org.biomage.BioAssayData
Class BioAssayDatum

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

All Implemented Interfaces:

HasBioAssay, HasDesignElement, HasPropertySets, HasQuantitationType, java.io.Serializable

public class BioAssayDatum

extends Extendable

implements java.io.Serializable, HasBioAssay, HasDesignElement, HasQuantitationType

A single cell of the quantitation, bioAssay, designElement matrix.

See Also:

Serialized Form

Nested Class Summary

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

HasPropertySets.PropertySets_list

Field Summary

protected BioAssay	bioAssay The BioAssay associated with the value of the BioAssayDatum.
protected DesignElement	designElement The DesignElement associated with the value of the BioAssayDatum.
protected QuantitationType	quantitationType The QuantitationType associated with the value of the BioAssayDatum.

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

BioAssayDatum()
Default constructor.

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

Method Summary

BioAssay	getBioAssay() Get method for bioAssay
DesignElement	getDesignElement() Get method for designElement
QuantitationType	getQuantitationType() Get method for quantitationType
java.lang.Object	getValue() Get method for value
void	setBioAssay(BioAssay bioAssay) Set method for bioAssay
void	setDesignElement(DesignElement designElement) Set method for designElement
void	setQuantitationType(QuantitationType quantitationType) Set method for quantitationType
void	setValue(java.lang.Object value) Set method for value
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.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

bioAssay

protected BioAssay bioAssay

The BioAssay associated with the value of the BioAssayDatum.

designElement

protected DesignElement designElement

The DesignElement associated with the value of the BioAssayDatum.

quantitationType

protected QuantitationType quantitationType

The QuantitationType associated with the value of the BioAssayDatum.

Constructor Detail

BioAssayDatum

public BioAssayDatum()

Default constructor.

BioAssayDatum

public BioAssayDatum(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 Extendable

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 Extendable

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 Extendable

java.io.IOException

setValue

public void setValue(java.lang.Object value)

Set method for value

Parameters:

value - to set

getValue

public java.lang.Object getValue()

Get method for value

Returns:

value of the attribute

setBioAssay

public void setBioAssay(BioAssay bioAssay)

Set method for bioAssay

Specified by:

setBioAssay in interface HasBioAssay

getBioAssay

public BioAssay getBioAssay()

Get method for bioAssay

Specified by:

getBioAssay in interface HasBioAssay

Returns:

value of the attribute

setDesignElement

public void setDesignElement(DesignElement designElement)

Set method for designElement

Specified by:

setDesignElement in interface HasDesignElement

getDesignElement

public DesignElement getDesignElement()

Get method for designElement

Specified by:

getDesignElement in interface HasDesignElement

Returns:

value of the attribute

setQuantitationType

public void setQuantitationType(QuantitationType quantitationType)

Set method for quantitationType

Specified by:

setQuantitationType in interface HasQuantitationType

getQuantitationType

public QuantitationType getQuantitationType()

Get method for quantitationType

Specified by:

getQuantitationType in interface HasQuantitationType

Returns:

value of the attribute