org.biomage.BioAssay
Class BioAssay

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

All Implemented Interfaces:

HasAuditTrail, HasBioAssayFactorValues, HasChannels, HasDescriptions, HasPropertySets, HasSecurity, java.io.Serializable

Direct Known Subclasses:

DerivedBioAssay, MeasuredBioAssay, PhysicalBioAssay

public abstract class BioAssay

extends Identifiable

implements java.io.Serializable, HasChannels, HasBioAssayFactorValues

An abstract class which represents both physical and computational groupings of arrays and biomaterials.

See Also:

Serialized Form

Nested Class Summary

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

HasChannels.Channels_list

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

HasBioAssayFactorValues.BioAssayFactorValues_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 HasBioAssayFactorValues.BioAssayFactorValues_list	bioAssayFactorValues The values that this BioAssay is associated with for the experiment.
protected HasChannels.Channels_list	channels Channels can be non-null for all subclasses.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

BioAssay()
Default constructor.

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

Method Summary

void	addToBioAssayFactorValues(FactorValue factorValue) Method to add FactorValue to BioAssayFactorValues_list
void	addToBioAssayFactorValues(int position, FactorValue factorValue) Method to add FactorValue at position to BioAssayFactorValues_list
void	addToChannels(Channel channel) Method to add Channel to Channels_list
void	addToChannels(int position, Channel channel) Method to add Channel at position to Channels_list
HasBioAssayFactorValues.BioAssayFactorValues_list	getBioAssayFactorValues() Get method for bioAssayFactorValues
HasChannels.Channels_list	getChannels() Get method for channels
FactorValue	getFromBioAssayFactorValues(int position) Method to get FactorValue from BioAssayFactorValues_list
Channel	getFromChannels(int position) Method to get Channel from Channels_list
void	removeElementAtFromBioAssayFactorValues(int position) Method to remove by position from BioAssayFactorValues_list
void	removeElementAtFromChannels(int position) Method to remove by position from Channels_list
void	removeFromBioAssayFactorValues(FactorValue factorValue) Method to remove first FactorValue from BioAssayFactorValues_list
void	removeFromChannels(Channel channel) Method to remove first Channel from Channels_list
void	setBioAssayFactorValues(HasBioAssayFactorValues.BioAssayFactorValues_list bioAssayFactorValues) Set method for bioAssayFactorValues
void	setChannels(HasChannels.Channels_list channels) Set method for channels
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

channels

protected HasChannels.Channels_list channels

Channels can be non-null for all subclasses. For instance, collapsing across replicate features will create a DerivedBioAssay that will potentially reference channels.

bioAssayFactorValues

protected HasBioAssayFactorValues.BioAssayFactorValues_list bioAssayFactorValues

The values that this BioAssay is associated with for the experiment.

Constructor Detail

BioAssay

public BioAssay()

Default constructor.

BioAssay

public BioAssay(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

setChannels

public void setChannels(HasChannels.Channels_list channels)

Set method for channels

Specified by:

setChannels in interface HasChannels

getChannels

public HasChannels.Channels_list getChannels()

Get method for channels

Specified by:

getChannels in interface HasChannels

Returns:

value of the attribute

addToChannels

public void addToChannels(Channel channel)

Method to add Channel to Channels_list

Specified by:

addToChannels in interface HasChannels

addToChannels

public void addToChannels(int position,
                          Channel channel)

Method to add Channel at position to Channels_list

Specified by:

addToChannels in interface HasChannels

getFromChannels

public Channel getFromChannels(int position)

Method to get Channel from Channels_list

Specified by:

getFromChannels in interface HasChannels

removeElementAtFromChannels

public void removeElementAtFromChannels(int position)

Method to remove by position from Channels_list

Specified by:

removeElementAtFromChannels in interface HasChannels

removeFromChannels

public void removeFromChannels(Channel channel)

Method to remove first Channel from Channels_list

Specified by:

removeFromChannels in interface HasChannels

setBioAssayFactorValues

public void setBioAssayFactorValues(HasBioAssayFactorValues.BioAssayFactorValues_list bioAssayFactorValues)

Set method for bioAssayFactorValues

Specified by:

setBioAssayFactorValues in interface HasBioAssayFactorValues

getBioAssayFactorValues

public HasBioAssayFactorValues.BioAssayFactorValues_list getBioAssayFactorValues()

Get method for bioAssayFactorValues

Specified by:

getBioAssayFactorValues in interface HasBioAssayFactorValues

Returns:

value of the attribute

addToBioAssayFactorValues

public void addToBioAssayFactorValues(FactorValue factorValue)

Method to add FactorValue to BioAssayFactorValues_list

Specified by:

addToBioAssayFactorValues in interface HasBioAssayFactorValues

addToBioAssayFactorValues

public void addToBioAssayFactorValues(int position,
                                      FactorValue factorValue)

Method to add FactorValue at position to BioAssayFactorValues_list

Specified by:

addToBioAssayFactorValues in interface HasBioAssayFactorValues

getFromBioAssayFactorValues

public FactorValue getFromBioAssayFactorValues(int position)

Method to get FactorValue from BioAssayFactorValues_list

Specified by:

getFromBioAssayFactorValues in interface HasBioAssayFactorValues

removeElementAtFromBioAssayFactorValues

public void removeElementAtFromBioAssayFactorValues(int position)

Method to remove by position from BioAssayFactorValues_list

Specified by:

removeElementAtFromBioAssayFactorValues in interface HasBioAssayFactorValues

removeFromBioAssayFactorValues

public void removeFromBioAssayFactorValues(FactorValue factorValue)

Method to remove first FactorValue from BioAssayFactorValues_list

Specified by:

removeFromBioAssayFactorValues in interface HasBioAssayFactorValues