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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:

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

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public class MeasuredBioAssay

extends BioAssay

implements java.io.Serializable, org.biomage.Interface.HasFeatureExtraction, org.biomage.Interface.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.

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Nested Class Summary

 

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

org.biomage.Interface.HasMeasuredBioAssayData.MeasuredBioAssayData_list

 

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

org.biomage.Interface.HasChannels.Channels_list

 

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

org.biomage.Interface.HasBioAssayFactorValues.BioAssayFactorValues_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  FeatureExtraction	featureExtraction           The association between the MeasuredBioAssay and the FeatureExtraction Event.
private  org.biomage.Interface.HasMeasuredBioAssayData.MeasuredBioAssayData_list	measuredBioAssayData           The data associated with the MeasuredBioAssay.

 

Fields inherited from class org.biomage.BioAssay.BioAssay

 

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

MeasuredBioAssay()           Default constructor.

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

 

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

private FeatureExtraction featureExtraction

The association between the MeasuredBioAssay and the FeatureExtraction Event.

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measuredBioAssayData

private org.biomage.Interface.HasMeasuredBioAssayData.MeasuredBioAssayData_list measuredBioAssayData

The data associated with the MeasuredBioAssay.

Constructor Detail

MeasuredBioAssay

public MeasuredBioAssay()

Default constructor.

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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

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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

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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

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setFeatureExtraction

public void setFeatureExtraction(FeatureExtraction featureExtraction)

Set method for featureExtraction

Specified by:

setFeatureExtraction in interface org.biomage.Interface.HasFeatureExtraction

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getFeatureExtraction

public FeatureExtraction getFeatureExtraction()

Get method for featureExtraction

Specified by:

getFeatureExtraction in interface org.biomage.Interface.HasFeatureExtraction

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setMeasuredBioAssayData

public void setMeasuredBioAssayData(org.biomage.Interface.HasMeasuredBioAssayData.MeasuredBioAssayData_list measuredBioAssayData)

Set method for measuredBioAssayData

Specified by:

setMeasuredBioAssayData in interface org.biomage.Interface.HasMeasuredBioAssayData

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getMeasuredBioAssayData

public org.biomage.Interface.HasMeasuredBioAssayData.MeasuredBioAssayData_list getMeasuredBioAssayData()

Get method for measuredBioAssayData

Specified by:

getMeasuredBioAssayData in interface org.biomage.Interface.HasMeasuredBioAssayData

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addToMeasuredBioAssayData

public void addToMeasuredBioAssayData(org.biomage.BioAssayData.MeasuredBioAssayData measuredBioAssayData)

Method to add MeasuredBioAssayData to MeasuredBioAssayData_list

Specified by:

addToMeasuredBioAssayData in interface org.biomage.Interface.HasMeasuredBioAssayData

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addToMeasuredBioAssayData

public void addToMeasuredBioAssayData(int position,
                                      org.biomage.BioAssayData.MeasuredBioAssayData measuredBioAssayData)

Method to add MeasuredBioAssayData at position to MeasuredBioAssayData_list

Specified by:

addToMeasuredBioAssayData in interface org.biomage.Interface.HasMeasuredBioAssayData

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getFromMeasuredBioAssayData

public org.biomage.BioAssayData.MeasuredBioAssayData getFromMeasuredBioAssayData(int position)

Method to get MeasuredBioAssayData from MeasuredBioAssayData_list

Specified by:

getFromMeasuredBioAssayData in interface org.biomage.Interface.HasMeasuredBioAssayData

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removeElementAtFromMeasuredBioAssayData

public void removeElementAtFromMeasuredBioAssayData(int position)

Method to remove by position from MeasuredBioAssayData_list

Specified by:

removeElementAtFromMeasuredBioAssayData in interface org.biomage.Interface.HasMeasuredBioAssayData

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removeFromMeasuredBioAssayData

public void removeFromMeasuredBioAssayData(org.biomage.BioAssayData.MeasuredBioAssayData measuredBioAssayData)

Method to remove first MeasuredBioAssayData from MeasuredBioAssayData_list

Specified by:

removeFromMeasuredBioAssayData in interface org.biomage.Interface.HasMeasuredBioAssayData

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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

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