Class StructureAlignmentOptimizer


  • public class StructureAlignmentOptimizer
    extends java.lang.Object
    • Constructor Summary

      Constructors 
      Constructor Description
      StructureAlignmentOptimizer​(int b1, int end1, Atom[] c1, int b2, int end2, Atom[] c2, int iniLen, int[][] iniSet)
      optimize the structural alignment by update the equivalent residues and then run dynamic programming input: len1 the length of structure 1; c1: the structure information of 1 len2 the length of structure 2; c2: the structure information of 2 iniLen and iniSet is the length and list of initial equivalent residues
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      double optimizeResult​(int[] optLen, int optLenpos, int[][] list)  
      void runOptimization​(int maxi)
      run the optimization
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • StructureAlignmentOptimizer

        public StructureAlignmentOptimizer​(int b1,
                                           int end1,
                                           Atom[] c1,
                                           int b2,
                                           int end2,
                                           Atom[] c2,
                                           int iniLen,
                                           int[][] iniSet)
                                    throws StructureException
        optimize the structural alignment by update the equivalent residues and then run dynamic programming input: len1 the length of structure 1; c1: the structure information of 1 len2 the length of structure 2; c2: the structure information of 2 iniLen and iniSet is the length and list of initial equivalent residues
        Throws:
        StructureException
    • Method Detail

      • runOptimization

        public void runOptimization​(int maxi)
                             throws StructureException
        run the optimization
        Parameters:
        maxi - maximum nr. of iterations
        Throws:
        StructureException
      • optimizeResult

        public double optimizeResult​(int[] optLen,
                                     int optLenpos,
                                     int[][] list)