Class AFPOptimizer
- java.lang.Object
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- org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer
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public class AFPOptimizer extends Object
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Field Summary
Fields Modifier and Type Field Description static boolean
debug
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Constructor Summary
Constructors Constructor Description AFPOptimizer()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static void
blockInfo(AFPChain afpChain)
get the afp list and residue list for each blockstatic void
optimizeAln(FatCatParameters params, AFPChain afpChain, Atom[] ca1, Atom[] ca2)
optimize the alignment by dynamic programmingstatic 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
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Field Detail
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debug
public static final boolean debug
- See Also:
- Constant Field Values
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Constructor Detail
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AFPOptimizer
public AFPOptimizer()
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Method Detail
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optimizeAln
public static void optimizeAln(FatCatParameters params, AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws StructureException
optimize the alignment by dynamic programming- Throws:
StructureException
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blockInfo
public static void blockInfo(AFPChain afpChain)
get the afp list and residue list for each block
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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
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