org.biomage.BioAssayData
Class BioAssayDimension

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.BioAssayData.BioAssayDimension

All Implemented Interfaces:

HasAuditTrail, HasBioAssays, HasDescriptions, HasPropertySets, HasSecurity, java.io.Serializable

public class BioAssayDimension

extends Identifiable

implements java.io.Serializable, HasBioAssays

An ordered list of bioAssays.

See Also:

Serialized Form

Nested Class Summary

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

HasBioAssays.BioAssays_list

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

HasAuditTrail.AuditTrail_list

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

HasDescriptions.Descriptions_list

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

HasPropertySets.PropertySets_list

Field Summary

protected HasBioAssays.BioAssays_list

bioAssays The BioAssays for this Dimension

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

BioAssayDimension()
Default constructor.

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

Method Summary

void	addToBioAssays(BioAssay bioAssay) Method to add BioAssay to BioAssays_list
void	addToBioAssays(int position, BioAssay bioAssay) Method to add BioAssay at position to BioAssays_list
HasBioAssays.BioAssays_list	getBioAssays() Get method for bioAssays
BioAssay	getFromBioAssays(int position) Method to get BioAssay from BioAssays_list
void	removeElementAtFromBioAssays(int position) Method to remove by position from BioAssays_list
void	removeFromBioAssays(BioAssay bioAssay) Method to remove first BioAssay from BioAssays_list
void	setBioAssays(HasBioAssays.BioAssays_list bioAssays) Set method for bioAssays
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.Identifiable

getIdentifier, getName, setIdentifier, setName

Methods inherited from class org.biomage.Common.Describable

addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAuditTrail, setDescriptions, setSecurity

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

bioAssays

protected HasBioAssays.BioAssays_list bioAssays

The BioAssays for this Dimension

Constructor Detail

BioAssayDimension

public BioAssayDimension()

Default constructor.

BioAssayDimension

public BioAssayDimension(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 Identifiable

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 Identifiable

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 Identifiable

java.io.IOException

setBioAssays

public void setBioAssays(HasBioAssays.BioAssays_list bioAssays)

Set method for bioAssays

Specified by:

setBioAssays in interface HasBioAssays

getBioAssays

public HasBioAssays.BioAssays_list getBioAssays()

Get method for bioAssays

Specified by:

getBioAssays in interface HasBioAssays

Returns:

value of the attribute

addToBioAssays

public void addToBioAssays(BioAssay bioAssay)

Method to add BioAssay to BioAssays_list

Specified by:

addToBioAssays in interface HasBioAssays

addToBioAssays

public void addToBioAssays(int position,
                           BioAssay bioAssay)

Method to add BioAssay at position to BioAssays_list

Specified by:

addToBioAssays in interface HasBioAssays

getFromBioAssays

public BioAssay getFromBioAssays(int position)

Method to get BioAssay from BioAssays_list

Specified by:

getFromBioAssays in interface HasBioAssays

removeElementAtFromBioAssays

public void removeElementAtFromBioAssays(int position)

Method to remove by position from BioAssays_list

Specified by:

removeElementAtFromBioAssays in interface HasBioAssays

removeFromBioAssays

public void removeFromBioAssays(BioAssay bioAssay)

Method to remove first BioAssay from BioAssays_list

Specified by:

removeFromBioAssays in interface HasBioAssays