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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.BioEvent.BioEvent
org.biomage.BioMaterial.Treatment
public class Treatment
The process by which a biomaterial is created (from source biomaterials). Treatments have an order and an action.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasCompoundMeasurements |
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HasCompoundMeasurements.CompoundMeasurements_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasSourceBioMaterialMeasurements |
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HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasProtocolApplications |
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HasProtocolApplications.ProtocolApplications_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail |
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HasAuditTrail.AuditTrail_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions |
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HasDescriptions.Descriptions_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets |
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HasPropertySets.PropertySets_list |
Field Summary | |
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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 |
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security |
Fields inherited from class org.biomage.Common.Extendable |
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editable, id, securedElementId |
Constructor Summary | |
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Treatment()
Default constructor. |
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Treatment(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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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()
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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()
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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 |
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addToProtocolApplications, addToProtocolApplications, getFromProtocolApplications, getProtocolApplications, removeElementAtFromProtocolApplications, removeFromProtocolApplications, setProtocolApplications |
Methods inherited from class org.biomage.Common.Identifiable |
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getIdentifier, getName, setIdentifier, setName, toString |
Methods inherited from class org.biomage.Common.Describable |
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addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAuditTrail, setDescriptions, setSecurity |
Methods inherited from class org.biomage.Common.Extendable |
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addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId |
Methods inherited from class java.lang.Object |
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clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected OntologyEntry action
protected Measurement actionMeasurement
protected java.util.List compoundMeasurements
protected java.util.List sourceBioMaterialMeasurements
Constructor Detail |
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public Treatment()
public Treatment(org.xml.sax.Attributes atts)
atts:
- the attribute list.Method Detail |
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public void setAttributes(org.xml.sax.Attributes atts)
setAttributes
in class BioEvent
public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class BioEvent
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class BioEvent
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class BioEvent
java.io.IOException
public void setOrder(java.lang.Integer order)
value
- to setpublic java.lang.Integer getOrder()
public java.lang.String getModelClassName()
getModelClassName
in class BioEvent
public void setAction(OntologyEntry action)
setAction
in interface HasAction
value
- to setpublic OntologyEntry getAction()
getAction
in interface HasAction
public void setActionMeasurement(Measurement actionMeasurement)
setActionMeasurement
in interface HasActionMeasurement
value
- to setpublic Measurement getActionMeasurement()
getActionMeasurement
in interface HasActionMeasurement
public void setCompoundMeasurements(HasCompoundMeasurements.CompoundMeasurements_list compoundMeasurements)
setCompoundMeasurements
in interface HasCompoundMeasurements
value
- to setpublic HasCompoundMeasurements.CompoundMeasurements_list getCompoundMeasurements()
getCompoundMeasurements
in interface HasCompoundMeasurements
public void addToCompoundMeasurements(CompoundMeasurement compoundMeasurement)
addToCompoundMeasurements
in interface HasCompoundMeasurements
public void addToCompoundMeasurements(int position, CompoundMeasurement compoundMeasurement)
addToCompoundMeasurements
in interface HasCompoundMeasurements
public CompoundMeasurement getFromCompoundMeasurements(int position)
getFromCompoundMeasurements
in interface HasCompoundMeasurements
public void removeElementAtFromCompoundMeasurements(int position)
removeElementAtFromCompoundMeasurements
in interface HasCompoundMeasurements
public void removeFromCompoundMeasurements(CompoundMeasurement compoundMeasurement)
removeFromCompoundMeasurements
in interface HasCompoundMeasurements
public void setSourceBioMaterialMeasurements(HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list sourceBioMaterialMeasurements)
setSourceBioMaterialMeasurements
in interface HasSourceBioMaterialMeasurements
value
- to setpublic HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list getSourceBioMaterialMeasurements()
getSourceBioMaterialMeasurements
in interface HasSourceBioMaterialMeasurements
public void addToSourceBioMaterialMeasurements(BioMaterialMeasurement bioMaterialMeasurement)
addToSourceBioMaterialMeasurements
in interface HasSourceBioMaterialMeasurements
public void addToSourceBioMaterialMeasurements(int position, BioMaterialMeasurement bioMaterialMeasurement)
addToSourceBioMaterialMeasurements
in interface HasSourceBioMaterialMeasurements
public BioMaterialMeasurement getFromSourceBioMaterialMeasurements(int position)
getFromSourceBioMaterialMeasurements
in interface HasSourceBioMaterialMeasurements
public void removeElementAtFromSourceBioMaterialMeasurements(int position)
removeElementAtFromSourceBioMaterialMeasurements
in interface HasSourceBioMaterialMeasurements
public void removeFromSourceBioMaterialMeasurements(BioMaterialMeasurement bioMaterialMeasurement)
removeFromSourceBioMaterialMeasurements
in interface HasSourceBioMaterialMeasurements
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