, and CNWAligner::x_GetDiagTS().

Referenced by CPSSMAligner::x_AlignProfile(), and CPSSMAligner::x_AlignPSSM().

x_FindFingerPrint64()

const char * CNWAligner::x_FindFingerPrint64 ( const char *  beg, const char *  end, unsigned char  fingerprint, size_t  size, size_t &  err_index  )

protected

Definition at line 1419 of file nw_aligner.cpp.

References fp, ncbi::grid::netcache::search::fields::size, and CNWAligner::x_CalcFingerPrint64().

Referenced by CNWAligner::MakePattern().

x_GetDiagTS() [1/2]

CNWAligner::ETranscriptSymbol CNWAligner::x_GetDiagTS ( size_t  i1, size_t  i2  ) const

protectedvirtual

Reimplemented in CPSSMAligner.

Definition at line 707 of file nw_aligner.cpp.

References CNWAligner::eTS_Match, CNWAligner::eTS_Replace, CNWAligner::m_PositivesAsMatches, CNWAligner::m_ScoreMatrix, CNWAligner::m_Seq1, CNWAligner::m_Seq2, SNCBIFullScoreMatrix::s, and toupper().

Referenced by CNWAligner::GetTranscriptString(), CBandAligner::x_DoBackTrace(), CNWAligner::x_DoBackTrace(), CSplicedAligner16::x_DoBackTrace(), CSplicedAligner32::x_DoBackTrace(), CPSSMAligner::x_GetDiagTS(), and CNWAligner::x_SWDoBackTrace().

x_GetDiagTS() [2/2]

CNWAligner::ETranscriptSymbol CPSSMAligner::x_GetDiagTS ( size_t  i1, size_t  i2  ) const

protectedvirtual

Reimplemented from CNWAligner.

Definition at line 183 of file nw_pssm_aligner.cpp.

References CNWAligner::eTS_Match, CPSSMAligner::m_Freq1, CPSSMAligner::m_Pssm1, and CNWAligner::x_GetDiagTS().

x_Run()

CNWAligner::TScore CNWAligner::x_Run ( void  )

protectedvirtual

Reimplemented in CMMAligner.

Definition at line 533 of file nw_aligner.cpp.

References CNWAligner::CNWAlignerThread_Align, copy(), data, CNWAligner::eTS_Match, g_msg_OutOfSpace, CNWAligner::GetTranscript(), i, ITERATE, CNWAligner::m_esf_L1, CNWAligner::m_esf_L2, CNWAligner::m_esf_R1, CNWAligner::m_esf_R2, CNWAligner::m_guides, CNWAligner::m_maxthreads, CNWAligner::m_mt, CNWAligner::m_score, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, CNWAligner::m_terminate, CNWAligner::m_Transcript, NCBI_THROW, NON_CONST_ITERATE, NW_RequestNewThread(), CNWAligner::SAlignInOut::PSpace(), CThread::Run(), CNWAligner::ScoreFromTranscript(), and CNWAligner::x_Align().

Referenced by CNWAligner::Run(), and CPSSMAligner::Run().

x_SWDoBackTrace()

void CNWAligner::x_SWDoBackTrace ( const CBacktraceMatrix4 &  backtrace, SAlignInOut *  data  )

private

Definition at line 778 of file nw_aligner.cpp.

References CNWAligner::CBacktraceMatrix4::BestPos(), CNWAligner::CBacktraceMatrix4::BestScore(), data, CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, kMaskD, kMaskE, kMaskEc, kMaskFc, CNWAligner::m_ScoreMatrix, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CNWAligner::m_SmithWaterman, CNWAligner::m_Wg, CNWAligner::m_Ws, NCBI_FSM_DIM, NCBI_THROW, SNCBIFullScoreMatrix::s, and CNWAligner::x_GetDiagTS().

Referenced by CNWAligner::x_Align().

~CBacktraceMatrix4()

CNWAligner::CBacktraceMatrix4::~CBacktraceMatrix4 ( )

inline

Definition at line 344 of file nw_aligner.hpp.

~CBandAligner()

virtual CBandAligner::~CBandAligner ( void  )

inlinevirtual

Definition at line 71 of file nw_band_aligner.hpp.

~CNWAligner()

virtual CNWAligner::~CNWAligner ( void  )

inlinevirtual

Definition at line 88 of file nw_aligner.hpp.

~CPSSMAligner()

virtual CPSSMAligner::~CPSSMAligner ( void  )

inlinevirtual

Definition at line 76 of file nw_pssm_aligner.hpp.

Variable Documentation

kPSSM_ColumnSize

const int CPSSMAligner::kPSSM_ColumnSize = 28

staticprotected

Definition at line 131 of file nw_pssm_aligner.hpp.

Referenced by CPSSMAligner::ScoreFromTranscript(), CPSSMAligner::SetScoreMatrix(), CPSSMAligner::SetSequences(), and CPSSMAligner::x_AlignProfile().

m_abc

const char* CNWAligner::m_abc

protected

Definition at line 280 of file nw_aligner.hpp.

Referenced by CNWAligner::SetScoreMatrix(), and CNWAligner::x_CheckSequence().

m_band

size_t CBandAligner::m_band

protected

Definition at line 84 of file nw_band_aligner.hpp.

Referenced by CBandAligner::GetBand(), CBandAligner::SetBand(), CBandAligner::x_Align(), CBandAligner::x_CheckMemoryLimit(), CBandAligner::x_CheckParameters(), and CBandAligner::x_DoBackTrace().

m_BestPos

size_t CNWAligner::CBacktraceMatrix4::m_BestPos

private

Definition at line 383 of file nw_aligner.hpp.

m_BestScore

TNCBIScore CNWAligner::CBacktraceMatrix4::m_BestScore

private

Definition at line 384 of file nw_aligner.hpp.

m_Buf

Uint1* CNWAligner::CBacktraceMatrix4::m_Buf

private

Definition at line 381 of file nw_aligner.hpp.

m_data

void* CNWAligner::SProgressInfo::m_data

Definition at line 150 of file nw_aligner.hpp.

Referenced by s_ProgressCallback(), and CNWAligner::SetProgressCallback().

m_DScoreMatrix

double CPSSMAligner::m_DScoreMatrix[kPSSM_ColumnSize][kPSSM_ColumnSize]

protected

Definition at line 156 of file nw_pssm_aligner.hpp.

Referenced by CPSSMAligner::SetScoreMatrix(), and CPSSMAligner::x_AlignProfile().

m_Elem

Uint1 CNWAligner::CBacktraceMatrix4::m_Elem

private

Definition at line 382 of file nw_aligner.hpp.

m_EndWg

TScore CPSSMAligner::m_EndWg

protected

Definition at line 145 of file nw_pssm_aligner.hpp.

Referenced by CPSSMAligner::GetEndWg(), CPSSMAligner::ScoreFromTranscript(), CPSSMAligner::SetEndWg(), CPSSMAligner::SetWg(), CPSSMAligner::x_AlignProfile(), and CPSSMAligner::x_AlignPSSM().

m_EndWs

TScore CPSSMAligner::m_EndWs

protected

Definition at line 146 of file nw_pssm_aligner.hpp.

Referenced by CPSSMAligner::GetEndWs(), CPSSMAligner::ScoreFromTranscript(), CPSSMAligner::SetEndWs(), CPSSMAligner::SetWs(), CPSSMAligner::x_AlignProfile(), and CPSSMAligner::x_AlignPSSM().

m_esf_L1 [1/2]

bool CNWAligner::m_esf_L1

protected

Definition at line 274 of file nw_aligner.hpp.

Referenced by CNWAligner::GetEndSpaceFree(), CPSSMAligner::ScoreFromTranscript(), CNWAligner::ScoreFromTranscript(), CSplicedAligner16::ScoreFromTranscript(), CSplicedAligner32::ScoreFromTranscript(), CNWAligner::SetEndSpaceFree(), CNWAligner::SetSmithWaterman(), CNWAligner::x_Run(), CMMAligner::x_RunTerm(), and CMMAligner::x_RunTop().

m_esf_L1 [2/2]

bool CNWAligner::SAlignInOut::m_esf_L1

Definition at line 421 of file nw_aligner.hpp.

m_esf_L2 [1/2]

bool CNWAligner::m_esf_L2

protected

Definition at line 274 of file nw_aligner.hpp.

Referenced by CNWAligner::GetEndSpaceFree(), CPSSMAligner::ScoreFromTranscript(), CNWAligner::ScoreFromTranscript(), CSplicedAligner16::ScoreFromTranscript(), CSplicedAligner32::ScoreFromTranscript(), CNWAligner::SetEndSpaceFree(), CNWAligner::SetSmithWaterman(), CMMAligner::x_FindBestJ(), CNWAligner::x_Run(), CMMAligner::x_RunBtm(), CMMAligner::x_RunTerm(), and CMMAligner::x_RunTop().

m_esf_L2 [2/2]

bool CNWAligner::SAlignInOut::m_esf_L2

Definition at line 426 of file nw_aligner.hpp.

m_esf_R1 [1/2]

bool CNWAligner::m_esf_R1

protected

Definition at line 274 of file nw_aligner.hpp.

Referenced by CNWAligner::GetEndSpaceFree(), CPSSMAligner::ScoreFromTranscript(), CNWAligner::ScoreFromTranscript(), CSplicedAligner16::ScoreFromTranscript(), CSplicedAligner32::ScoreFromTranscript(), CNWAligner::SetEndSpaceFree(), CNWAligner::SetSmithWaterman(), CNWAligner::x_Run(), CMMAligner::x_RunBtm(), and CMMAligner::x_RunTerm().

m_esf_R1 [2/2]

bool CNWAligner::SAlignInOut::m_esf_R1

Definition at line 421 of file nw_aligner.hpp.

m_esf_R2 [1/2]

bool CNWAligner::m_esf_R2

protected

Definition at line 274 of file nw_aligner.hpp.

Referenced by CNWAligner::GetEndSpaceFree(), CPSSMAligner::ScoreFromTranscript(), CNWAligner::ScoreFromTranscript(), CSplicedAligner16::ScoreFromTranscript(), CSplicedAligner32::ScoreFromTranscript(), CNWAligner::SetEndSpaceFree(), CNWAligner::SetSmithWaterman(), CMMAligner::x_FindBestJ(), CNWAligner::x_Run(), CMMAligner::x_RunBtm(), CMMAligner::x_RunTerm(), and CMMAligner::x_RunTop().

m_esf_R2 [2/2]

bool CNWAligner::SAlignInOut::m_esf_R2

Definition at line 426 of file nw_aligner.hpp.

m_Finish

template<class THit >

TCoord CHitCoverageAccumulator< THit >::m_Finish

private

Definition at line 104 of file hit_filter.hpp.

Referenced by CHitCoverageAccumulator< THit >::operator()().

m_Freq1

const double** CPSSMAligner::m_Freq1

protected

Definition at line 135 of file nw_pssm_aligner.hpp.

Referenced by CPSSMAligner::GetFreq1(), CPSSMAligner::ScoreFromTranscript(), CPSSMAligner::SetSequences(), CPSSMAligner::x_Align(), CPSSMAligner::x_AlignProfile(), and CPSSMAligner::x_GetDiagTS().

m_Freq2

const double** CPSSMAligner::m_Freq2

protected

Definition at line 138 of file nw_pssm_aligner.hpp.

Referenced by CPSSMAligner::GetFreq2(), CPSSMAligner::ScoreFromTranscript(), CPSSMAligner::SetSequences(), and CPSSMAligner::x_AlignProfile().

m_FreqScale

int CPSSMAligner::m_FreqScale

protected

Definition at line 141 of file nw_pssm_aligner.hpp.

Referenced by CPSSMAligner::GetFreqScale(), CPSSMAligner::ScoreFromTranscript(), CPSSMAligner::SetFreqScale(), CPSSMAligner::SetSequences(), and CPSSMAligner::x_AlignProfile().

m_GapPreference

EGapPreference CNWAligner::m_GapPreference

protected

Definition at line 277 of file nw_aligner.hpp.

Referenced by CNWAligner::GetGapPreference(), CNWAligner::SetGapPreference(), and CNWAligner::x_Align().

m_guides

vector<size_t> CNWAligner::m_guides

protected

Definition at line 317 of file nw_aligner.hpp.

Referenced by CNWAligner::MakePattern(), CNWAligner::Run(), CNWAligner::SetPattern(), CNWAligner::x_CheckMemoryLimit(), CBandAligner::x_CheckMemoryLimit(), and CNWAligner::x_Run().

m_i1

template<class THit >

Uint1 CHitCoverageAccumulator< THit >::m_i1

private

Definition at line 105 of file hit_filter.hpp.

Referenced by CHitCoverageAccumulator< THit >::CHitCoverageAccumulator(), and CHitCoverageAccumulator< THit >::operator()().

m_i2

template<class THit >

Uint1 CHitCoverageAccumulator< THit >::m_i2

private

Definition at line 105 of file hit_filter.hpp.

Referenced by CHitCoverageAccumulator< THit >::CHitCoverageAccumulator(), and CHitCoverageAccumulator< THit >::operator()().

m_iter_done

size_t CNWAligner::SProgressInfo::m_iter_done

Definition at line 148 of file nw_aligner.hpp.

Referenced by s_ProgressCallback(), CBandAligner::x_Align(), CSplicedAligner16::x_Align(), CNWAligner::x_Align(), CPSSMAligner::x_AlignProfile(), CPSSMAligner::x_AlignPSSM(), CMMAligner::x_Run(), CMMAligner::x_RunBtm(), and CMMAligner::x_RunTop().

m_iter_total

size_t CNWAligner::SProgressInfo::m_iter_total

Definition at line 149 of file nw_aligner.hpp.

Referenced by s_ProgressCallback(), CBandAligner::x_Align(), CSplicedAligner16::x_Align(), CNWAligner::x_Align(), CPSSMAligner::x_AlignProfile(), CPSSMAligner::x_AlignPSSM(), and CMMAligner::x_Run().

m_LastCoordSeq1

size_t CBandAligner::m_LastCoordSeq1

protected

Definition at line 91 of file nw_band_aligner.hpp.

Referenced by CBandAligner::x_Align(), and CBandAligner::x_DoBackTrace().

m_LastCoordSeq2

size_t CBandAligner::m_LastCoordSeq2

protected

Definition at line 92 of file nw_band_aligner.hpp.

Referenced by CBandAligner::x_Align(), and CBandAligner::x_DoBackTrace().

m_len1

size_t CNWAligner::SAlignInOut::m_len1

Definition at line 420 of file nw_aligner.hpp.

Referenced by CNWAligner::SAlignInOut::SAlignInOut().

m_len2

size_t CNWAligner::SAlignInOut::m_len2

Definition at line 425 of file nw_aligner.hpp.

Referenced by CNWAligner::SAlignInOut::FillEdgeGaps(), and CNWAligner::SAlignInOut::SAlignInOut().

m_MaxMem

size_t CNWAligner::m_MaxMem

protected

Definition at line 324 of file nw_aligner.hpp.

Referenced by CNWAligner::x_CheckMemoryLimit(), and CBandAligner::x_CheckMemoryLimit().

m_maxthreads

size_t CNWAligner::m_maxthreads

protected

Definition at line 321 of file nw_aligner.hpp.

Referenced by CNWAligner::EnableMultipleThreads(), CMMAligner::x_DoSubmatrix(), and CNWAligner::x_Run().

m_mt

bool CNWAligner::m_mt

protected

Definition at line 320 of file nw_aligner.hpp.

Referenced by CNWAligner::EnableMultipleThreads(), CMMAligner::x_DoSubmatrix(), and CNWAligner::x_Run().

m_offset1

size_t CNWAligner::SAlignInOut::m_offset1

Definition at line 419 of file nw_aligner.hpp.

m_offset2

size_t CNWAligner::SAlignInOut::m_offset2

Definition at line 424 of file nw_aligner.hpp.

m_Point

template<class THit >

Uint1 CHitFilter< THit >::SHitEnd::m_Point

Definition at line 592 of file hit_filter.hpp.

Referenced by CHitFilter< THit >::SHitEnd::operator<(), CHitFilter< THit >::s_MergeAbutting(), CHitFilter< THit >::s_RunGreedy(), CHitFilter< THit >::sx_AddMidIfNeeded(), CHitFilter< THit >::sx_GetEndsInRange(), and CHitFilter< THit >::sx_TM().

m_PositivesAsMatches

bool CNWAligner::m_PositivesAsMatches

protected

Definition at line 315 of file nw_aligner.hpp.

Referenced by CNWAligner::x_GetDiagTS().

m_prg_callback

FProgressCallback CNWAligner::m_prg_callback

protected

Definition at line 285 of file nw_aligner.hpp.

Referenced by CNWAligner::SetProgressCallback(), CBandAligner::x_Align(), CSplicedAligner16::x_Align(), CNWAligner::x_Align(), CPSSMAligner::x_AlignProfile(), CPSSMAligner::x_AlignPSSM(), CMMAligner::x_Run(), CMMAligner::x_RunBtm(), and CMMAligner::x_RunTop().

m_prg_info

SProgressInfo CNWAligner::m_prg_info

mutableprotected

Definition at line 288 of file nw_aligner.hpp.

Referenced by CNWAligner::SetProgressCallback(), CBandAligner::x_Align(), CSplicedAligner16::x_Align(), CNWAligner::x_Align(), CPSSMAligner::x_AlignProfile(), CPSSMAligner::x_AlignPSSM(), CMMAligner::x_Run(), CMMAligner::x_RunBtm(), and CMMAligner::x_RunTop().

m_Pssm1

const TScore** CPSSMAligner::m_Pssm1

protected

Definition at line 134 of file nw_pssm_aligner.hpp.

Referenced by CPSSMAligner::GetPssm1(), CPSSMAligner::ScoreFromTranscript(), CPSSMAligner::SetSequences(), CPSSMAligner::x_Align(), CPSSMAligner::x_AlignPSSM(), and CPSSMAligner::x_GetDiagTS().

m_Ptr

template<class THit >

THitRef* CHitFilter< THit >::SHitEnd::m_Ptr

Definition at line 593 of file hit_filter.hpp.

Referenced by CHitFilter< THit >::SHitEnd::operator<(), CHitFilter< THit >::s_MergeAbutting(), CHitFilter< THit >::s_RunGreedy(), CHitFilter< THit >::sx_AddMidIfNeeded(), CHitFilter< THit >::sx_GetEndsInRange(), and CHitFilter< THit >::sx_TM().

m_score

TScore CNWAligner::m_score

protected

Definition at line 316 of file nw_aligner.hpp.

Referenced by CNWAligner::GetScore(), CNWAligner::Run(), CPSSMAligner::Run(), CNWAligner::SetTranscript(), CMMAligner::x_DoSubmatrix(), CMMAligner::x_Run(), and CNWAligner::x_Run().

m_ScoreMatrix

SNCBIFullScoreMatrix CNWAligner::m_ScoreMatrix

protected

Definition at line 281 of file nw_aligner.hpp.

Referenced by CPSSMAligner::GetMatrix(), CPSSMAligner::ScoreFromTranscript(), CNWAligner::ScoreFromTranscript(), CSplicedAligner16::ScoreFromTranscript(), CSplicedAligner32::ScoreFromTranscript(), CNWAligner::SetScoreMatrix(), CPSSMAligner::SetScoreMatrix(), CBandAligner::x_Align(), CSplicedAligner16::x_Align(), CSplicedAligner32::x_Align(), CNWAligner::x_Align(), CNWAligner::x_GetDiagTS(), CMMAligner::x_RunBtm(), CMMAligner::x_RunTerm(), CMMAligner::x_RunTop(), and CNWAligner::x_SWDoBackTrace().

m_ScoreMatrixInvalid

bool CNWAligner::m_ScoreMatrixInvalid

protected

Definition at line 282 of file nw_aligner.hpp.

Referenced by CNWAligner::Run(), CNWAligner::SetScoreMatrix(), CNWAligner::SetWm(), and CNWAligner::SetWms().

m_Seq1

const char* CNWAligner::m_Seq1

protected

Definition at line 295 of file nw_aligner.hpp.

Referenced by CNWAligner::GetLeftSeg(), CNWAligner::GetLongestSeg(), CNWAligner::GetRightSeg(), CPSSMAligner::GetSeq1(), CNWAligner::GetTranscriptString(), CNWAligner::MakePattern(), CNWAligner::Run(), CNWAligner::ScoreFromTranscript(), CSplicedAligner16::ScoreFromTranscript(), CSplicedAligner32::ScoreFromTranscript(), CNWAligner::SetSequences(), CPSSMAligner::SetSequences(), CBandAligner::x_Align(), CSplicedAligner16::x_Align(), CSplicedAligner32::x_Align(), CNWAligner::x_Align(), CNWAligner::x_GetDiagTS(), CMMAligner::x_RunBtm(), CMMAligner::x_RunTerm(), CMMAligner::x_RunTop(), and CNWAligner::x_SWDoBackTrace().

m_Seq1Vec

vector<char> CNWAligner::m_Seq1Vec

protected

Definition at line 294 of file nw_aligner.hpp.

Referenced by CNWAligner::SetSequences().

m_Seq2 [1/2]

const char* CNWAligner::m_Seq2

protected

Definition at line 298 of file nw_aligner.hpp.

Referenced by CNWAligner::GetLeftSeg(), CNWAligner::GetLongestSeg(), CNWAligner::GetRightSeg(), CNWAligner::GetTranscriptString(), CNWAligner::MakePattern(), CNWAligner::Run(), CNWAligner::ScoreFromTranscript(), CSplicedAligner16::ScoreFromTranscript(), CSplicedAligner32::ScoreFromTranscript(), CNWAligner::SetSequences(), CPSSMAligner::SetSequences(), CBandAligner::x_Align(), CSplicedAligner16::x_Align(), CSplicedAligner32::x_Align(), CNWAligner::x_Align(), CNWAligner::x_GetDiagTS(), CMMAligner::x_RunBtm(), CMMAligner::x_RunTerm(), CMMAligner::x_RunTop(), and CNWAligner::x_SWDoBackTrace().

m_Seq2 [2/2]

const char* CPSSMAligner::m_Seq2

protected

Definition at line 137 of file nw_pssm_aligner.hpp.

Referenced by CPSSMAligner::ScoreFromTranscript(), CPSSMAligner::SetSequences(), and CPSSMAligner::x_AlignPSSM().

m_Seq2Vec

vector<char> CNWAligner::m_Seq2Vec

protected

Definition at line 297 of file nw_aligner.hpp.

Referenced by CNWAligner::SetSequences().

m_SeqLen1

size_t CNWAligner::m_SeqLen1

protected

Definition at line 296 of file nw_aligner.hpp.

Referenced by CNWAligner::GetRightSeg(), CNWAligner::MakePattern(), CPSSMAligner::ScoreFromTranscript(), CNWAligner::SetPattern(), CNWAligner::SetSequences(), CPSSMAligner::SetSequences(), CSplicedAligner16::x_Align(), CSplicedAligner32::x_Align(), CNWAligner::x_Align(), CPSSMAligner::x_AlignProfile(), CPSSMAligner::x_AlignPSSM(), CNWAligner::x_CheckMemoryLimit(), CBandAligner::x_CheckMemoryLimit(), CMMAligner::x_DoSubmatrix(), CMMAligner::x_Run(), CNWAligner::x_Run(), CMMAligner::x_RunBtm(), and CMMAligner::x_RunTerm().

m_SeqLen2

size_t CNWAligner::m_SeqLen2

protected

Definition at line 299 of file nw_aligner.hpp.

Referenced by CNWAligner::GetRightSeg(), CNWAligner::MakePattern(), CPSSMAligner::ScoreFromTranscript(), CNWAligner::SetPattern(), CNWAligner::SetSequences(), CPSSMAligner::SetSequences(), CSplicedAligner16::x_Align(), CSplicedAligner32::x_Align(), CNWAligner::x_Align(), CPSSMAligner::x_AlignProfile(), CPSSMAligner::x_AlignPSSM(), CNWAligner::x_CheckMemoryLimit(), CBandAligner::x_CheckMemoryLimit(), CMMAligner::x_DoSubmatrix(), CMMAligner::x_FindBestJ(), CMMAligner::x_Run(), CNWAligner::x_Run(), CMMAligner::x_RunBtm(), CMMAligner::x_RunTerm(), and CMMAligner::x_RunTop().

m_Shift

long CBandAligner::m_Shift

protected

Definition at line 87 of file nw_band_aligner.hpp.

Referenced by CBandAligner::GetShift(), CBandAligner::SetShift(), CBandAligner::x_Align(), CBandAligner::x_CheckParameters(), and CBandAligner::x_DoBackTrace().

m_SmithWaterman

bool CNWAligner::m_SmithWaterman

protected

Definition at line 275 of file nw_aligner.hpp.

Referenced by CNWAligner::IsSmithWaterman(), CNWAligner::Run(), CNWAligner::SetSmithWaterman(), CNWAligner::x_Align(), and CNWAligner::x_SWDoBackTrace().

m_space

size_t CNWAligner::SAlignInOut::m_space

private

Definition at line 451 of file nw_aligner.hpp.

Referenced by CNWAligner::SAlignInOut::GetSpace(), CNWAligner::SAlignInOut::PSpace(), and CNWAligner::SAlignInOut::SAlignInOut().

m_StartWg

TScore CPSSMAligner::m_StartWg

protected

Definition at line 143 of file nw_pssm_aligner.hpp.

Referenced by CPSSMAligner::GetStartWg(), CPSSMAligner::ScoreFromTranscript(), CPSSMAligner::SetStartWg(), CPSSMAligner::SetWg(), CPSSMAligner::x_AlignProfile(), and CPSSMAligner::x_AlignPSSM().

m_StartWs

TScore CPSSMAligner::m_StartWs

protected

Definition at line 144 of file nw_pssm_aligner.hpp.

Referenced by CPSSMAligner::GetStartWs(), CPSSMAligner::ScoreFromTranscript(), CPSSMAligner::SetStartWs(), CPSSMAligner::SetWs(), CPSSMAligner::x_AlignProfile(), and CPSSMAligner::x_AlignPSSM().

m_terminate

bool CNWAligner::m_terminate

mutableprotected

Definition at line 291 of file nw_aligner.hpp.

Referenced by CBandAligner::x_Align(), CSplicedAligner16::x_Align(), CNWAligner::x_Align(), CPSSMAligner::x_AlignProfile(), CPSSMAligner::x_AlignPSSM(), CMMAligner::x_DoSubmatrix(), CMMAligner::x_Run(), CNWAligner::x_Run(), CMMAligner::x_RunBtm(), CMMAligner::x_RunTerm(), and CMMAligner::x_RunTop().

m_TermK

size_t CBandAligner::m_TermK

protected

Definition at line 90 of file nw_band_aligner.hpp.

Referenced by CBandAligner::x_Align(), and CBandAligner::x_DoBackTrace().

m_text_buffer

char CNWAligner::SProgressInfo::m_text_buffer[1024]

Definition at line 151 of file nw_aligner.hpp.

m_Transcript

TTranscript CNWAligner::m_Transcript

protected

Definition at line 314 of file nw_aligner.hpp.

Referenced by CSplicedAligner::CheckPreferences(), CNWAligner::GetLeftSeg(), CNWAligner::GetLongestSeg(), CNWAligner::GetRightSeg(), CNWAligner::GetScore(), CNWAligner::GetTranscript(), CNWAligner::GetTranscriptString(), CNWAligner::SetSequences(), CNWAligner::SetTranscript(), CMMAligner::x_Run(), and CNWAligner::x_Run().

m_transcript

TTranscript CNWAligner::SAlignInOut::m_transcript

Definition at line 429 of file nw_aligner.hpp.

Referenced by CNWAligner::SAlignInOut::FillEdgeGaps().

m_Wg

TScore CNWAligner::m_Wg

protected

Definition at line 270 of file nw_aligner.hpp.

Referenced by CPSSMAligner::ScoreFromTranscript(), CNWAligner::ScoreFromTranscript(), CSplicedAligner16::ScoreFromTranscript(), CSplicedAligner32::ScoreFromTranscript(), CPSSMAligner::SetWg(), CBandAligner::x_Align(), CSplicedAligner16::x_Align(), CSplicedAligner32::x_Align(), CNWAligner::x_Align(), CPSSMAligner::x_AlignProfile(), CPSSMAligner::x_AlignPSSM(), CMMAligner::x_FindBestJ(), CMMAligner::x_RunBtm(), CMMAligner::x_RunTerm(), CMMAligner::x_RunTop(), and CNWAligner::x_SWDoBackTrace().

m_Where

template<class THit >

Uint1 CHitCoverageAccumulator< THit >::m_Where

private

Definition at line 103 of file hit_filter.hpp.

Referenced by CHitCoverageAccumulator< THit >::CHitCoverageAccumulator().

m_Wm

TScore CNWAligner::m_Wm

protected

Definition at line 268 of file nw_aligner.hpp.

Referenced by CNWAligner::ScoreFromTranscript(), CSplicedAligner16::ScoreFromTranscript(), CSplicedAligner32::ScoreFromTranscript(), CNWAligner::SetScoreMatrix(), and CNWAligner::SetWm().

m_Wms

TScore CNWAligner::m_Wms

protected

Definition at line 269 of file nw_aligner.hpp.

Referenced by CNWAligner::ScoreFromTranscript(), CSplicedAligner16::ScoreFromTranscript(), CSplicedAligner32::ScoreFromTranscript(), CNWAligner::SetScoreMatrix(), and CNWAligner::SetWms().

m_Ws

TScore CNWAligner::m_Ws

protected

Definition at line 271 of file nw_aligner.hpp.

Referenced by CPSSMAligner::ScoreFromTranscript(), CNWAligner::ScoreFromTranscript(), CSplicedAligner16::ScoreFromTranscript(), CSplicedAligner32::ScoreFromTranscript(), CPSSMAligner::SetWs(), CBandAligner::x_Align(), CSplicedAligner16::x_Align(), CSplicedAligner32::x_Align(), CNWAligner::x_Align(), CPSSMAligner::x_AlignProfile(), CPSSMAligner::x_AlignPSSM(), CMMAligner::x_RunBtm(), CMMAligner::x_RunTerm(), CMMAligner::x_RunTop(), and CNWAligner::x_SWDoBackTrace().

m_X

template<class THit >

TCoord CHitFilter< THit >::SHitEnd::m_X

Definition at line 594 of file hit_filter.hpp.

Referenced by CHitFilter< THit >::SHitEnd::operator<(), CHitFilter< THit >::s_MergeAbutting(), CHitFilter< THit >::s_RunGreedy(), CHitFilter< THit >::sx_AddMidIfNeeded(), CHitFilter< THit >::sx_GetEndsInRange(), and CHitFilter< THit >::sx_TM().

Friends

CNWAlignerThread_Align

friend class CNWAlignerThread_Align

friend

Definition at line 400 of file nw_aligner.hpp.

Referenced by CNWAligner::x_Run().

operator<<

template<class THit >

ostream& operator<< ( ostream &  ostr, const SHitEnd &  he  )

friend

Definition at line 607 of file hit_filter.hpp.