org.biomage.Common
Class Extendable

java.lang.Object
  |
  +--org.biomage.Common.Extendable

All Implemented Interfaces:

HasPropertySets, java.io.Serializable

Direct Known Subclasses:

ArrayManufactureDeviation, BioAssayDatum, BioAssayMapping, BioDataValues, BioMaterialMeasurement, CompoundMeasurement, DatabaseEntry, Describable, DesignElementMapping, ExternalReference, FeatureDefect, FeatureInformation, Measurement, MismatchInformation, NodeValue, OntologyEntry, ParameterValue, Position, PositionDelta, QuantitationTypeMapping, SeqFeatureLocation, SequencePosition, Unit, ZoneDefect, ZoneGroup, ZoneLayout

public abstract class Extendable

extends java.lang.Object

implements java.io.Serializable, HasPropertySets

Abstract class that specifies for subclasses an association to NameValueTypes. These can be used, for instance, to specify proprietary properties and in-house processing hints.

See Also:

Serialized Form

Nested Class Summary

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

HasPropertySets.PropertySets_list

Field Summary

protected HasPropertySets.PropertySets_list

propertySets Allows specification of name/value pairs.

Constructor Summary

Extendable()
Default constructor.

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

Method Summary

void	addToPropertySets(int position, NameValueType nameValueType) Method to add NameValueType at position to PropertySets_list
void	addToPropertySets(NameValueType nameValueType) Method to add NameValueType to PropertySets_list
NameValueType	getFromPropertySets(int position) Method to get NameValueType from PropertySets_list
HasPropertySets.PropertySets_list	getPropertySets() Get method for propertySets
void	removeElementAtFromPropertySets(int position) Method to remove by position from PropertySets_list
void	removeFromPropertySets(NameValueType nameValueType) Method to remove first NameValueType from PropertySets_list
void	setPropertySets(HasPropertySets.PropertySets_list propertySets) Set method for propertySets
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

propertySets

protected HasPropertySets.PropertySets_list propertySets

Allows specification of name/value pairs. Meant to primarily help in-house, pipeline processing of instances by providing a place for values that aren't part of the specification proper.

Constructor Detail

Extendable

public Extendable()

Default constructor.

Extendable

public Extendable(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

setPropertySets

public void setPropertySets(HasPropertySets.PropertySets_list propertySets)

Set method for propertySets

Specified by:

setPropertySets in interface HasPropertySets

getPropertySets

public HasPropertySets.PropertySets_list getPropertySets()

Get method for propertySets

Specified by:

getPropertySets in interface HasPropertySets

Returns:

value of the attribute

addToPropertySets

public void addToPropertySets(NameValueType nameValueType)

Method to add NameValueType to PropertySets_list

Specified by:

addToPropertySets in interface HasPropertySets

addToPropertySets

public void addToPropertySets(int position,
                              NameValueType nameValueType)

Method to add NameValueType at position to PropertySets_list

Specified by:

addToPropertySets in interface HasPropertySets

getFromPropertySets

public NameValueType getFromPropertySets(int position)

Method to get NameValueType from PropertySets_list

Specified by:

getFromPropertySets in interface HasPropertySets

removeElementAtFromPropertySets

public void removeElementAtFromPropertySets(int position)

Method to remove by position from PropertySets_list

Specified by:

removeElementAtFromPropertySets in interface HasPropertySets

removeFromPropertySets

public void removeFromPropertySets(NameValueType nameValueType)

Method to remove first NameValueType from PropertySets_list

Specified by:

removeFromPropertySets in interface HasPropertySets