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## 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)`

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