org.biojava.nbio.structure.align.cemc

Class CeMcOptimizer

java.lang.Object

org.biojava.nbio.structure.align.cemc.CeMcOptimizer

All Implemented Interfaces:

Callable<MultipleAlignment>

public class CeMcOptimizer
extends Object
implements Callable<MultipleAlignment>

This class takes a MultipleAlignment seed previously generated by the CECP algorithm and runs a Monte Carlo optimization.

It assumes that the seed alignment is not flexible, since only CP are supported but not alignment flexibility.

It implements Callable to be run in parallel.

Author:

Aleix Lafita

Constructor Summary

Constructors

Constructor and Description
CeMcOptimizer(MultipleAlignment seedAln, long randomSeed, int reference) Constructor.

Method Summary

Methods

Modifier and Type	Method and Description
MultipleAlignment	call()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CeMcOptimizer

public CeMcOptimizer(MultipleAlignment seedAln,
             long randomSeed,
             int reference)
              throws StructureException

Constructor.

Parameters:

seedAln - MultipleAlignment to be optimized.

randomSeed - seed to use in the random number generator

reference - the index of the most similar structure to all others

Throws:

StructureException

Method Detail

call

public MultipleAlignment call()
                       throws Exception

Specified by:

call in interface Callable<MultipleAlignment>

Throws:

Exception