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

class ArcMatches with additional mapping More...

#include <arc_matches.hh>

Inheritance diagram for LocARNA::ArcMatchesIndexed:
LocARNA::ArcMatches

List of all members.

Public Member Functions

 ArcMatchesIndexed (const Sequence &seqA_, const Sequence &seqB_, const std::string &arcmatch_scores_file, int probability_scale, size_type max_length_diff, size_type max_diff_at_am, const MatchController &trace_controller, const AnchorConstraints &constraints)
 construct with explicit arc match score list
 ArcMatchesIndexed (const RnaData &rnadataA, const RnaData &rnadataB, double min_prob, size_type max_length_diff, size_type max_diff_at_am, const MatchController &trace_controller, const AnchorConstraints &constraints)
 construct from single base pair probabilities.
const ArcMatch::idx_type invalid_am_index () const
 the invalid arc match index
const ArcMatch::idx_type am_index (const size_type &arcAIdx, const size_type &arcBIdx) const
 Lookup arc match index by pair of arc indices.
const ArcMatcham_index (const Arc &arcA, const Arc &arcB) const
 Lookup arc match by pair of arcs.

Detailed Description

class ArcMatches with additional mapping

Like ArcMatches, maintain the relevant arc matches and their scores. Additionally, build an index to support mapping from pairs of arcs to arc matches.


Constructor & Destructor Documentation

LocARNA::ArcMatchesIndexed::ArcMatchesIndexed ( const Sequence seqA_,
const Sequence seqB_,
const std::string &  arcmatch_scores_file,
int  probability_scale,
size_type  max_length_diff,
size_type  max_diff_at_am,
const MatchController trace_controller,
const AnchorConstraints constraints 
) [inline]

construct with explicit arc match score list

construct from seqnames and explicit list of all scored arc matches together with their score.

Note:
registers constraints and heuristics and then calls read_arcmatch_scores. The constructed object explicitely represents/maintains the scores of arc matchs.
Parameters:
seqA_sequence A
seqB_sequence B
arcmatch_scores_filefile containing arc match scores
probability_scaleif >=0 read probabilities and multiply them by probability_scale
max_length_diffaccept arc matches only up to maximal length difference
trace_controlleraccept only due to trace controller
constraintsaccept only due to constraints
LocARNA::ArcMatchesIndexed::ArcMatchesIndexed ( const RnaData rnadataA,
const RnaData rnadataB,
double  min_prob,
size_type  max_length_diff,
size_type  max_diff_at_am,
const MatchController trace_controller,
const AnchorConstraints constraints 
) [inline]

construct from single base pair probabilities.

In this case, the object filters for relevant base pairs/arcs by min_prob. Registers constraints and heuristics and then calls read_arcmatch_scores. Constructs BasePairs objects for each single object and registers them. Generates adjacency lists of arc matches for internal use and sorts them. Lists contain only valid arc matches according to constraints and heuristics (see is_valid_arcmatch()). The constructed object does not explicitely represent/maintain the scores of arc matchs.

Parameters:
rnadataAdata for RNA A
rnadataBdata for RNA B
min_probconsider only arcs with this minimal probability
max_length_diffconsider arc matches only up to maximal length difference
trace_controllerarc matches only due to trace controller
constraintsarc matches only due to constraints

Member Function Documentation

const ArcMatch::idx_type LocARNA::ArcMatchesIndexed::am_index ( const size_type arcAIdx,
const size_type arcBIdx 
) const [inline]

Lookup arc match index by pair of arc indices.

Parameters:
arcAIdxindex of arc in A
arcBIdxindex of arc in B
Returns:
index of arcmatch of arcA and arcB or invalid_am_index()
const ArcMatch& LocARNA::ArcMatchesIndexed::am_index ( const Arc arcA,
const Arc arcB 
) const [inline]

Lookup arc match by pair of arcs.

Parameters:
arcAarc in A
arcBarc in B
Returns:
arcmatch of arcA and arcB (or an invalid arc match with index invalid_am_index())

the invalid arc match index

Returns:
invalid arc match index
Note:
this index is returned by am_index if the queried pair of arcs does not correspond to a valid arcmatch

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