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

Class MaxConflicts

java.lang.Object

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

pl.poznan.put.structure.pseudoknots.elimination.MaxConflicts

All Implemented Interfaces:

RegionRemover, PseudoknotFinder

Direct Known Subclasses:

ImmutableMaxConflicts

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

Java implementation of Elimination Conflicts 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
MaxConflicts()

Method Summary

Modifier and Type	Method	Description
final Region	selectRegionToRemove(ConflictGraph conflictGraph)	Selects a region which has the most conflicts with other regions.

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

MaxConflicts

public MaxConflicts()

Method Details

selectRegionToRemove

public final Region selectRegionToRemove(ConflictGraph conflictGraph)

Selects a region which has the most conflicts with other regions. In case of a tie, selects one with has the least gain. 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.