org.biomage.BioAssay
Class MeasuredBioAssay

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.BioAssay.BioAssay
                  extended by org.biomage.BioAssay.MeasuredBioAssay
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasBioAssayFactorValues, HasChannels, HasDescriptions, HasFeatureExtraction, HasMeasuredBioAssayData, HasPropertySets, HasSecurity

public class MeasuredBioAssay
extends BioAssay
implements java.io.Serializable, HasFeatureExtraction, 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.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasMeasuredBioAssayData
HasMeasuredBioAssayData.MeasuredBioAssayData_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasChannels
HasChannels.Channels_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasBioAssayFactorValues
HasBioAssayFactorValues.BioAssayFactorValues_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  FeatureExtraction featureExtraction
          The association between the MeasuredBioAssay and the FeatureExtraction Event.
protected  java.util.List measuredBioAssayData
          The data associated with the MeasuredBioAssay.
 
Fields inherited from class org.biomage.BioAssay.BioAssay
bioAssayFactorValues, channels, deleted, ojbConcreteClass
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
MeasuredBioAssay()
          Default constructor.
MeasuredBioAssay(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToMeasuredBioAssayData(int position, MeasuredBioAssayData measuredBioAssayData)
          Method to add MeasuredBioAssayData at position to MeasuredBioAssayData_list
 void addToMeasuredBioAssayData(MeasuredBioAssayData measuredBioAssayData)
          Method to add MeasuredBioAssayData to MeasuredBioAssayData_list
 boolean emptyMAGEobject()
           
 FeatureExtraction getFeatureExtraction()
          Get method for featureExtraction
 MeasuredBioAssayData getFromMeasuredBioAssayData(int position)
          Method to get MeasuredBioAssayData from MeasuredBioAssayData_list
 HasMeasuredBioAssayData.MeasuredBioAssayData_list getMeasuredBioAssayData()
          Get method for measuredBioAssayData
 java.lang.String getModelClassName()
           
 void removeElementAtFromMeasuredBioAssayData(int position)
          Method to remove by position from MeasuredBioAssayData_list
 void removeFromMeasuredBioAssayData(MeasuredBioAssayData measuredBioAssayData)
          Method to remove first MeasuredBioAssayData from MeasuredBioAssayData_list
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setFeatureExtraction(FeatureExtraction featureExtraction)
          Set method for featureExtraction
 void setMeasuredBioAssayData(HasMeasuredBioAssayData.MeasuredBioAssayData_list measuredBioAssayData)
          Set method for measuredBioAssayData
 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.BioAssay.BioAssay
addToBioAssayFactorValues, addToBioAssayFactorValues, addToChannels, addToChannels, getBioAssayFactorValues, getChannels, getFromBioAssayFactorValues, getFromChannels, isDeleted, removeElementAtFromBioAssayFactorValues, removeElementAtFromChannels, removeFromBioAssayFactorValues, removeFromChannels, setBioAssayFactorValues, setChannels, setDeleted
 
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

featureExtraction

protected FeatureExtraction featureExtraction
The association between the MeasuredBioAssay and the FeatureExtraction Event.


measuredBioAssayData

protected java.util.List measuredBioAssayData
The data associated with the MeasuredBioAssay.

Constructor Detail

MeasuredBioAssay

public MeasuredBioAssay()
Default constructor.


MeasuredBioAssay

public MeasuredBioAssay(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 BioAssay

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
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 BioAssay
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 BioAssay
Throws:
java.io.IOException

getModelClassName

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

setFeatureExtraction

public void setFeatureExtraction(FeatureExtraction featureExtraction)
Set method for featureExtraction

Specified by:
setFeatureExtraction in interface HasFeatureExtraction
Parameters:
value - to set

getFeatureExtraction

public FeatureExtraction getFeatureExtraction()
Get method for featureExtraction

Specified by:
getFeatureExtraction in interface HasFeatureExtraction
Returns:
value of the attribute

setMeasuredBioAssayData

public void setMeasuredBioAssayData(HasMeasuredBioAssayData.MeasuredBioAssayData_list measuredBioAssayData)
Set method for measuredBioAssayData

Specified by:
setMeasuredBioAssayData in interface HasMeasuredBioAssayData
Parameters:
value - to set

getMeasuredBioAssayData

public HasMeasuredBioAssayData.MeasuredBioAssayData_list getMeasuredBioAssayData()
Get method for measuredBioAssayData

Specified by:
getMeasuredBioAssayData in interface HasMeasuredBioAssayData
Returns:
value of the attribute

addToMeasuredBioAssayData

public void addToMeasuredBioAssayData(MeasuredBioAssayData measuredBioAssayData)
Method to add MeasuredBioAssayData to MeasuredBioAssayData_list

Specified by:
addToMeasuredBioAssayData in interface HasMeasuredBioAssayData

addToMeasuredBioAssayData

public void addToMeasuredBioAssayData(int position,
                                      MeasuredBioAssayData measuredBioAssayData)
Method to add MeasuredBioAssayData at position to MeasuredBioAssayData_list

Specified by:
addToMeasuredBioAssayData in interface HasMeasuredBioAssayData

getFromMeasuredBioAssayData

public MeasuredBioAssayData getFromMeasuredBioAssayData(int position)
Method to get MeasuredBioAssayData from MeasuredBioAssayData_list

Specified by:
getFromMeasuredBioAssayData in interface HasMeasuredBioAssayData

removeElementAtFromMeasuredBioAssayData

public void removeElementAtFromMeasuredBioAssayData(int position)
Method to remove by position from MeasuredBioAssayData_list

Specified by:
removeElementAtFromMeasuredBioAssayData in interface HasMeasuredBioAssayData

removeFromMeasuredBioAssayData

public void removeFromMeasuredBioAssayData(MeasuredBioAssayData measuredBioAssayData)
Method to remove first MeasuredBioAssayData from MeasuredBioAssayData_list

Specified by:
removeFromMeasuredBioAssayData in interface HasMeasuredBioAssayData