org.biomage.Description
Class Database

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.Description.Database

All Implemented Interfaces:

HasAuditTrail, HasContacts, HasDescriptions, HasPropertySets, HasSecurity, java.io.Serializable

public class Database

extends Identifiable

implements java.io.Serializable, HasContacts

An address to a repository.

See Also:

Serialized Form

Nested Class Summary

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

HasContacts.Contacts_list

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

HasAuditTrail.AuditTrail_list

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

HasDescriptions.Descriptions_list

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

HasPropertySets.PropertySets_list

Field Summary

protected HasContacts.Contacts_list

contacts Information on the contacts for the database

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

Database()
Default constructor.

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

Method Summary

void	addToContacts(Contact contact) Method to add Contact to Contacts_list
void	addToContacts(int position, Contact contact) Method to add Contact at position to Contacts_list
HasContacts.Contacts_list	getContacts() Get method for contacts
Contact	getFromContacts(int position) Method to get Contact from Contacts_list
java.lang.String	getURI() Get method for URI
java.lang.String	getVersion() Get method for version
void	removeElementAtFromContacts(int position) Method to remove by position from Contacts_list
void	removeFromContacts(Contact contact) Method to remove first Contact from Contacts_list
void	setContacts(HasContacts.Contacts_list contacts) Set method for contacts
void	setURI(java.lang.String URI) Set method for URI
void	setVersion(java.lang.String version) Set method for version
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.Identifiable

getIdentifier, getName, setIdentifier, setName

Methods inherited from class org.biomage.Common.Describable

addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAuditTrail, setDescriptions, setSecurity

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

contacts

protected HasContacts.Contacts_list contacts

Information on the contacts for the database

Constructor Detail

Database

public Database()

Default constructor.

Database

public Database(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 Identifiable

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 Identifiable

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 Identifiable

java.io.IOException

setVersion

public void setVersion(java.lang.String version)

Set method for version

getVersion

public java.lang.String getVersion()

Get method for version

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

setContacts

public void setContacts(HasContacts.Contacts_list contacts)

Set method for contacts

Specified by:

setContacts in interface HasContacts

getContacts

public HasContacts.Contacts_list getContacts()

Get method for contacts

Specified by:

getContacts in interface HasContacts

Returns:

value of the attribute

addToContacts

public void addToContacts(Contact contact)

Method to add Contact to Contacts_list

Specified by:

addToContacts in interface HasContacts

addToContacts

public void addToContacts(int position,
                          Contact contact)

Method to add Contact at position to Contacts_list

Specified by:

addToContacts in interface HasContacts

getFromContacts

public Contact getFromContacts(int position)

Method to get Contact from Contacts_list

Specified by:

getFromContacts in interface HasContacts

removeElementAtFromContacts

public void removeElementAtFromContacts(int position)

Method to remove by position from Contacts_list

Specified by:

removeElementAtFromContacts in interface HasContacts

removeFromContacts

public void removeFromContacts(Contact contact)

Method to remove first Contact from Contacts_list

Specified by:

removeFromContacts in interface HasContacts