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

Packages that use CECalculator

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

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

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

Modifier and Type	Field and Description
protected CECalculator	CeMain.calculator

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

Modifier and Type	Method and Description
CECalculator	CeMain.getCECalculator()

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

Modifier and Type	Method and Description
static AFPChain	CeCPMain.filterDuplicateAFPs(AFPChain afpChain, CECalculator ceCalc, Atom[] ca1, Atom[] ca2duplicated) Takes as input an AFPChain where ca2 has been artificially duplicated.
static AFPChain	CeCPMain.filterDuplicateAFPs(AFPChain afpChain, CECalculator ceCalc, Atom[] ca1, Atom[] ca2duplicated, CECPParameters params)
static AFPChain	CeCPMain.postProcessAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2m, CECalculator calculator) Circular permutation specific code to be run after the standard CE alignment
static AFPChain	CeCPMain.postProcessAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2m, CECalculator calculator, CECPParameters param) Circular permutation specific code to be run after the standard CE alignment