Package com.milaboratory.core.alignment.kaligner1

Interface Summary

Interface	Description
AbstractKAlignerParameters

Class Summary

Class	Description
KAligner<P>	KAligner is a comprehensive aligner for nucleotide sequences.
KAlignerParameters
KAlignmentHit<P>	KAlignmentHit - class which represents single hit for KAlignmentResult
KAlignmentResult<P>	KAlignmentResult - class which is result of KAligner.align(com.milaboratory.core.sequence.NucleotideSequence), KAligner.align(com.milaboratory.core.sequence.NucleotideSequence, int, int), KAligner#align(com.milaboratory.core.sequence.NucleotideSequence, int, int, boolean) methods.
KAlignmentResultP<P,Q>	Piped version of KAlignmentResult.
KMapper	KMapper - class to perform fast alignment based only on matches between kMers of target and one of reference sequences.
KMappingHit	KMappingHit - class which represents single hit for KMappingResult
KMappingResult	KMappingResult - class which is result of KMapper#align(com.milaboratory.core.sequence.nucleotide.NucleotideSequence, int, int), KMapper.align(com.milaboratory.core.sequence.NucleotideSequence) methods.