ESAT: broad.core.primer3.HairpinKmer Class Reference

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Public Member Functions
	HairpinKmer (String kmer, int relativeStart, int relativeEnd)

	HairpinKmer (String kmer, int relativeStart, int relativeEnd, Map< String, Double > mirLookup, Set< String > lookup2, Set< String > rcLookup2)

void	addTranscript (RNAiGeneAnnotation transcript)

Collection< RNAiGeneAnnotation >	getTranscripts ()

void	setPercentVariantsCovered (double percent)

double	getPercentVariantsCovered ()

String	getKmerSequence ()

int	getKmerStartPosition ()

int	getKmerEndPosition ()

double	getRS8Score ()

double	getOriginalScore ()

double	getMirScore ()

int	compareTo (HairpinKmer kmer)

boolean	setRS8Score (double score)

boolean	setOriginalScore (double score)

boolean	setMirScore (double score)

void	setBlastHit (boolean b)

boolean	getBlastHit ()

List< SequenceRegion >	getRelativePositions (RNAiGeneAnnotation transcript) throws SearchException

int	getOverlap (HairpinKmer hp)

double	getPercentGC ()

int	maxSelfComplementarity ()

Constructor & Destructor Documentation

broad.core.primer3.HairpinKmer.HairpinKmer	(	String	kmer,
		int	relativeStart,
		int	relativeEnd
	)

broad.core.primer3.HairpinKmer.HairpinKmer	(	String	kmer,
		int	relativeStart,
		int	relativeEnd,
		Map< String, Double >	mirLookup,
		Set< String >	lookup2,
		Set< String >	rcLookup2
	)

Member Function Documentation

void broad.core.primer3.HairpinKmer.addTranscript ( RNAiGeneAnnotation transcript )

int broad.core.primer3.HairpinKmer.compareTo ( HairpinKmer kmer )

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boolean broad.core.primer3.HairpinKmer.getBlastHit ( )

int broad.core.primer3.HairpinKmer.getKmerEndPosition ( )

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String broad.core.primer3.HairpinKmer.getKmerSequence ( )

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int broad.core.primer3.HairpinKmer.getKmerStartPosition ( )

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double broad.core.primer3.HairpinKmer.getMirScore ( )

double broad.core.primer3.HairpinKmer.getOriginalScore ( )

int broad.core.primer3.HairpinKmer.getOverlap ( HairpinKmer hp )

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double broad.core.primer3.HairpinKmer.getPercentGC ( )

double broad.core.primer3.HairpinKmer.getPercentVariantsCovered ( )

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List<SequenceRegion> broad.core.primer3.HairpinKmer.getRelativePositions ( RNAiGeneAnnotation transcript ) throws SearchException

double broad.core.primer3.HairpinKmer.getRS8Score ( )

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Collection<RNAiGeneAnnotation> broad.core.primer3.HairpinKmer.getTranscripts ( )

int broad.core.primer3.HairpinKmer.maxSelfComplementarity ( )

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void broad.core.primer3.HairpinKmer.setBlastHit ( boolean b )

boolean broad.core.primer3.HairpinKmer.setMirScore ( double score )

boolean broad.core.primer3.HairpinKmer.setOriginalScore ( double score )

void broad.core.primer3.HairpinKmer.setPercentVariantsCovered ( double percent )

boolean broad.core.primer3.HairpinKmer.setRS8Score ( double score )

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

java/broad/core/primer3/HairpinKmer.java