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

Methods in org.biojava.bio.structure.gui with parameters of type AlternativeAlignment
 void SequenceDisplay.setAlternativeAlignment(AlternativeAlignment alig)
           
 void JMatrixPanel.setAlternativeAligs(AlternativeAlignment[] aligs)
           
 void ScaleableMatrixPanel.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)