Uses of Interface
org.biojavax.CrossRef

Packages that use CrossRef

Package	Description
org.biojavax	The Biojava extensions packages, classes that extend the core biojava functionality The biojavax packages contain a number of extensions to the core biojava interfaces.
org.biojavax.bio.db.biosql	Interface between biojava and biosql databases
org.biojavax.bio.seq	Rich implementations of Sequences, Locations and Features.

Uses of CrossRef in org.biojavax

Classes in org.biojavax that implement CrossRef

Modifier and Type	Class and Description
class	SimpleCrossRef A basic CrossRef implementation.

Methods in org.biojavax that return CrossRef

Modifier and Type	Method and Description
CrossRef	SimpleDocRef.getCrossref() The document reference may refer to an object in another database.
CrossRef	DocRef.getCrossref() The document reference may refer to an object in another database.
CrossRef	SimpleRankedCrossRef.getCrossRef() Return the cross reference associated with this object.
CrossRef	RankedCrossRef.getCrossRef() Return the cross reference associated with this object.

Methods in org.biojavax with parameters of type CrossRef

Modifier and Type	Method and Description
BioEntry	DummyCrossReferenceResolver.getRemoteBioEntry(CrossRef cr) Given the CrossRef return the corresponding BioEntry
BioEntry	CrossReferenceResolver.getRemoteBioEntry(CrossRef cr) Given the CrossRef return the corresponding BioEntry
SymbolList	DummyCrossReferenceResolver.getRemoteSymbolList(CrossRef cr, Alphabet a) Given a cross reference, return the corresponding symbol list.
SymbolList	CrossReferenceResolver.getRemoteSymbolList(CrossRef cr, Alphabet a) Given a cross reference, return the corresponding symbol list.
void	SimpleDocRef.setCrossref(CrossRef crossref) The document reference may refer to an object in another database.
void	DocRef.setCrossref(CrossRef crossref) The document reference may refer to an object in another database.

Constructors in org.biojavax with parameters of type CrossRef

Constructor and Description
SimpleRankedCrossRef(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 CrossRef

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

Modifier and Type	Method and Description
CrossRef	SimpleRichLocation.getCrossRef() Retrieves the crossref associated with this location.
CrossRef	RichLocation.getCrossRef() Retrieves the crossref associated with this location.
CrossRef	MultiSourceCompoundRichLocation.getCrossRef() Retrieves the crossref associated with this location.
CrossRef	EmptyRichLocation.getCrossRef() Retrieves the crossref associated with this location.

Methods in org.biojavax.bio.seq with parameters of type CrossRef

Modifier and Type	Method and Description
protected void	SimpleRichLocation.setCrossRef(CrossRef crossRef)

Constructors in org.biojavax.bio.seq with parameters of type CrossRef

Constructor and Description
SimpleRichLocation(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.