Docjar: A Java Source and Docuemnt Enginecom.*    java.*    javax.*    org.*    all    new    plug-in

Quick Search    Search Deep

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

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.BioAssay.BioAssay
                  extended byorg.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

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.


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.


measuredBioAssayData

private org.biomage.Interface.HasMeasuredBioAssayData.MeasuredBioAssayData_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

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

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

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

setFeatureExtraction

public void setFeatureExtraction(FeatureExtraction featureExtraction)
Set method for featureExtraction

Specified by:
setFeatureExtraction in interface org.biomage.Interface.HasFeatureExtraction

getFeatureExtraction

public FeatureExtraction getFeatureExtraction()
Get method for featureExtraction

Specified by:
getFeatureExtraction in interface org.biomage.Interface.HasFeatureExtraction

setMeasuredBioAssayData

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

Specified by:
setMeasuredBioAssayData in interface org.biomage.Interface.HasMeasuredBioAssayData

getMeasuredBioAssayData

public org.biomage.Interface.HasMeasuredBioAssayData.MeasuredBioAssayData_list getMeasuredBioAssayData()
Get method for measuredBioAssayData

Specified by:
getMeasuredBioAssayData in interface org.biomage.Interface.HasMeasuredBioAssayData

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

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

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

removeElementAtFromMeasuredBioAssayData

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

Specified by:
removeElementAtFromMeasuredBioAssayData in interface org.biomage.Interface.HasMeasuredBioAssayData

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