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org.biomage.BioMaterial
Class Treatment  view Treatment download Treatment.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.BioMaterial.Treatment
All Implemented Interfaces:
org.biomage.Interface.HasAction, org.biomage.Interface.HasActionMeasurement, org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasCompoundMeasurements, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasProtocolApplications, org.biomage.Interface.HasSecurity, org.biomage.Interface.HasSourceBioMaterialMeasurements, java.io.Serializable

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

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


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasCompoundMeasurements
org.biomage.Interface.HasCompoundMeasurements.CompoundMeasurements_list
 
Nested classes inherited from class org.biomage.Interface.HasSourceBioMaterialMeasurements
org.biomage.Interface.HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_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.Description.OntologyEntry action
          The event that occurred (e.g.
private  org.biomage.Measurement.Measurement actionMeasurement
          Measures events like duration, centrifuge speed, etc.
private  org.biomage.Interface.HasCompoundMeasurements.CompoundMeasurements_list compoundMeasurements
          The compounds and their amounts used in the treatment.
(package private)  int order
          The chronological order in which a treatment occurred (in relation to other treatments).
private  org.biomage.Interface.HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list sourceBioMaterialMeasurements
          The BioMaterials and the amounts used in the treatment
 
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
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
 org.biomage.Description.OntologyEntry getAction()
          Get method for action
 org.biomage.Measurement.Measurement getActionMeasurement()
          Get method for actionMeasurement
 org.biomage.Interface.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
 int getOrder()
          Get method for order
 org.biomage.Interface.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(org.biomage.Description.OntologyEntry action)
          Set method for action
 void setActionMeasurement(org.biomage.Measurement.Measurement actionMeasurement)
          Set method for actionMeasurement
 void setCompoundMeasurements(org.biomage.Interface.HasCompoundMeasurements.CompoundMeasurements_list compoundMeasurements)
          Set method for compoundMeasurements
 void setOrder(int order)
          Set method for order
 void setSourceBioMaterialMeasurements(org.biomage.Interface.HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list sourceBioMaterialMeasurements)
          Set method for sourceBioMaterialMeasurements
 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

order

int order
The chronological order in which a treatment occurred (in relation to other treatments). More than one treatment can have the same chronological order indicating that they happened (or were caused to happen) simultaneously.


compoundMeasurements

private org.biomage.Interface.HasCompoundMeasurements.CompoundMeasurements_list compoundMeasurements
The compounds and their amounts used in the treatment.


sourceBioMaterialMeasurements

private org.biomage.Interface.HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list sourceBioMaterialMeasurements
The BioMaterials and the amounts used in the treatment


actionMeasurement

private org.biomage.Measurement.Measurement actionMeasurement
Measures events like duration, centrifuge speed, etc.


action

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

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

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.


setOrder

public void setOrder(int order)
Set method for order


getOrder

public int getOrder()
Get method for order


setCompoundMeasurements

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

Specified by:
setCompoundMeasurements in interface org.biomage.Interface.HasCompoundMeasurements

getCompoundMeasurements

public org.biomage.Interface.HasCompoundMeasurements.CompoundMeasurements_list getCompoundMeasurements()
Get method for compoundMeasurements

Specified by:
getCompoundMeasurements in interface org.biomage.Interface.HasCompoundMeasurements

addToCompoundMeasurements

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

Specified by:
addToCompoundMeasurements in interface org.biomage.Interface.HasCompoundMeasurements

addToCompoundMeasurements

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

Specified by:
addToCompoundMeasurements in interface org.biomage.Interface.HasCompoundMeasurements

getFromCompoundMeasurements

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

Specified by:
getFromCompoundMeasurements in interface org.biomage.Interface.HasCompoundMeasurements

removeElementAtFromCompoundMeasurements

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

Specified by:
removeElementAtFromCompoundMeasurements in interface org.biomage.Interface.HasCompoundMeasurements

removeFromCompoundMeasurements

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

Specified by:
removeFromCompoundMeasurements in interface org.biomage.Interface.HasCompoundMeasurements

setSourceBioMaterialMeasurements

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

Specified by:
setSourceBioMaterialMeasurements in interface org.biomage.Interface.HasSourceBioMaterialMeasurements

getSourceBioMaterialMeasurements

public org.biomage.Interface.HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list getSourceBioMaterialMeasurements()
Get method for sourceBioMaterialMeasurements

Specified by:
getSourceBioMaterialMeasurements in interface org.biomage.Interface.HasSourceBioMaterialMeasurements

addToSourceBioMaterialMeasurements

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

Specified by:
addToSourceBioMaterialMeasurements in interface org.biomage.Interface.HasSourceBioMaterialMeasurements

addToSourceBioMaterialMeasurements

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

Specified by:
addToSourceBioMaterialMeasurements in interface org.biomage.Interface.HasSourceBioMaterialMeasurements

getFromSourceBioMaterialMeasurements

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

Specified by:
getFromSourceBioMaterialMeasurements in interface org.biomage.Interface.HasSourceBioMaterialMeasurements

removeElementAtFromSourceBioMaterialMeasurements

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

Specified by:
removeElementAtFromSourceBioMaterialMeasurements in interface org.biomage.Interface.HasSourceBioMaterialMeasurements

removeFromSourceBioMaterialMeasurements

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

Specified by:
removeFromSourceBioMaterialMeasurements in interface org.biomage.Interface.HasSourceBioMaterialMeasurements

setActionMeasurement

public void setActionMeasurement(org.biomage.Measurement.Measurement actionMeasurement)
Set method for actionMeasurement

Specified by:
setActionMeasurement in interface org.biomage.Interface.HasActionMeasurement

getActionMeasurement

public org.biomage.Measurement.Measurement getActionMeasurement()
Get method for actionMeasurement

Specified by:
getActionMeasurement in interface org.biomage.Interface.HasActionMeasurement

setAction

public void setAction(org.biomage.Description.OntologyEntry action)
Set method for action

Specified by:
setAction in interface org.biomage.Interface.HasAction

getAction

public org.biomage.Description.OntologyEntry getAction()
Get method for action

Specified by:
getAction in interface org.biomage.Interface.HasAction