PseudoknotFinder (BioCommons 3.0.4 API)

All Known Subinterfaces:

RegionRemover

All Known Implementing Classes:

AbstractRegionRemover, DynamicProgrammingAll, ImmutableDynamicProgrammingAll, ImmutableMaxConflicts, ImmutableMinGain, MaxConflicts, MinGain

Functional Interface:

This is a functional interface and can therefore be used as the assignment target for a lambda expression or method reference.
```
@FunctionalInterface
public interface PseudoknotFinder
```
A finder of pseudoknots in RNA secondary structure.

- Method Summary
  
  All Methods Instance Methods Abstract Methods
  Modifier and Type Method Description
  
  List<BpSeq> findPseudoknots(BpSeq bpSeq)
  Finds pseudoknots in BPSEQ data.

- Method Detail
  - findPseudoknots
```
List<BpSeq> findPseudoknots(BpSeq bpSeq)
```
    Finds pseudoknots in BPSEQ data. Pseudoknots are defined here as BPSEQ entries which if removed will make the RNA secondary structure fully nested. There may be many subsets of pairs considered pseudoknots for a single BPSEQ input.
    
    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.