Package com.milaboratory.core.alignment

Interface Summary

Interface	Description
AlignerCustom.MatrixCache
AlignmentIterator<S extends Sequence<S>>	Iterates over all positions in alignment
AlignmentScoring<S extends Sequence<S>>	AlignmentScoring - interface which is to be implemented by any scoring system

Class Summary

Class	Description
AbstractAlignmentScoring<S extends Sequence<S>>	AbstractAlignmentScoring - abstract scoring system class used for alignment procedure.
AffineGapAlignmentScoring<S extends Sequence<S>>	AffineGapAlignmentScoring - scoring which uses different penalties for gap opening and gap extension
AffineGapAlignmentScoring.SerializationObject
Aligner
AlignerCustom	Collection of custom aligners
AlignerCustom.AffineMatrixCache
AlignerCustom.LinearMatrixCache
AlignerCustom.Matrix
Alignment<S extends Sequence<S>>
AlignmentCache	AlignmentCache - class which is providing cached array for BandedLinearAligner.
AlignmentHelper
AlignmentIteratorForward<S extends Sequence<S>>	Iterates over all positions in alignment
AlignmentIteratorReverse<S extends Sequence<S>>	Iterates over all positions in alignment
AlignmentTrimmer
AlignmentUtils
BandedAffineAligner
BandedAffineAligner.MatrixCache
BandedAligner
BandedAlignerParameters<S extends Sequence<S>>
BandedLinearAligner
BandedMatrix	BandedMatrix - class which used to store alignment matrix for BandedLinearAligner.
BandedSemiLocalResult	BandedSemiLocalResult - class which is result of BandedSemiLocal alignment.
CachedIntArray	CachedIntArray - class which is used for storing alignment matrix.
LinearGapAlignmentScoring<S extends Sequence<S>>	LinearGapAlignmentScoring - scoring system which uses penalty for gap
LinearGapAlignmentScoring.SerializationObject
MultiAlignmentHelper
MultiAlignmentHelper.Settings
ScoringUtils	ScoringUtils - class which contains some useful helpers used in scoring systems

Enum Summary

Enum	Description
BLASTMatrix	BLASTMatrix - enum of available BLAST AminoAcid substitution matrices