net.sourceforge.cilib.bioinf.rnaprediction
Class GreedyRNAFolder

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

public class GreedyRNAFolder
extends RNAFolder

Author:

mneethling This subclass uses a greedy algorithm to add the 'close stems' to the 'currentStem' RNAStem. It will add the stems from 'closeStems' that reduces the free energy of the RNAStem the most, first, until no more stems can be added.

Constructor Summary

GreedyRNAFolder(RNAFitness fitness)

Method Summary

void	refold(RNAConformation currentFolding, RNAConformation openStems, RNAConformation closeStems) This method modifies the 'currentFolding' HashSet.

Methods inherited from class java.lang.Object

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

Constructor Detail

GreedyRNAFolder

public GreedyRNAFolder(RNAFitness fitness)

Method Detail

refold

public void refold(RNAConformation currentFolding,
                   RNAConformation openStems,
                   RNAConformation closeStems)

This method modifies the 'currentFolding' HashSet. HashSet is passed by reference.

Specified by:

refold in class RNAFolder

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.