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org.biomage.BioAssayData
Class Transformation  view Transformation download Transformation.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.BioEvent.BioEvent
                  extended byorg.biomage.BioAssayData.Transformation
All Implemented Interfaces:
org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasBioAssayDataSources, org.biomage.Interface.HasBioAssayMapping, org.biomage.Interface.HasDerivedBioAssayDataTarget, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasDesignElementMapping, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasProtocolApplications, org.biomage.Interface.HasQuantitationTypeMapping, org.biomage.Interface.HasSecurity, java.io.Serializable

public class Transformation
extends org.biomage.BioEvent.BioEvent
implements java.io.Serializable, org.biomage.Interface.HasBioAssayDataSources, org.biomage.Interface.HasBioAssayMapping, org.biomage.Interface.HasDerivedBioAssayDataTarget, org.biomage.Interface.HasQuantitationTypeMapping, org.biomage.Interface.HasDesignElementMapping

The process by which derivedBioAssays are created from measuredBioAssays and/or derivedBioAssays. It uses mappings to indicate the input and output dimensions.


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasBioAssayDataSources
org.biomage.Interface.HasBioAssayDataSources.BioAssayDataSources_list
 
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  org.biomage.Interface.HasBioAssayDataSources.BioAssayDataSources_list bioAssayDataSources
          The BioAssayData sources that the Transformation event uses to produce the target DerivedBioAssayData.
private  BioAssayMapping bioAssayMapping
          The collection of mappings for the BioAssays.
private  DerivedBioAssayData derivedBioAssayDataTarget
          The association between the DerivedBioAssayData and the Transformation event that produced it.
private  DesignElementMapping designElementMapping
          The collection of mappings for the DesignElements.
private  QuantitationTypeMapping quantitationTypeMapping
          The collection of mappings for the QuantitationTypes.
 
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
Transformation()
          Default constructor.
Transformation(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToBioAssayDataSources(BioAssayData bioAssayData)
          Method to add BioAssayData to BioAssayDataSources_list
 void addToBioAssayDataSources(int position, BioAssayData bioAssayData)
          Method to add BioAssayData at position to BioAssayDataSources_list
 org.biomage.Interface.HasBioAssayDataSources.BioAssayDataSources_list getBioAssayDataSources()
          Get method for bioAssayDataSources
 BioAssayMapping getBioAssayMapping()
          Get method for bioAssayMapping
 DerivedBioAssayData getDerivedBioAssayDataTarget()
          Get method for derivedBioAssayDataTarget
 DesignElementMapping getDesignElementMapping()
          Get method for designElementMapping
 BioAssayData getFromBioAssayDataSources(int position)
          Method to get BioAssayData from BioAssayDataSources_list
 QuantitationTypeMapping getQuantitationTypeMapping()
          Get method for quantitationTypeMapping
 void removeElementAtFromBioAssayDataSources(int position)
          Method to remove by position from BioAssayDataSources_list
 void removeFromBioAssayDataSources(BioAssayData bioAssayData)
          Method to remove first BioAssayData from BioAssayDataSources_list
 void setBioAssayDataSources(org.biomage.Interface.HasBioAssayDataSources.BioAssayDataSources_list bioAssayDataSources)
          Set method for bioAssayDataSources
 void setBioAssayMapping(BioAssayMapping bioAssayMapping)
          Set method for bioAssayMapping
 void setDerivedBioAssayDataTarget(DerivedBioAssayData derivedBioAssayDataTarget)
          Set method for derivedBioAssayDataTarget
 void setDesignElementMapping(DesignElementMapping designElementMapping)
          Set method for designElementMapping
 void setQuantitationTypeMapping(QuantitationTypeMapping quantitationTypeMapping)
          Set method for quantitationTypeMapping
 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

bioAssayDataSources

private org.biomage.Interface.HasBioAssayDataSources.BioAssayDataSources_list bioAssayDataSources
The BioAssayData sources that the Transformation event uses to produce the target DerivedBioAssayData.


bioAssayMapping

private BioAssayMapping bioAssayMapping
The collection of mappings for the BioAssays.


derivedBioAssayDataTarget

private DerivedBioAssayData derivedBioAssayDataTarget
The association between the DerivedBioAssayData and the Transformation event that produced it.


quantitationTypeMapping

private QuantitationTypeMapping quantitationTypeMapping
The collection of mappings for the QuantitationTypes.


designElementMapping

private DesignElementMapping designElementMapping
The collection of mappings for the DesignElements.

Constructor Detail

Transformation

public Transformation()
Default constructor.


Transformation

public Transformation(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.


setBioAssayDataSources

public void setBioAssayDataSources(org.biomage.Interface.HasBioAssayDataSources.BioAssayDataSources_list bioAssayDataSources)
Set method for bioAssayDataSources

Specified by:
setBioAssayDataSources in interface org.biomage.Interface.HasBioAssayDataSources

getBioAssayDataSources

public org.biomage.Interface.HasBioAssayDataSources.BioAssayDataSources_list getBioAssayDataSources()
Get method for bioAssayDataSources

Specified by:
getBioAssayDataSources in interface org.biomage.Interface.HasBioAssayDataSources

addToBioAssayDataSources

public void addToBioAssayDataSources(BioAssayData bioAssayData)
Method to add BioAssayData to BioAssayDataSources_list

Specified by:
addToBioAssayDataSources in interface org.biomage.Interface.HasBioAssayDataSources

addToBioAssayDataSources

public void addToBioAssayDataSources(int position,
                                     BioAssayData bioAssayData)
Method to add BioAssayData at position to BioAssayDataSources_list

Specified by:
addToBioAssayDataSources in interface org.biomage.Interface.HasBioAssayDataSources

getFromBioAssayDataSources

public BioAssayData getFromBioAssayDataSources(int position)
Method to get BioAssayData from BioAssayDataSources_list

Specified by:
getFromBioAssayDataSources in interface org.biomage.Interface.HasBioAssayDataSources

removeElementAtFromBioAssayDataSources

public void removeElementAtFromBioAssayDataSources(int position)
Method to remove by position from BioAssayDataSources_list

Specified by:
removeElementAtFromBioAssayDataSources in interface org.biomage.Interface.HasBioAssayDataSources

removeFromBioAssayDataSources

public void removeFromBioAssayDataSources(BioAssayData bioAssayData)
Method to remove first BioAssayData from BioAssayDataSources_list

Specified by:
removeFromBioAssayDataSources in interface org.biomage.Interface.HasBioAssayDataSources

setBioAssayMapping

public void setBioAssayMapping(BioAssayMapping bioAssayMapping)
Set method for bioAssayMapping

Specified by:
setBioAssayMapping in interface org.biomage.Interface.HasBioAssayMapping

getBioAssayMapping

public BioAssayMapping getBioAssayMapping()
Get method for bioAssayMapping

Specified by:
getBioAssayMapping in interface org.biomage.Interface.HasBioAssayMapping

setDerivedBioAssayDataTarget

public void setDerivedBioAssayDataTarget(DerivedBioAssayData derivedBioAssayDataTarget)
Set method for derivedBioAssayDataTarget

Specified by:
setDerivedBioAssayDataTarget in interface org.biomage.Interface.HasDerivedBioAssayDataTarget

getDerivedBioAssayDataTarget

public DerivedBioAssayData getDerivedBioAssayDataTarget()
Get method for derivedBioAssayDataTarget

Specified by:
getDerivedBioAssayDataTarget in interface org.biomage.Interface.HasDerivedBioAssayDataTarget

setQuantitationTypeMapping

public void setQuantitationTypeMapping(QuantitationTypeMapping quantitationTypeMapping)
Set method for quantitationTypeMapping

Specified by:
setQuantitationTypeMapping in interface org.biomage.Interface.HasQuantitationTypeMapping

getQuantitationTypeMapping

public QuantitationTypeMapping getQuantitationTypeMapping()
Get method for quantitationTypeMapping

Specified by:
getQuantitationTypeMapping in interface org.biomage.Interface.HasQuantitationTypeMapping

setDesignElementMapping

public void setDesignElementMapping(DesignElementMapping designElementMapping)
Set method for designElementMapping

Specified by:
setDesignElementMapping in interface org.biomage.Interface.HasDesignElementMapping

getDesignElementMapping

public DesignElementMapping getDesignElementMapping()
Get method for designElementMapping

Specified by:
getDesignElementMapping in interface org.biomage.Interface.HasDesignElementMapping