LocARNA::LCSEPM Class Reference

computes the best chain of EPMs, the LCS-EPM More...

#include <exact_matcher.hh>

Public Member Functions
	LCSEPM (const Sequence &seqA_, const Sequence &seqB_, const PatternPairMap &myPatterns, PatternPairMap &myLCSEPM)
virtual	~LCSEPM ()
	Destructor.
void	MapToPS (const std::string &sequenceA, const std::string &sequenceB, PatternPairMap &myMap, const std::string &file1, const std::string &file2)
	output chained EPMs to PS files More...
void	calculateLCSEPM (bool quiet)
	calculates the best chain of EPMs, the LCS-EPM
std::pair< SequenceAnnotation, SequenceAnnotation >	anchor_annotation ()
	get anchor annotation
void	output_locarna (const std::string &sequenceA, const std::string &sequenceB, const std::string &outfile)
	outputs anchor constraints to be used as input for locarna
void	output_clustal (const std::string &outfile_name)
	writes chain as clustal alignment

Detailed Description

computes the best chain of EPMs, the LCS-EPM

Constructor & Destructor Documentation

LCSEPM()

LocARNA::LCSEPM::LCSEPM ( const Sequence &  seqA_, const Sequence &  seqB_, const PatternPairMap &  myPatterns, PatternPairMap &  myLCSEPM  )

inline

Constructor

Parameters

seqA_	first sequence
seqB_	second sequence
myPatterns	input PatternPairMap
myLCSEPM	output PatternPairMap

Member Function Documentation

MapToPS()

void LocARNA::LCSEPM::MapToPS	(	const std::string &	sequenceA,
		const std::string &	sequenceB,
		PatternPairMap &	myMap,
		const std::string &	file1,
		const std::string &	file2
	)

output chained EPMs to PS files

Parameters

sequenceA	first sequence
sequenceB	second sequence
myMap	PatternPairMap for the two sequences
file1	name of the output file for the first sequence
file2	name of the output file for the second sequence

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

• src/LocARNA/exact_matcher.hh
• src/LocARNA/exact_matcher.cc