LocARNA::LCSEPM Class Reference

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

#include <exact_matcher.hh>

List of all members.

Classes
struct	HoleCompare2
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
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

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Detailed Description

computes the best chain of EPMs, the LCS-EPM

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Constructor & Destructor Documentation

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

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Member Function Documentation

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