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.gui
org.biojava.nbio.structure.align.multiple.mc
org.biojava.nbio.structure.align.seq
org.biojava.nbio.structure.symmetry.internal

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

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

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

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

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

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

Modifier	Constructor	Description
	CallableStructureAlignment(Atom[] ca1, Atom[] ca2, String algorithmName, ConfigStrucAligParams params)	Constructor for all-to-all alignment calculation.

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	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	Description
ConfigStrucAligParams	CeMain.getParameters()
ConfigStrucAligParams	CeSideChainMain.getParameters()
ConfigStrucAligParams	OptimalCECPMain.getParameters()

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

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

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

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

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

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

Modifier	Constructor	Description
	ParameterGUI(ConfigStrucAligParams params, String algorithm)	Constructor for a ParameterGUI.

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

Classes in org.biojava.nbio.structure.align.multiple.mc that implement ConfigStrucAligParams

Modifier and Type	Class	Description
class	MultipleMcParameters	Contains the parameters to be sent to the MC optimization.

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

Modifier and Type	Method	Description
ConfigStrucAligParams	MultipleMcMain.getParameters()

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

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

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	Description
class	SmithWaterman3DParameters

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

Modifier and Type	Method	Description
ConfigStrucAligParams	SmithWaterman3Daligner.getParameters()

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

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

Uses of ConfigStrucAligParams in org.biojava.nbio.structure.symmetry.internal

Classes in org.biojava.nbio.structure.symmetry.internal that implement ConfigStrucAligParams

Modifier and Type	Class	Description
class	CESymmParameters	Provides parameters to CeSymm.