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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/nw__pssm__aligner_8hpp_source.html below:

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

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1 #ifndef ALGO___NW_PSSM_ALIGNER__HPP 2 #define ALGO___NW_PSSM_ALIGNER__HPP 69  const char

* seq2,

size_t

len2);

72  const double

** freq2,

size_t

len2,

83  const char

* seq2,

size_t

len2,

87  const char

* seq2,

size_t

len2,

91  const double

** freq2,

size_t

len2,

100

m_StartWg = m_Wg = m_EndWg =

value

;

104

m_StartWs = m_Ws = m_EndWs =

value

;

114  const double

**

GetFreq1

()

const

{

return

m_Freq1;}

115  const double

**

GetFreq2

()

const

{

return

m_Freq2;}

126  size_t

start2 = 0)

const

;

131  static const int

kPSSM_ColumnSize = 28;

156  double

m_DScoreMatrix[kPSSM_ColumnSize][kPSSM_ColumnSize];

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

void SetStartWg(TScore value)

const CNWAligner::TScore ** GetPssm1() const

const double ** GetFreq1() const

const char * GetSeq1() const

virtual TScore x_Align(SAlignInOut *data)

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

virtual ETranscriptSymbol x_GetDiagTS(size_t i1, size_t i2) const

const double ** GetFreq2() const

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

SNCBIFullScoreMatrix m_ScoreMatrix

void SetEndWs(TScore value)

TScore GetStartWs() const

SNCBIFullScoreMatrix & GetMatrix()

void SetFreqScale(const int scale)

void SetEndWg(TScore value)

virtual ~CPSSMAligner(void)

void SetScoreMatrix(const SNCBIPackedScoreMatrix *scoremat)

TScore GetStartWg() const

void SetStartWs(TScore value)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_XALGOALIGN_EXPORT

const GenericPointer< typename T::ValueType > T2 value

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

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