org.biojava.nbio.structure.align.fatcat.calc

Class StructureAlignmentOptimizer

java.lang.Object

org.biojava.nbio.structure.align.fatcat.calc.StructureAlignmentOptimizer

public class StructureAlignmentOptimizer
extends Object

Constructor Summary

Constructors

Constructor and 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

Methods

Modifier and Type	Method and 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)