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 theCrossRefreturn the correspondingBioEntryDummyCrossReferenceResolver.getRemoteBioEntry(CrossRef cr) Given theCrossRefreturn the correspondingBioEntry -
Uses of BioEntry in org.biojavax.bio
Classes in org.biojavax.bio that implement BioEntryModifier and TypeClassDescriptionclassReference 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 TypeMethodDescriptionvoidAbstractBioEntryDB.addBioEntry(BioEntry seq) voidAbstractRichSequenceDB.addBioEntry(BioEntry seq) voidBioEntryDBLite.addBioEntry(BioEntry seq) Adds a sequence to the database.protected voidHashBioEntryDB.addBioEntry(String id, BioEntry seq) voidHashBioEntryDB.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 theCrossRefreturn the correspondingBioEntryMethods in org.biojavax.bio.db.biosql with parameters of type BioEntryModifier and TypeMethodDescriptionvoidBioSQLBioEntryDB._addBioEntry(BioEntry seq) voidBioSQLBioEntryDB.addBioEntry(BioEntry seq) -
Uses of BioEntry in org.biojavax.bio.seq
Subinterfaces of BioEntry in org.biojavax.bio.seqModifier and TypeInterfaceDescriptioninterfaceA rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.Classes in org.biojavax.bio.seq that implement BioEntryModifier and TypeClassDescriptionclassA simple implementation of RichSequence.classA 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()