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

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1 #ifndef ALGO_ALIGN__NW_FORMAT__HPP 2 #define ALGO_ALIGN__NW_FORMAT__HPP 76

eSAFF_DynProgScore = 1,

88 void

AsText(

string

output

, ETextFormatType

type

89 size_t

line_width = 100)

const

;

97 int

SAFF_flags = eSAFF_None)

const

;

102 int

SAFF_flags = eSAFF_None)

const

;

122 void

ImproveFromLeft(

const char

* seq1,

const char

* seq2,

124 void

ImproveFromRight(

const char

* seq1,

const char

* seq2,

128 void

ImproveFromLeft1(

const char

* seq1,

const char

* seq2,

130 void

ImproveFromRight1(

const char

* seq1,

const char

* seq2,

134 bool

IsLowComplexityExon(

const char

*rna_seq);

137 int

CanExtendRight(

const

vector<char>& mrna,

const

vector<char>& genomic)

const

;

138 int

CanExtendLeft(

const

vector<char>& mrna,

const

vector<char>& genomic)

const

;

141 void

ExtendRight(

const

vector<char>& mrna,

const

vector<char>& genomic,

Int8

ext_len,

const CNWAligner

* aligner);

142 void

ExtendLeft(

const

vector<char>& mrna,

const

vector<char>& genomic,

Int8

ext_len,

const CNWAligner

* aligner);

145 const char

GetDonor

(

void

)

const

;

149 static bool

s_IsConsensusSplice(

const char

* donor,

const char

* acceptor,

150 bool

semi_as_cons =

false

);

159 void

MakeSegments(vector<SSegment>* psegments)

const

;

160 void

MakeSegments(deque<SSegment>* psegments)

const

;

167 size_t

x_ApplyTranscript(vector<char>* seq1_transformed,

168

vector<char>* seq2_transformed)

const

;

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

static SQLCHAR output[256]

const CNWAligner * m_aligner

CConstRef< objects::CSeq_id > m_Seq2Id

vector< char > TNetCacheBuffer

unsigned int TSeqPos

Type for sequence locations and lengths.

int64_t Int8

8-byte (64-bit) signed 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.

#define NCBI_XALGOALIGN_EXPORT

ENa_strand

strand of nucleic acid

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

string GetAcceptor(const objects::CSpliced_exon &exon)

string GetDonor(const objects::CSpliced_exon &exon)

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