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 final 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 Details
- debug
  
  public static final boolean debug
  See Also:
  
  Constant Field Values
Constructor Details
- AFPOptimizer
  
  public AFPOptimizer()
Method Details
- 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