LocARNA-1.9.2
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LocARNA::ExtRnaDataImpl Class Reference

Implementation of ExtRnaData. More...

#include <ext_rna_data_impl.hh>

List of all members.

Public Types

typedef SparseVector< double > arc_prob_vector_t
 vector of arc probabilities
typedef
RnaDataImpl::arc_prob_matrix_t 
arc_prob_matrix_t
 matrix of arc probabilities
typedef SparseMatrix
< arc_prob_vector_t
arc_prob_vector_matrix_t
 matrix of arc probability vectors
typedef SparseMatrix
< arc_prob_matrix_t
arc_prob_matrix_matrix_t
 matrix of arc probability matrices

Public Member Functions

 ExtRnaDataImpl (ExtRnaData *self, double p_bpilcut, double p_uilcut)
 Construct.
void init_from_fixed_structure (const RnaStructure &structure)
 initialize in loop probabilities from fixed structure
void init_from_ext_rna_ensemble (const RnaEnsemble &rna_ensemble)
 initialize from rna ensemble
std::istream & read_pp_in_loop_probabilities (std::istream &in)
 read in loop probability section of pp-format
void read_pp_in_loop_probabilities_kwline (const std::string &line)
 read keyword line in loop probability section of pp-format
void read_pp_in_loop_probabilities_line (const std::string &line)
 read probability line in loop probability section of pp-format
std::ostream & write_pp_in_loop_probabilities (std::ostream &out, double p_outbpcut, double p_outbpilcut, double p_outuilcut) const
 Write in loop probability section of pp 2.0.
std::ostream & write_pp_in_loop_probability_line (std::ostream &out, size_t i, size_t j, double p_bpcut, double p_ucut) const
 Write a line of in loop probabilities for one base pair.
std::ostream & write_pp_basepair_in_loop_probabilities (std::ostream &out, const arc_prob_matrix_t &probs, double p_cut) const
 Write in loop base pair probabilities for a specific base pair.
std::ostream & write_pp_unpaired_in_loop_probabilities (std::ostream &out, const arc_prob_vector_t &probs, double p_cut) const
 Write in loop unpaired probabilities for a specific base pair.
void drop_worst_bps (size_t keep)
 Drop in loop bases and base pairs without base pairs.
void drop_worst_uil (size_t keep)
 Drop unpaired bases in loops with lowest probability.
void drop_worst_bpil (size_t keep)
 Drop base pairs in loops with lowest probability.
void drop_worst_bpil_precise (double ratio)
 Drop base pairs in loops with lowest probability based on loop length.

Public Attributes

ExtRnaDataself_
double p_bpilcut_
 cutoff probabilitiy for base pair in loop
double p_uilcut_
 cutoff probabilitiy for unpaired base in loop
arc_prob_matrix_matrix_t arc_in_loop_probs_
 in loop probabilities of base pairs
arc_prob_vector_matrix_t unpaired_in_loop_probs_
 in loop probabilities of unpaired bases
bool has_in_loop_probs_

Detailed Description

Implementation of ExtRnaData.


Constructor & Destructor Documentation

LocARNA::ExtRnaDataImpl::ExtRnaDataImpl ( ExtRnaData self,
double  p_bpilcut,
double  p_uilcut 
)

Construct.

Parameters:
selfself pointer
p_bpilcutprobability cutoff base pair in loop
p_uilcutprobability cutoff unpaired in loop
Note:
autodetects file format, see corresponding RnaDataImpl constructor

Member Function Documentation

Drop base pairs in loops with lowest probability.

Parameters:
keepthe maximum total number of base pairs in loops to keep

Drop base pairs in loops with lowest probability based on loop length.

Parameters:
ratiolimit on number of base pairs closed by a loop divided by loop length

Drop in loop bases and base pairs without base pairs.

Parameters:
keepthe maximum number of base pairs to keep

Drop unpaired bases in loops with lowest probability.

Parameters:
keepthe maximum total number of unpaired bases in loops to keep

initialize from rna ensemble

Parameters:
rna_ensemblerna ensemble
Note:
overloaded to initialize with additional information (in loop probabilities)
rna_ensemble must have in loop probabilities

initialize in loop probabilities from fixed structure

Parameters:
structurefixed structure
Note:
this initializes only the inloop probabilities; itdoes not initialize base pair probabilities, which is done by the corresponding method of RnaDataImpl.
std::istream & LocARNA::ExtRnaDataImpl::read_pp_in_loop_probabilities ( std::istream &  in)

read in loop probability section of pp-format

Parameters:
ininput stream
Returns:
stream

Reads only base pairs with probabilities greater than p_bpcut_; base pairs in loops, p_bpilcut_; unpaired bases in loops, p_uilcut_

read keyword line in loop probability section of pp-format

Parameters:
lineinput line

read probability line in loop probability section of pp-format

Parameters:
lineinput line
std::ostream & LocARNA::ExtRnaDataImpl::write_pp_basepair_in_loop_probabilities ( std::ostream &  out,
const arc_prob_matrix_t probs,
double  p_cut 
) const

Write in loop base pair probabilities for a specific base pair.

Parameters:
outoutput stream
probsin loop probability matrix of a base pair
p_cutbase pair in loop probability cutoff
Returns:
output stream
std::ostream & LocARNA::ExtRnaDataImpl::write_pp_in_loop_probabilities ( std::ostream &  out,
double  p_outbpcut,
double  p_outbpilcut,
double  p_outuilcut 
) const

Write in loop probability section of pp 2.0.

Parameters:
outoutput stream
p_outbpcutbase pair probability cutoff
p_outbpilcutbase pair in loop probability cutoff
p_outuilcutunpaired in loop probability cutoff
Returns:
output stream
std::ostream & LocARNA::ExtRnaDataImpl::write_pp_in_loop_probability_line ( std::ostream &  out,
size_t  i,
size_t  j,
double  p_bpcut,
double  p_ucut 
) const

Write a line of in loop probabilities for one base pair.

Parameters:
outoutput stream
ileft end
jright end
p_bpcutbase pair in loop probability cutoff
p_ucutunpaired in loop probability cutoff
Returns:
output stream
std::ostream & LocARNA::ExtRnaDataImpl::write_pp_unpaired_in_loop_probabilities ( std::ostream &  out,
const arc_prob_vector_t probs,
double  p_cut 
) const

Write in loop unpaired probabilities for a specific base pair.

Parameters:
outoutput stream
probsin loop probability vector of a base pair
p_cutunpaired in loop probability cutoff
Returns:
output stream

Member Data Documentation

used in initialization, to check whether in loop probs still have to be computed

  • pointer to corresponding non-impl object

The documentation for this class was generated from the following files:
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