org.biojavax.bio.seq

Class SimpleRichFeatureRelationship

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.bio.seq.SimpleRichFeatureRelationship

All Implemented Interfaces:

Comparable, Changeable, RichFeatureRelationship

public class SimpleRichFeatureRelationship
extends AbstractChangeable
implements RichFeatureRelationship

Represents a relationship between two features that is described by a term.

Since:

1.5

Author:

Richard Holland, Mark Schreiber

Field Summary

Fields inherited from interface org.biojavax.bio.seq.RichFeatureRelationship

RANK

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	SimpleRichFeatureRelationship()
	SimpleRichFeatureRelationship(RichFeature object, RichFeature subject, ComparableTerm term, int rank) Creates a new instance of SimpleRichFeatureRelationship.

Method Summary

Methods

Modifier and Type	Method and Description
int	compareTo(Object o) Relations are compared first by rank, then object, subject, then finally term.
boolean	equals(Object obj) Relations are equal if their objects, subjects and terms are equal.
static ComparableTerm	getContainsTerm() Gets the default CONTAINS term used for defining the relationship between features.
Integer	getId() Gets the Hibernate ID.
RichFeature	getObject() Returns the object of this relationship (ie. the feature which this relationship starts from).
int	getRank() Gets the rank of this relationship.
RichFeature	getSubject() Gets the feature that this relationship refers to.
ComparableTerm	getTerm() Gets the term that describes this relationship.
int	hashCode()
void	setId(Integer id) Sets the Hibernate ID.
void	setRank(int rank) Sets the rank of this relationship.
String	toString() Form: "(#rank) term(object,subject)"

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

SimpleRichFeatureRelationship

public SimpleRichFeatureRelationship(RichFeature object,
                             RichFeature subject,
                             ComparableTerm term,
                             int rank)

Creates a new instance of SimpleRichFeatureRelationship.

Parameters:

subject - The subject RichFeature.

term - The relationship term.

rank - the rank of the relationship.

SimpleRichFeatureRelationship

protected SimpleRichFeatureRelationship()

Method Detail

getContainsTerm

public static ComparableTerm getContainsTerm()

Gets the default CONTAINS term used for defining the relationship between features.

Returns:

the default CONTAINS term.

setRank

public void setRank(int rank)
             throws ChangeVetoException

Sets the rank of this relationship.

Specified by:

setRank in interface RichFeatureRelationship

Parameters:

rank - Value of property rank.

Throws:

ChangeVetoException - if the rank is untasty.

getRank

public int getRank()

Gets the rank of this relationship.

Specified by:

getRank in interface RichFeatureRelationship

Returns:

Value of property rank.

getObject

public RichFeature getObject()

Returns the object of this relationship (ie. the feature which this relationship starts from). This is an immutable property set by the constructor of an instantiating class.

Specified by:

getObject in interface RichFeatureRelationship

Returns:

Value of property object.

getSubject

public RichFeature getSubject()

Gets the feature that this relationship refers to. This is set at constructor time and is immutable.

Specified by:

getSubject in interface RichFeatureRelationship

Returns:

Value of property subject.

getTerm

public ComparableTerm getTerm()

Gets the term that describes this relationship. This is set at constructor time and is immutable.

Specified by:

getTerm in interface RichFeatureRelationship

Returns:

Value of property term.

compareTo

public int compareTo(Object o)

Relations are compared first by rank, then object, subject, then finally term.

Specified by:

compareTo in interface Comparable

equals

public boolean equals(Object obj)

Relations are equal if their objects, subjects and terms are equal.

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Form: "(#rank) term(object,subject)"

Overrides:

toString in class Object

getId

public Integer getId()

Gets the Hibernate ID. Should be used with caution.

Returns:

the Hibernate ID, if using Hibernate.

setId

public void setId(Integer id)

Sets the Hibernate ID. Should be used with caution.

Parameters:

id - the Hibernate ID, if using Hibernate.