org.biomage.HigherLevelAnalysis
Class NodeContents

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.HigherLevelAnalysis.NodeContents

All Implemented Interfaces:

HasAuditTrail, HasBioAssayDimension, HasDescriptions, HasDesignElementDimension, HasPropertySets, HasQuantitationDimension, HasSecurity, java.io.Serializable

public class NodeContents

extends Describable

implements java.io.Serializable, HasDesignElementDimension, HasQuantitationDimension, HasBioAssayDimension

The contents of a node for any or all of the three Dimensions. If a node only contained genes just the DesignElementDimension would be defined.

See Also:

Serialized Form

Nested Class Summary

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

HasAuditTrail.AuditTrail_list

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

HasDescriptions.Descriptions_list

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

HasPropertySets.PropertySets_list

Field Summary

protected BioAssayDimension	bioAssayDimension The relevant BioAssays for this NodeContents from the BioAssayData.
protected DesignElementDimension	designElementDimension The relevant DesignElements for this NodeContents from the BioAssayData.
protected QuantitationTypeDimension	quantitationDimension The relevant QuantitationTypes for this NodeContents from the BioAssayData.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

NodeContents()
Default constructor.

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

Method Summary

BioAssayDimension	getBioAssayDimension() Get method for bioAssayDimension
DesignElementDimension	getDesignElementDimension() Get method for designElementDimension
QuantitationTypeDimension	getQuantitationDimension() Get method for quantitationDimension
void	setBioAssayDimension(BioAssayDimension bioAssayDimension) Set method for bioAssayDimension
void	setDesignElementDimension(DesignElementDimension designElementDimension) Set method for designElementDimension
void	setQuantitationDimension(QuantitationTypeDimension quantitationDimension) Set method for quantitationDimension
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.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, 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

bioAssayDimension

protected BioAssayDimension bioAssayDimension

The relevant BioAssays for this NodeContents from the BioAssayData.

designElementDimension

protected DesignElementDimension designElementDimension

The relevant DesignElements for this NodeContents from the BioAssayData.

quantitationDimension

protected QuantitationTypeDimension quantitationDimension

The relevant QuantitationTypes for this NodeContents from the BioAssayData.

Constructor Detail

NodeContents

public NodeContents()

Default constructor.

NodeContents

public NodeContents(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 Describable

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 Describable

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 Describable

java.io.IOException

setBioAssayDimension

public void setBioAssayDimension(BioAssayDimension bioAssayDimension)

Set method for bioAssayDimension

Specified by:

setBioAssayDimension in interface HasBioAssayDimension

getBioAssayDimension

public BioAssayDimension getBioAssayDimension()

Get method for bioAssayDimension

Specified by:

getBioAssayDimension in interface HasBioAssayDimension

Returns:

value of the attribute

setDesignElementDimension

public void setDesignElementDimension(DesignElementDimension designElementDimension)

Set method for designElementDimension

Specified by:

setDesignElementDimension in interface HasDesignElementDimension

getDesignElementDimension

public DesignElementDimension getDesignElementDimension()

Get method for designElementDimension

Specified by:

getDesignElementDimension in interface HasDesignElementDimension

Returns:

value of the attribute

setQuantitationDimension

public void setQuantitationDimension(QuantitationTypeDimension quantitationDimension)

Set method for quantitationDimension

Specified by:

setQuantitationDimension in interface HasQuantitationDimension

getQuantitationDimension

public QuantitationTypeDimension getQuantitationDimension()

Get method for quantitationDimension

Specified by:

getQuantitationDimension in interface HasQuantitationDimension

Returns:

value of the attribute