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.
org.biojava.nbio.structure.gui	A few convenience classes to view protein structures with Jmol (if it is on the classpath), to calculate a protein structure alignment and to investigate the internals of the protein structure alignment algorithm.
org.biojava.nbio.structure.gui.util	Some utility classes for the protein structure GUIs.

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

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

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

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

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

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

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

Modifier and Type	Method	Description
AlternativeAlignment[]	JMatrixPanel.getAlternativeAligs()
AlternativeAlignment[]	ScaleableMatrixPanel.getAlternativeAligs()

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

Modifier and Type	Method	Description
void	SequenceDisplay.setAlternativeAlignment(AlternativeAlignment alig)
void	JMatrixPanel.setAlternativeAligs(AlternativeAlignment[] aligs)
void	ScaleableMatrixPanel.setAlternativeAligs(AlternativeAlignment[] aligs)

Uses of AlternativeAlignment in org.biojava.nbio.structure.gui.util

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

Modifier and Type	Method	Description
void	AlternativeAlignmentFrame.setAlternativeAlignments(AlternativeAlignment[] aligs)