Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ BioAssay overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

---

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:

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

---

Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ BioAssay overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

---