Package pl.poznan.put.rna

Class InteractionType

java.lang.Object

pl.poznan.put.rna.InteractionType

All Implemented Interfaces:

Serializable, Comparable<InteractionType>

Direct Known Subclasses:

ImmutableInteractionType

@Immutable
public abstract class InteractionType
extends Object
implements Serializable, Comparable<InteractionType>

A type of interaction between two nucleotides.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static InteractionType	BASE_BASE	A base-base interaction, base pair.
static InteractionType	BASE_BASE_1H	A weak base-base interaction, based on a single hydrogen bond only.
static InteractionType	BASE_PHOSPHATE	A base-phosphate interaction (see BPh).
static InteractionType	BASE_RIBOSE	A base-ribose interaction (see BR).
static InteractionType	OTHER	Another interaction type.
static InteractionType	STACKING	A stacking interaction.
static InteractionType	SUGAR_SUGAR	A ribose-ribose interaction.

Constructor Summary

Constructors

Constructor	Description
InteractionType()

Method Summary

Modifier and Type	Method	Description
int	compareTo(InteractionType t)
String	description()
InteractionType	invert()
abstract boolean	isPairing()	Checks if this interaction is a basis for base pairing.
abstract NucleotideComponentType	left()
abstract NucleotideComponentType	right()
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

BASE_BASE

public static final InteractionType BASE_BASE

A base-base interaction, base pair.

BASE_BASE_1H

public static final InteractionType BASE_BASE_1H

A weak base-base interaction, based on a single hydrogen bond only.

BASE_PHOSPHATE

public static final InteractionType BASE_PHOSPHATE

A base-phosphate interaction (see BPh).

BASE_RIBOSE

public static final InteractionType BASE_RIBOSE

A base-ribose interaction (see BR).

SUGAR_SUGAR

public static final InteractionType SUGAR_SUGAR

A ribose-ribose interaction.

STACKING

public static final InteractionType STACKING

A stacking interaction.

OTHER

public static final InteractionType OTHER

Another interaction type.

Constructor Detail

InteractionType

public InteractionType()

Method Detail

left

public abstract NucleotideComponentType left()

Returns:

The first interacting partner.

right

public abstract NucleotideComponentType right()

Returns:

The second interacting partner.

isPairing

public abstract boolean isPairing()

Checks if this interaction is a basis for base pairing.

Returns:

True for BASE_BASE, false for all other types.

description

@Default
public String description()

Returns:

The description of this interaction type.

toString

public final String toString()

Overrides:

toString in class Object

compareTo

public final int compareTo(InteractionType t)

Specified by:

compareTo in interface Comparable<InteractionType>

invert

public final InteractionType invert()

Returns:

An instance where first and second interacting partners are inverted.