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 and Description
ConfigStrucAligParams	BioJavaStructureAlignment.getParameters()
ConfigStrucAligParams	StructureAlignment.getParameters() Return the paramers for this algorithm.
ConfigStrucAligParams	MultipleStructureAligner.getParameters() Return the parameters of this algorithm instance.
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	StructureAlignment.setParameters(ConfigStrucAligParams parameters) Set the default parameters for this algorithm to use
void	MultipleStructureAligner.setParameters(ConfigStrucAligParams parameters) Set the parameters for this algorithm to use.
void	CallableStructureAlignment.setParameters(ConfigStrucAligParams parameters)
abstract void	AbstractStructureAlignment.setParameters(ConfigStrucAligParams parameters)

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

Constructor and 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 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	CeMain.getParameters()
ConfigStrucAligParams	CeSideChainMain.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	CeMain.setParameters(ConfigStrucAligParams params)
void	CeSideChainMain.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.gui

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

Constructor and 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 and 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 and Description
ConfigStrucAligParams	MultipleMcMain.getParameters()

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

Modifier and Type	Method and 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 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)

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 and Description
class	CESymmParameters Provides parameters to CeSymm.