Implements the stral-like scoring function.
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#include <stral_score.hh>
Implements the stral-like scoring function.
- Note
- unlike the integer scores in locarna, which are scaled by factor 100, the double scores in this class are usually not scaled.
◆ StralScore()
| LocARNA::StralScore::StralScore |
( |
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, 4 > & |
alphabet, |
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double |
pf_struct_weight, |
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double |
indel_opening, |
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double |
indel |
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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 |
| struct_weight | structure weight |
| indel_opening | gap opening cost |
| indel | gap extension cost |
◆ indel()
| double LocARNA::StralScore::indel |
( |
| ) |
const |
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inline |
Read gap extension cost.
- Returns
- gap extension cost
◆ indel_opening()
| double LocARNA::StralScore::indel_opening |
( |
| ) |
const |
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inline |
Read gap opening cost.
- Returns
- gap opening cost
◆ reverse()
| void LocARNA::StralScore::reverse |
( |
| ) |
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Reverse the scoring.
- Postcondition
- the object scores the reverted RNAs
◆ sigma()
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:
