Uses of Interface
org.biojava.nbio.structure.align.StructureAlignment

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

Uses of StructureAlignment in org.biojava.nbio.structure.align

Classes in org.biojava.nbio.structure.align that implement StructureAlignment

Modifier and Type	Class and Description
class	AbstractStructureAlignment
class	BioJavaStructureAlignment Wrapper for the BioJava Structure Alignment Implementation

Methods in org.biojava.nbio.structure.align that return StructureAlignment

Modifier and Type	Method and 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 and 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 and Description
MultiThreadedDBSearch(String name, Structure structure, String outFile, StructureAlignment algorithm, int nrCPUs, boolean domainSplit)

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 and Description
class	CeCPMain A wrapper for CeMain 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 for CeMain 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 and Description
StructureAlignment	CeSideChainUserArgumentProcessor.getAlgorithm()
StructureAlignment	CeCPUserArgumentProcessor.getAlgorithm()
StructureAlignment	CeUserArgumentProcessor.getAlgorithm()
abstract StructureAlignment	AbstractUserArgumentProcessor.getAlgorithm()

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 and Description
class	FatCatFlexible
class	FatCatRigid

Methods in org.biojava.nbio.structure.align.fatcat that return StructureAlignment

Modifier and Type	Method and Description
StructureAlignment	FatCatUserArgumentProcessor.getAlgorithm()

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 and Description
StructureAlignment	AlignmentCalcDB.getAlgorithm()
StructureAlignment	MultipleAlignmentGUI.getPairwiseStructureAligner()
StructureAlignment	DBSearchGUI.getStructureAlignment()
StructureAlignment	AlignmentGui.getStructureAlignment()

Methods in org.biojava.nbio.structure.align.gui with parameters of type StructureAlignment

Modifier and Type	Method and Description
void	AlignmentCalcDB.setAlgorithm(StructureAlignment algo)

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 and 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 and Description
class	SmithWaterman3Daligner provides a 3D superimposition based on the sequence alignment

Methods in org.biojava.nbio.structure.align.seq that return StructureAlignment

Modifier and Type	Method and Description
StructureAlignment	SmithWatermanUserArgumentProcessor.getAlgorithm()