org.biomage.BioAssay
Class FeatureExtraction

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

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/interfaces inherited from interface org.biomage.Interface.HasProtocolApplications
HasProtocolApplications.ProtocolApplications_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail
HasAuditTrail.AuditTrail_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions
HasDescriptions.Descriptions_list
 
Nested classes/interfaces inherited from interface 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.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
FeatureExtraction()
          Default constructor.
FeatureExtraction(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 boolean emptyMAGEobject()
           
 MeasuredBioAssay getMeasuredBioAssayTarget()
          Get method for measuredBioAssayTarget
 java.lang.String getModelClassName()
           
 PhysicalBioAssay getPhysicalBioAssaySource()
          Get method for physicalBioAssaySource
 void setAttributes(org.xml.sax.Attributes atts)
           
 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, toString
 
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, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, 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

Parameters:
atts: - the attribute list.
Method Detail

setAttributes

public void setAttributes(org.xml.sax.Attributes atts)
Overrides:
setAttributes in class BioEvent

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
Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

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
Throws:
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
Throws:
java.io.IOException

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class BioEvent

setPhysicalBioAssaySource

public void setPhysicalBioAssaySource(PhysicalBioAssay physicalBioAssaySource)
Set method for physicalBioAssaySource

Specified by:
setPhysicalBioAssaySource in interface HasPhysicalBioAssaySource
Parameters:
value - to set

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
Parameters:
value - to set

getMeasuredBioAssayTarget

public MeasuredBioAssay getMeasuredBioAssayTarget()
Get method for measuredBioAssayTarget

Specified by:
getMeasuredBioAssayTarget in interface HasMeasuredBioAssayTarget
Returns:
value of the attribute