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hmm_score.hh
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1 //------------------------------------------------------------------------------
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18 //------------------------------------------------------------------------------
19 
20 #ifndef OST_SEQ_ALG_HMM_SCORE_HH
21 #define OST_SEQ_ALG_HMM_SCORE_HH
22 
25 
26 namespace ost{ namespace seq{ namespace alg{
27 
28 Real HMMScore(const ost::seq::ProfileHandle& profile_0,
29  const ost::seq::ProfileHandle& profile_1,
30  const ost::seq::AlignmentHandle& aln,
31  int seq_0_idx, int seq_1_idx,
32  Real match_score_offset = -0.03,
33  Real correl_score_weight = 0.1,
34  Real del_start_penalty_factor=0.6,
35  Real del_extend_penalty_factor=0.6,
36  Real ins_start_penalty_factor=0.6,
37  Real ins_extend_penalty_factor=0.6);
38 
39 }}} // ns
40 
41 #endif
float Real
Definition: base.hh:44
Provides a profile for a sequence.
Real HMMScore(const ost::seq::ProfileHandle &profile_0, const ost::seq::ProfileHandle &profile_1, const ost::seq::AlignmentHandle &aln, int seq_0_idx, int seq_1_idx, Real match_score_offset=-0.03, Real correl_score_weight=0.1, Real del_start_penalty_factor=0.6, Real del_extend_penalty_factor=0.6, Real ins_start_penalty_factor=0.6, Real ins_extend_penalty_factor=0.6)
representation of a multiple sequence alignemnt consisting of two or more sequences ...