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org.biomage.BioAssay
Class FeatureExtraction  view FeatureExtraction download FeatureExtraction.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.BioEvent.BioEvent
                  extended byorg.biomage.BioAssay.FeatureExtraction
All Implemented Interfaces:
org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasMeasuredBioAssayTarget, org.biomage.Interface.HasPhysicalBioAssaySource, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasProtocolApplications, org.biomage.Interface.HasSecurity, java.io.Serializable

public class FeatureExtraction
extends org.biomage.BioEvent.BioEvent
implements java.io.Serializable, org.biomage.Interface.HasPhysicalBioAssaySource, org.biomage.Interface.HasMeasuredBioAssayTarget

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


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasProtocolApplications
org.biomage.Interface.HasProtocolApplications.ProtocolApplications_list
 
Nested classes inherited from class org.biomage.Interface.HasAuditTrail
org.biomage.Interface.HasAuditTrail.AuditTrail_list
 
Nested classes inherited from class org.biomage.Interface.HasDescriptions
org.biomage.Interface.HasDescriptions.Descriptions_list
 
Nested classes inherited from class org.biomage.Interface.HasPropertySets
org.biomage.Interface.HasPropertySets.PropertySets_list
 
Field Summary
private  MeasuredBioAssay measuredBioAssayTarget
          The association between the MeasuredBioAssay and the FeatureExtraction Event.
private  PhysicalBioAssay physicalBioAssaySource
          The PhysicalBioAssay used in the FeatureExtraction event.
 
Fields inherited from class org.biomage.BioEvent.BioEvent
 
Fields inherited from class org.biomage.Common.Identifiable
 
Fields inherited from class org.biomage.Common.Describable
 
Fields inherited from class org.biomage.Common.Extendable
 
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
 void writeAttributes(java.io.Writer out)
          writeAttributes
 void writeMAGEML(java.io.Writer out)
          writeMAGEML
 
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

private PhysicalBioAssay physicalBioAssaySource
The PhysicalBioAssay used in the FeatureExtraction event.


measuredBioAssayTarget

private 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.


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.


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.


setPhysicalBioAssaySource

public void setPhysicalBioAssaySource(PhysicalBioAssay physicalBioAssaySource)
Set method for physicalBioAssaySource

Specified by:
setPhysicalBioAssaySource in interface org.biomage.Interface.HasPhysicalBioAssaySource

getPhysicalBioAssaySource

public PhysicalBioAssay getPhysicalBioAssaySource()
Get method for physicalBioAssaySource

Specified by:
getPhysicalBioAssaySource in interface org.biomage.Interface.HasPhysicalBioAssaySource

setMeasuredBioAssayTarget

public void setMeasuredBioAssayTarget(MeasuredBioAssay measuredBioAssayTarget)
Set method for measuredBioAssayTarget

Specified by:
setMeasuredBioAssayTarget in interface org.biomage.Interface.HasMeasuredBioAssayTarget

getMeasuredBioAssayTarget

public MeasuredBioAssay getMeasuredBioAssayTarget()
Get method for measuredBioAssayTarget

Specified by:
getMeasuredBioAssayTarget in interface org.biomage.Interface.HasMeasuredBioAssayTarget