Uses of Class
de.jstacs.algorithms.alignment.PairwiseStringAlignment

Packages that use PairwiseStringAlignment

Package	Description
de.jstacs.algorithms.alignment	Provides classes for alignments.

Uses of PairwiseStringAlignment in de.jstacs.algorithms.alignment

Methods in de.jstacs.algorithms.alignment that return PairwiseStringAlignment

Modifier and Type	Method and Description
PairwiseStringAlignment	Alignment.getAlignment(Alignment.AlignmentType type, Sequence s1, int startS1, int endS1, Sequence s2, int startS2, int endS2) Computes and returns the alignment of s1 and s2 (Alignment.Alignment(Costs)).
PairwiseStringAlignment	Alignment.getAlignment(Alignment.AlignmentType type, Sequence s1, Sequence s2) Computes and returns the alignment of s1 and s2 (Alignment.Alignment(Costs)).
protected PairwiseStringAlignment	Alignment.getAlignment(int[] index) Returns the optimal alignment (backtrace) according to matrix index[0] until positions index[1] and index[2] in the first and second sequence, respectively.