org.biomage.Description
Class Description_package

java.lang.Object
  extended by org.biomage.Description.Description_package
All Implemented Interfaces:
java.io.Serializable

public class Description_package
extends java.lang.Object
implements java.io.Serializable

The classes in this package allow a variety of references to third party annotation and direct annotation by the experimenter.

See Also:
Serialized Form

Nested Class Summary
 class Description_package.Database_list
          Inner list class for holding multiple entries for attribute database.
 
Field Summary
 Description_package.Database_list database_list
          An address to a repository.
 
Constructor Summary
Description_package()
          Default constructor.
Description_package(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToDatabase_list(Database database)
          Method to add Database to Database_list
 void addToDatabase_list(int position, Database database)
          Method to add Database at position to Database_list
 boolean emptyMAGEobject()
           
 Description_package.Database_list getDatabase_list()
          Get method for database_list
 Database getFromDatabase_list(int position)
          Method to get Database from Database_list
 java.lang.String getModelClassName()
           
 void removeElementAtFromDatabase_list(int position)
          Method to remove by position from Database_list
 void removeFromDatabase_list(Database database)
          Method to remove first Database from Database_list
 void setDatabase_list(Description_package.Database_list database_list)
          Set method for database_list
 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 java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

database_list

public Description_package.Database_list database_list
An address to a repository.

Constructor Detail

Description_package

public Description_package()
Default constructor.


Description_package

public Description_package(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

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.

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.

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.

Throws:
java.io.IOException

getModelClassName

public java.lang.String getModelClassName()

setDatabase_list

public void setDatabase_list(Description_package.Database_list database_list)
Set method for database_list

Parameters:
value - to set

getDatabase_list

public Description_package.Database_list getDatabase_list()
Get method for database_list

Returns:
value of the attribute

addToDatabase_list

public void addToDatabase_list(Database database)
Method to add Database to Database_list


addToDatabase_list

public void addToDatabase_list(int position,
                               Database database)
Method to add Database at position to Database_list


getFromDatabase_list

public Database getFromDatabase_list(int position)
Method to get Database from Database_list


removeElementAtFromDatabase_list

public void removeElementAtFromDatabase_list(int position)
Method to remove by position from Database_list


removeFromDatabase_list

public void removeFromDatabase_list(Database database)
Method to remove first Database from Database_list