Package pl.poznan.put.structure.pseudoknots.elimination

Class MinGain

java.lang.Object

pl.poznan.put.structure.pseudoknots.elimination.AbstractRegionRemover

pl.poznan.put.structure.pseudoknots.elimination.MinGain

All Implemented Interfaces:

RegionRemover, PseudoknotFinder

Direct Known Subclasses:

ImmutableMinGain

@Immutable(singleton=true)
public abstract class MinGain
extends AbstractRegionRemover

Java implementation of Elimination Gain algorithm as presented in: Smit, S. et al., 2008. From knotted to nested RNA structures: A variety of computational methods for pseudoknot removal. RNA, 14, pp.410–416.

Constructor Summary

Constructors

Constructor	Description
MinGain()

Method Summary

Modifier and Type	Method	Description
final Region	selectRegionToRemove(ConflictGraph conflictGraph)	Selects a region which has the least gain (sum of length of all regions in conflict).

Methods inherited from class pl.poznan.put.structure.pseudoknots.elimination.AbstractRegionRemover

findPseudoknots

Methods inherited from class java.lang.Object

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

Constructor Details

MinGain

public MinGain()

Method Details

selectRegionToRemove

public final Region selectRegionToRemove(ConflictGraph conflictGraph)

Selects a region which has the least gain (sum of length of all regions in conflict). In case of a tie, selects one with has the maximum conflict count. In case of another tie, select one which is closer to 5' end.

Parameters:

conflictGraph - The graph of conflicts between regions.

Returns:

A region to be removed.