org.biojava.bio.structure.align.fatcat.calc
Class StructureAlignmentOptimizer

java.lang.Object
  extended by org.biojava.bio.structure.align.fatcat.calc.StructureAlignmentOptimizer

public class StructureAlignmentOptimizer
extends Object


Constructor Summary
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
 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)