Package pl.poznan.put.structure

Interface ClassifiedBasePair

All Superinterfaces:
Comparable<ClassifiedBasePair>, Serializable
All Known Implementing Classes:
AnalyzedBasePair, ImmutableAnalyzedBasePair, ImmutableQuantifiedBasePair, QuantifiedBasePair
public interface ClassifiedBasePair extends Serializable, Comparable<ClassifiedBasePair>
A pair of interacting nucleotides with classification info.

  • Method Details

    • basePair

      BasePair basePair()
      Returns:
      The pair of nucleotides which interact.

    • interactionType

      default InteractionType interactionType()
      Returns:
      The type of interaction.

    • saenger

      default Saenger saenger()
      Returns:
      The classification by Saenger (if applicable).

    • leontisWesthof

      default LeontisWesthof leontisWesthof()
      Returns:
      The classification by Leontis and Westhof (if applicable).

    • bph

      default BPh bph()
      Returns:
      The classification of base-phosphate interaction (if applicable).

    • br

      default BR br()
      Returns:
      The classification of base-ribose interaction (if applicable).

    • stackingTopology

      default StackingTopology stackingTopology()
      Returns:
      The classification of stacking interaction (if applicable).

    • isRepresented

      default boolean isRepresented()
      Returns:
      True if this interaction is represented in secondary structure.

    • invert

      ClassifiedBasePair invert()
      Returns:
      An instance of this class, but with interacting partners inverted.

    • generateComment

      default String generateComment()
      Returns:
      A comment containing Saenger and Leontis-Westhof classifications.

    • isBaseRibose

      default boolean isBaseRibose()
      Returns:
      True if this instance describes a base-ribose interaction.

    • isStacking

      default boolean isStacking()
      Returns:
      True if this instance describes a stacking interaction.

    • isBasePhosphate

      default boolean isBasePhosphate()
      Returns:
      True if this instance describes a base-phosphate interaction.

    • isPairing

      default boolean isPairing()
      Returns:
      True if this instance describes a base-base interaction.

    • isNonCanonical

      default boolean isNonCanonical()
      Returns:
      True if this instance describes a non-canonical base-base interaction.

    • isCanonical

      default boolean isCanonical()
      Returns:
      True if this instance describes a canonical base-base interaction.

    • compareTo

      default int compareTo(ClassifiedBasePair t)
      Specified by:
      compareTo in interface Comparable<ClassifiedBasePair>