Uses of Interface
org.biojavax.bio.BioEntry

Packages that use BioEntry

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

BioEntry	DummyCrossReferenceResolver.getRemoteBioEntry(CrossRef cr) Given the CrossRef return the corresponding BioEntry All responses are null.
BioEntry	CrossReferenceResolver.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

class

SimpleBioEntry Reference implementation of a BioEntry object which has no features or sequence.

Methods in org.biojavax.bio that return BioEntry

BioEntry	SimpleBioEntryRelationship.getObject() Returns the object of this relationship (ie.
BioEntry	BioEntryRelationship.getObject() Returns the object of this relationship (ie.
BioEntry	SimpleBioEntryRelationship.getSubject() Returns the subject of this relationship (ie.
BioEntry	BioEntryRelationship.getSubject() Returns the subject of this relationship (ie.
BioEntry	BioEntryIterator.nextBioEntry()

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

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

BioEntry	HashBioEntryDB.getBioEntry(String id)
BioEntry	BioEntryDBLite.getBioEntry(String id) Retrieve a single BioEntry by its id.
BioEntry	AbstractRichSequenceDB.getBioEntry(String id)

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

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

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

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

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

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

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

class	SimpleRichSequence A simple implementation of RichSequence.
class	ThinRichSequence A simple implementation of RichSequence.

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

BioEntry

RichSequence.IOTools.SingleRichSeqIterator.nextBioEntry()

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

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

BioEntry	RichStreamReader.nextBioEntry()
BioEntry	HashedFastaIterator.nextBioEntry()