Uses of Class
org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

Packages that use FatCatParameters

Package	Description
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

Uses of FatCatParameters in org.biojava.nbio.structure.align.fatcat

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

Modifier and Type	Method	Description
protected AFPChain	FatCat.align(Atom[] ca1, Atom[] ca2, FatCatParameters params, boolean doRigid)
AFPChain	FatCat.alignFlexible(Atom[] ca1, Atom[] ca2, FatCatParameters params)
AFPChain	FatCat.alignRigid(Atom[] ca1, Atom[] ca2, FatCatParameters params)

Uses of FatCatParameters in org.biojava.nbio.structure.align.fatcat.calc

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

Modifier and Type	Method	Description
static boolean	AFPChainer.afpPairConn(int afp1, int afp2, FatCatParameters params, AFPChain afpChain)	//Key function: calculate the connectivity of AFP pairs //no compatibility criteria is executed //note: afp1 is previous to afp2 in terms of the position //this module must be optimized
void	FatCatAligner.align(Atom[] ca1, Atom[] ca2, boolean doRigid, FatCatParameters params)
double	SigEva.calNS(FatCatParameters params, AFPChain afpChain)
double	SigEva.calSigAll(FatCatParameters params, AFPChain afpChain)
static void	AFPChainer.doChainAfp(FatCatParameters params, AFPChain afpChain, Atom[] ca1, Atom[] ca2)	// Key function: chain (assembly) the AFPs // a AFP (k) is defined as (i, j, k), with i and j are staring points // AFP extension (eg.
static void	AFPCalculator.extractAFPChains(FatCatParameters params, AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static void	AFPOptimizer.optimizeAln(FatCatParameters params, AFPChain afpChain, Atom[] ca1, Atom[] ca2)	optimize the alignment by dynamic programming
static void	AFPPostProcessor.postProcess(FatCatParameters params, AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static void	AFPOptimizer.updateScore(FatCatParameters params, AFPChain afpChain)	to update the chaining score after block delete and merge processed the blockScore value is important for significance evaluation