org.biomage.Description
Class Description_package

java.lang.Object
  |
  +--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
Description_package.Database_list	getDatabase_list() Get method for database_list
Database	getFromDatabase_list(int position) Method to get Database from Database_list
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

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.

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.

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.

java.io.IOException

setDatabase_list

public void setDatabase_list(Description_package.Database_list database_list)

Set method for database_list

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