Uses of Interface
org.biojavax.ontology.ComparableTerm

Packages that use ComparableTerm

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

ComparableTerm	SimpleNote.getTerm() Gets the term that defines this note.
ComparableTerm	Note.getTerm() Gets the term that defines this note.

Methods in org.biojavax with parameters of type ComparableTerm

void	SimpleNote.setTerm(ComparableTerm term) Sets the term for this note.
void	Note.setTerm(ComparableTerm term) Sets the term for this note.

Constructors in org.biojavax with parameters of type ComparableTerm

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

ComparableTerm	SimpleBioEntryRelationship.getTerm() Returns the term describing the relationship.
ComparableTerm	BioEntryRelationship.getTerm() Returns the term describing the relationship.

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

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

ComparableTerm	BioSQLFeatureFilter.BySourceTerm.getSourceTerm()
ComparableTerm	BioSQLFeatureFilter.ByNoteTermOnly.getTerm()
ComparableTerm	BioSQLFeatureFilter.ByTypeTerm.getTypeTerm()

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

BioSQLFeatureFilter.ByNoteTermOnly(ComparableTerm term)

BioSQLFeatureFilter.BySourceTerm(ComparableTerm sourceTerm)
Create a BySourceTerm filter that filters in all features with sourceTerm fields equal to source.

BioSQLFeatureFilter.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

protected ComparableTerm

SimpleRichLocation.term

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

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	SimpleRichLocation.getTerm() Retrieves the term associated with this location.
ComparableTerm	SimpleRichFeatureRelationship.getTerm() Gets the term that describes this relationship.
ComparableTerm	RichLocation.getTerm() Retrieves the term associated with this location.
ComparableTerm	RichFeatureRelationship.getTerm() Gets the term that describes this relationship.
ComparableTerm	EmptyRichLocation.getTerm() Retrieves the term associated with this location. ALWAYS RETURNS NULL
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

void	SimpleRichLocation.setTerm(ComparableTerm term) Sets the term for this location.
void	RichLocation.setTerm(ComparableTerm term) Sets the term for this location.
void	EmptyRichLocation.setTerm(ComparableTerm term) Sets the term for this location. NOT IMPLEMENTED
void	CompoundRichLocation.setTerm(ComparableTerm term) Sets the term for this location.

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

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

static ComparableTerm	EMBLxmlFormat.Terms.getDataClassTerm() Getter for the Ensembl-specific 'dataClass' term
static ComparableTerm	EMBLFormat.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	UniProtXMLFormat.Terms.getProteinExistsTerm() Getter for the protein exists term
static ComparableTerm	UniProtFormat.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

class

SimpleComparableTerm A Term object that can be compared and thus sorted.

Methods in org.biojavax.ontology that return ComparableTerm

ComparableTerm	SimpleComparableOntology.getOrCreateTerm(String name) Looks for a term with the given name and returns it. If the term has to be created, it is added with the description "auto-generated by biojavax".
ComparableTerm	ComparableOntology.getOrCreateTerm(String name) Looks for a term with the given name and returns it.
ComparableTerm	SimpleComparableOntology.getOrImportTerm(Term term) Looks for a term with the same name as the given term and returns it.
ComparableTerm	ComparableOntology.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

void	SimpleComparableTriple.addDescriptor(ComparableTerm desc) Adds a descriptor.
void	ComparableTriple.addDescriptor(ComparableTerm desc) Adds a descriptor.
boolean	SimpleComparableTriple.removeDescriptor(ComparableTerm desc) Removes a descriptor.
boolean	ComparableTriple.removeDescriptor(ComparableTerm desc) Removes a descriptor.