## 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)`