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org.biomage.BioAssay
Class DerivedBioAssay  view DerivedBioAssay download DerivedBioAssay.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.DerivedBioAssay
All Implemented Interfaces:
org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasBioAssayFactorValues, org.biomage.Interface.HasChannels, org.biomage.Interface.HasDerivedBioAssayData, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasSecurity, org.biomage.Interface.HasType, java.io.Serializable

public class DerivedBioAssay
extends BioAssay
implements java.io.Serializable, org.biomage.Interface.HasDerivedBioAssayData, org.biomage.Interface.HasType

A BioAssay that is created by the Transformation BioEvent from one or more MeasuredBioAssays or DerivedBioAssays.


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasDerivedBioAssayData
org.biomage.Interface.HasDerivedBioAssayData.DerivedBioAssayData_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  org.biomage.Interface.HasDerivedBioAssayData.DerivedBioAssayData_list derivedBioAssayData
          The data associated with the DerivedBioAssay.
private  org.biomage.Description.OntologyEntry type
          The derivation type, for instance collapsed spot replicate, ratio, averaged intensity, bioassay replicates, etc.
 
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
DerivedBioAssay()
          Default constructor.
DerivedBioAssay(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToDerivedBioAssayData(org.biomage.BioAssayData.DerivedBioAssayData derivedBioAssayData)
          Method to add DerivedBioAssayData to DerivedBioAssayData_list
 void addToDerivedBioAssayData(int position, org.biomage.BioAssayData.DerivedBioAssayData derivedBioAssayData)
          Method to add DerivedBioAssayData at position to DerivedBioAssayData_list
 org.biomage.Interface.HasDerivedBioAssayData.DerivedBioAssayData_list getDerivedBioAssayData()
          Get method for derivedBioAssayData
 org.biomage.BioAssayData.DerivedBioAssayData getFromDerivedBioAssayData(int position)
          Method to get DerivedBioAssayData from DerivedBioAssayData_list
 org.biomage.Description.OntologyEntry getType()
          Get method for type
 void removeElementAtFromDerivedBioAssayData(int position)
          Method to remove by position from DerivedBioAssayData_list
 void removeFromDerivedBioAssayData(org.biomage.BioAssayData.DerivedBioAssayData derivedBioAssayData)
          Method to remove first DerivedBioAssayData from DerivedBioAssayData_list
 void setDerivedBioAssayData(org.biomage.Interface.HasDerivedBioAssayData.DerivedBioAssayData_list derivedBioAssayData)
          Set method for derivedBioAssayData
 void setType(org.biomage.Description.OntologyEntry type)
          Set method for type
 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

derivedBioAssayData

private org.biomage.Interface.HasDerivedBioAssayData.DerivedBioAssayData_list derivedBioAssayData
The data associated with the DerivedBioAssay.


type

private org.biomage.Description.OntologyEntry type
The derivation type, for instance collapsed spot replicate, ratio, averaged intensity, bioassay replicates, etc.

Constructor Detail

DerivedBioAssay

public DerivedBioAssay()
Default constructor.


DerivedBioAssay

public DerivedBioAssay(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

setDerivedBioAssayData

public void setDerivedBioAssayData(org.biomage.Interface.HasDerivedBioAssayData.DerivedBioAssayData_list derivedBioAssayData)
Set method for derivedBioAssayData

Specified by:
setDerivedBioAssayData in interface org.biomage.Interface.HasDerivedBioAssayData

getDerivedBioAssayData

public org.biomage.Interface.HasDerivedBioAssayData.DerivedBioAssayData_list getDerivedBioAssayData()
Get method for derivedBioAssayData

Specified by:
getDerivedBioAssayData in interface org.biomage.Interface.HasDerivedBioAssayData

addToDerivedBioAssayData

public void addToDerivedBioAssayData(org.biomage.BioAssayData.DerivedBioAssayData derivedBioAssayData)
Method to add DerivedBioAssayData to DerivedBioAssayData_list

Specified by:
addToDerivedBioAssayData in interface org.biomage.Interface.HasDerivedBioAssayData

addToDerivedBioAssayData

public void addToDerivedBioAssayData(int position,
                                     org.biomage.BioAssayData.DerivedBioAssayData derivedBioAssayData)
Method to add DerivedBioAssayData at position to DerivedBioAssayData_list

Specified by:
addToDerivedBioAssayData in interface org.biomage.Interface.HasDerivedBioAssayData

getFromDerivedBioAssayData

public org.biomage.BioAssayData.DerivedBioAssayData getFromDerivedBioAssayData(int position)
Method to get DerivedBioAssayData from DerivedBioAssayData_list

Specified by:
getFromDerivedBioAssayData in interface org.biomage.Interface.HasDerivedBioAssayData

removeElementAtFromDerivedBioAssayData

public void removeElementAtFromDerivedBioAssayData(int position)
Method to remove by position from DerivedBioAssayData_list

Specified by:
removeElementAtFromDerivedBioAssayData in interface org.biomage.Interface.HasDerivedBioAssayData

removeFromDerivedBioAssayData

public void removeFromDerivedBioAssayData(org.biomage.BioAssayData.DerivedBioAssayData derivedBioAssayData)
Method to remove first DerivedBioAssayData from DerivedBioAssayData_list

Specified by:
removeFromDerivedBioAssayData in interface org.biomage.Interface.HasDerivedBioAssayData

setType

public void setType(org.biomage.Description.OntologyEntry type)
Set method for type

Specified by:
setType in interface org.biomage.Interface.HasType

getType

public org.biomage.Description.OntologyEntry getType()
Get method for type

Specified by:
getType in interface org.biomage.Interface.HasType