Uses of Class
org.biojava.nbio.structure.align.pairwise.AlternativeAlignment
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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 org.biojava.nbio.structure.gui.util -
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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 structuresMethods 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)
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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)
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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)
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