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

Class AbstractRegionRemover

java.lang.Object

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

All Implemented Interfaces:

RegionRemover, PseudoknotFinder

Direct Known Subclasses:

MaxConflicts, MinGain

public abstract class AbstractRegionRemover
extends Object
implements RegionRemover

Java implementation of region removal 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
AbstractRegionRemover()

Method Summary

Modifier and Type	Method	Description
final List<BpSeq>	findPseudoknots(BpSeq bpSeq)	Finds pseudoknots by removing one region at a time until there are any conflicts.

Methods inherited from class java.lang.Object

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

Methods inherited from interface pl.poznan.put.structure.pseudoknots.elimination.RegionRemover

selectRegionToRemove

Constructor Details

AbstractRegionRemover

public AbstractRegionRemover()

Method Details

findPseudoknots

public final List<BpSeq> findPseudoknots(BpSeq bpSeq)

Finds pseudoknots by removing one region at a time until there are any conflicts. The region to remove is selected according to a heuristic (see MinGain and MaxConflicts).

Specified by:

findPseudoknots in interface PseudoknotFinder

Parameters:

bpSeq - An input BPSEQ structure with all pairs.

Returns:

A list of BPSEQ structures where each contains only pairs considered to be pseudoknots. Each BPSEQ is a full copy of original one, but contains zeroed 'pair' columns for entries which are non-pseudoknots.