Class AFPOptimizer


  • public class AFPOptimizer
    extends java.lang.Object
    • Field Summary

      Fields 
      Modifier and Type Field Description
      static boolean debug  
    • Constructor Summary

      Constructors 
      Constructor Description
      AFPOptimizer()  
    • 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 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
    • Constructor Detail

      • AFPOptimizer

        public AFPOptimizer()
    • Method Detail

      • 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