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 Summary

All Methods Instance Methods Abstract Methods Default Methods
Modifier and Type	Method	Description
`BasePair`	`basePair()`
`default BPh`	`bph()`
`default BR`	`br()`
`default int`	`compareTo(ClassifiedBasePair t)`
`default String`	`generateComment()`
`default InteractionType`	`interactionType()`
`ClassifiedBasePair`	`invert()`
`default boolean`	`isBasePhosphate()`
`default boolean`	`isBaseRibose()`
`default boolean`	`isCanonical()`
`default boolean`	`isNonCanonical()`
`default boolean`	`isPairing()`
`default boolean`	`isRepresented()`
`default boolean`	`isStacking()`
`default LeontisWesthof`	`leontisWesthof()`
`default Saenger`	`saenger()`

- Method Detail
  - 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).
  - 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>

Interface ClassifiedBasePair

Method Summary

Method Detail

basePair

interactionType

saenger

leontisWesthof

bph

br

isRepresented

invert

generateComment

isBaseRibose

isStacking

isBasePhosphate

isPairing

isNonCanonical

isCanonical

compareTo