org.biomage.Protocol
Class Protocol

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

All Implemented Interfaces:

HasAuditTrail, HasDescriptions, HasHardwares, HasParameterTypes, HasPropertySets, HasSecurity, HasSoftwares, HasType, java.io.Serializable

public class Protocol

extends Parameterizable

implements java.io.Serializable, HasSoftwares, HasHardwares, HasType

A Protocol is a parameterizable description of a method. ProtocolApplication is used to specify the ParameterValues of it's Protocol's Parameters.

See Also:

Serialized Form

Nested Class Summary

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

HasSoftwares.Softwares_list

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

HasHardwares.Hardwares_list

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 HasHardwares.Hardwares_list	hardwares Hardware used by this protocol.
protected HasSoftwares.Softwares_list	softwares Software used by this Protocol.
protected OntologyEntry	type The type of a Protocol, a user should provide/use a recommended vocabulary.

Fields inherited from class org.biomage.Protocol.Parameterizable

parameterTypes

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

Protocol()
Default constructor.

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

Method Summary

void	addToHardwares(Hardware hardware) Method to add Hardware to Hardwares_list
void	addToHardwares(int position, Hardware hardware) Method to add Hardware at position to Hardwares_list
void	addToSoftwares(int position, Software software) Method to add Software at position to Softwares_list
void	addToSoftwares(Software software) Method to add Software to Softwares_list
Hardware	getFromHardwares(int position) Method to get Hardware from Hardwares_list
Software	getFromSoftwares(int position) Method to get Software from Softwares_list
HasHardwares.Hardwares_list	getHardwares() Get method for hardwares
HasSoftwares.Softwares_list	getSoftwares() Get method for softwares
java.lang.String	getText() Get method for text
java.lang.String	getTitle() Get method for title
OntologyEntry	getType() Get method for type
void	removeElementAtFromHardwares(int position) Method to remove by position from Hardwares_list
void	removeElementAtFromSoftwares(int position) Method to remove by position from Softwares_list
void	removeFromHardwares(Hardware hardware) Method to remove first Hardware from Hardwares_list
void	removeFromSoftwares(Software software) Method to remove first Software from Softwares_list
void	setHardwares(HasHardwares.Hardwares_list hardwares) Set method for hardwares
void	setSoftwares(HasSoftwares.Softwares_list softwares) Set method for softwares
void	setText(java.lang.String text) Set method for text
void	setTitle(java.lang.String title) Set method for title
void	setType(OntologyEntry type) Set method for type
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.Protocol.Parameterizable

addToParameterTypes, addToParameterTypes, getFromParameterTypes, getParameterTypes, getURI, removeElementAtFromParameterTypes, removeFromParameterTypes, setParameterTypes, setURI

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

type

protected OntologyEntry type

The type of a Protocol, a user should provide/use a recommended vocabulary. Examples of types include: RNA extraction, array washing, etc...

hardwares

protected HasHardwares.Hardwares_list hardwares

Hardware used by this protocol.

softwares

protected HasSoftwares.Softwares_list softwares

Software used by this Protocol.

Constructor Detail

Protocol

public Protocol()

Default constructor.

Protocol

public Protocol(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 Parameterizable

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 Parameterizable

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 Parameterizable

java.io.IOException

setText

public void setText(java.lang.String text)

Set method for text

getText

public java.lang.String getText()

Get method for text

Returns:

value of the attribute

setTitle

public void setTitle(java.lang.String title)

Set method for title

getTitle

public java.lang.String getTitle()

Get method for title

Returns:

value of the attribute

setType

public void setType(OntologyEntry type)

Set method for type

Specified by:

setType in interface HasType

getType

public OntologyEntry getType()

Get method for type

Specified by:

getType in interface HasType

Returns:

value of the attribute

setHardwares

public void setHardwares(HasHardwares.Hardwares_list hardwares)

Set method for hardwares

Specified by:

setHardwares in interface HasHardwares

getHardwares

public HasHardwares.Hardwares_list getHardwares()

Get method for hardwares

Specified by:

getHardwares in interface HasHardwares

Returns:

value of the attribute

addToHardwares

public void addToHardwares(Hardware hardware)

Method to add Hardware to Hardwares_list

Specified by:

addToHardwares in interface HasHardwares

addToHardwares

public void addToHardwares(int position,
                           Hardware hardware)

Method to add Hardware at position to Hardwares_list

Specified by:

addToHardwares in interface HasHardwares

getFromHardwares

public Hardware getFromHardwares(int position)

Method to get Hardware from Hardwares_list

Specified by:

getFromHardwares in interface HasHardwares

removeElementAtFromHardwares

public void removeElementAtFromHardwares(int position)

Method to remove by position from Hardwares_list

Specified by:

removeElementAtFromHardwares in interface HasHardwares

removeFromHardwares

public void removeFromHardwares(Hardware hardware)

Method to remove first Hardware from Hardwares_list

Specified by:

removeFromHardwares in interface HasHardwares

setSoftwares

public void setSoftwares(HasSoftwares.Softwares_list softwares)

Set method for softwares

Specified by:

setSoftwares in interface HasSoftwares

getSoftwares

public HasSoftwares.Softwares_list getSoftwares()

Get method for softwares

Specified by:

getSoftwares in interface HasSoftwares

Returns:

value of the attribute

addToSoftwares

public void addToSoftwares(Software software)

Method to add Software to Softwares_list

Specified by:

addToSoftwares in interface HasSoftwares

addToSoftwares

public void addToSoftwares(int position,
                           Software software)

Method to add Software at position to Softwares_list

Specified by:

addToSoftwares in interface HasSoftwares

getFromSoftwares

public Software getFromSoftwares(int position)

Method to get Software from Softwares_list

Specified by:

getFromSoftwares in interface HasSoftwares

removeElementAtFromSoftwares

public void removeElementAtFromSoftwares(int position)

Method to remove by position from Softwares_list

Specified by:

removeElementAtFromSoftwares in interface HasSoftwares

removeFromSoftwares

public void removeFromSoftwares(Software software)

Method to remove first Software from Softwares_list

Specified by:

removeFromSoftwares in interface HasSoftwares