org.biomage.BioMaterial
Class Treatment

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.BioEvent.BioEvent
                          |
                          +--org.biomage.BioMaterial.Treatment

All Implemented Interfaces:

HasAction, HasActionMeasurement, HasAuditTrail, HasCompoundMeasurements, HasDescriptions, HasPropertySets, HasProtocolApplications, HasSecurity, HasSourceBioMaterialMeasurements, java.io.Serializable

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 inherited from class org.biomage.Interface.HasCompoundMeasurements

HasCompoundMeasurements.CompoundMeasurements_list

Nested classes inherited from class org.biomage.Interface.HasSourceBioMaterialMeasurements

HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list

Nested classes inherited from class org.biomage.Interface.HasProtocolApplications

HasProtocolApplications.ProtocolApplications_list

Nested classes inherited from class org.biomage.Interface.HasAuditTrail

HasAuditTrail.AuditTrail_list

Nested classes inherited from class org.biomage.Interface.HasDescriptions

HasDescriptions.Descriptions_list

Nested classes inherited from class 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 HasCompoundMeasurements.CompoundMeasurements_list	compoundMeasurements The compounds and their amounts used in the treatment.
protected HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list	sourceBioMaterialMeasurements The BioMaterials and the amounts used in the treatment

Fields inherited from class org.biomage.BioEvent.BioEvent

protocolApplications

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

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
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
int	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	setCompoundMeasurements(HasCompoundMeasurements.CompoundMeasurements_list compoundMeasurements) Set method for compoundMeasurements
void	setOrder(int 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

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

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 HasCompoundMeasurements.CompoundMeasurements_list compoundMeasurements

The compounds and their amounts used in the treatment.

sourceBioMaterialMeasurements

protected HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_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

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 BioEvent

java.io.IOException

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

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

java.io.IOException

setOrder

public void setOrder(int order)

Set method for order

getOrder

public int getOrder()

Get method for order

Returns:

value of the attribute

setAction

public void setAction(OntologyEntry action)

Set method for action

Specified by:

setAction in interface HasAction

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

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

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

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