Uses of Interface org.biojavax.ontology.ComparableTerm (BioJava-1.5-beta API)

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV NEXT | FRAMES NO FRAMES

## 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 |
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` | `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
`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
`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` | `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
`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
`ComparableTerm` | `SimpleRichFeatureRelationship.getTerm()` Gets the term that describes this relationship.
`ComparableTerm` | `SimpleRichLocation.getTerm()` Retrieves the term associated with this location.
`ComparableTerm` | `EmptyRichLocation.getTerm()` Retrieves the term associated with this location. ALWAYS RETURNS NULL
`ComparableTerm` | `RichFeatureRelationship.getTerm()` Gets the term that describes this relationship.
`ComparableTerm` | `RichLocation.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
`void` | `SimpleRichLocation.setTerm(ComparableTerm term)` Sets the term for this location.
`void` | `EmptyRichLocation.setTerm(ComparableTerm term)` Sets the term for this location. NOT IMPLEMENTED
`void` | `RichLocation.setTerm(ComparableTerm term)` Sets the term for this location.
`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` | `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` | `UniProtXMLFormat.Terms.getProteinTypeTerm()` Getter for the protein type 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` | `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.

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV NEXT | FRAMES NO FRAMES