Uses of Interface
org.biojavax.ontology.ComparableTerm

Packages that use ComparableTerm

Package	Description
org.biojavax	The Biojava extensions packages, classes that extend the core biojava functionality
org.biojavax.bio	Classes to represent biological entities and their relationships.
org.biojavax.bio.db.biosql	Interface between biojava and biosql databases
org.biojavax.bio.seq	Rich implementations of Sequences, Locations and Features.
org.biojavax.bio.seq.io	Classes to support the I/O of RichSequence and Bioentry objects.
org.biojavax.ontology	Extensions to the biojava ontology model that represent BioSQL ontology.

Uses of ComparableTerm in org.biojavax

Methods in org.biojavax that return ComparableTerm

Modifier and Type	Method	Description
ComparableTerm	Note.getTerm()	Gets the term that defines this note.
ComparableTerm	SimpleNote.getTerm()	Gets the term that defines this note.

Methods in org.biojavax with parameters of type ComparableTerm

Modifier and Type	Method	Description
void	Note.setTerm(ComparableTerm term)	Sets the term for this note.
void	SimpleNote.setTerm(ComparableTerm term)	Sets the term for this note.

Constructors in org.biojavax with parameters of type ComparableTerm

Constructor	Description
SimpleNote(ComparableTerm term, String value, int rank)	Creates a new instance of SimpleNote with a given term, value and rank.

Uses of ComparableTerm in org.biojavax.bio

Methods in org.biojavax.bio that return ComparableTerm

Modifier and Type	Method	Description
ComparableTerm	BioEntryRelationship.getTerm()	Returns the term describing the relationship.
ComparableTerm	SimpleBioEntryRelationship.getTerm()	Returns the term describing the relationship.

Constructors in org.biojavax.bio with parameters of type ComparableTerm

Constructor	Description
SimpleBioEntryRelationship(BioEntry object, BioEntry subject, ComparableTerm term, Integer rank)	Creates a new instance of SimpleBioEntryRelationship.

Uses of ComparableTerm in org.biojavax.bio.db.biosql

Methods in org.biojavax.bio.db.biosql that return ComparableTerm

Modifier and Type	Method	Description
ComparableTerm	BioSQLFeatureFilter.BySourceTerm.getSourceTerm()
ComparableTerm	BioSQLFeatureFilter.ByNoteTermOnly.getTerm()
ComparableTerm	BioSQLFeatureFilter.ByTypeTerm.getTypeTerm()

Constructors in org.biojavax.bio.db.biosql with parameters of type ComparableTerm

Constructor	Description
ByNoteTermOnly(ComparableTerm term)
BySourceTerm(ComparableTerm sourceTerm)	Create a BySourceTerm filter that filters in all features with sourceTerm fields equal to source.
ByTypeTerm(ComparableTerm typeTerm)	Create a ByTypeTerm filter that filters in all features with typeTerm fields equal to typeTerm.

Uses of ComparableTerm in org.biojavax.bio.seq

Fields in org.biojavax.bio.seq declared as ComparableTerm

Modifier and Type	Field	Description
protected ComparableTerm	SimpleRichLocation.term

Methods in org.biojavax.bio.seq that return ComparableTerm

Modifier and Type	Method	Description
static ComparableTerm	RichSequence.Terms.getAdditionalAccessionTerm()	Getter for the secondary/tertiary/additional accession term
static ComparableTerm	SimpleRichFeatureRelationship.getContainsTerm()	Gets the default CONTAINS term used for defining the relationship between features.
static ComparableTerm	RichSequence.Terms.getCopyrightTerm()	Getter for the copyright term
static ComparableTerm	RichSequence.Terms.getDataClassTerm()	Getter for the DataClass term
static ComparableTerm	RichSequence.Terms.getDateAnnotatedTerm()	Getter for the date annotated term
static ComparableTerm	RichSequence.Terms.getDateCreatedTerm()	Getter for the date created term
static ComparableTerm	RichSequence.Terms.getDateUpdatedTerm()	Getter for the date updated term
static ComparableTerm	RichSequence.Terms.getFeatureDescTerm()	Getter for the FeatureDesc term
static ComparableTerm	RichSequence.Terms.getFTIdTerm()	Getter for the FTId term
static ComparableTerm	RichSequence.Terms.getGeneNameTerm()	Getter for the GeneName term
static ComparableTerm	RichSequence.Terms.getGeneSynonymTerm()	Getter for the GeneSynonym term
static ComparableTerm	CompoundRichLocation.getJoinTerm()	Getter for the "join" term
static ComparableTerm	RichSequence.Terms.getKeywordTerm()	Getter for the keyword term
static ComparableTerm	RichSequence.Terms.getMolTypeTerm()	getter for the MolType term
static ComparableTerm	RichSequence.Terms.getOrderedLocusNameTerm()	Getter for the OrderedLocusName term
static ComparableTerm	CompoundRichLocation.getOrderTerm()	Getter for the "order" term
static ComparableTerm	RichSequence.Terms.getORFNameTerm()	Getter for the ORFName term
static ComparableTerm	RichSequence.Terms.getOrganelleTerm()	Getter for the Organelle term
static ComparableTerm	RichSequence.Terms.getPlasmidTerm()	Getter for the Plasmid term
static ComparableTerm	RichSequence.Terms.getRelAnnotatedTerm()	Getter for the release annotated term
static ComparableTerm	RichSequence.Terms.getRelCreatedTerm()	Getter for the release created term
static ComparableTerm	RichSequence.Terms.getRelUpdatedTerm()	Getter for the release updated term
static ComparableTerm	RichSequence.Terms.getSpeciesTerm()	Getter for the Species term
static ComparableTerm	RichSequence.Terms.getStrainTerm()	Getter for the Strain term
static ComparableTerm	RichSequence.Terms.getStrandedTerm()	Getter for the Strand term; legal values are "single", "double", and "mixed".
ComparableTerm	EmptyRichLocation.getTerm()	Retrieves the term associated with this location.
ComparableTerm	RichFeatureRelationship.getTerm()	Gets the term that describes this relationship.
ComparableTerm	RichLocation.getTerm()	Retrieves the term associated with this location.
ComparableTerm	SimpleRichFeatureRelationship.getTerm()	Gets the term that describes this relationship.
ComparableTerm	SimpleRichLocation.getTerm()	Retrieves the term associated with this location.
static ComparableTerm	RichSequence.Terms.getTissueTerm()	Getter for the Tissue term
static ComparableTerm	RichSequence.Terms.getTransposonTerm()	Getter for the Transposon term

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

Modifier and Type	Method	Description
void	CompoundRichLocation.setTerm(ComparableTerm term)	Sets the term for this location.
void	EmptyRichLocation.setTerm(ComparableTerm term)	Sets the term for this location.
void	RichLocation.setTerm(ComparableTerm term)	Sets the term for this location.
void	SimpleRichLocation.setTerm(ComparableTerm term)	Sets the term for this location.

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

Constructor	Description
CompoundRichLocation(ComparableTerm term, Collection members)	Constructs a CompoundRichLocation from the given set of members.
MultiSourceCompoundRichLocation(ComparableTerm term, Collection members)	Constructs a MultiSourceCompoundRichLocation from the given set of members.
SimpleRichFeatureRelationship(RichFeature object, RichFeature subject, ComparableTerm term, int rank)	Creates a new instance of SimpleRichFeatureRelationship.

Uses of ComparableTerm in org.biojavax.bio.seq.io

Methods in org.biojavax.bio.seq.io that return ComparableTerm

Modifier and Type	Method	Description
static ComparableTerm	EMBLFormat.Terms.getDataClassTerm()	Getter for the Ensembl-specific 'dataClass' term
static ComparableTerm	EMBLxmlFormat.Terms.getDataClassTerm()	Getter for the Ensembl-specific 'dataClass' term
static ComparableTerm	EMBLFormat.Terms.getEMBLTerm()	Getter for the EMBL term
static ComparableTerm	EMBLxmlFormat.Terms.getEMBLxmlTerm()	Getter for the EMBLxml term
static ComparableTerm	UniProtXMLFormat.Terms.getEvidenceAttrTerm()	Getter for the evidence attr term
static ComparableTerm	UniProtXMLFormat.Terms.getEvidenceCategoryTerm()	Getter for the evidence category term
static ComparableTerm	UniProtXMLFormat.Terms.getEvidenceDateTerm()	Getter for the evidence date term
static ComparableTerm	UniProtXMLFormat.Terms.getEvidenceTypeTerm()	Getter for the evidence type term
static ComparableTerm	UniProtXMLFormat.Terms.getFeatureOriginalTerm()	Getter for the feature original term
static ComparableTerm	UniProtXMLFormat.Terms.getFeatureRefTerm()	Getter for the feature ref term
static ComparableTerm	UniProtXMLFormat.Terms.getFeatureStatusTerm()	Getter for the feature status term
static ComparableTerm	UniProtXMLFormat.Terms.getFeatureVariationTerm()	Getter for the feature variation term
static ComparableTerm	GenbankFormat.Terms.getGenBankTerm()	Getter for the Genbank term
static ComparableTerm	EMBLFormat.Terms.getGenomicTerm()	Getter for the Ensembl-specific 'genomic' term
static ComparableTerm	INSDseqFormat.Terms.getINSDseqTerm()	Getter for the INSDseq term
static ComparableTerm	UniProtXMLFormat.Terms.getLocationSequenceTerm()	Getter for the location seq term
static ComparableTerm	INSDseqFormat.Terms.getOtherSeqIdTerm()	Getter for the INSDseq term
static ComparableTerm	EMBLxmlFormat.Terms.getProjectAccessionTerm()	Getter for the ProjectAccession term
static ComparableTerm	UniProtFormat.Terms.getProteinExistsTerm()	Getter for the protein exists term
static ComparableTerm	UniProtXMLFormat.Terms.getProteinExistsTerm()	Getter for the protein exists term
static ComparableTerm	UniProtXMLFormat.Terms.getProteinTypeTerm()	Getter for the protein type term
static ComparableTerm	EMBLFormat.Terms.getRelUpdatedRecordVersionTerm()	Getter for the RelUpdatedRecordVersion term
static ComparableTerm	EMBLxmlFormat.Terms.getStatusDateTerm()	Getter for the StatusDate term
static ComparableTerm	EMBLxmlFormat.Terms.getStatusTerm()	Getter for the Status term
static ComparableTerm	EMBLxmlFormat.Terms.getSubmitterAccessionTerm()	Getter for the SubmitterAccession term
static ComparableTerm	EMBLxmlFormat.Terms.getSubmitterVersionTerm()	Getter for the SubmitterVersion term
static ComparableTerm	EMBLxmlFormat.Terms.getSubmitterWgsVersionTerm()	Getter for the SubmitterWgsVersion term
static ComparableTerm	UniProtFormat.Terms.getUniProtDBNameTerm()	Getter for the UniProt combined database term
static ComparableTerm	UniProtFormat.Terms.getUniProtTerm()	Getter for the UniProt term
static ComparableTerm	UniProtXMLFormat.Terms.getUniProtXMLTerm()	Getter for the UniProtXML term
static ComparableTerm	EMBLFormat.Terms.getVersionLineTerm()	Getter for the Ensembl-specific 'versionLine' term

Uses of ComparableTerm in org.biojavax.ontology

Classes in org.biojavax.ontology that implement ComparableTerm

Modifier and Type	Class	Description
class	SimpleComparableTerm	A Term object that can be compared and thus sorted.

Methods in org.biojavax.ontology that return ComparableTerm

Modifier and Type	Method	Description
ComparableTerm	ComparableOntology.getOrCreateTerm(String name)	Looks for a term with the given name and returns it.
ComparableTerm	SimpleComparableOntology.getOrCreateTerm(String name)	Looks for a term with the given name and returns it.
ComparableTerm	ComparableOntology.getOrImportTerm(Term term)	Looks for a term with the same name as the given term and returns it.
ComparableTerm	SimpleComparableOntology.getOrImportTerm(Term term)	Looks for a term with the same name as the given term and returns it.

Methods in org.biojavax.ontology with parameters of type ComparableTerm

Modifier and Type	Method	Description
void	ComparableTriple.addDescriptor(ComparableTerm desc)	Adds a descriptor.
void	SimpleComparableTriple.addDescriptor(ComparableTerm desc)	Adds a descriptor.
boolean	ComparableTriple.removeDescriptor(ComparableTerm desc)	Removes a descriptor.
boolean	SimpleComparableTriple.removeDescriptor(ComparableTerm desc)	Removes a descriptor.