Uses of Class
org.biomage.Description.DatabaseEntry

Packages that use DatabaseEntry
org.biomage.Array   
org.biomage.BioMaterial   
org.biomage.BioSequence   
org.biomage.BQS   
org.biomage.Description   
org.biomage.Description.Ontology   
org.biomage.Interface   
org.biomage.tools.helpers   
 

Uses of DatabaseEntry in org.biomage.Array
 

Fields in org.biomage.Array declared as DatabaseEntry
protected  DatabaseEntry ManufactureLIMS.identifierLIMS
          Association to a LIMS data source for further information on the manufacturing process.
 

Methods in org.biomage.Array that return DatabaseEntry
 DatabaseEntry ManufactureLIMS.getIdentifierLIMS()
          Get method for identifierLIMS
 

Methods in org.biomage.Array with parameters of type DatabaseEntry
 void ManufactureLIMS.setIdentifierLIMS(DatabaseEntry identifierLIMS)
          Set method for identifierLIMS
 

Uses of DatabaseEntry in org.biomage.BioMaterial
 

Fields in org.biomage.BioMaterial declared as DatabaseEntry
protected  DatabaseEntry Compound.externalLIMS
          Reference to an entry in an external LIMS data source.
 

Methods in org.biomage.BioMaterial that return DatabaseEntry
 DatabaseEntry Compound.getExternalLIMS()
          Get method for externalLIMS
 

Methods in org.biomage.BioMaterial with parameters of type DatabaseEntry
 void Compound.setExternalLIMS(DatabaseEntry externalLIMS)
          Set method for externalLIMS
 

Uses of DatabaseEntry in org.biomage.BioSequence
 

Methods in org.biomage.BioSequence that return DatabaseEntry
 DatabaseEntry BioSequence.getFromSequenceDatabases(int position)
          Method to get DatabaseEntry from SequenceDatabases_list
 

Methods in org.biomage.BioSequence with parameters of type DatabaseEntry
 void BioSequence.addToSequenceDatabases(DatabaseEntry databaseEntry)
          Method to add DatabaseEntry to SequenceDatabases_list
 void BioSequence.addToSequenceDatabases(int position, DatabaseEntry databaseEntry)
          Method to add DatabaseEntry at position to SequenceDatabases_list
 void BioSequence.removeFromSequenceDatabases(DatabaseEntry databaseEntry)
          Method to remove first DatabaseEntry from SequenceDatabases_list
 

Uses of DatabaseEntry in org.biomage.BQS
 

Methods in org.biomage.BQS that return DatabaseEntry
 DatabaseEntry BibliographicReference.getFromAccessions(int position)
          Method to get DatabaseEntry from Accessions_list
 

Methods in org.biomage.BQS with parameters of type DatabaseEntry
 void BibliographicReference.addToAccessions(DatabaseEntry databaseEntry)
          Method to add DatabaseEntry to Accessions_list
 void BibliographicReference.addToAccessions(int position, DatabaseEntry databaseEntry)
          Method to add DatabaseEntry at position to Accessions_list
 void BibliographicReference.removeFromAccessions(DatabaseEntry databaseEntry)
          Method to remove first DatabaseEntry from Accessions_list
 

Uses of DatabaseEntry in org.biomage.Description
 

Fields in org.biomage.Description declared as DatabaseEntry
protected  DatabaseEntry OntologyEntry.ontologyReference
          Many ontology entries will not yet have formalized ontologies.
 

Methods in org.biomage.Description that return DatabaseEntry
 DatabaseEntry Description.getFromDatabaseReferences(int position)
          Method to get DatabaseEntry from DatabaseReferences_list
 DatabaseEntry OntologyEntry.getOntologyReference()
          Get method for ontologyReference
 

Methods in org.biomage.Description with parameters of type DatabaseEntry
 void Description.addToDatabaseReferences(DatabaseEntry databaseEntry)
          Method to add DatabaseEntry to DatabaseReferences_list
 void Description.addToDatabaseReferences(int position, DatabaseEntry databaseEntry)
          Method to add DatabaseEntry at position to DatabaseReferences_list
 void Description.removeFromDatabaseReferences(DatabaseEntry databaseEntry)
          Method to remove first DatabaseEntry from DatabaseReferences_list
 void OntologyEntry.setOntologyReference(DatabaseEntry ontologyReference)
          Set method for ontologyReference
 

Uses of DatabaseEntry in org.biomage.Description.Ontology
 

Methods in org.biomage.Description.Ontology that return DatabaseEntry
abstract  DatabaseEntry BioMaterialCharacteristic.getOntologyReference()
          Get method for ontologyReference
 

Methods in org.biomage.Description.Ontology with parameters of type DatabaseEntry
abstract  void BioMaterialCharacteristic.setOntologyReference(DatabaseEntry ontologyReference)
           
 

Uses of DatabaseEntry in org.biomage.Interface
 

Methods in org.biomage.Interface that return DatabaseEntry
 DatabaseEntry HasExternalLIMS.getExternalLIMS()
          Get method for externalLIMS
 DatabaseEntry HasAccessions.getFromAccessions(int position)
          Method to get DatabaseEntry from Accessions_list
 DatabaseEntry HasDatabaseReferences.getFromDatabaseReferences(int position)
          Method to get DatabaseEntry from DatabaseReferences_list
 DatabaseEntry HasSequenceDatabases.getFromSequenceDatabases(int position)
          Method to get DatabaseEntry from SequenceDatabases_list
 DatabaseEntry HasIdentifierLIMS.getIdentifierLIMS()
          Get method for identifierLIMS
 DatabaseEntry HasOntologyReference.getOntologyReference()
          Get method for ontologyReference
 

Methods in org.biomage.Interface with parameters of type DatabaseEntry
 void HasAccessions.addToAccessions(DatabaseEntry databaseEntry)
          Method to add DatabaseEntry to Accessions_list
 void HasAccessions.addToAccessions(int position, DatabaseEntry databaseEntry)
          Method to add DatabaseEntry at position to Accessions_list
 void HasDatabaseReferences.addToDatabaseReferences(DatabaseEntry databaseEntry)
          Method to add DatabaseEntry to DatabaseReferences_list
 void HasDatabaseReferences.addToDatabaseReferences(int position, DatabaseEntry databaseEntry)
          Method to add DatabaseEntry at position to DatabaseReferences_list
 void HasSequenceDatabases.addToSequenceDatabases(DatabaseEntry databaseEntry)
          Method to add DatabaseEntry to SequenceDatabases_list
 void HasSequenceDatabases.addToSequenceDatabases(int position, DatabaseEntry databaseEntry)
          Method to add DatabaseEntry at position to SequenceDatabases_list
 void HasAccessions.removeFromAccessions(DatabaseEntry databaseEntry)
          Method to remove first DatabaseEntry from Accessions_list
 void HasDatabaseReferences.removeFromDatabaseReferences(DatabaseEntry databaseEntry)
          Method to remove first DatabaseEntry from DatabaseReferences_list
 void HasSequenceDatabases.removeFromSequenceDatabases(DatabaseEntry databaseEntry)
          Method to remove first DatabaseEntry from SequenceDatabases_list
 void HasExternalLIMS.setExternalLIMS(DatabaseEntry externalLIMS)
          Set method for externalLIMS
 void HasIdentifierLIMS.setIdentifierLIMS(DatabaseEntry identifierLIMS)
          Set method for identifierLIMS
 void HasOntologyReference.setOntologyReference(DatabaseEntry ontologyReference)
          Set method for ontologyReference
 

Uses of DatabaseEntry in org.biomage.tools.helpers
 

Subclasses of DatabaseEntry in org.biomage.tools.helpers
static class MGEDOntologyEntry.OntologyDatabaseEntry
           
 

Methods in org.biomage.tools.helpers that return DatabaseEntry
 DatabaseEntry OntologyHelper.getOntologyReference(java.lang.String term)