org.biomage.BioAssayData
Class Transformation

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.BioEvent.BioEvent
                  extended by org.biomage.BioAssayData.Transformation
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasBioAssayDataSources, HasBioAssayMapping, HasDerivedBioAssayDataTarget, HasDescriptions, HasDesignElementMapping, HasPropertySets, HasProtocolApplications, HasQuantitationTypeMapping, HasSecurity

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

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

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasBioAssayDataSources
HasBioAssayDataSources.BioAssayDataSources_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasProtocolApplications
HasProtocolApplications.ProtocolApplications_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  java.util.List bioAssayDataSources
          The BioAssayData sources that the Transformation event uses to produce the target DerivedBioAssayData.
protected  BioAssayMapping bioAssayMapping
          The collection of mappings for the BioAssays.
protected  DerivedBioAssayData derivedBioAssayDataTarget
          The association between the DerivedBioAssayData and the Transformation event that produced it.
protected  DesignElementMapping designElementMapping
          The collection of mappings for the DesignElements.
protected  QuantitationTypeMapping quantitationTypeMapping
          The collection of mappings for the QuantitationTypes.
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
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
 boolean emptyMAGEobject()
           
 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
 java.lang.String getModelClassName()
           
 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 setAttributes(org.xml.sax.Attributes atts)
           
 void setBioAssayDataSources(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 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.BioEvent.BioEvent
addToProtocolApplications, addToProtocolApplications, getFromProtocolApplications, getProtocolApplications, removeElementAtFromProtocolApplications, removeFromProtocolApplications, setProtocolApplications
 
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

bioAssayDataSources

protected java.util.List bioAssayDataSources
The BioAssayData sources that the Transformation event uses to produce the target DerivedBioAssayData.


derivedBioAssayDataTarget

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


quantitationTypeMapping

protected QuantitationTypeMapping quantitationTypeMapping
The collection of mappings for the QuantitationTypes.


designElementMapping

protected DesignElementMapping designElementMapping
The collection of mappings for the DesignElements.


bioAssayMapping

protected BioAssayMapping bioAssayMapping
The collection of mappings for the BioAssays.

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

Parameters:
atts: - the attribute list.
Method Detail

setAttributes

public void setAttributes(org.xml.sax.Attributes atts)
Overrides:
setAttributes in class BioEvent

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 BioEvent
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 BioEvent
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 BioEvent
Throws:
java.io.IOException

getModelClassName

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

setBioAssayDataSources

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

Specified by:
setBioAssayDataSources in interface HasBioAssayDataSources
Parameters:
value - to set

getBioAssayDataSources

public HasBioAssayDataSources.BioAssayDataSources_list getBioAssayDataSources()
Get method for bioAssayDataSources

Specified by:
getBioAssayDataSources in interface HasBioAssayDataSources
Returns:
value of the attribute

addToBioAssayDataSources

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

Specified by:
addToBioAssayDataSources in interface HasBioAssayDataSources

addToBioAssayDataSources

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

Specified by:
addToBioAssayDataSources in interface HasBioAssayDataSources

getFromBioAssayDataSources

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

Specified by:
getFromBioAssayDataSources in interface HasBioAssayDataSources

removeElementAtFromBioAssayDataSources

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

Specified by:
removeElementAtFromBioAssayDataSources in interface HasBioAssayDataSources

removeFromBioAssayDataSources

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

Specified by:
removeFromBioAssayDataSources in interface HasBioAssayDataSources

setDerivedBioAssayDataTarget

public void setDerivedBioAssayDataTarget(DerivedBioAssayData derivedBioAssayDataTarget)
Set method for derivedBioAssayDataTarget

Specified by:
setDerivedBioAssayDataTarget in interface HasDerivedBioAssayDataTarget
Parameters:
value - to set

getDerivedBioAssayDataTarget

public DerivedBioAssayData getDerivedBioAssayDataTarget()
Get method for derivedBioAssayDataTarget

Specified by:
getDerivedBioAssayDataTarget in interface HasDerivedBioAssayDataTarget
Returns:
value of the attribute

setQuantitationTypeMapping

public void setQuantitationTypeMapping(QuantitationTypeMapping quantitationTypeMapping)
Set method for quantitationTypeMapping

Specified by:
setQuantitationTypeMapping in interface HasQuantitationTypeMapping
Parameters:
value - to set

getQuantitationTypeMapping

public QuantitationTypeMapping getQuantitationTypeMapping()
Get method for quantitationTypeMapping

Specified by:
getQuantitationTypeMapping in interface HasQuantitationTypeMapping
Returns:
value of the attribute

setDesignElementMapping

public void setDesignElementMapping(DesignElementMapping designElementMapping)
Set method for designElementMapping

Specified by:
setDesignElementMapping in interface HasDesignElementMapping
Parameters:
value - to set

getDesignElementMapping

public DesignElementMapping getDesignElementMapping()
Get method for designElementMapping

Specified by:
getDesignElementMapping in interface HasDesignElementMapping
Returns:
value of the attribute

setBioAssayMapping

public void setBioAssayMapping(BioAssayMapping bioAssayMapping)
Set method for bioAssayMapping

Specified by:
setBioAssayMapping in interface HasBioAssayMapping
Parameters:
value - to set

getBioAssayMapping

public BioAssayMapping getBioAssayMapping()
Get method for bioAssayMapping

Specified by:
getBioAssayMapping in interface HasBioAssayMapping
Returns:
value of the attribute