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NCBI C++ ToolKit: include/algo/align/nw/nw_aligner.hpp Source File

* seq2,

len2,

TScore

(

);

objects::CSeq_loc &loc1,

objects::CSeq_loc &loc2,

trim_end_gaps =

);

objects::CSeq_id &id1,

objects::CSeq_id &id2,

trim_end_gaps =

);

SetSequences(

* seq1,

len1,

* seq2,

len2,

SetSequences(

& seq1,

SetWm (TScore

);

SetWms (TScore

);

SetEndSpaceFree(

Left1,

Right1,

Left2,

Right2);

SetSmithWaterman(

);

SetGapPreference(EGapPreference p);

SetPattern(

vector<size_t>& pattern);

m_text_buffer [1024];

SetProgressCallback ( FProgressCallback prg_callback,

*

);

*

(

)

{

m_Seq1; }

*

(

)

{

m_Seq2; }

GetEndSpaceFree(

* L1,

* R1,

* L2,

* R2)

IsSmithWaterman()

;

EGapPreference GetGapPreference()

;

TScore GetScore(

)

;

GetTranscript(

reversed =

)

;

SetTranscript(

& transcript);

GetTranscriptString(

)

;

m_PositivesAsMatches = positives_as_matches;

m_PositivesAsMatches;

GetLeftSeg(

* q0,

* q1,

* s0,

* s1,

min_size)

;

GetRightSeg(

* q0,

* q1,

* s0,

* s1,

min_size)

;

GetLongestSeg(

* q0,

* q1,

* s0,

* s1)

;

TScore ScoreFromTranscript(

TTranscript& transcript,

EnableMultipleThreads(

enable =

);

MakePattern(

hit_size = 100,

core_size = 28);

trim_end_gaps =

)

objects::CSeq_id& query_id,

objects::CSeq_id& subj_id,

trim_end_gaps =

)

x_CheckSequence(

* seq,

)

;

x_CheckMemoryLimit(

);

x_CalcFingerPrint64(

* beg,

& err_index );

* x_FindFingerPrint64(

* beg,

fingerprint,

& err_index );

x_Run (

);

m_Buf =

[dim / 2 + 1];

m_Buf[

>> 1] = m_Elem | (v << 4);

m_Buf[

>> 1] = m_Elem;

0x0F & ((m_Buf[

>> 1]) >> ((

& 1) << 2));

(

offset1,

len1,

esfL1,

esfR1,

offset2,

len2,

esfL2,

esfR2):

g_nwaligner_nucleotides [] =

;

Include a standard set of the NCBI C++ Toolkit most basic headers.

void SetBestPos(size_t k)

void SetAt(size_t i, Uint1 v)

size_t GetSpaceLimit(void) const

void SetSpaceLimit(const size_t &maxmem)

static TScore GetDefaultWg(void)

void FillEdgeGaps(size_t len, bool seq1_gap_fist)

const char * GetSeq2(void) const

const SNCBIFullScoreMatrix & GetScoreMatrix(void) const

vector< size_t > m_guides

SNCBIFullScoreMatrix m_ScoreMatrix

const char * GetSeq1(void) const

CBacktraceMatrix4(size_t dim)

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

bool GetPositivesAsMatches(void) const

void SetBestScore(TNCBIScore score)

static size_t GetDefaultSpaceLimit(void)

static TScore GetDefaultWms(void)

static TScore GetDefaultWs(void)

size_t GetSeqLen2(void) const

TScore GetWms(void) const

bool m_ScoreMatrixInvalid

FProgressCallback m_prg_callback

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

size_t GetSpace(void) const

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

TNCBIScore BestScore() const

vector< ETranscriptSymbol > TTranscript

size_t GetSeqLen1(void) const

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

bool m_PositivesAsMatches

EGapPreference m_GapPreference

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

virtual size_t GetElemSize(void) const

virtual ~CNWAligner(void)

void SetPositivesAsMatches(bool positives_as_matches=true)

static TScore GetDefaultWm(void)

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

unsigned int TSeqPos

Type for sequence locations and lengths.

uint8_t Uint1

1-byte (8-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

void Run(void)

Enter the main loop.

#define NCBI_XALGOALIGN_EXPORT

ENa_strand

strand of nucleic acid

const struct ncbi::grid::netcache::search::fields::SIZE size

const GenericPointer< typename T::ValueType > T2 value

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

int TNCBIScore

data types

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