Uses of Interface
org.biojavax.CrossRef

Packages that use CrossRef

org.biojavax	The Biojava extensions packages, classes that extend the core biojava functionality
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

class

SimpleCrossRef A basic CrossRef implementation.

Methods in org.biojavax that return CrossRef

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

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
SymbolList	DummyCrossReferenceResolver.getRemoteSymbolList(CrossRef cr, Alphabet a) Given a cross reference, return the corresponding symbol list. All responses are instances of InfinitelyAmbiguousSymbolList.
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

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

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

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. ALWAYS RETURNS NULL
CrossRef	EmptyRichLocation.getCrossRef() Retrieves the crossref associated with this location. ALWAYS RETURNS NULL

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

protected void

SimpleRichLocation.setCrossRef(CrossRef crossRef)

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

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.