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A
- accession - Variable in class org.biomage.Description.DatabaseEntry
- The identifier used to look up the record.
- accessionVersion - Variable in class org.biomage.Description.DatabaseEntry
- The appropriate version of the accession (if applicable).
- addToAnnotations(OntologyEntry) - Method in class org.biomage.Description.Description
- Method to add OntologyEntry to Annotations_list
- addToAnnotations(int, OntologyEntry) - Method in class org.biomage.Description.Description
- Method to add OntologyEntry at position to Annotations_list
- addToBibliographicReferences(BibliographicReference) - Method in class org.biomage.Description.Description
- Method to add BibliographicReference to BibliographicReferences_list
- addToBibliographicReferences(int, BibliographicReference) - Method in class org.biomage.Description.Description
- Method to add BibliographicReference at position to BibliographicReferences_list
- addToContacts(Contact) - Method in class org.biomage.Description.Database
- Method to add Contact to Contacts_list
- addToContacts(int, Contact) - Method in class org.biomage.Description.Database
- Method to add Contact at position to Contacts_list
- addToDatabaseReferences(DatabaseEntry) - Method in class org.biomage.Description.Description
- Method to add DatabaseEntry to DatabaseReferences_list
- addToDatabaseReferences(int, DatabaseEntry) - Method in class org.biomage.Description.Description
- Method to add DatabaseEntry at position to DatabaseReferences_list
- addToDatabase_list(Database) - Method in class org.biomage.Description.Description_package
- Method to add Database to Database_list
- addToDatabase_list(int, Database) - Method in class org.biomage.Description.Description_package
- Method to add Database at position to Database_list
- annotations - Variable in class org.biomage.Description.Description
- Allows specification of ontology entries related to the instance being described.
B
- bibliographicReferences - Variable in class org.biomage.Description.Description
- References to existing literature.
C
- category - Variable in class org.biomage.Description.OntologyEntry
- The category to which this entry belongs.
- contacts - Variable in class org.biomage.Description.Database
- Information on the contacts for the database
D
- Database - class org.biomage.Description.Database.
- An address to a repository.
- Database() - Constructor for class org.biomage.Description.Database
- Default constructor.
- Database(Attributes) - Constructor for class org.biomage.Description.Database
- Attribute constructor.
- DatabaseEntry - class org.biomage.Description.DatabaseEntry.
- A reference to a record in a database.
- DatabaseEntry() - Constructor for class org.biomage.Description.DatabaseEntry
- Default constructor.
- DatabaseEntry(Attributes) - Constructor for class org.biomage.Description.DatabaseEntry
- Attribute constructor.
- Description - class org.biomage.Description.Description.
- A free text description of an object.
- Description() - Constructor for class org.biomage.Description.Description
- Default constructor.
- Description(Attributes) - Constructor for class org.biomage.Description.Description
- Attribute constructor.
- Description_package - class org.biomage.Description.Description_package.
- The classes in this package allow a variety of references to third party annotation and direct annotation by the experimenter.
- Description_package() - Constructor for class org.biomage.Description.Description_package
- Default constructor.
- Description_package(Attributes) - Constructor for class org.biomage.Description.Description_package
- Attribute constructor.
- Description_package.Database_list - class org.biomage.Description.Description_package.Database_list.
- Inner list class for holding multiple entries for attribute database_list.
- Description_package.Database_list() - Constructor for class org.biomage.Description.Description_package.Database_list
- database - Variable in class org.biomage.Description.DatabaseEntry
- Reference to the database where the DataEntry instance can be found.
- databaseReferences - Variable in class org.biomage.Description.Description
- References to entries in databases.
- database_list - Variable in class org.biomage.Description.Description_package
- An address to a repository.
- description - Variable in class org.biomage.Description.OntologyEntry
- The description of the meaning for this entry.
E
- ExternalReference - class org.biomage.Description.ExternalReference.
- A reference to the originating source for the object.
- ExternalReference() - Constructor for class org.biomage.Description.ExternalReference
- Default constructor.
- ExternalReference(Attributes) - Constructor for class org.biomage.Description.ExternalReference
- Attribute constructor.
- exportID - Variable in class org.biomage.Description.ExternalReference
- The identifier of the object at the originating source.
- exportName - Variable in class org.biomage.Description.ExternalReference
- The name of the object at the originating source.
- exportedFromDB - Variable in class org.biomage.Description.ExternalReference
- Name of the database, if applicable, that the object was exported from.
- exportedFromServer - Variable in class org.biomage.Description.ExternalReference
- The originating server for the object, a network address or common name.
- externalReference - Variable in class org.biomage.Description.Description
- Specifies where the described instance was originally obtained from.
G
- getAccession() - Method in class org.biomage.Description.DatabaseEntry
- Get method for accession
- getAccessionVersion() - Method in class org.biomage.Description.DatabaseEntry
- Get method for accessionVersion
- getAnnotations() - Method in class org.biomage.Description.Description
- Get method for annotations
- getBibliographicReferences() - Method in class org.biomage.Description.Description
- Get method for bibliographicReferences
- getCategory() - Method in class org.biomage.Description.OntologyEntry
- Get method for category
- getContacts() - Method in class org.biomage.Description.Database
- Get method for contacts
- getDatabase() - Method in class org.biomage.Description.DatabaseEntry
- Get method for database
- getDatabaseReferences() - Method in class org.biomage.Description.Description
- Get method for databaseReferences
- getDatabase_list() - Method in class org.biomage.Description.Description_package
- Get method for database_list
- getDescription() - Method in class org.biomage.Description.OntologyEntry
- Get method for description
- getExportID() - Method in class org.biomage.Description.ExternalReference
- Get method for exportID
- getExportName() - Method in class org.biomage.Description.ExternalReference
- Get method for exportName
- getExportedFromDB() - Method in class org.biomage.Description.ExternalReference
- Get method for exportedFromDB
- getExportedFromServer() - Method in class org.biomage.Description.ExternalReference
- Get method for exportedFromServer
- getExternalReference() - Method in class org.biomage.Description.Description
- Get method for externalReference
- getFromAnnotations(int) - Method in class org.biomage.Description.Description
- Method to get OntologyEntry from Annotations_list
- getFromBibliographicReferences(int) - Method in class org.biomage.Description.Description
- Method to get BibliographicReference from BibliographicReferences_list
- getFromContacts(int) - Method in class org.biomage.Description.Database
- Method to get Contact from Contacts_list
- getFromDatabaseReferences(int) - Method in class org.biomage.Description.Description
- Method to get DatabaseEntry from DatabaseReferences_list
- getFromDatabase_list(int) - Method in class org.biomage.Description.Description_package
- Method to get Database from Database_list
- getOntologyReference() - Method in class org.biomage.Description.OntologyEntry
- Get method for ontologyReference
- getText() - Method in class org.biomage.Description.Description
- Get method for text
- getType() - Method in class org.biomage.Description.DatabaseEntry
- Get method for type
- getURI() - Method in class org.biomage.Description.Database
- Get method for URI
- getURI() - Method in class org.biomage.Description.DatabaseEntry
- Get method for URI
- getValue() - Method in class org.biomage.Description.OntologyEntry
- Get method for value
- getVersion() - Method in class org.biomage.Description.Database
- Get method for version
O
- OntologyEntry - class org.biomage.Description.OntologyEntry.
- A single entry from an ontology or a controlled vocabulary.
- OntologyEntry() - Constructor for class org.biomage.Description.OntologyEntry
- Default constructor.
- OntologyEntry(Attributes) - Constructor for class org.biomage.Description.OntologyEntry
- Attribute constructor.
- ontologyReference - Variable in class org.biomage.Description.OntologyEntry
- Many ontology entries will not yet have formalized ontologies.
- org.biomage.Description - package org.biomage.Description
R
- removeElementAtFromAnnotations(int) - Method in class org.biomage.Description.Description
- Method to remove by position from Annotations_list
- removeElementAtFromBibliographicReferences(int) - Method in class org.biomage.Description.Description
- Method to remove by position from BibliographicReferences_list
- removeElementAtFromContacts(int) - Method in class org.biomage.Description.Database
- Method to remove by position from Contacts_list
- removeElementAtFromDatabaseReferences(int) - Method in class org.biomage.Description.Description
- Method to remove by position from DatabaseReferences_list
- removeElementAtFromDatabase_list(int) - Method in class org.biomage.Description.Description_package
- Method to remove by position from Database_list
- removeFromAnnotations(OntologyEntry) - Method in class org.biomage.Description.Description
- Method to remove first OntologyEntry from Annotations_list
- removeFromBibliographicReferences(BibliographicReference) - Method in class org.biomage.Description.Description
- Method to remove first BibliographicReference from BibliographicReferences_list
- removeFromContacts(Contact) - Method in class org.biomage.Description.Database
- Method to remove first Contact from Contacts_list
- removeFromDatabaseReferences(DatabaseEntry) - Method in class org.biomage.Description.Description
- Method to remove first DatabaseEntry from DatabaseReferences_list
- removeFromDatabase_list(Database) - Method in class org.biomage.Description.Description_package
- Method to remove first Database from Database_list
S
- setAccession(String) - Method in class org.biomage.Description.DatabaseEntry
- Set method for accession
- setAccessionVersion(String) - Method in class org.biomage.Description.DatabaseEntry
- Set method for accessionVersion
- setAnnotations(HasAnnotations.Annotations_list) - Method in class org.biomage.Description.Description
- Set method for annotations
- setBibliographicReferences(HasBibliographicReferences.BibliographicReferences_list) - Method in class org.biomage.Description.Description
- Set method for bibliographicReferences
- setCategory(String) - Method in class org.biomage.Description.OntologyEntry
- Set method for category
- setContacts(HasContacts.Contacts_list) - Method in class org.biomage.Description.Database
- Set method for contacts
- setDatabase(Database) - Method in class org.biomage.Description.DatabaseEntry
- Set method for database
- setDatabaseReferences(HasDatabaseReferences.DatabaseReferences_list) - Method in class org.biomage.Description.Description
- Set method for databaseReferences
- setDatabase_list(Description_package.Database_list) - Method in class org.biomage.Description.Description_package
- Set method for database_list
- setDescription(String) - Method in class org.biomage.Description.OntologyEntry
- Set method for description
- setExportID(String) - Method in class org.biomage.Description.ExternalReference
- Set method for exportID
- setExportName(String) - Method in class org.biomage.Description.ExternalReference
- Set method for exportName
- setExportedFromDB(String) - Method in class org.biomage.Description.ExternalReference
- Set method for exportedFromDB
- setExportedFromServer(String) - Method in class org.biomage.Description.ExternalReference
- Set method for exportedFromServer
- setExternalReference(ExternalReference) - Method in class org.biomage.Description.Description
- Set method for externalReference
- setOntologyReference(DatabaseEntry) - Method in class org.biomage.Description.OntologyEntry
- Set method for ontologyReference
- setText(String) - Method in class org.biomage.Description.Description
- Set method for text
- setType(OntologyEntry) - Method in class org.biomage.Description.DatabaseEntry
- Set method for type
- setURI(String) - Method in class org.biomage.Description.Database
- Set method for URI
- setURI(String) - Method in class org.biomage.Description.DatabaseEntry
- Set method for URI
- setValue(String) - Method in class org.biomage.Description.OntologyEntry
- Set method for value
- setVersion(String) - Method in class org.biomage.Description.Database
- Set method for version
T
- text - Variable in class org.biomage.Description.Description
- The description.
- type - Variable in class org.biomage.Description.DatabaseEntry
- The type of record (e.g.
U
- URI - Variable in class org.biomage.Description.Database
- The location of the Database.
- URI - Variable in class org.biomage.Description.DatabaseEntry
- The location of the record.
V
- value - Variable in class org.biomage.Description.OntologyEntry
- The value for this entry in this category.
- version - Variable in class org.biomage.Description.Database
- The version for which a DatabaseReference applies.
W
- writeAssociations(Writer) - Method in class org.biomage.Description.Database
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.Description.DatabaseEntry
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.Description.Description
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.Description.Description_package
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.Description.ExternalReference
- writeAssociations
- writeAssociations(Writer) - Method in class org.biomage.Description.OntologyEntry
- writeAssociations
- writeAttributes(Writer) - Method in class org.biomage.Description.Database
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.Description.DatabaseEntry
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.Description.Description
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.Description.Description_package
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.Description.ExternalReference
- writeAttributes
- writeAttributes(Writer) - Method in class org.biomage.Description.OntologyEntry
- writeAttributes
- writeMAGEML(Writer) - Method in class org.biomage.Description.Database
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.Description.DatabaseEntry
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.Description.Description
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.Description.Description_package
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.Description.ExternalReference
- writeMAGEML
- writeMAGEML(Writer) - Method in class org.biomage.Description.OntologyEntry
- writeMAGEML
A B C D E G O R S T U V W
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