org.biomage.Description
Class Database

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Common.Describable
          extended by org.biomage.Common.Identifiable
              extended by org.biomage.Description.Database
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasContacts, HasDescriptions, HasPropertySets, HasSecurity

public class Database
extends Identifiable
implements java.io.Serializable, HasContacts

An address to a repository.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasContacts
HasContacts.Contacts_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail
HasAuditTrail.AuditTrail_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions
HasDescriptions.Descriptions_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets
HasPropertySets.PropertySets_list
 
Field Summary
protected  java.util.List contacts
          Information on the contacts for the database
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
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
 boolean emptyMAGEobject()
           
 java.lang.String getCategory()
           
 HasContacts.Contacts_list getContacts()
          Get method for contacts
 Contact getFromContacts(int position)
          Method to get Contact from Contacts_list
 java.lang.String getModelClassName()
           
 java.lang.String getURI()
          Get method for URI
 boolean getUserDefined()
           
 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 setAttributes(org.xml.sax.Attributes atts)
           
 void setCategory(java.lang.String category)
           
 void setContacts(HasContacts.Contacts_list contacts)
          Set method for contacts
 void setURI(java.lang.String URI)
          Set method for URI
 void setUserDefined(boolean b)
           
 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, toString
 
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, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

contacts

protected java.util.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

Parameters:
atts: - the attribute list.
Method Detail

setAttributes

public void setAttributes(org.xml.sax.Attributes atts)
Overrides:
setAttributes in class Identifiable

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
Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

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
Throws:
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
Throws:
java.io.IOException

setVersion

public void setVersion(java.lang.String version)
Set method for version

Parameters:
value - to set

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

Parameters:
value - to set

getURI

public java.lang.String getURI()
Get method for URI

Returns:
value of the attribute

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class Identifiable

setContacts

public void setContacts(HasContacts.Contacts_list contacts)
Set method for contacts

Specified by:
setContacts in interface HasContacts
Parameters:
value - to set

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

getCategory

public java.lang.String getCategory()
Returns:

setCategory

public void setCategory(java.lang.String category)
Parameters:
string -

getUserDefined

public boolean getUserDefined()
Returns:

setUserDefined

public void setUserDefined(boolean b)
Parameters:
b -