org.biojavax.bio

Interface BioEntry

All Superinterfaces:

Annotatable, Changeable, Comparable, RankedCrossRefable, RichAnnotatable

All Known Subinterfaces:

RichSequence

All Known Implementing Classes:

SimpleBioEntry, SimpleRichSequence, ThinRichSequence

public interface BioEntry
extends RichAnnotatable, RankedCrossRefable, Comparable, Changeable

This class relates to the bioentry table in BioSQL. It holds everything you need to define a non-sequence bearing bioentry.

Since:

1.5

Author:

Mark Schreiber, Richard Holland

See Also:

BioEntryRelationship

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Field Summary

Fields

Modifier and Type	Field and Description
static ChangeType	COMMENT
static ChangeType	DESCRIPTION
static ChangeType	DIVISION
static ChangeType	IDENTIFIER
static ChangeType	RANKEDCROSSREF
static ChangeType	RANKEDDOCREF
static ChangeType	RELATIONS
static ChangeType	SEQVERSION
static ChangeType	TAXON

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Method Summary

Methods

Modifier and Type	Method and Description
void	addComment(Comment comment) Adds a comment instance to this bioentry.
void	addRankedDocRef(RankedDocRef docref) Adds a ranked docref instance to this bioentry.
void	addRelationship(BioEntryRelationship relation) Adds a relation instance to this bioentry.
String	getAccession() Returns the accession of this bioentry.
Set<Comment>	getComments() Returns a set of all comments associated with this bioentry.
String	getDescription() Returns a description of this sequence.
String	getDivision() Returns the division of this bioentry.
String	getIdentifier() Returns the identifier of this bioentry.
String	getName() Returns the name of this bioentry.
Namespace	getNamespace() Returns the namespace of this bioentry.
Set<RankedDocRef>	getRankedDocRefs() Returns a set of all bioentrydocrefs associated with this bioentry.
Set<BioEntryRelationship>	getRelationships() Returns a set of all relationships associated with this bioentry.
NCBITaxon	getTaxon() Gets the taxon associated with this bioentry.
int	getVersion() Gets the version of this bioentry.
void	removeComment(Comment comment) Removes a comment instance from this bioentry.
void	removeRankedDocRef(RankedDocRef docref) Removes a ranked docref instance from this bioentry.
void	removeRelationship(BioEntryRelationship relation) Removes a relation instance from this bioentry.
void	setDescription(String description) Sets the description for this bioentry.
void	setDivision(String division) Sets the division of this bioentry.
void	setIdentifier(String identifier) Sets the identifier of this bioentry.
void	setTaxon(NCBITaxon taxon) Sets the taxon for this bioentry.

Methods inherited from interface org.biojavax.RichAnnotatable

getNoteSet, getRichAnnotation, setNoteSet

Methods inherited from interface org.biojava.bio.Annotatable

getAnnotation

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojavax.RankedCrossRefable

addRankedCrossRef, getRankedCrossRefs, removeRankedCrossRef, setRankedCrossRefs

Methods inherited from interface java.lang.Comparable

compareTo

Field Detail

IDENTIFIER

static final ChangeType IDENTIFIER

DESCRIPTION

static final ChangeType DESCRIPTION

DIVISION

static final ChangeType DIVISION

TAXON

static final ChangeType TAXON

SEQVERSION

static final ChangeType SEQVERSION

RANKEDCROSSREF

static final ChangeType RANKEDCROSSREF

RANKEDDOCREF

static final ChangeType RANKEDDOCREF

COMMENT

static final ChangeType COMMENT

RELATIONS

static final ChangeType RELATIONS

Method Detail

getNamespace

Namespace getNamespace()

Returns the namespace of this bioentry. The namespace is supposed to be an immutable property set by the constructor.

Returns:

the namespace of this bioentry.

getName

String getName()

Returns the name of this bioentry. The name is supposed to be an immutable property set by the constructor.

Returns:

Value of property name.

getAccession

String getAccession()

Returns the accession of this bioentry. The accession is supposed to be an immutable property set by the constructor.

Returns:

Value of property accession.

getIdentifier

String getIdentifier()

Returns the identifier of this bioentry.

Returns:

Value of property identifier.

setIdentifier

void setIdentifier(String identifier)
                   throws ChangeVetoException

Sets the identifier of this bioentry. Null is allowable.

Parameters:

identifier - New value of property identifier.

Throws:

ChangeVetoException - in case of objections.

getDivision

String getDivision()

Returns the division of this bioentry. Division relates to a division of the parent namespace.

Returns:

Value of property division.

setDivision

void setDivision(String division)
                 throws ChangeVetoException

Sets the division of this bioentry. Null is allowable.

Parameters:

division - New value of property division.

Throws:

ChangeVetoException - in case of objections.

getDescription

String getDescription()

Returns a description of this sequence.

Returns:

Value of property description.

setDescription

void setDescription(String description)
                    throws ChangeVetoException

Sets the description for this bioentry.

Parameters:

description - New value of property description.

Throws:

ChangeVetoException - in case of objections.

getVersion

int getVersion()

Gets the version of this bioentry. Bioentries with no versions return 0. The version is supposed to be immutable and set only by the constructor.

Returns:

Value of property version.

getTaxon

NCBITaxon getTaxon()

Gets the taxon associated with this bioentry. It may be null.

Returns:

Value of property taxon.

setTaxon

void setTaxon(NCBITaxon taxon)
              throws ChangeVetoException

Sets the taxon for this bioentry. It may be null, in which case the taxon is unset.

Parameters:

taxon - New value of property taxon.

Throws:

ChangeVetoException - in case of objections.

getRankedDocRefs

Set<RankedDocRef> getRankedDocRefs()

Returns a set of all bioentrydocrefs associated with this bioentry. This set is not mutable. If no docrefs are associated, you will get back an empty set.

Returns:

a set of RankedDocRef objects.

See Also:

RankedDocRef

getComments

Set<Comment> getComments()

Returns a set of all comments associated with this bioentry. This set is not mutable. If no comments are associated, you will get back an empty set.

Returns:

a set of Comment objects.

See Also:

Comment

getRelationships

Set<BioEntryRelationship> getRelationships()

Returns a set of all relationships associated with this bioentry. This set is not mutable. If no relationships are associated, you will get back an empty set.

Returns:

a set of BioEntryRelationship objects.

See Also:

BioEntryRelationship

addRankedDocRef

void addRankedDocRef(RankedDocRef docref)
                     throws ChangeVetoException

Adds a ranked docref instance to this bioentry. Must not be null.

Parameters:

docref - the item to add.

Throws:

ChangeVetoException - if it doesn't want to add it.

removeRankedDocRef

void removeRankedDocRef(RankedDocRef docref)
                        throws ChangeVetoException

Removes a ranked docref instance from this bioentry. If it was not found, nothing happens.

Parameters:

docref - the item to remove.

Throws:

ChangeVetoException - if it doesn't want to remove it.

addComment

void addComment(Comment comment)
                throws ChangeVetoException

Adds a comment instance to this bioentry. Must not be null.

Parameters:

comment - the item to add.

Throws:

ChangeVetoException - if it doesn't want to add it.

removeComment

void removeComment(Comment comment)
                   throws ChangeVetoException

Removes a comment instance from this bioentry. If it wasn't present, it nothing will happen.

Parameters:

comment - the item to remove.

Throws:

ChangeVetoException - if it doesn't want to remove it.

addRelationship

void addRelationship(BioEntryRelationship relation)
                     throws ChangeVetoException

Adds a relation instance to this bioentry. It must not be null.

Parameters:

relation - the item to add.

Throws:

ChangeVetoException - if it doesn't want to add it.

removeRelationship

void removeRelationship(BioEntryRelationship relation)
                        throws ChangeVetoException

Removes a relation instance from this bioentry. If it wasn't present, nothing will happen.

Parameters:

relation - the item to remove.

Throws:

ChangeVetoException - if it doesn't want to remove it.