Implements the stral-like scoring function.
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#include <stral_score.hh>
Implements the stral-like scoring function.
| LocARNA::StralScore::StralScore |
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const RnaData & |
rnaA, |
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const RnaData & |
rnaB, |
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const Matrix< double > & |
sim_mat_, |
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const Alphabet< char > & |
alphabet_, |
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double |
pf_struct_weight_, |
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double |
gap_opening_, |
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double |
gap_extension_ |
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) |
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Construct for pair of RNAs with parameters for alignment
- Parameters
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| rnaA | data of first RNA |
| rnaB | data of second RNA |
| sim_mat_ | similarity matrix for bases |
| alphabet_ | alphabet |
| pf_struct_weight_ | structure weight |
| gap_opening_ | gap opening cost |
| gap_extension_ | gap extension cost |
| double LocARNA::StralScore::alpha |
( |
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const |
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inline |
Read gap opening cost.
- Returns
- gap opening cost
| double LocARNA::StralScore::beta |
( |
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const |
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inline |
Read gap extension cost.
- Returns
- gap extension cost
| void LocARNA::StralScore::reverse |
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Reverse the scoring.
- Postcondition
- the object scores the reverted RNAs
Compute STRAL-like similarity of two residues in the two RNAs.
- Parameters
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| i | position in sequence A |
| j | position in sequence B |
- Note
- Computes the average similarity over all pairs of alignment rows in the RNA sequence, which are alignments in general.
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The treatment of gaps and unknown nucleotide symbols in the aligned alignments is quite ad hoc.
- Returns
- similarity of residues i in A and j in B.
The documentation for this class was generated from the following files:
1.8.11
