Uses of Interface
org.biojavax.bio.BioEntry
Packages that use BioEntry
Package
Description
The Biojava extensions packages, classes that extend the core biojava
functionality
Classes to represent biological entities and their relationships.
Interactions between biojavax objects and a DB.
Interface between biojava and biosql databases
Rich implementations of Sequences, Locations and Features.
Classes to support the I/O of RichSequence and
Bioentry objects.
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Uses of BioEntry in org.biojavax
Methods in org.biojavax that return BioEntryModifier and TypeMethodDescriptionCrossReferenceResolver.getRemoteBioEntry
(CrossRef cr) Given theCrossRef
return the correspondingBioEntry
DummyCrossReferenceResolver.getRemoteBioEntry
(CrossRef cr) Given theCrossRef
return the correspondingBioEntry
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Uses of BioEntry in org.biojavax.bio
Classes in org.biojavax.bio that implement BioEntryModifier and TypeClassDescriptionclass
Reference implementation of a BioEntry object which has no features or sequence.Methods in org.biojavax.bio that return BioEntryModifier and TypeMethodDescriptionBioEntryRelationship.getObject()
Returns the object of this relationship (ie. the BioEntry which this relationship starts from).SimpleBioEntryRelationship.getObject()
Returns the object of this relationship (ie. the BioEntry which this relationship starts from).BioEntryRelationship.getSubject()
Returns the subject of this relationship (ie. the BioEntry which this relationship targets).SimpleBioEntryRelationship.getSubject()
Returns the subject of this relationship (ie. the BioEntry which this relationship targets).BioEntryIterator.nextBioEntry()
Constructors in org.biojavax.bio with parameters of type BioEntryModifierConstructorDescriptionSimpleBioEntryRelationship
(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 BioEntryModifier and TypeMethodDescriptionAbstractRichSequenceDB.getBioEntry
(String id) BioEntryDBLite.getBioEntry
(String id) Retrieve a single BioEntry by its id.HashBioEntryDB.getBioEntry
(String id) Methods in org.biojavax.bio.db with parameters of type BioEntryModifier and TypeMethodDescriptionvoid
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 BioEntryModifier and TypeMethodDescriptionBioSQLBioEntryDB.getBioEntry
(String id) BioSQLCrossReferenceResolver.getRemoteBioEntry
(CrossRef cr) Given theCrossRef
return the correspondingBioEntry
Methods in org.biojavax.bio.db.biosql with parameters of type BioEntryModifier and TypeMethodDescriptionvoid
BioSQLBioEntryDB._addBioEntry
(BioEntry seq) void
BioSQLBioEntryDB.addBioEntry
(BioEntry seq) -
Uses of BioEntry in org.biojavax.bio.seq
Subinterfaces of BioEntry in org.biojavax.bio.seqModifier and TypeInterfaceDescriptioninterface
A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.Classes in org.biojavax.bio.seq that implement BioEntryModifier and TypeClassDescriptionclass
A simple implementation of RichSequence.class
A simple implementation of RichSequence.Methods in org.biojavax.bio.seq that return BioEntry -
Uses of BioEntry in org.biojavax.bio.seq.io
Methods in org.biojavax.bio.seq.io that return BioEntryModifier and TypeMethodDescriptionHashedFastaIterator.nextBioEntry()
RichStreamReader.nextBioEntry()