Collaboration diagram for umms.core.alignment.SmatchLike:

Public Member Functions
	SmatchLike (String kmer, List< Sequence > geneSequences, int seedNum)

	SmatchLike (String kmer, String primer, int seedNum)

	SmatchLike (String kmer2, Collection< Pair< String >> tailPrimers, Pair< String > subprimer1)

Collection< String >	getForwardTargets (int numMismatches) throws SearchException

Map< String, List < SequenceRegion > >	getForwardTargetRegions (int numMismatches) throws SearchException

Collection< String >	getReverseTargets (int numMismatches) throws SearchException

Collection< String >	getAllPossibleTargets (int numMismatches) throws SearchException

int	numPossibleTargets ()

Static Public Member Functions
static void	main (String[] args) throws IOException, SearchException

Constructor & Destructor Documentation

umms.core.alignment.SmatchLike.SmatchLike	(	String	kmer,
		List< Sequence >	geneSequences,
		int	seedNum
	)

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umms.core.alignment.SmatchLike.SmatchLike	(	String	kmer,
		String	primer,
		int	seedNum
	)

umms.core.alignment.SmatchLike.SmatchLike	(	String	kmer2,
		Collection< Pair< String >>	tailPrimers,
		Pair< String >	subprimer1
	)

Member Function Documentation

Collection<String> umms.core.alignment.SmatchLike.getAllPossibleTargets ( int numMismatches ) throws SearchException

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Map<String, List<SequenceRegion> > umms.core.alignment.SmatchLike.getForwardTargetRegions ( int numMismatches ) throws SearchException

Collection<String> umms.core.alignment.SmatchLike.getForwardTargets ( int numMismatches ) throws SearchException

Collection<String> umms.core.alignment.SmatchLike.getReverseTargets ( int numMismatches ) throws SearchException

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static void umms.core.alignment.SmatchLike.main ( String[] args ) throws IOException, SearchException

static

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int umms.core.alignment.SmatchLike.numPossibleTargets ( )

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