org.biomage.HigherLevelAnalysis
Class NodeContents

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Common.Describable
          extended by org.biomage.HigherLevelAnalysis.NodeContents
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasBioAssayDimension, HasDescriptions, HasDesignElementDimension, HasPropertySets, HasQuantitationDimension, HasSecurity

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/interfaces inherited from interface org.biomage.Interface.HasAuditTrail
HasAuditTrail.AuditTrail_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions
HasDescriptions.Descriptions_list
 
Nested classes/interfaces inherited from interface 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
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
NodeContents()
          Default constructor.
NodeContents(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 boolean emptyMAGEobject()
           
 BioAssayDimension getBioAssayDimension()
          Get method for bioAssayDimension
 DesignElementDimension getDesignElementDimension()
          Get method for designElementDimension
 java.lang.String getModelClassName()
           
 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, setAttributes, setAuditTrail, setDescriptions, setSecurity
 
Methods inherited from class org.biomage.Common.Extendable
addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId, toString
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, 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

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.

Overrides:
writeMAGEML in class Describable
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.

Overrides:
writeAttributes in class Describable
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.

Overrides:
writeAssociations in class Describable
Throws:
java.io.IOException

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class Describable

setBioAssayDimension

public void setBioAssayDimension(BioAssayDimension bioAssayDimension)
Set method for bioAssayDimension

Specified by:
setBioAssayDimension in interface HasBioAssayDimension
Parameters:
value - to set

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
Parameters:
value - to set

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
Parameters:
value - to set

getQuantitationDimension

public QuantitationTypeDimension getQuantitationDimension()
Get method for quantitationDimension

Specified by:
getQuantitationDimension in interface HasQuantitationDimension
Returns:
value of the attribute