org.biojava.bio.structure.align.fatcat.calc
Class AFPOptimizer
java.lang.Object
org.biojava.bio.structure.align.fatcat.calc.AFPOptimizer
public class AFPOptimizer
- extends Object
Field Summary |
static boolean |
debug
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
debug
public static final boolean debug
- See Also:
- Constant Field Values
AFPOptimizer
public AFPOptimizer()
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