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

Packages that use AlignmentPair

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

Uses of AlignmentPair in org.biojava.bio.alignment

Methods in org.biojava.bio.alignment that return AlignmentPair

Modifier and Type	Method	Description
static AlignmentPair	AlignmentPair.align(Sequence query, Sequence subject, AlignmentAlgorithm algorithm)
abstract AlignmentPair	AlignmentAlgorithm.pairwiseAlignment(SymbolList query, SymbolList subject)	Performs a pairwise sequence alignment of the two given sequences.
AlignmentPair	NeedlemanWunsch.pairwiseAlignment(SymbolList query, SymbolList subject)	Global pairwise sequence alignment of two BioJava-Sequence objects according to the Needleman-Wunsch-algorithm.
AlignmentPair	SmithWaterman.pairwiseAlignment(SymbolList query, SymbolList subject)	Overrides the method inherited from the NeedlemanWunsch and performs only a local alignment.

Methods in org.biojava.bio.alignment that return types with arguments of type AlignmentPair

Modifier and Type	Method	Description
List<AlignmentPair>	AlignmentAlgorithm.alignAll(SequenceIterator source, SequenceDB subjectDB)