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:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
AnalyzedBasePair()

Method Summary

Modifier and Type	Method	Description
abstract BasePair	basePair()
BPh	bph()
BR	br()
Boolean	getIsRepresented()	Returns the value of isRepresented(), but this naming is required by Spring.
InteractionType	interactionType()
ClassifiedBasePair	invert()
boolean	isRepresented()
LeontisWesthof	leontisWesthof()
Saenger	saenger()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface pl.poznan.put.structure.ClassifiedBasePair

compareTo, generateComment, isBasePhosphate, isBaseRibose, isCanonical, isNonCanonical, isPairing, isStacking

Constructor Detail

AnalyzedBasePair

public AnalyzedBasePair()

Method Detail

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).

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();