Package pl.poznan.put.structure.formats

Class BpSeq

java.lang.Object
pl.poznan.put.structure.formats.BpSeq
All Implemented Interfaces:
Serializable
Direct Known Subclasses:
ImmutableBpSeq
@Immutable public abstract class BpSeq extends Object implements Serializable
RNA secondary structure in BPSEQ format.
See Also:

  • Constructor Details

    • BpSeq

      public BpSeq()

  • Method Details

    • fromString

      public static BpSeq fromString(String data)
      Parses string into an instance of this class.
      Parameters:
      data - The string with BPSEQ data.
      Returns:
      An instance of this class with parsed data.

    • fromCt

      public static BpSeq fromCt(Ct ct)
      Converts RNA secondary structure in CT format to BPSEQ format.
      Parameters:
      ct - The data in CT format.
      Returns:
      An instance of this class with converted data.

    • fromDotBracket

      public static BpSeq fromDotBracket(DotBracket db)
      Converts RNA secondary structure in dot-bracket format to BPSEQ format.
      Parameters:
      db - The data in dot-bracket format.
      Returns:
      An instance of this class with converted data.

    • fromBasePairs

      public static BpSeq fromBasePairs(List<PdbNamedResidueIdentifier> residues, Collection<? extends ClassifiedBasePair> basePairs)
      Creates an instance of BPSEQ from a list of residue identifiers and a list of base pairs. The PDB chains are automatically reordered so that connecting ones are next to each other.
      Parameters:
      residues - The list of residue identifiers with names.
      basePairs - The list of base pairs.
      Returns:
      An instance of this class.

    • entries

      @Parameter(order=1) @NaturalOrder public abstract SortedSet<BpSeq.Entry> entries()
      Returns:
      The list of BPSEQ entries.

    • sequence

      public final String sequence()
      Returns:
      The sequence of nucleotides stored in this object.

    • paired

      public final SortedSet<BpSeq.Entry> paired()
      Returns:
      The set of paired BPSEQ entries without duplicates. For example, pair (4, 15) will not be repeated as (15, 4).

    • size

      public final int size()
      Returns:
      The number of BPSEQ entries.

    • hasAnyPair

      public final boolean hasAnyPair()
      Returns:
      True if at least one BPSEQ entry stands for a pair.

    • withoutIsolatedPairs

      public final BpSeq withoutIsolatedPairs()
      Finds all isolated base pairs and creates a copy of this instance without them.
      Returns:
      A copy of this instance, but with all isolated base pairs removed.

    • withoutPair

      public final BpSeq withoutPair(BpSeq.Entry entry)
      Creates a copy of this instance, but with the given pair removed.
      Parameters:
      entry - The pair to remove.
      Returns:
      A copy of this instance without the given pair.

    • toString

      public final String toString()
      Overrides:
      toString in class Object

    • validate

      @Check protected void validate()