org.biomage.BioMaterial
Class Treatment

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.BioMaterial.Treatment
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAction, HasActionMeasurement, HasAuditTrail, HasCompoundMeasurements, HasDescriptions, HasPropertySets, HasProtocolApplications, HasSecurity, HasSourceBioMaterialMeasurements

public class Treatment
extends BioEvent
implements java.io.Serializable, HasCompoundMeasurements, HasSourceBioMaterialMeasurements, HasActionMeasurement, HasAction

The process by which a biomaterial is created (from source biomaterials). Treatments have an order and an action.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasCompoundMeasurements
HasCompoundMeasurements.CompoundMeasurements_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasSourceBioMaterialMeasurements
HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_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  OntologyEntry action
          The event that occurred (e.g.
protected  Measurement actionMeasurement
          Measures events like duration, centrifuge speed, etc.
protected  java.util.List compoundMeasurements
          The compounds and their amounts used in the treatment.
protected  java.util.List sourceBioMaterialMeasurements
          The BioMaterials and the amounts used in the treatment
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
Treatment()
          Default constructor.
Treatment(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToCompoundMeasurements(CompoundMeasurement compoundMeasurement)
          Method to add CompoundMeasurement to CompoundMeasurements_list
 void addToCompoundMeasurements(int position, CompoundMeasurement compoundMeasurement)
          Method to add CompoundMeasurement at position to CompoundMeasurements_list
 void addToSourceBioMaterialMeasurements(BioMaterialMeasurement bioMaterialMeasurement)
          Method to add BioMaterialMeasurement to SourceBioMaterialMeasurements_list
 void addToSourceBioMaterialMeasurements(int position, BioMaterialMeasurement bioMaterialMeasurement)
          Method to add BioMaterialMeasurement at position to SourceBioMaterialMeasurements_list
 boolean emptyMAGEobject()
           
 OntologyEntry getAction()
          Get method for action
 Measurement getActionMeasurement()
          Get method for actionMeasurement
 HasCompoundMeasurements.CompoundMeasurements_list getCompoundMeasurements()
          Get method for compoundMeasurements
 CompoundMeasurement getFromCompoundMeasurements(int position)
          Method to get CompoundMeasurement from CompoundMeasurements_list
 BioMaterialMeasurement getFromSourceBioMaterialMeasurements(int position)
          Method to get BioMaterialMeasurement from SourceBioMaterialMeasurements_list
 java.lang.String getModelClassName()
           
 java.lang.Integer getOrder()
          Get method for order
 HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list getSourceBioMaterialMeasurements()
          Get method for sourceBioMaterialMeasurements
 void removeElementAtFromCompoundMeasurements(int position)
          Method to remove by position from CompoundMeasurements_list
 void removeElementAtFromSourceBioMaterialMeasurements(int position)
          Method to remove by position from SourceBioMaterialMeasurements_list
 void removeFromCompoundMeasurements(CompoundMeasurement compoundMeasurement)
          Method to remove first CompoundMeasurement from CompoundMeasurements_list
 void removeFromSourceBioMaterialMeasurements(BioMaterialMeasurement bioMaterialMeasurement)
          Method to remove first BioMaterialMeasurement from SourceBioMaterialMeasurements_list
 void setAction(OntologyEntry action)
          Set method for action
 void setActionMeasurement(Measurement actionMeasurement)
          Set method for actionMeasurement
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setCompoundMeasurements(HasCompoundMeasurements.CompoundMeasurements_list compoundMeasurements)
          Set method for compoundMeasurements
 void setOrder(java.lang.Integer order)
          Set method for order
 void setSourceBioMaterialMeasurements(HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list sourceBioMaterialMeasurements)
          Set method for sourceBioMaterialMeasurements
 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

action

protected OntologyEntry action
The event that occurred (e.g. grow, wait, add, etc...). The actions should be a recommended vocabulary


actionMeasurement

protected Measurement actionMeasurement
Measures events like duration, centrifuge speed, etc.


compoundMeasurements

protected java.util.List compoundMeasurements
The compounds and their amounts used in the treatment.


sourceBioMaterialMeasurements

protected java.util.List sourceBioMaterialMeasurements
The BioMaterials and the amounts used in the treatment

Constructor Detail

Treatment

public Treatment()
Default constructor.


Treatment

public Treatment(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

setOrder

public void setOrder(java.lang.Integer order)
Set method for order

Parameters:
value - to set

getOrder

public java.lang.Integer getOrder()
Get method for order

Returns:
value of the attribute

getModelClassName

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

setAction

public void setAction(OntologyEntry action)
Set method for action

Specified by:
setAction in interface HasAction
Parameters:
value - to set

getAction

public OntologyEntry getAction()
Get method for action

Specified by:
getAction in interface HasAction
Returns:
value of the attribute

setActionMeasurement

public void setActionMeasurement(Measurement actionMeasurement)
Set method for actionMeasurement

Specified by:
setActionMeasurement in interface HasActionMeasurement
Parameters:
value - to set

getActionMeasurement

public Measurement getActionMeasurement()
Get method for actionMeasurement

Specified by:
getActionMeasurement in interface HasActionMeasurement
Returns:
value of the attribute

setCompoundMeasurements

public void setCompoundMeasurements(HasCompoundMeasurements.CompoundMeasurements_list compoundMeasurements)
Set method for compoundMeasurements

Specified by:
setCompoundMeasurements in interface HasCompoundMeasurements
Parameters:
value - to set

getCompoundMeasurements

public HasCompoundMeasurements.CompoundMeasurements_list getCompoundMeasurements()
Get method for compoundMeasurements

Specified by:
getCompoundMeasurements in interface HasCompoundMeasurements
Returns:
value of the attribute

addToCompoundMeasurements

public void addToCompoundMeasurements(CompoundMeasurement compoundMeasurement)
Method to add CompoundMeasurement to CompoundMeasurements_list

Specified by:
addToCompoundMeasurements in interface HasCompoundMeasurements

addToCompoundMeasurements

public void addToCompoundMeasurements(int position,
                                      CompoundMeasurement compoundMeasurement)
Method to add CompoundMeasurement at position to CompoundMeasurements_list

Specified by:
addToCompoundMeasurements in interface HasCompoundMeasurements

getFromCompoundMeasurements

public CompoundMeasurement getFromCompoundMeasurements(int position)
Method to get CompoundMeasurement from CompoundMeasurements_list

Specified by:
getFromCompoundMeasurements in interface HasCompoundMeasurements

removeElementAtFromCompoundMeasurements

public void removeElementAtFromCompoundMeasurements(int position)
Method to remove by position from CompoundMeasurements_list

Specified by:
removeElementAtFromCompoundMeasurements in interface HasCompoundMeasurements

removeFromCompoundMeasurements

public void removeFromCompoundMeasurements(CompoundMeasurement compoundMeasurement)
Method to remove first CompoundMeasurement from CompoundMeasurements_list

Specified by:
removeFromCompoundMeasurements in interface HasCompoundMeasurements

setSourceBioMaterialMeasurements

public void setSourceBioMaterialMeasurements(HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list sourceBioMaterialMeasurements)
Set method for sourceBioMaterialMeasurements

Specified by:
setSourceBioMaterialMeasurements in interface HasSourceBioMaterialMeasurements
Parameters:
value - to set

getSourceBioMaterialMeasurements

public HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list getSourceBioMaterialMeasurements()
Get method for sourceBioMaterialMeasurements

Specified by:
getSourceBioMaterialMeasurements in interface HasSourceBioMaterialMeasurements
Returns:
value of the attribute

addToSourceBioMaterialMeasurements

public void addToSourceBioMaterialMeasurements(BioMaterialMeasurement bioMaterialMeasurement)
Method to add BioMaterialMeasurement to SourceBioMaterialMeasurements_list

Specified by:
addToSourceBioMaterialMeasurements in interface HasSourceBioMaterialMeasurements

addToSourceBioMaterialMeasurements

public void addToSourceBioMaterialMeasurements(int position,
                                               BioMaterialMeasurement bioMaterialMeasurement)
Method to add BioMaterialMeasurement at position to SourceBioMaterialMeasurements_list

Specified by:
addToSourceBioMaterialMeasurements in interface HasSourceBioMaterialMeasurements

getFromSourceBioMaterialMeasurements

public BioMaterialMeasurement getFromSourceBioMaterialMeasurements(int position)
Method to get BioMaterialMeasurement from SourceBioMaterialMeasurements_list

Specified by:
getFromSourceBioMaterialMeasurements in interface HasSourceBioMaterialMeasurements

removeElementAtFromSourceBioMaterialMeasurements

public void removeElementAtFromSourceBioMaterialMeasurements(int position)
Method to remove by position from SourceBioMaterialMeasurements_list

Specified by:
removeElementAtFromSourceBioMaterialMeasurements in interface HasSourceBioMaterialMeasurements

removeFromSourceBioMaterialMeasurements

public void removeFromSourceBioMaterialMeasurements(BioMaterialMeasurement bioMaterialMeasurement)
Method to remove first BioMaterialMeasurement from SourceBioMaterialMeasurements_list

Specified by:
removeFromSourceBioMaterialMeasurements in interface HasSourceBioMaterialMeasurements