org.biomage.BioAssayData
Class BioAssayTuple

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.BioAssayData.BioAssayTuple
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasDesignElementTuples, HasPropertySets

public class BioAssayTuple
extends Extendable
implements java.io.Serializable, HasDesignElementTuples

Transformed container to specify a BioAssay and the Design Elements and their data for that BioAssay.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDesignElementTuples
HasDesignElementTuples.DesignElementTuples_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets
HasPropertySets.PropertySets_list
 
Field Summary
protected  BioAssay bioAssay
          The BioAssay associated with the value of the BioAssayDatum.
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
BioAssayTuple()
          Default constructor.
BioAssayTuple(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToDesignElementTuples(DesignElementTuple designElementTuple)
          Method to add DesignElementTuple to DesignElementTuples_list
 void addToDesignElementTuples(int position, DesignElementTuple designElementTuple)
          Method to add DesignElementTuple at position to DesignElementTuples_list
 boolean emptyMAGEobject()
           
 BioAssay getBioAssay()
          Get method for bioAssay
 HasDesignElementTuples.DesignElementTuples_list getDesignElementTuples()
          Get method for designElementTuples
 DesignElementTuple getFromDesignElementTuples(int position)
          Method to get DesignElementTuple from DesignElementTuples_list
 java.lang.String getModelClassName()
           
 void removeElementAtFromDesignElementTuples(int position)
          Method to remove by position from DesignElementTuples_list
 void removeFromDesignElementTuples(DesignElementTuple designElementTuple)
          Method to remove first DesignElementTuple from DesignElementTuples_list
 void setBioAssay(BioAssay bioAssay)
          Set method for bioAssay
 void setDesignElementTuples(HasDesignElementTuples.DesignElementTuples_list designElementTuples)
          Set method for designElementTuples
 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, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setAttributes, setId, setIsEditable, setPropertySets, setSecuredElementId, toString
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

bioAssay

protected BioAssay bioAssay
The BioAssay associated with the value of the BioAssayDatum.

Constructor Detail

BioAssayTuple

public BioAssayTuple()
Default constructor.


BioAssayTuple

public BioAssayTuple(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 Extendable
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 Extendable
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 Extendable
Throws:
java.io.IOException

getModelClassName

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

setBioAssay

public void setBioAssay(BioAssay bioAssay)
Set method for bioAssay

Parameters:
value - to set

getBioAssay

public BioAssay getBioAssay()
Get method for bioAssay

Returns:
value of the attribute

setDesignElementTuples

public void setDesignElementTuples(HasDesignElementTuples.DesignElementTuples_list designElementTuples)
Set method for designElementTuples

Specified by:
setDesignElementTuples in interface HasDesignElementTuples
Parameters:
value - to set

getDesignElementTuples

public HasDesignElementTuples.DesignElementTuples_list getDesignElementTuples()
Get method for designElementTuples

Specified by:
getDesignElementTuples in interface HasDesignElementTuples
Returns:
value of the attribute

addToDesignElementTuples

public void addToDesignElementTuples(DesignElementTuple designElementTuple)
Method to add DesignElementTuple to DesignElementTuples_list

Specified by:
addToDesignElementTuples in interface HasDesignElementTuples

addToDesignElementTuples

public void addToDesignElementTuples(int position,
                                     DesignElementTuple designElementTuple)
Method to add DesignElementTuple at position to DesignElementTuples_list

Specified by:
addToDesignElementTuples in interface HasDesignElementTuples

getFromDesignElementTuples

public DesignElementTuple getFromDesignElementTuples(int position)
Method to get DesignElementTuple from DesignElementTuples_list

Specified by:
getFromDesignElementTuples in interface HasDesignElementTuples

removeElementAtFromDesignElementTuples

public void removeElementAtFromDesignElementTuples(int position)
Method to remove by position from DesignElementTuples_list

Specified by:
removeElementAtFromDesignElementTuples in interface HasDesignElementTuples

removeFromDesignElementTuples

public void removeFromDesignElementTuples(DesignElementTuple designElementTuple)
Method to remove first DesignElementTuple from DesignElementTuples_list

Specified by:
removeFromDesignElementTuples in interface HasDesignElementTuples