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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/hmm__inlines_8hpp_source.html below:

NCBI C++ ToolKit: src/algo/gnomon/hmm_inlines.hpp Source File

1 #ifndef ALGO_GNOMON___HMM_INLINES__HPP 2 #define ALGO_GNOMON___HMM_INLINES__HPP 54

CMarkov_chain_params::TProbabilities::const_iterator

i

= from.

GetProbabilities

().begin();

55

m_next[

enA

].Init((*

i

++)->GetPrev_order());

56

m_next[

enC

].Init((*

i

++)->GetPrev_order());

57

m_next[

enG

].Init((*

i

++)->GetPrev_order());

58

m_next[

enT

].Init((*

i

++)->GetPrev_order());

61

m_next[

enN

].Average(m_next[

enA

],m_next[

enC

],m_next[

enG

],m_next[

enT

]);

70

m_next[

enN

].Average(m_next[

enA

],m_next[

enC

],m_next[

enG

],m_next[

enT

]);

75

m_next[

enA

].toScore();

76

m_next[

enC

].toScore();

77

m_next[

enG

].toScore();

78

m_next[

enT

].toScore();

79

m_next[

enN

].toScore();

85  for

(

int i

= 0;

i

< m_length; ++

i

)

87  double

s = m_mc[

i

].Score(seq+

i

);

97

m_mc.resize(m_length);

98

CMarkov_chain_array::TMatrix::const_iterator mc = from.

GetMatrix

().begin();

99  for

(

int i

= 0;

i

< m_length; ++

i

) m_mc[

i

].InitScore(**mc++);

104 template

<

int

order>

108  int last

=

i

+m_right;

109  if

(

first

-order < 0 || last >= (

int

)seq.size())

return BadScore

();

113  return

m_matrix.Score(&seq[

first

]);

116 template

<

int

order>

123

m_right = m_inintron;

125

m_matrix.InitScore(m_inexon+m_inintron,from.

GetDonor

());

129 template

<

int

order>

133  int last

=

i

+m_right;

134  if

(

first

-order < 0 || last >= (

int

)seq.size())

return BadScore

();

137  return

m_matrix.Score(&seq[

first

]);

140 template

<

int

order>

149

m_matrix.InitScore(m_inexon+m_inintron,from.

GetAcceptor

());

153 template

<

int

order>

159

m_matrix[

i

++].InitScore(**p);

165 template

<

int

order>

170  else return

m_matrix[codonshift].Score(&seq[

i

]);

173 template

<

int

order>

179 template

<

int

order>

183  return

m_matrix.Score(&seq[

i

]);

188  int len

=

r

.Stop()-

r

.Start()+1;

189  if

(

len

>=

r

.MaxLen() ||

r

.StopInside())

return

;

199  if

(

len

< minlen)

return

;

203  if

(

r

.NoRightEnd())

205

score =

r

.ThroughLengthScore();

209

score =

r

.InitialLengthScore();

218  if

(!

r

.NoRightEnd())

220

scr =

r

.TermScore();

225  if

(

r

.OpenRgn())

r

.UpdateScore(score);

static void Error(const string &label)

double Score(const CEResidueVec &seq, int i, int codonshift) const

CMC3_CodingRegion(const objects::CGnomon_param::C_Param &from)

double Score(const CEResidueVec &seq, int i) const

CMC_NonCodingRegion(const objects::CGnomon_param::C_Param &from)

void InitScore(int l, const objects::CMarkov_chain_array &from)

double Score(const EResidue *seq) const

void Init(const objects::CMarkov_chain_params &hmm_param_asn)

CMarkovChain< order-1 > m_next[5]

void Average(Type &mc0, Type &mc1, Type &mc2, Type &mc3)

CMarkov_chain_params –.

CWAM_Acceptor(const objects::CGnomon_param::C_Param &from)

double Score(const CEResidueVec &seq, int i) const

double Score(const CEResidueVec &seq, int i) const

CWAM_Donor(const objects::CGnomon_param::C_Param &from)

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

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

static DLIST_TYPE *DLIST_NAME() last(DLIST_LIST_TYPE *list)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

void Error(CExceptionArgs_Base &args)

#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.

const TNon_coding_region & GetNon_coding_region(void) const

Get the variant data.

TIn_intron GetIn_intron(void) const

Get the In_intron member data.

TIn_exon GetIn_exon(void) const

Get the In_exon member data.

const TProbabilities & GetProbabilities(void) const

Get the Probabilities member data.

const TDonor & GetDonor(void) const

Get the variant data.

const TAcceptor & GetAcceptor(void) const

Get the variant data.

list< CRef< CMarkov_chain_params > > TCoding_region

const TCoding_region & GetCoding_region(void) const

Get the variant data.

const TMatrix & GetMatrix(void) const

Get the Matrix member data.

TOrder GetOrder(void) const

Get the Order member data.

void EvaluateInitialScore(State &r)

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

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