org.biomage.BioAssayData
Class BioAssayMapping

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

All Implemented Interfaces:

HasBioAssayMaps, HasPropertySets, java.io.Serializable

public class BioAssayMapping

extends Extendable

implements java.io.Serializable, HasBioAssayMaps

Container of the mappings of the input BioAssay dimensions to the output BioAssay dimension.

See Also:

Serialized Form

Nested Class Summary

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

HasBioAssayMaps.BioAssayMaps_list

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

HasPropertySets.PropertySets_list

Field Summary

protected HasBioAssayMaps.BioAssayMaps_list

bioAssayMaps The maps for the BioAssays.

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

BioAssayMapping()
Default constructor.

BioAssayMapping(org.xml.sax.Attributes atts)
Attribute constructor.

Method Summary

void	addToBioAssayMaps(BioAssayMap bioAssayMap) Method to add BioAssayMap to BioAssayMaps_list
void	addToBioAssayMaps(int position, BioAssayMap bioAssayMap) Method to add BioAssayMap at position to BioAssayMaps_list
HasBioAssayMaps.BioAssayMaps_list	getBioAssayMaps() Get method for bioAssayMaps
BioAssayMap	getFromBioAssayMaps(int position) Method to get BioAssayMap from BioAssayMaps_list
void	removeElementAtFromBioAssayMaps(int position) Method to remove by position from BioAssayMaps_list
void	removeFromBioAssayMaps(BioAssayMap bioAssayMap) Method to remove first BioAssayMap from BioAssayMaps_list
void	setBioAssayMaps(HasBioAssayMaps.BioAssayMaps_list bioAssayMaps) Set method for bioAssayMaps
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

bioAssayMaps

protected HasBioAssayMaps.BioAssayMaps_list bioAssayMaps

The maps for the BioAssays.

Constructor Detail

BioAssayMapping

public BioAssayMapping()

Default constructor.

BioAssayMapping

public BioAssayMapping(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 Extendable

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 Extendable

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

java.io.IOException

setBioAssayMaps

public void setBioAssayMaps(HasBioAssayMaps.BioAssayMaps_list bioAssayMaps)

Set method for bioAssayMaps

Specified by:

setBioAssayMaps in interface HasBioAssayMaps

getBioAssayMaps

public HasBioAssayMaps.BioAssayMaps_list getBioAssayMaps()

Get method for bioAssayMaps

Specified by:

getBioAssayMaps in interface HasBioAssayMaps

Returns:

value of the attribute

addToBioAssayMaps

public void addToBioAssayMaps(BioAssayMap bioAssayMap)

Method to add BioAssayMap to BioAssayMaps_list

Specified by:

addToBioAssayMaps in interface HasBioAssayMaps

addToBioAssayMaps

public void addToBioAssayMaps(int position,
                              BioAssayMap bioAssayMap)

Method to add BioAssayMap at position to BioAssayMaps_list

Specified by:

addToBioAssayMaps in interface HasBioAssayMaps

getFromBioAssayMaps

public BioAssayMap getFromBioAssayMaps(int position)

Method to get BioAssayMap from BioAssayMaps_list

Specified by:

getFromBioAssayMaps in interface HasBioAssayMaps

removeElementAtFromBioAssayMaps

public void removeElementAtFromBioAssayMaps(int position)

Method to remove by position from BioAssayMaps_list

Specified by:

removeElementAtFromBioAssayMaps in interface HasBioAssayMaps

removeFromBioAssayMaps

public void removeFromBioAssayMaps(BioAssayMap bioAssayMap)

Method to remove first BioAssayMap from BioAssayMaps_list

Specified by:

removeFromBioAssayMaps in interface HasBioAssayMaps