org.biomage.BioAssayData
Class BioDataTuples

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

public class BioDataTuples
extends BioDataValues
implements java.io.Serializable, HasBioAssayTupleData

A relational, tuple representation of the data.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasBioAssayTupleData
HasBioAssayTupleData.BioAssayTuples_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets
HasPropertySets.PropertySets_list
 
Field Summary
 
Fields inherited from class org.biomage.BioAssayData.BioDataValues
ojbConcreteClass
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
BioDataTuples()
          Default constructor.
BioDataTuples(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToBioAssayTuples(BioAssayTuple bioAssayTuple)
          Method to add BioAssayTuple to BioAssayTuples_list
 void addToBioAssayTuples(int position, BioAssayTuple bioAssayTuple)
          Method to add BioAssayTuple at position to BioAssayTuples_list
 boolean emptyMAGEobject()
           
 HasBioAssayTupleData.BioAssayTuples_list getBioAssayTuples()
          Get method for bioAssayTuples
 BioAssayTuple getFromBioAssayTuples(int position)
          Method to get BioAssayTuple from BioAssayTuples_list
 java.lang.String getModelClassName()
           
 void removeElementAtFromBioAssayTuples(int position)
          Method to remove by position from BioAssayTuples_list
 void removeFromBioAssayTuples(BioAssayTuple bioAssayTuple)
          Method to remove first BioAssayTuple from BioAssayTuples_list
 void setBioAssayTuples(HasBioAssayTupleData.BioAssayTuples_list bioAssayTuples)
          Set method for bioAssayTuples
 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
 

Constructor Detail

BioDataTuples

public BioDataTuples()
Default constructor.


BioDataTuples

public BioDataTuples(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 BioDataValues
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 BioDataValues
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 BioDataValues
Throws:
java.io.IOException

getModelClassName

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

setBioAssayTuples

public void setBioAssayTuples(HasBioAssayTupleData.BioAssayTuples_list bioAssayTuples)
Set method for bioAssayTuples

Specified by:
setBioAssayTuples in interface HasBioAssayTupleData
Parameters:
value - to set

getBioAssayTuples

public HasBioAssayTupleData.BioAssayTuples_list getBioAssayTuples()
Get method for bioAssayTuples

Specified by:
getBioAssayTuples in interface HasBioAssayTupleData
Returns:
value of the attribute

addToBioAssayTuples

public void addToBioAssayTuples(BioAssayTuple bioAssayTuple)
Method to add BioAssayTuple to BioAssayTuples_list

Specified by:
addToBioAssayTuples in interface HasBioAssayTupleData

addToBioAssayTuples

public void addToBioAssayTuples(int position,
                                BioAssayTuple bioAssayTuple)
Method to add BioAssayTuple at position to BioAssayTuples_list

Specified by:
addToBioAssayTuples in interface HasBioAssayTupleData

getFromBioAssayTuples

public BioAssayTuple getFromBioAssayTuples(int position)
Method to get BioAssayTuple from BioAssayTuples_list

Specified by:
getFromBioAssayTuples in interface HasBioAssayTupleData

removeElementAtFromBioAssayTuples

public void removeElementAtFromBioAssayTuples(int position)
Method to remove by position from BioAssayTuples_list

Specified by:
removeElementAtFromBioAssayTuples in interface HasBioAssayTupleData

removeFromBioAssayTuples

public void removeFromBioAssayTuples(BioAssayTuple bioAssayTuple)
Method to remove first BioAssayTuple from BioAssayTuples_list

Specified by:
removeFromBioAssayTuples in interface HasBioAssayTupleData