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

Description

protected

SimpleRichFeatureRelationship()

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

Creates a new instance of SimpleRichFeatureRelationship.
Method Summary

Modifier and Type

Method

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 Details
- 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 Details
- 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.

Class SimpleRichFeatureRelationship

Field Summary

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

Constructor Summary

Method Summary

Methods inherited from class org.biojava.utils.AbstractChangeable

Methods inherited from class java.lang.Object

Methods inherited from interface org.biojava.utils.Changeable

Constructor Details

SimpleRichFeatureRelationship

SimpleRichFeatureRelationship

Method Details

getContainsTerm

setRank

getRank

getObject

getSubject

getTerm

compareTo

equals

hashCode

toString

getId

setId