Package pl.poznan.put.structure

Class AnalyzedBasePair

java.lang.Object
pl.poznan.put.structure.AnalyzedBasePair
All Implemented Interfaces:
Serializable, Comparable<ClassifiedBasePair>, ClassifiedBasePair
Direct Known Subclasses:
ImmutableAnalyzedBasePair
@Immutable public abstract class AnalyzedBasePair extends Object implements ClassifiedBasePair
A pair of residues with metadata taken from analysis tool.
See Also:

  • Constructor Details

    • AnalyzedBasePair

      public AnalyzedBasePair()

  • 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

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

    • invert

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

    • getIsRepresented

      public final Boolean getIsRepresented()
      Returns the value of isRepresented(), but this naming is required by Spring.
      Returns:
      The value of isRepresented();