Uses of Interface
org.biojava.nbio.structure.align.StructureAlignment
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Packages that use StructureAlignment Package Description org.biojava.nbio.structure.align Classes for the alignment of structures.org.biojava.nbio.structure.align.ce Classes related to the implementation of the CE alignment algorithm, here called jCE.org.biojava.nbio.structure.align.fatcat Classes related to the implementation of the FATCAT alignment algorithm, here called jFATCAT.org.biojava.nbio.structure.align.gui org.biojava.nbio.structure.align.multiple.mc org.biojava.nbio.structure.align.seq -
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Uses of StructureAlignment in org.biojava.nbio.structure.align
Classes in org.biojava.nbio.structure.align that implement StructureAlignment Modifier and Type Class Description class
AbstractStructureAlignment
class
BioJavaStructureAlignment
Wrapper for the BioJava Structure Alignment ImplementationMethods in org.biojava.nbio.structure.align that return StructureAlignment Modifier and Type Method Description StructureAlignment
MultiThreadedDBSearch. getAlgorithm()
static StructureAlignment
StructureAlignmentFactory. getAlgorithm(String name)
static StructureAlignment[]
StructureAlignmentFactory. getAllAlgorithms()
Methods in org.biojava.nbio.structure.align with parameters of type StructureAlignment Modifier and Type Method Description static void
StructureAlignmentFactory. addAlgorithm(StructureAlignment alg)
Adds a new StructureAlignment algorithm to the list.void
MultiThreadedDBSearch. setAlgorithm(StructureAlignment algo)
Constructors in org.biojava.nbio.structure.align with parameters of type StructureAlignment Constructor Description MultiThreadedDBSearch(String name, Structure structure, String outFile, StructureAlignment algorithm, int nrCPUs, boolean domainSplit)
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Uses of StructureAlignment in org.biojava.nbio.structure.align.ce
Classes in org.biojava.nbio.structure.align.ce that implement StructureAlignment Modifier and Type Class Description class
CeCPMain
A wrapper forCeMain
which sets default parameters to be appropriate for finding circular permutations.class
CeMain
The main class of the Java implementation of the Combinatorial Extension Algorithm (CE), as has been originally developed by I.class
CeSideChainMain
class
OptimalCECPMain
A wrapper forCeMain
which sets default parameters to be appropriate for finding circular permutations.Methods in org.biojava.nbio.structure.align.ce that return StructureAlignment Modifier and Type Method Description abstract StructureAlignment
AbstractUserArgumentProcessor. getAlgorithm()
StructureAlignment
CeCPUserArgumentProcessor. getAlgorithm()
StructureAlignment
CeSideChainUserArgumentProcessor. getAlgorithm()
StructureAlignment
CeUserArgumentProcessor. getAlgorithm()
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Uses of StructureAlignment in org.biojava.nbio.structure.align.fatcat
Classes in org.biojava.nbio.structure.align.fatcat that implement StructureAlignment Modifier and Type Class Description class
FatCatFlexible
class
FatCatRigid
Methods in org.biojava.nbio.structure.align.fatcat that return StructureAlignment Modifier and Type Method Description StructureAlignment
FatCatUserArgumentProcessor. getAlgorithm()
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Uses of StructureAlignment in org.biojava.nbio.structure.align.gui
Methods in org.biojava.nbio.structure.align.gui that return StructureAlignment Modifier and Type Method Description StructureAlignment
AlignmentCalcDB. getAlgorithm()
StructureAlignment
MultipleAlignmentGUI. getPairwiseStructureAligner()
StructureAlignment
AlignmentGui. getStructureAlignment()
StructureAlignment
DBSearchGUI. getStructureAlignment()
Methods in org.biojava.nbio.structure.align.gui with parameters of type StructureAlignment Modifier and Type Method Description void
AlignmentCalcDB. setAlgorithm(StructureAlignment algo)
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Uses of StructureAlignment in org.biojava.nbio.structure.align.multiple.mc
Constructors in org.biojava.nbio.structure.align.multiple.mc with parameters of type StructureAlignment Constructor Description MultipleMcMain(StructureAlignment pairwiseAlgo)
Default constructor. -
Uses of StructureAlignment in org.biojava.nbio.structure.align.seq
Classes in org.biojava.nbio.structure.align.seq that implement StructureAlignment Modifier and Type Class Description class
SmithWaterman3Daligner
Provides a 3D superimposition of two structures based on their sequence alignment.Methods in org.biojava.nbio.structure.align.seq that return StructureAlignment Modifier and Type Method Description StructureAlignment
SmithWatermanUserArgumentProcessor. getAlgorithm()
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