org.biomage.Protocol
Class Parameter

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.Protocol.Parameter
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasDataType, HasDefaultValue, HasDescriptions, HasPropertySets, HasSecurity

public class Parameter
extends Identifiable
implements java.io.Serializable, HasDataType, HasDefaultValue

A Parameter is a replaceable value in a Parameterizable class. Examples of Parameters include: scanning wavelength, laser power, centrifuge speed, multiplicative errors, the number of input nodes to a SOM, and PCR temperatures.

See Also:
Serialized Form

Nested Class Summary
 
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 dataType
          The type of data generated by the parameter i.e.
protected  Measurement defaultValue
          Allows the optional specification of a default values and the unit for the Parameter
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
Parameter()
          Default constructor.
Parameter(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 boolean emptyMAGEobject()
           
 OntologyEntry getDataType()
          Get method for dataType
 Measurement getDefaultValue()
          Get method for defaultValue
 java.lang.String getModelClassName()
           
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setDataType(OntologyEntry dataType)
          Set method for dataType
 void setDefaultValue(Measurement defaultValue)
          Set method for defaultValue
 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.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

defaultValue

protected Measurement defaultValue
Allows the optional specification of a default values and the unit for the Parameter


dataType

protected OntologyEntry dataType
The type of data generated by the parameter i.e. Boolean, float, etc...

Constructor Detail

Parameter

public Parameter()
Default constructor.


Parameter

public Parameter(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 Identifiable

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 Identifiable
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 Identifiable
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 Identifiable
Throws:
java.io.IOException

getModelClassName

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

setDefaultValue

public void setDefaultValue(Measurement defaultValue)
Set method for defaultValue

Specified by:
setDefaultValue in interface HasDefaultValue
Parameters:
value - to set

getDefaultValue

public Measurement getDefaultValue()
Get method for defaultValue

Specified by:
getDefaultValue in interface HasDefaultValue
Returns:
value of the attribute

setDataType

public void setDataType(OntologyEntry dataType)
Set method for dataType

Specified by:
setDataType in interface HasDataType
Parameters:
value - to set

getDataType

public OntologyEntry getDataType()
Get method for dataType

Specified by:
getDataType in interface HasDataType
Returns:
value of the attribute