org.biomage.BioAssay
Class FeatureExtraction

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

All Implemented Interfaces:

HasAuditTrail, HasDescriptions, HasMeasuredBioAssayTarget, HasPhysicalBioAssaySource, HasPropertySets, HasProtocolApplications, HasSecurity, java.io.Serializable

public class FeatureExtraction

extends BioEvent

implements java.io.Serializable, HasPhysicalBioAssaySource, HasMeasuredBioAssayTarget

The process by which data is extracted from an image producing a measuredBioAssayData and a measuredBioAssay.

See Also:

Serialized Form

Nested Class Summary

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

HasProtocolApplications.ProtocolApplications_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 MeasuredBioAssay	measuredBioAssayTarget The association between the MeasuredBioAssay and the FeatureExtraction Event.
protected PhysicalBioAssay	physicalBioAssaySource The PhysicalBioAssay used in the FeatureExtraction event.

Fields inherited from class org.biomage.BioEvent.BioEvent

protocolApplications

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

FeatureExtraction()
Default constructor.

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

Method Summary

MeasuredBioAssay	getMeasuredBioAssayTarget() Get method for measuredBioAssayTarget
PhysicalBioAssay	getPhysicalBioAssaySource() Get method for physicalBioAssaySource
void	setMeasuredBioAssayTarget(MeasuredBioAssay measuredBioAssayTarget) Set method for measuredBioAssayTarget
void	setPhysicalBioAssaySource(PhysicalBioAssay physicalBioAssaySource) Set method for physicalBioAssaySource
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.BioEvent.BioEvent

addToProtocolApplications, addToProtocolApplications, getFromProtocolApplications, getProtocolApplications, removeElementAtFromProtocolApplications, removeFromProtocolApplications, setProtocolApplications

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

physicalBioAssaySource

protected PhysicalBioAssay physicalBioAssaySource

The PhysicalBioAssay used in the FeatureExtraction event.

measuredBioAssayTarget

protected MeasuredBioAssay measuredBioAssayTarget

The association between the MeasuredBioAssay and the FeatureExtraction Event.

Constructor Detail

FeatureExtraction

public FeatureExtraction()

Default constructor.

FeatureExtraction

public FeatureExtraction(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 BioEvent

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 BioEvent

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 BioEvent

java.io.IOException

setPhysicalBioAssaySource

public void setPhysicalBioAssaySource(PhysicalBioAssay physicalBioAssaySource)

Set method for physicalBioAssaySource

Specified by:

setPhysicalBioAssaySource in interface HasPhysicalBioAssaySource

getPhysicalBioAssaySource

public PhysicalBioAssay getPhysicalBioAssaySource()

Get method for physicalBioAssaySource

Specified by:

getPhysicalBioAssaySource in interface HasPhysicalBioAssaySource

Returns:

value of the attribute

setMeasuredBioAssayTarget

public void setMeasuredBioAssayTarget(MeasuredBioAssay measuredBioAssayTarget)

Set method for measuredBioAssayTarget

Specified by:

setMeasuredBioAssayTarget in interface HasMeasuredBioAssayTarget

getMeasuredBioAssayTarget

public MeasuredBioAssay getMeasuredBioAssayTarget()

Get method for measuredBioAssayTarget

Specified by:

getMeasuredBioAssayTarget in interface HasMeasuredBioAssayTarget

Returns:

value of the attribute