org.biomage.BioAssay
Class DerivedBioAssay

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

All Implemented Interfaces:

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

public class DerivedBioAssay

extends BioAssay

implements java.io.Serializable, HasDerivedBioAssayData, HasType

A BioAssay that is created by the Transformation BioEvent from one or more MeasuredBioAssays or DerivedBioAssays.

See Also:

Serialized Form

Nested Class Summary

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

HasDerivedBioAssayData.DerivedBioAssayData_list

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 HasDerivedBioAssayData.DerivedBioAssayData_list	derivedBioAssayData The data associated with the DerivedBioAssay.
protected OntologyEntry	type The derivation type, for instance collapsed spot replicate, ratio, averaged intensity, bioassay replicates, etc.

Fields inherited from class org.biomage.BioAssay.BioAssay

bioAssayFactorValues, channels

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

DerivedBioAssay()
Default constructor.

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

Method Summary

void	addToDerivedBioAssayData(DerivedBioAssayData derivedBioAssayData) Method to add DerivedBioAssayData to DerivedBioAssayData_list
void	addToDerivedBioAssayData(int position, DerivedBioAssayData derivedBioAssayData) Method to add DerivedBioAssayData at position to DerivedBioAssayData_list
HasDerivedBioAssayData.DerivedBioAssayData_list	getDerivedBioAssayData() Get method for derivedBioAssayData
DerivedBioAssayData	getFromDerivedBioAssayData(int position) Method to get DerivedBioAssayData from DerivedBioAssayData_list
OntologyEntry	getType() Get method for type
void	removeElementAtFromDerivedBioAssayData(int position) Method to remove by position from DerivedBioAssayData_list
void	removeFromDerivedBioAssayData(DerivedBioAssayData derivedBioAssayData) Method to remove first DerivedBioAssayData from DerivedBioAssayData_list
void	setDerivedBioAssayData(HasDerivedBioAssayData.DerivedBioAssayData_list derivedBioAssayData) Set method for derivedBioAssayData
void	setType(OntologyEntry type) Set method for type
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.BioAssay.BioAssay

addToBioAssayFactorValues, addToBioAssayFactorValues, addToChannels, addToChannels, getBioAssayFactorValues, getChannels, getFromBioAssayFactorValues, getFromChannels, removeElementAtFromBioAssayFactorValues, removeElementAtFromChannels, removeFromBioAssayFactorValues, removeFromChannels, setBioAssayFactorValues, setChannels

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

type

protected OntologyEntry type

The derivation type, for instance collapsed spot replicate, ratio, averaged intensity, bioassay replicates, etc.

derivedBioAssayData

protected HasDerivedBioAssayData.DerivedBioAssayData_list derivedBioAssayData

The data associated with the DerivedBioAssay.

Constructor Detail

DerivedBioAssay

public DerivedBioAssay()

Default constructor.

DerivedBioAssay

public DerivedBioAssay(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 BioAssay

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 BioAssay

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 BioAssay

java.io.IOException

setType

public void setType(OntologyEntry type)

Set method for type

Specified by:

setType in interface HasType

getType

public OntologyEntry getType()

Get method for type

Specified by:

getType in interface HasType

Returns:

value of the attribute

setDerivedBioAssayData

public void setDerivedBioAssayData(HasDerivedBioAssayData.DerivedBioAssayData_list derivedBioAssayData)

Set method for derivedBioAssayData

Specified by:

setDerivedBioAssayData in interface HasDerivedBioAssayData

getDerivedBioAssayData

public HasDerivedBioAssayData.DerivedBioAssayData_list getDerivedBioAssayData()

Get method for derivedBioAssayData

Specified by:

getDerivedBioAssayData in interface HasDerivedBioAssayData

Returns:

value of the attribute

addToDerivedBioAssayData

public void addToDerivedBioAssayData(DerivedBioAssayData derivedBioAssayData)

Method to add DerivedBioAssayData to DerivedBioAssayData_list

Specified by:

addToDerivedBioAssayData in interface HasDerivedBioAssayData

addToDerivedBioAssayData

public void addToDerivedBioAssayData(int position,
                                     DerivedBioAssayData derivedBioAssayData)

Method to add DerivedBioAssayData at position to DerivedBioAssayData_list

Specified by:

addToDerivedBioAssayData in interface HasDerivedBioAssayData

getFromDerivedBioAssayData

public DerivedBioAssayData getFromDerivedBioAssayData(int position)

Method to get DerivedBioAssayData from DerivedBioAssayData_list

Specified by:

getFromDerivedBioAssayData in interface HasDerivedBioAssayData

removeElementAtFromDerivedBioAssayData

public void removeElementAtFromDerivedBioAssayData(int position)

Method to remove by position from DerivedBioAssayData_list

Specified by:

removeElementAtFromDerivedBioAssayData in interface HasDerivedBioAssayData

removeFromDerivedBioAssayData

public void removeFromDerivedBioAssayData(DerivedBioAssayData derivedBioAssayData)

Method to remove first DerivedBioAssayData from DerivedBioAssayData_list

Specified by:

removeFromDerivedBioAssayData in interface HasDerivedBioAssayData