Uses of Class
org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

Packages that use AlternativeAlignment

Package	Description
org.biojava.nbio.structure.align	Classes for the alignment of structures.
org.biojava.nbio.structure.align.pairwise	Classes for the pairwise alignment of structures.

Uses of AlternativeAlignment in org.biojava.nbio.structure.align

Methods in org.biojava.nbio.structure.align that return AlternativeAlignment

Modifier and Type	Method and Description
AlternativeAlignment[]	StructurePairAligner.getAlignments() return the alternative alignments that can be found for the two structures

Methods in org.biojava.nbio.structure.align with parameters of type AlternativeAlignment

Modifier and Type	Method and Description
static void	ClusterAltAligs.cluster(AlternativeAlignment[] aligs)
static void	ClusterAltAligs.cluster(AlternativeAlignment[] aligs, int cutoff)

Uses of AlternativeAlignment in org.biojava.nbio.structure.align.pairwise

Methods in org.biojava.nbio.structure.align.pairwise that return AlternativeAlignment

Modifier and Type	Method and Description
AlternativeAlignment[]	AlignmentResult.getAlignments()

Methods in org.biojava.nbio.structure.align.pairwise with parameters of type AlternativeAlignment

Modifier and Type	Method and Description
int	AltAligComparator.compare(AlternativeAlignment a, AlternativeAlignment b)
void	AlignmentResult.setAlignments(AlternativeAlignment[] alignments) we only keep the first alternative...