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org.biomage.Description
Class DatabaseEntry  

java.lang.Object
  org.biomage.Common.Extendable
      org.biomage.Description.DatabaseEntry

All Implemented Interfaces:

org.biomage.Interface.HasDatabase, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasType, java.io.Serializable

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public class DatabaseEntry

extends org.biomage.Common.Extendable

implements java.io.Serializable, org.biomage.Interface.HasDatabase, org.biomage.Interface.HasType

A reference to a record in a database.

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Nested Class Summary

 

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

org.biomage.Interface.HasPropertySets.PropertySets_list

 

Field Summary
(package private)  java.lang.String	accession           The identifier used to look up the record.
(package private)  java.lang.String	accessionVersion           The appropriate version of the accession (if applicable).
private  Database	database           Reference to the database where the DataEntry instance can be found.
private  OntologyEntry	type           The type of record (e.g.
(package private)  java.lang.String	URI           The location of the record.

 

Fields inherited from class org.biomage.Common.Extendable

 

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
void	writeAttributes(java.io.Writer out)           writeAttributes
void	writeMAGEML(java.io.Writer out)           writeMAGEML

 

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

accession

java.lang.String accession

The identifier used to look up the record.

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accessionVersion

java.lang.String accessionVersion

The appropriate version of the accession (if applicable).

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URI

java.lang.String URI

The location of the record.

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database

private Database database

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

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type

private OntologyEntry type

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

Constructor Detail

DatabaseEntry

public DatabaseEntry()

Default constructor.

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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.

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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.

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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.

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setAccession

public void setAccession(java.lang.String accession)

Set method for accession

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getAccession

public java.lang.String getAccession()

Get method for accession

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setAccessionVersion

public void setAccessionVersion(java.lang.String accessionVersion)

Set method for accessionVersion

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getAccessionVersion

public java.lang.String getAccessionVersion()

Get method for accessionVersion

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setURI

public void setURI(java.lang.String URI)

Set method for URI

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getURI

public java.lang.String getURI()

Get method for URI

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setDatabase

public void setDatabase(Database database)

Set method for database

Specified by:

setDatabase in interface org.biomage.Interface.HasDatabase

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getDatabase

public Database getDatabase()

Get method for database

Specified by:

getDatabase in interface org.biomage.Interface.HasDatabase

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setType

public void setType(OntologyEntry type)

Set method for type

Specified by:

setType in interface org.biomage.Interface.HasType

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getType

public OntologyEntry getType()

Get method for type

Specified by:

getType in interface org.biomage.Interface.HasType

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ Description overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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