Package org.biojava.nbio.structure.align.fatcat.calc

Class AFPOptimizer

java.lang.Object

org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer

public class AFPOptimizer
extends Object

Field Summary

Fields

Modifier and Type	Field	Description
static boolean	debug

Constructor Summary

Constructors

Constructor	Description
AFPOptimizer()

Method Summary

Modifier and Type	Method	Description
static void	blockInfo(AFPChain afpChain)	get the afp list and residue list for each block
static void	optimizeAln(FatCatParameters params, AFPChain afpChain, Atom[] ca1, Atom[] ca2)	optimize the alignment by dynamic programming
static void	updateScore(FatCatParameters params, AFPChain afpChain)	to update the chaining score after block delete and merge processed the blockScore value is important for significance evaluation

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

debug

public static final boolean debug

See Also:

Constant Field Values

Constructor Detail

AFPOptimizer

public AFPOptimizer()

Method Detail

optimizeAln

public static void optimizeAln(FatCatParameters params,
                               AFPChain afpChain,
                               Atom[] ca1,
                               Atom[] ca2)
                        throws StructureException

optimize the alignment by dynamic programming

Throws:

StructureException

blockInfo

public static void blockInfo(AFPChain afpChain)

get the afp list and residue list for each block

updateScore

public static void updateScore(FatCatParameters params,
                               AFPChain afpChain)

to update the chaining score after block delete and merge processed the blockScore value is important for significance evaluation