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

Packages that use AlternativeAlignment

org.biojava.bio.structure.align	Classes for the super-imposition of structures.
org.biojava.bio.structure.align.pairwise	Classes for the pairwise alignment of structures.
org.biojava.bio.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.bio.structure.gui.util	Some utility classes for the protein structure GUIs.

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

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

AlternativeAlignment[]

StructurePairAligner.getAlignments() return the alternative alignments that can be found for the two structures

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

static void	ClusterAltAligs.cluster(AlternativeAlignment[] aligs)
static void	ClusterAltAligs.cluster(AlternativeAlignment[] aligs, int cutoff)

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

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

int	AltAligComparator.compare(AlternativeAlignment a, AlternativeAlignment b)

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

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

AlternativeAlignment[]	ScaleableMatrixPanel.getAlternativeAligs()
AlternativeAlignment[]	JMatrixPanel.getAlternativeAligs()

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

void	SequenceDisplay.setAlternativeAlignment(AlternativeAlignment alig)
void	ScaleableMatrixPanel.setAlternativeAligs(AlternativeAlignment[] aligs)
void	JMatrixPanel.setAlternativeAligs(AlternativeAlignment[] aligs)

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

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

void	AlternativeAlignmentFrame.setAlternativeAlignments(AlternativeAlignment[] aligs)