org.biomage.Protocol
Class Parameterizable

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.Protocol.Parameterizable

All Implemented Interfaces:

HasAuditTrail, HasDescriptions, HasParameterTypes, HasPropertySets, HasSecurity, java.io.Serializable

Direct Known Subclasses:

Hardware, Protocol, Software

public abstract class Parameterizable

extends Identifiable

implements java.io.Serializable, HasParameterTypes

The Parameterizable interface encapsulates the association of Parameters with ParameterValues.

See Also:

Serialized Form

Nested Class Summary

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

HasParameterTypes.ParameterTypes_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 HasParameterTypes.ParameterTypes_list

parameterTypes The description of the parameters for the Parameterizable class instance.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

Parameterizable()
Default constructor.

Parameterizable(org.xml.sax.Attributes atts)
Attribute constructor.

Method Summary

void	addToParameterTypes(int position, Parameter parameter) Method to add Parameter at position to ParameterTypes_list
void	addToParameterTypes(Parameter parameter) Method to add Parameter to ParameterTypes_list
Parameter	getFromParameterTypes(int position) Method to get Parameter from ParameterTypes_list
HasParameterTypes.ParameterTypes_list	getParameterTypes() Get method for parameterTypes
java.lang.String	getURI() Get method for URI
void	removeElementAtFromParameterTypes(int position) Method to remove by position from ParameterTypes_list
void	removeFromParameterTypes(Parameter parameter) Method to remove first Parameter from ParameterTypes_list
void	setParameterTypes(HasParameterTypes.ParameterTypes_list parameterTypes) Set method for parameterTypes
void	setURI(java.lang.String URI) Set method for URI
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

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

parameterTypes

protected HasParameterTypes.ParameterTypes_list parameterTypes

The description of the parameters for the Parameterizable class instance.

Constructor Detail

Parameterizable

public Parameterizable()

Default constructor.

Parameterizable

public Parameterizable(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 Identifiable

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 Identifiable

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

java.io.IOException

setURI

public void setURI(java.lang.String URI)

Set method for URI

getURI

public java.lang.String getURI()

Get method for URI

Returns:

value of the attribute

setParameterTypes

public void setParameterTypes(HasParameterTypes.ParameterTypes_list parameterTypes)

Set method for parameterTypes

Specified by:

setParameterTypes in interface HasParameterTypes

getParameterTypes

public HasParameterTypes.ParameterTypes_list getParameterTypes()

Get method for parameterTypes

Specified by:

getParameterTypes in interface HasParameterTypes

Returns:

value of the attribute

addToParameterTypes

public void addToParameterTypes(Parameter parameter)

Method to add Parameter to ParameterTypes_list

Specified by:

addToParameterTypes in interface HasParameterTypes

addToParameterTypes

public void addToParameterTypes(int position,
                                Parameter parameter)

Method to add Parameter at position to ParameterTypes_list

Specified by:

addToParameterTypes in interface HasParameterTypes

getFromParameterTypes

public Parameter getFromParameterTypes(int position)

Method to get Parameter from ParameterTypes_list

Specified by:

getFromParameterTypes in interface HasParameterTypes

removeElementAtFromParameterTypes

public void removeElementAtFromParameterTypes(int position)

Method to remove by position from ParameterTypes_list

Specified by:

removeElementAtFromParameterTypes in interface HasParameterTypes

removeFromParameterTypes

public void removeFromParameterTypes(Parameter parameter)

Method to remove first Parameter from ParameterTypes_list

Specified by:

removeFromParameterTypes in interface HasParameterTypes