Package pl.poznan.put.structure.pseudoknots

Interface PseudoknotFinder

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

    Modifier and Type
    Method
    Description
    List<BpSeq>
    findPseudoknots(BpSeq bpSeq)
    Finds pseudoknots in BPSEQ data.

  • Method Details

    • 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.