MinGain (BioCommons 3.0.4 API)

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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`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 Detail
  - MinGain
```
public MinGain()
```
- Method Detail
  - 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.