Package org.biojavax.bio
Interface BioEntry
- All Superinterfaces:
Annotatable
,Changeable
,Comparable
,RankedCrossRefable
,RichAnnotatable
- All Known Subinterfaces:
RichSequence
- All Known Implementing Classes:
SimpleBioEntry
,SimpleRichSequence
,ThinRichSequence
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:
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Nested Class Summary
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final ChangeType
static final ChangeType
static final ChangeType
static final ChangeType
static final ChangeType
static final ChangeType
static final ChangeType
static final ChangeType
static final ChangeType
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
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Method Summary
Modifier and TypeMethodDescriptionvoid
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.Returns the accession of this bioentry.Returns a set of all comments associated with this bioentry.Returns a description of this sequence.Returns the division of this bioentry.Returns the identifier of this bioentry.getName()
Returns the name of this bioentry.Returns the namespace of this bioentry.Returns a set of all bioentrydocrefs associated with this bioentry.Returns a set of all relationships associated with this bioentry.getTaxon()
Gets the taxon associated with this bioentry.int
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
Sets the taxon for this bioentry.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 java.lang.Comparable
compareTo
Methods inherited from interface org.biojavax.RankedCrossRefable
addRankedCrossRef, getRankedCrossRefs, removeRankedCrossRef, setRankedCrossRefs
Methods inherited from interface org.biojavax.RichAnnotatable
getNoteSet, getRichAnnotation, setNoteSet
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Field Details
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IDENTIFIER
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DESCRIPTION
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DIVISION
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TAXON
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SEQVERSION
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RANKEDCROSSREF
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RANKEDDOCREF
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COMMENT
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RELATIONS
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Method Details
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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.
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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.
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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.
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getIdentifier
Returns the identifier of this bioentry.- Returns:
- Value of property identifier.
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setIdentifier
Sets the identifier of this bioentry. Null is allowable.- Parameters:
identifier
- New value of property identifier.- Throws:
ChangeVetoException
- in case of objections.
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getDivision
Returns the division of this bioentry. Division relates to a division of the parent namespace.- Returns:
- Value of property division.
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setDivision
Sets the division of this bioentry. Null is allowable.- Parameters:
division
- New value of property division.- Throws:
ChangeVetoException
- in case of objections.
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getDescription
Returns a description of this sequence.- Returns:
- Value of property description.
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setDescription
Sets the description for this bioentry.- Parameters:
description
- New value of property description.- Throws:
ChangeVetoException
- in case of objections.
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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.
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getTaxon
Gets the taxon associated with this bioentry. It may be null.- Returns:
- Value of property taxon.
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setTaxon
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.
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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:
-
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:
-
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:
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addRankedDocRef
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.
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removeRankedDocRef
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.
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addComment
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.
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removeComment
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.
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addRelationship
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.
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removeRelationship
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.
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