Package pl.poznan.put.structure

Class QuantifiedBasePair

java.lang.Object
pl.poznan.put.structure.QuantifiedBasePair
All Implemented Interfaces:
Serializable, Comparable<ClassifiedBasePair>, ClassifiedBasePair
Direct Known Subclasses:
ImmutableQuantifiedBasePair
@Immutable public abstract class QuantifiedBasePair extends Object implements ClassifiedBasePair
A base pair which is classified and quantified with numerical parameters.
See Also:

  • Constructor Details

    • QuantifiedBasePair

      public QuantifiedBasePair()

  • Method Details

    • basePair

      @Parameter(order=1) public abstract BasePair basePair()
      Specified by:
      basePair in interface ClassifiedBasePair
      Returns:
      The pair of nucleotides which interact.

    • interactionType

      @Default public InteractionType interactionType()
      Specified by:
      interactionType in interface ClassifiedBasePair
      Returns:
      The type of interaction.

    • saenger

      @Default public Saenger saenger()
      Specified by:
      saenger in interface ClassifiedBasePair
      Returns:
      The classification by Saenger (if applicable).

    • leontisWesthof

      @Default public LeontisWesthof leontisWesthof()
      Specified by:
      leontisWesthof in interface ClassifiedBasePair
      Returns:
      The classification by Leontis and Westhof (if applicable).

    • bph

      @Default public BPh bph()
      Specified by:
      bph in interface ClassifiedBasePair
      Returns:
      The classification of base-phosphate interaction (if applicable).

    • br

      @Default public BR br()
      Specified by:
      br in interface ClassifiedBasePair
      Returns:
      The classification of base-ribose interaction (if applicable).

    • stackingTopology

      @Default public StackingTopology stackingTopology()
      Specified by:
      stackingTopology in interface ClassifiedBasePair
      Returns:
      The classification of stacking interaction (if applicable).

    • isRepresented

      @Default @Auxiliary public boolean isRepresented()
      Specified by:
      isRepresented in interface ClassifiedBasePair
      Returns:
      True if this interaction is represented in secondary structure.

    • invert

      public ClassifiedBasePair invert()
      Specified by:
      invert in interface ClassifiedBasePair
      Returns:
      An instance of this class, but with interacting partners inverted.

    • shear

      @Parameter(order=2) @Auxiliary public abstract double shear()
      Returns:
      The value of shear parameter.

    • stretch

      @Parameter(order=3) @Auxiliary public abstract double stretch()
      Returns:
      The value of stretch parameter.

    • stagger

      @Parameter(order=4) @Auxiliary public abstract double stagger()
      Returns:
      The value of stagger parameter.

    • buckle

      @Parameter(order=5) @Auxiliary public abstract double buckle()
      Returns:
      The value of buckle parameter.

    • propeller

      @Parameter(order=6) @Auxiliary public abstract double propeller()
      Returns:
      The value of propeller parameter.

    • opening

      @Parameter(order=7) @Auxiliary public abstract double opening()
      Returns:
      The value of opening parameter.