LocARNA-1.9.2
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Public Member Functions
LocARNA::StralScore Class Reference

Implements the stral-like scoring function. More...

#include <stral_score.hh>

List of all members.

Public Member Functions

 StralScore (const RnaData &rnaA, const RnaData &rnaB, const Matrix< double > &sim_mat_, const Alphabet< char > &alphabet_, double pf_struct_weight_, double gap_opening_, double gap_extension_)
double sigma (size_type i, size_type j) const
 Compute STRAL-like similarity of two residues in the two RNAs.
double alpha () const
 Read gap opening cost.
double beta () const
 Read gap extension cost.
void reverse ()
 Reverse the scoring.

Detailed Description

Implements the stral-like scoring function.


Constructor & Destructor Documentation

LocARNA::StralScore::StralScore ( const RnaData rnaA,
const RnaData rnaB,
const Matrix< double > &  sim_mat_,
const Alphabet< char > &  alphabet_,
double  pf_struct_weight_,
double  gap_opening_,
double  gap_extension_ 
)

Construct for pair of RNAs with parameters for alignment

Parameters:
rnaAdata of first RNA
rnaBdata 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

Member Function Documentation

double LocARNA::StralScore::alpha ( ) const [inline]

Read gap opening cost.

Returns:
gap opening cost
double LocARNA::StralScore::beta ( ) const [inline]

Read gap extension cost.

Returns:
gap extension cost

Reverse the scoring.

Postcondition:
the object scores the reverted RNAs
double LocARNA::StralScore::sigma ( size_type  i,
size_type  j 
) const

Compute STRAL-like similarity of two residues in the two RNAs.

Parameters:
iposition in sequence A
jposition in sequence B
Note:
Computes the average similarity over all pairs of alignment rows in the RNA sequence, which are alignments in general.
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:
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