net.sourceforge.cilib.bioinf.rnaprediction
Class RNAFolder

java.lang.Object
  net.sourceforge.cilib.bioinf.rnaprediction.RNAFolder

Direct Known Subclasses:

GreedyRNAFolder

public abstract class RNAFolder
extends Object

Author:

mneethling This is an abstract class (Strategy design pattern) that takes care of 'folding' a given conformation into a new/different conformation. Several methods to do this is possible, the simplest being a greedy algorithm that first adds stems that has the greatest effect on the fitness of the particle. Another option is to use an optimising algorithm (like PSO) to do a local search to find the best configuration for adding the new stems.

Constructor Summary

RNAFolder()

Method Summary

abstract void

refold(RNAConformation currentfolding, RNAConformation openStems, RNAConformation closeStems)

Methods inherited from class java.lang.Object

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

Constructor Detail

RNAFolder

public RNAFolder()

Method Detail

refold

public abstract void refold(RNAConformation currentfolding,
                            RNAConformation openStems,
                            RNAConformation closeStems)

Parameters:

currentfolding - - This is a input/output parameter (passed by reference. The new folding is returned in this parameter.

openStems - - The stems to remove from the conformation.

closeStems - - The stems to attempt to add to the conformation.