Uses of Interface
org.biojava.nbio.structure.align.ce.ConfigStrucAligParams

Packages that use ConfigStrucAligParams

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.fatcat.calc
org.biojava.nbio.structure.align.seq

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

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

Modifier and Type	Method and Description
ConfigStrucAligParams	BioJavaStructureAlignment.getParameters()
ConfigStrucAligParams	StructureAlignment.getParameters() Return the paramers for this algorithm.
abstract ConfigStrucAligParams	AbstractStructureAlignment.getParameters()

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

Modifier and Type	Method and Description
void	BioJavaStructureAlignment.setParameters(ConfigStrucAligParams o)
void	CallableStructureAlignment.setParameters(ConfigStrucAligParams parameters)
void	StructureAlignment.setParameters(ConfigStrucAligParams parameters) Set the default parameters for this algorithm to use
abstract void	AbstractStructureAlignment.setParameters(ConfigStrucAligParams parameters)

Uses of ConfigStrucAligParams in org.biojava.nbio.structure.align.ce

Classes in org.biojava.nbio.structure.align.ce that implement ConfigStrucAligParams

Modifier and Type	Class and Description
class	CECPParameters Provides parameters to CeCPMain
class	CeParameters Contains the parameters that can be sent to CE
class	OptimalCECPParameters Contains the parameters that can be sent to CE

Methods in org.biojava.nbio.structure.align.ce that return ConfigStrucAligParams

Modifier and Type	Method and Description
ConfigStrucAligParams	OptimalCECPMain.getParameters()
ConfigStrucAligParams	CeSideChainMain.getParameters()
ConfigStrucAligParams	CeMain.getParameters()

Methods in org.biojava.nbio.structure.align.ce with parameters of type ConfigStrucAligParams

Modifier and Type	Method and Description
void	OptimalCECPMain.setParameters(ConfigStrucAligParams params)
void	CeSideChainMain.setParameters(ConfigStrucAligParams params)
void	CeMain.setParameters(ConfigStrucAligParams params)

Uses of ConfigStrucAligParams in org.biojava.nbio.structure.align.fatcat

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

Modifier and Type	Method and Description
ConfigStrucAligParams	FatCatRigid.getParameters()
ConfigStrucAligParams	FatCatFlexible.getParameters()

Methods in org.biojava.nbio.structure.align.fatcat with parameters of type ConfigStrucAligParams

Modifier and Type	Method and Description
void	FatCatRigid.setParameters(ConfigStrucAligParams parameters)
void	FatCatFlexible.setParameters(ConfigStrucAligParams parameters)

Uses of ConfigStrucAligParams in org.biojava.nbio.structure.align.fatcat.calc

Classes in org.biojava.nbio.structure.align.fatcat.calc that implement ConfigStrucAligParams

Modifier and Type	Class and Description
class	FatCatParameters

Uses of ConfigStrucAligParams in org.biojava.nbio.structure.align.seq

Classes in org.biojava.nbio.structure.align.seq that implement ConfigStrucAligParams

Modifier and Type	Class and Description
class	SmithWaterman3DParameters

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

Modifier and Type	Method and Description
ConfigStrucAligParams	SmithWaterman3Daligner.getParameters()

Methods in org.biojava.nbio.structure.align.seq with parameters of type ConfigStrucAligParams

Modifier and Type	Method and Description
void	SmithWaterman3Daligner.setParameters(ConfigStrucAligParams parameters)