org.biojava.bio.structure.align.fatcat.calc
Class AFPOptimizer

java.lang.Object
  extended by org.biojava.bio.structure.align.fatcat.calc.AFPOptimizer

public class AFPOptimizer
extends Object


Field Summary
static boolean debug
           
 
Constructor Summary
AFPOptimizer()
           
 
Method Summary
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