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:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
QuantifiedBasePair()

Method Summary

Modifier and Type	Method	Description
abstract BasePair	basePair()
BPh	bph()
BR	br()
abstract double	buckle()
InteractionType	interactionType()
ClassifiedBasePair	invert()
boolean	isRepresented()
LeontisWesthof	leontisWesthof()
abstract double	opening()
abstract double	propeller()
Saenger	saenger()
abstract double	shear()
abstract double	stagger()
abstract double	stretch()

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

QuantifiedBasePair

public QuantifiedBasePair()

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

@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.