Uses of Interface
org.biojavax.CrossRef
Packages that use CrossRef
Package
Description
The Biojava extensions packages, classes that extend the core biojava
functionality
Interface between biojava and biosql databases
Rich implementations of Sequences, Locations and Features.
-
Uses of CrossRef in org.biojavax
Classes in org.biojavax that implement CrossRefMethods in org.biojavax that return CrossRefModifier and TypeMethodDescriptionDocRef.getCrossref()
The document reference may refer to an object in another database.SimpleDocRef.getCrossref()
The document reference may refer to an object in another database.RankedCrossRef.getCrossRef()
Return the cross reference associated with this object.SimpleRankedCrossRef.getCrossRef()
Return the cross reference associated with this object.Methods in org.biojavax with parameters of type CrossRefModifier and TypeMethodDescriptionCrossReferenceResolver.getRemoteBioEntry
(CrossRef cr) Given theCrossRef
return the correspondingBioEntry
DummyCrossReferenceResolver.getRemoteBioEntry
(CrossRef cr) Given theCrossRef
return the correspondingBioEntry
CrossReferenceResolver.getRemoteSymbolList
(CrossRef cr, Alphabet a) Given a cross reference, return the corresponding symbol list.DummyCrossReferenceResolver.getRemoteSymbolList
(CrossRef cr, Alphabet a) Given a cross reference, return the corresponding symbol list.void
DocRef.setCrossref
(CrossRef crossref) The document reference may refer to an object in another database.void
SimpleDocRef.setCrossref
(CrossRef crossref) The document reference may refer to an object in another database.Constructors in org.biojavax with parameters of type CrossRefModifierConstructorDescriptionSimpleRankedCrossRef
(CrossRef crossref, int rank) Constructs a new crossref with a rank. -
Uses of CrossRef in org.biojavax.bio.db.biosql
Methods in org.biojavax.bio.db.biosql with parameters of type CrossRefModifier and TypeMethodDescriptionBioSQLCrossReferenceResolver.getRemoteBioEntry
(CrossRef cr) Given theCrossRef
return the correspondingBioEntry
BioSQLCrossReferenceResolver.getRemoteSymbolList
(CrossRef cr, Alphabet a) Given a cross reference, return the corresponding symbol list. -
Uses of CrossRef in org.biojavax.bio.seq
Methods in org.biojavax.bio.seq that return CrossRefModifier and TypeMethodDescriptionEmptyRichLocation.getCrossRef()
Retrieves the crossref associated with this location.MultiSourceCompoundRichLocation.getCrossRef()
Retrieves the crossref associated with this location.RichLocation.getCrossRef()
Retrieves the crossref associated with this location.SimpleRichLocation.getCrossRef()
Retrieves the crossref associated with this location.Methods in org.biojavax.bio.seq with parameters of type CrossRefModifier and TypeMethodDescriptionprotected void
SimpleRichLocation.setCrossRef
(CrossRef crossRef) Constructors in org.biojavax.bio.seq with parameters of type CrossRefModifierConstructorDescriptionSimpleRichLocation
(Position pos, int rank, RichLocation.Strand strand, CrossRef crossRef) Creates a new instance of SimpleRichSequenceLocation that points to a single position on another sequence.SimpleRichLocation
(Position min, Position max, int rank, RichLocation.Strand strand, CrossRef crossRef) Creates a new instance of SimpleRichSequenceLocation that points to a range position on another sequence.