Uses of Interface
org.biojavax.bio.BioEntry

Packages that use BioEntry

Package	Description
org.biojavax	The Biojava extensions packages, classes that extend the core biojava functionality
org.biojavax.bio	Classes to represent biological entities and their relationships.
org.biojavax.bio.db	Interactions between biojavax objects and a DB.
org.biojavax.bio.db.biosql	Interface between biojava and biosql databases
org.biojavax.bio.seq	Rich implementations of Sequences, Locations and Features.
org.biojavax.bio.seq.io	Classes to support the I/O of RichSequence and Bioentry objects.

Uses of BioEntry in org.biojavax

Methods in org.biojavax that return BioEntry

Modifier and Type	Method	Description
BioEntry	CrossReferenceResolver.getRemoteBioEntry(CrossRef cr)	Given the CrossRef return the corresponding BioEntry
BioEntry	DummyCrossReferenceResolver.getRemoteBioEntry(CrossRef cr)	Given the CrossRef return the corresponding BioEntry

Uses of BioEntry in org.biojavax.bio

Classes in org.biojavax.bio that implement BioEntry

Modifier and Type	Class	Description
class	SimpleBioEntry	Reference implementation of a BioEntry object which has no features or sequence.

Methods in org.biojavax.bio that return BioEntry

Modifier and Type	Method	Description
BioEntry	BioEntryRelationship.getObject()	Returns the object of this relationship (ie. the BioEntry which this relationship starts from).
BioEntry	SimpleBioEntryRelationship.getObject()	Returns the object of this relationship (ie. the BioEntry which this relationship starts from).
BioEntry	BioEntryRelationship.getSubject()	Returns the subject of this relationship (ie. the BioEntry which this relationship targets).
BioEntry	SimpleBioEntryRelationship.getSubject()	Returns the subject of this relationship (ie. the BioEntry which this relationship targets).
BioEntry	BioEntryIterator.nextBioEntry()

Constructors in org.biojavax.bio with parameters of type BioEntry

Constructor	Description
SimpleBioEntryRelationship(BioEntry object, BioEntry subject, ComparableTerm term, Integer rank)	Creates a new instance of SimpleBioEntryRelationship.

Uses of BioEntry in org.biojavax.bio.db

Methods in org.biojavax.bio.db that return BioEntry

Modifier and Type	Method	Description
BioEntry	AbstractRichSequenceDB.getBioEntry(String id)
BioEntry	BioEntryDBLite.getBioEntry(String id)	Retrieve a single BioEntry by its id.
BioEntry	HashBioEntryDB.getBioEntry(String id)

Methods in org.biojavax.bio.db with parameters of type BioEntry

Modifier and Type	Method	Description
void	AbstractBioEntryDB.addBioEntry(BioEntry seq)
void	AbstractRichSequenceDB.addBioEntry(BioEntry seq)
void	BioEntryDBLite.addBioEntry(BioEntry seq)	Adds a sequence to the database.
protected void	HashBioEntryDB.addBioEntry(String id, BioEntry seq)
void	HashBioEntryDB.addBioEntry(BioEntry seq)	Add a BioEntry, the name of the BioEntry will be used as the ID

Uses of BioEntry in org.biojavax.bio.db.biosql

Methods in org.biojavax.bio.db.biosql that return BioEntry

Modifier and Type	Method	Description
BioEntry	BioSQLBioEntryDB.getBioEntry(String id)
BioEntry	BioSQLCrossReferenceResolver.getRemoteBioEntry(CrossRef cr)	Given the CrossRef return the corresponding BioEntry

Methods in org.biojavax.bio.db.biosql with parameters of type BioEntry

Modifier and Type	Method	Description
void	BioSQLBioEntryDB._addBioEntry(BioEntry seq)
void	BioSQLBioEntryDB.addBioEntry(BioEntry seq)

Uses of BioEntry in org.biojavax.bio.seq

Subinterfaces of BioEntry in org.biojavax.bio.seq

Modifier and Type	Interface	Description
interface	RichSequence	A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.

Classes in org.biojavax.bio.seq that implement BioEntry

Modifier and Type	Class	Description
class	SimpleRichSequence	A simple implementation of RichSequence.
class	ThinRichSequence	A simple implementation of RichSequence.

Methods in org.biojavax.bio.seq that return BioEntry

Modifier and Type	Method	Description
BioEntry	RichSequence.IOTools.SingleRichSeqIterator.nextBioEntry()

Uses of BioEntry in org.biojavax.bio.seq.io

Methods in org.biojavax.bio.seq.io that return BioEntry

Modifier and Type	Method	Description
BioEntry	HashedFastaIterator.nextBioEntry()
BioEntry	RichStreamReader.nextBioEntry()