Search Java Classes and Packages
#Org.biojava.nbio.ontology Classes and Interfaces - 39 results found.
| Name | Description | Type | Package | Framework |
| AbstractAnnotation | A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map. | Class | org.biojava.nbio.ontology.utils | BioJava |
| AbstractTerm | Abstract implementation of term This provides basic change-forwarding functionality from | Class | org.biojava.nbio.ontology | BioJava |
| AlreadyExistsException | Thrown to indicate that a term or triple can't be added to an ontology because it is already present. | Class | org.biojava.nbio.ontology | BioJava |
| Annotatable | Indicates that an object has an associated annotation. | Interface | org.biojava.nbio.ontology.utils | BioJava |
| Annotation | Arbitrary annotation associated with one or more objects. | Interface | org.biojava.nbio.ontology.utils | BioJava |
| App | Class | org.biojava.nbio.ontology | BioJava | |
| AssertionFailure | An unchecked exception representing an Assertion failure. | Class | org.biojava.nbio.ontology.utils | BioJava |
| DefaultOps | Default implementation of OntologyOps. | Class | org.biojava.nbio.ontology | BioJava |
| GOParser | Simple parser for the Gene Ontology (GO) flatfile format. | Class | org.biojava.nbio.ontology.io | BioJava |
| IntegerOntology | Class | org.biojava.nbio.ontology | BioJava | |
| InvalidTermException | Thrown to indicate that an ontology term is not acceptable or appropriate in a given context | Class | org.biojava.nbio.ontology | BioJava |
| KeyedWeakReference | Subclass of WeakReference which includes and extra field (the key) which can be used to help cleanup once this reference has been | Class | org.biojava.nbio.ontology.utils | BioJava |
| OboFileEventListener | an interface for events that occur during parsing of . | Interface | org.biojava.nbio.ontology.obo | BioJava |
| OboFileHandler | A file handler for . | Class | org.biojava.nbio.ontology.obo | BioJava |
| OboFileParser | A class to parse the content of an OBO file. | Class | org.biojava.nbio.ontology.obo | BioJava |
| OboFileParser .SOPair | Class | org.biojava.nbio.ontology.obo | BioJava | |
| OboParser | OboParser parser = new OboParser(); InputStream inStream = this. | Class | org.biojava.nbio.ontology.io | BioJava |
| Ontology | This is just a set of Term objects, and a set of Triple objects describing relationships between these terms. | Interface | org.biojava.nbio.ontology | BioJava |
| Ontology .Impl | A basic in-memory implementation of an ontologySince:1. | Class | org.biojava.nbio.ontology | BioJava |
| OntologyException | Thrown to indicate an error in an Ontology objectSince:1. | Class | org.biojava.nbio.ontology | BioJava |
| OntologyFactory | A factory for Ontology instances. | Interface | org.biojava.nbio.ontology | BioJava |
| OntologyOps | This is an interface for optimizing ontology operators. | Interface | org.biojava.nbio.ontology | BioJava |
| OntologyTerm | A term in an ontology which identifies another ontology. | Interface | org.biojava.nbio.ontology | BioJava |
| OntologyTerm .Impl | Simple in-memory implementation of a remote ontology term. | Class | org.biojava.nbio.ontology | BioJava |
| OntoTools | Tools for manipulating ontologies. | Class | org.biojava.nbio.ontology | BioJava |
| RemoteTerm | A term in another ontology. | Interface | org.biojava.nbio.ontology | BioJava |
| RemoteTerm .Impl | Simple in-memory implementation of a remote ontology term. | Class | org.biojava.nbio.ontology | BioJava |
| SmallAnnotation | Annotation that is optimized for memory usage. | Class | org.biojava.nbio.ontology.utils | BioJava |
| SmallMap | Lightweight implementation of Map which uses little memory to store a small number of mappings, at the expense of scalability. | Class | org.biojava.nbio.ontology.utils | BioJava |
| StaticMemberPlaceHolder | Class | org.biojava.nbio.ontology.utils | BioJava | |
| Synonym | Class | org.biojava.nbio.ontology | BioJava | |
| TabDelimParser | Parse tab-delimited ontology files into Ontology objects. | Class | org.biojava.nbio.ontology.io | BioJava |
| Term | A term in an ontology. | Interface | org.biojava.nbio.ontology | BioJava |
| Term .Impl | Simple in-memory implementation of an ontology term. | Class | org.biojava.nbio.ontology | BioJava |
| Triple | A triple in an ontology. | Interface | org.biojava.nbio.ontology | BioJava |
| Triple .Impl | Basic in-memory implementation of a Triple in an ontology This can be used to implement Ontology. | Class | org.biojava.nbio.ontology | BioJava |
| Variable | Interface | org.biojava.nbio.ontology | BioJava | |
| Variable .Impl | Class | org.biojava.nbio.ontology | BioJava | |
| WeakValueHashMap | Map implementation which keeps weak references to values. | Class | org.biojava.nbio.ontology.utils | BioJava |