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org.biomage.BioAssayData
Class BioDataTuples  view BioDataTuples download BioDataTuples.java

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

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

A relational, tuple representation of the data.


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasBioAssayTupleData
org.biomage.Interface.HasBioAssayTupleData.BioAssayTupleData_list
 
Nested classes inherited from class org.biomage.Interface.HasPropertySets
org.biomage.Interface.HasPropertySets.PropertySets_list
 
Field Summary
private  org.biomage.Interface.HasBioAssayTupleData.BioAssayTupleData_list bioAssayTupleData
          The collection of BioAssayData tuples.
 
Fields inherited from class org.biomage.Common.Extendable
 
Constructor Summary
BioDataTuples()
          Default constructor.
BioDataTuples(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToBioAssayTupleData(BioAssayDatum bioAssayDatum)
          Method to add BioAssayDatum to BioAssayTupleData_list
 void addToBioAssayTupleData(int position, BioAssayDatum bioAssayDatum)
          Method to add BioAssayDatum at position to BioAssayTupleData_list
 org.biomage.Interface.HasBioAssayTupleData.BioAssayTupleData_list getBioAssayTupleData()
          Get method for bioAssayTupleData
 BioAssayDatum getFromBioAssayTupleData(int position)
          Method to get BioAssayDatum from BioAssayTupleData_list
 void removeElementAtFromBioAssayTupleData(int position)
          Method to remove by position from BioAssayTupleData_list
 void removeFromBioAssayTupleData(BioAssayDatum bioAssayDatum)
          Method to remove first BioAssayDatum from BioAssayTupleData_list
 void setBioAssayTupleData(org.biomage.Interface.HasBioAssayTupleData.BioAssayTupleData_list bioAssayTupleData)
          Set method for bioAssayTupleData
 void writeAssociations(java.io.Writer out)
          writeAssociations
 void writeAttributes(java.io.Writer out)
          writeAttributes
 void writeMAGEML(java.io.Writer out)
          writeMAGEML
 
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

bioAssayTupleData

private org.biomage.Interface.HasBioAssayTupleData.BioAssayTupleData_list bioAssayTupleData
The collection of BioAssayData tuples.

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

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

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

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

setBioAssayTupleData

public void setBioAssayTupleData(org.biomage.Interface.HasBioAssayTupleData.BioAssayTupleData_list bioAssayTupleData)
Set method for bioAssayTupleData

Specified by:
setBioAssayTupleData in interface org.biomage.Interface.HasBioAssayTupleData

getBioAssayTupleData

public org.biomage.Interface.HasBioAssayTupleData.BioAssayTupleData_list getBioAssayTupleData()
Get method for bioAssayTupleData

Specified by:
getBioAssayTupleData in interface org.biomage.Interface.HasBioAssayTupleData

addToBioAssayTupleData

public void addToBioAssayTupleData(BioAssayDatum bioAssayDatum)
Method to add BioAssayDatum to BioAssayTupleData_list

Specified by:
addToBioAssayTupleData in interface org.biomage.Interface.HasBioAssayTupleData

addToBioAssayTupleData

public void addToBioAssayTupleData(int position,
                                   BioAssayDatum bioAssayDatum)
Method to add BioAssayDatum at position to BioAssayTupleData_list

Specified by:
addToBioAssayTupleData in interface org.biomage.Interface.HasBioAssayTupleData

getFromBioAssayTupleData

public BioAssayDatum getFromBioAssayTupleData(int position)
Method to get BioAssayDatum from BioAssayTupleData_list

Specified by:
getFromBioAssayTupleData in interface org.biomage.Interface.HasBioAssayTupleData

removeElementAtFromBioAssayTupleData

public void removeElementAtFromBioAssayTupleData(int position)
Method to remove by position from BioAssayTupleData_list

Specified by:
removeElementAtFromBioAssayTupleData in interface org.biomage.Interface.HasBioAssayTupleData

removeFromBioAssayTupleData

public void removeFromBioAssayTupleData(BioAssayDatum bioAssayDatum)
Method to remove first BioAssayDatum from BioAssayTupleData_list

Specified by:
removeFromBioAssayTupleData in interface org.biomage.Interface.HasBioAssayTupleData