Uses of Class
org.biojava.nbio.structure.align.ce.CeParameters

Packages that use CeParameters

Package	Description
org.biojava.nbio.structure.align.ce	Classes related to the implementation of the CE alignment algorithm, here called jCE.
org.biojava.nbio.structure.symmetry.internal

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

Subclasses of CeParameters in org.biojava.nbio.structure.align.ce

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

Fields in org.biojava.nbio.structure.align.ce declared as CeParameters

Modifier and Type	Field	Description
protected CeParameters	CECalculator.params
protected CeParameters	CeCalculatorEnhanced.params
protected CeParameters	CeMain.params

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

Modifier and Type	Method	Description
static double[][]	CECalculator.updateMatrixWithSequenceConservation(double[][] max, Atom[] ca1, Atom[] ca2, CeParameters params)	Modifies an alignment matrix by favoring the alignment of similar and identical amino acids and penalizing the alignment of unrelated ones.
static double[][]	CeCalculatorEnhanced.updateMatrixWithSequenceConservation(double[][] max, Atom[] ca1, Atom[] ca2, CeParameters params)	Modifies an alignment matrix by favoring the alignment of similar and identical amino acids and penalizing the alignment of unrelated ones.

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

Constructor	Description
CECalculator(CeParameters params)
CeCalculatorEnhanced(CeParameters params)

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

Subclasses of CeParameters in org.biojava.nbio.structure.symmetry.internal

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