org.biomage.Description
Class DatabaseEntry

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Description.DatabaseEntry

All Implemented Interfaces:

HasDatabase, HasPropertySets, HasType, java.io.Serializable

public class DatabaseEntry

extends Extendable

implements java.io.Serializable, HasDatabase, HasType

A reference to a record in a database.

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class org.biomage.Interface.HasPropertySets

HasPropertySets.PropertySets_list

Field Summary

protected Database	database Reference to the database where the DataEntry instance can be found.
protected OntologyEntry	type The type of record (e.g.

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

DatabaseEntry()
Default constructor.

DatabaseEntry(org.xml.sax.Attributes atts)
Attribute constructor.

Method Summary

java.lang.String	getAccession() Get method for accession
java.lang.String	getAccessionVersion() Get method for accessionVersion
Database	getDatabase() Get method for database
OntologyEntry	getType() Get method for type
java.lang.String	getURI() Get method for URI
void	setAccession(java.lang.String accession) Set method for accession
void	setAccessionVersion(java.lang.String accessionVersion) Set method for accessionVersion
void	setDatabase(Database database) Set method for database
void	setType(OntologyEntry type) Set method for type
void	setURI(java.lang.String URI) Set method for URI
void	writeAssociations(java.io.Writer out) writeAssociations This method is responsible for assembling the association data into XML.
void	writeAttributes(java.io.Writer out) writeAttributes This method is responsible for assembling the attribute data into XML.
void	writeMAGEML(java.io.Writer out) writeMAGEML This method is responsible for assembling the attribute and association data into XML.

Methods inherited from class org.biomage.Common.Extendable

addToPropertySets, addToPropertySets, getFromPropertySets, getPropertySets, removeElementAtFromPropertySets, removeFromPropertySets, setPropertySets

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

type

protected OntologyEntry type

The type of record (e.g. a protein in SwissProt, or a yeast strain in SGD).

database

protected Database database

Reference to the database where the DataEntry instance can be found.

Constructor Detail

DatabaseEntry

public DatabaseEntry()

Default constructor.

DatabaseEntry

public DatabaseEntry(org.xml.sax.Attributes atts)

Attribute constructor. Looks up the attributes in the parameter and casts them from strings appropriately

Method Detail

writeMAGEML

public void writeMAGEML(java.io.Writer out)
                 throws java.io.IOException

writeMAGEML This method is responsible for assembling the attribute and association data into XML. It creates the object tag and then calls the writeAttributes and writeAssociation methods.

Overrides:

writeMAGEML in class Extendable

java.io.IOException

writeAttributes

public void writeAttributes(java.io.Writer out)
                     throws java.io.IOException

writeAttributes This method is responsible for assembling the attribute data into XML. It calls the super method to write out all attributes of this class and it's ancestors.

Overrides:

writeAttributes in class Extendable

java.io.IOException

writeAssociations

public void writeAssociations(java.io.Writer out)
                       throws java.io.IOException

writeAssociations This method is responsible for assembling the association data into XML. It calls the super method to write out all associations of this class's ancestors.

Overrides:

writeAssociations in class Extendable

java.io.IOException

setAccession

public void setAccession(java.lang.String accession)

Set method for accession

getAccession

public java.lang.String getAccession()

Get method for accession

Returns:

value of the attribute

setAccessionVersion

public void setAccessionVersion(java.lang.String accessionVersion)

Set method for accessionVersion

getAccessionVersion

public java.lang.String getAccessionVersion()

Get method for accessionVersion

Returns:

value of the attribute

setURI

public void setURI(java.lang.String URI)

Set method for URI

getURI

public java.lang.String getURI()

Get method for URI

Returns:

value of the attribute

setType

public void setType(OntologyEntry type)

Set method for type

Specified by:

setType in interface HasType

getType

public OntologyEntry getType()

Get method for type

Specified by:

getType in interface HasType

Returns:

value of the attribute

setDatabase

public void setDatabase(Database database)

Set method for database

Specified by:

setDatabase in interface HasDatabase

getDatabase

public Database getDatabase()

Get method for database

Specified by:

getDatabase in interface HasDatabase

Returns:

value of the attribute