org.biomage.BioAssayData
Class BioDataTuples

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.BioAssayData.BioDataValues
              |
              +--org.biomage.BioAssayData.BioDataTuples

All Implemented Interfaces:

HasBioAssayTupleData, HasPropertySets, java.io.Serializable

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 inherited from class org.biomage.Interface.HasBioAssayTupleData

HasBioAssayTupleData.BioAssayTupleData_list

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

HasPropertySets.PropertySets_list

Field Summary

protected HasBioAssayTupleData.BioAssayTupleData_list

bioAssayTupleData The collection of BioAssayData tuples.

Fields inherited from class org.biomage.Common.Extendable

propertySets

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
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(HasBioAssayTupleData.BioAssayTupleData_list bioAssayTupleData) Set method for bioAssayTupleData
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, 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

protected 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

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 BioDataValues

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

java.io.IOException

setBioAssayTupleData

public void setBioAssayTupleData(HasBioAssayTupleData.BioAssayTupleData_list bioAssayTupleData)

Set method for bioAssayTupleData

Specified by:

setBioAssayTupleData in interface HasBioAssayTupleData

getBioAssayTupleData

public HasBioAssayTupleData.BioAssayTupleData_list getBioAssayTupleData()

Get method for bioAssayTupleData

Specified by:

getBioAssayTupleData in interface HasBioAssayTupleData

Returns:

value of the attribute

addToBioAssayTupleData

public void addToBioAssayTupleData(BioAssayDatum bioAssayDatum)

Method to add BioAssayDatum to BioAssayTupleData_list

Specified by:

addToBioAssayTupleData in interface HasBioAssayTupleData

addToBioAssayTupleData

public void addToBioAssayTupleData(int position,
                                   BioAssayDatum bioAssayDatum)

Method to add BioAssayDatum at position to BioAssayTupleData_list

Specified by:

addToBioAssayTupleData in interface HasBioAssayTupleData

getFromBioAssayTupleData

public BioAssayDatum getFromBioAssayTupleData(int position)

Method to get BioAssayDatum from BioAssayTupleData_list

Specified by:

getFromBioAssayTupleData in interface HasBioAssayTupleData

removeElementAtFromBioAssayTupleData

public void removeElementAtFromBioAssayTupleData(int position)

Method to remove by position from BioAssayTupleData_list

Specified by:

removeElementAtFromBioAssayTupleData in interface HasBioAssayTupleData

removeFromBioAssayTupleData

public void removeFromBioAssayTupleData(BioAssayDatum bioAssayDatum)

Method to remove first BioAssayDatum from BioAssayTupleData_list

Specified by:

removeFromBioAssayTupleData in interface HasBioAssayTupleData