org.biomage.BioAssay
Class MeasuredBioAssay

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

All Implemented Interfaces:

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

public class MeasuredBioAssay

extends BioAssay

implements java.io.Serializable, HasFeatureExtraction, HasMeasuredBioAssayData

A measured bioAssay is the direct processing of information in a physical bioAssay by the featureExtraction event. Often uses images which are referenced through the physical bioAssay.

See Also:

Serialized Form

Nested Class Summary

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

HasMeasuredBioAssayData.MeasuredBioAssayData_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 FeatureExtraction	featureExtraction The association between the MeasuredBioAssay and the FeatureExtraction Event.
protected HasMeasuredBioAssayData.MeasuredBioAssayData_list	measuredBioAssayData The data associated with the MeasuredBioAssay.

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

MeasuredBioAssay()
Default constructor.

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

Method Summary

void	addToMeasuredBioAssayData(int position, MeasuredBioAssayData measuredBioAssayData) Method to add MeasuredBioAssayData at position to MeasuredBioAssayData_list
void	addToMeasuredBioAssayData(MeasuredBioAssayData measuredBioAssayData) Method to add MeasuredBioAssayData to MeasuredBioAssayData_list
FeatureExtraction	getFeatureExtraction() Get method for featureExtraction
MeasuredBioAssayData	getFromMeasuredBioAssayData(int position) Method to get MeasuredBioAssayData from MeasuredBioAssayData_list
HasMeasuredBioAssayData.MeasuredBioAssayData_list	getMeasuredBioAssayData() Get method for measuredBioAssayData
void	removeElementAtFromMeasuredBioAssayData(int position) Method to remove by position from MeasuredBioAssayData_list
void	removeFromMeasuredBioAssayData(MeasuredBioAssayData measuredBioAssayData) Method to remove first MeasuredBioAssayData from MeasuredBioAssayData_list
void	setFeatureExtraction(FeatureExtraction featureExtraction) Set method for featureExtraction
void	setMeasuredBioAssayData(HasMeasuredBioAssayData.MeasuredBioAssayData_list measuredBioAssayData) Set method for measuredBioAssayData
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

featureExtraction

protected FeatureExtraction featureExtraction

The association between the MeasuredBioAssay and the FeatureExtraction Event.

measuredBioAssayData

protected HasMeasuredBioAssayData.MeasuredBioAssayData_list measuredBioAssayData

The data associated with the MeasuredBioAssay.

Constructor Detail

MeasuredBioAssay

public MeasuredBioAssay()

Default constructor.

MeasuredBioAssay

public MeasuredBioAssay(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

setFeatureExtraction

public void setFeatureExtraction(FeatureExtraction featureExtraction)

Set method for featureExtraction

Specified by:

setFeatureExtraction in interface HasFeatureExtraction

getFeatureExtraction

public FeatureExtraction getFeatureExtraction()

Get method for featureExtraction

Specified by:

getFeatureExtraction in interface HasFeatureExtraction

Returns:

value of the attribute

setMeasuredBioAssayData

public void setMeasuredBioAssayData(HasMeasuredBioAssayData.MeasuredBioAssayData_list measuredBioAssayData)

Set method for measuredBioAssayData

Specified by:

setMeasuredBioAssayData in interface HasMeasuredBioAssayData

getMeasuredBioAssayData

public HasMeasuredBioAssayData.MeasuredBioAssayData_list getMeasuredBioAssayData()

Get method for measuredBioAssayData

Specified by:

getMeasuredBioAssayData in interface HasMeasuredBioAssayData

Returns:

value of the attribute

addToMeasuredBioAssayData

public void addToMeasuredBioAssayData(MeasuredBioAssayData measuredBioAssayData)

Method to add MeasuredBioAssayData to MeasuredBioAssayData_list

Specified by:

addToMeasuredBioAssayData in interface HasMeasuredBioAssayData

addToMeasuredBioAssayData

public void addToMeasuredBioAssayData(int position,
                                      MeasuredBioAssayData measuredBioAssayData)

Method to add MeasuredBioAssayData at position to MeasuredBioAssayData_list

Specified by:

addToMeasuredBioAssayData in interface HasMeasuredBioAssayData

getFromMeasuredBioAssayData

public MeasuredBioAssayData getFromMeasuredBioAssayData(int position)

Method to get MeasuredBioAssayData from MeasuredBioAssayData_list

Specified by:

getFromMeasuredBioAssayData in interface HasMeasuredBioAssayData

removeElementAtFromMeasuredBioAssayData

public void removeElementAtFromMeasuredBioAssayData(int position)

Method to remove by position from MeasuredBioAssayData_list

Specified by:

removeElementAtFromMeasuredBioAssayData in interface HasMeasuredBioAssayData

removeFromMeasuredBioAssayData

public void removeFromMeasuredBioAssayData(MeasuredBioAssayData measuredBioAssayData)

Method to remove first MeasuredBioAssayData from MeasuredBioAssayData_list

Specified by:

removeFromMeasuredBioAssayData in interface HasMeasuredBioAssayData