Uses of Class
org.biojava.bio.alignment.AlignmentAlgorithm

Packages that use AlignmentAlgorithm

Package	Description
org.biojava.bio.alignment	Classes to generate and describe sequence alignments.

Uses of AlignmentAlgorithm in org.biojava.bio.alignment

Subclasses of AlignmentAlgorithm in org.biojava.bio.alignment

Modifier and Type	Class	Description
class	NeedlemanWunsch	Needleman and Wunsch defined the problem of global sequence alignments, from the first till the last symbol of a sequence.
class	SmithWaterman	Smith and Waterman developed an efficient dynamic programming algorithm to perform local sequence alignments, which returns the most conserved region of two sequences (longest common substring with modifications).

Methods in org.biojava.bio.alignment with parameters of type AlignmentAlgorithm

Modifier and Type	Method	Description
static AlignmentPair	AlignmentPair.align(Sequence query, Sequence subject, AlignmentAlgorithm algorithm)