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.
org.biojava.nbio.structure.symmetry.utils

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

Uses of CECalculator in org.biojava.nbio.structure.symmetry.utils

Methods in org.biojava.nbio.structure.symmetry.utils with parameters of type CECalculator

Modifier and Type	Method and Description
static boolean[][]	SymmetryTools.blankOutBreakFlag(AFPChain afpChain, Atom[] ca2, int rows, int cols, CECalculator calculator, boolean[][] breakFlag, int blankWindowSize)
static Matrix	SymmetryTools.blankOutCEOrig(Atom[] ca2, int rows, int cols, CECalculator calculator, Matrix origM, int blankWindowSize)
static Matrix	SymmetryTools.blankOutPreviousAlignment(AFPChain afpChain, Atom[] ca2, int rows, int cols, CECalculator calculator, Matrix max, int blankWindowSize)
static Matrix	SymmetryTools.grayOutCEOrig(Atom[] ca2, int rows, int cols, CECalculator calculator, Matrix origM, int blankWindowSize, double[] gradientPolyCoeff, double gradientExpCoeff) Grays out the main diagonal of a duplicated distance matrix.
static Matrix	SymmetryTools.grayOutPreviousAlignment(AFPChain afpChain, Atom[] ca2, int rows, int cols, CECalculator calculator, Matrix max, int blankWindowSize, double[] gradientPolyCoeff, double gradientExpCoeff)