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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:

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

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public class Protocol

extends Parameterizable

implements java.io.Serializable, org.biomage.Interface.HasSoftwares, org.biomage.Interface.HasHardwares, org.biomage.Interface.HasType

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

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Nested Class Summary

 

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

org.biomage.Interface.HasSoftwares.Softwares_list

 

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

org.biomage.Interface.HasHardwares.Hardwares_list

 

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

org.biomage.Interface.HasParameterTypes.ParameterTypes_list

 

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

org.biomage.Interface.HasAuditTrail.AuditTrail_list

 

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

org.biomage.Interface.HasDescriptions.Descriptions_list

 

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

org.biomage.Interface.HasPropertySets.PropertySets_list

 

Field Summary
private  org.biomage.Interface.HasHardwares.Hardwares_list	hardwares           Hardware used by this protocol.
private  org.biomage.Interface.HasSoftwares.Softwares_list	softwares           Software used by this Protocol.
(package private)  java.lang.String	text           The text description of the Protocol.
(package private)  java.lang.String	title           The title of the Protocol
private  org.biomage.Description.OntologyEntry	type           The type of a Protocol, a user should provide/use a recommended vocabulary.

 

Fields inherited from class org.biomage.Protocol.Parameterizable

URI

 

Fields inherited from class org.biomage.Common.Identifiable

 

Fields inherited from class org.biomage.Common.Describable

 

Fields inherited from class org.biomage.Common.Extendable

 

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
org.biomage.Interface.HasHardwares.Hardwares_list	getHardwares()           Get method for hardwares
org.biomage.Interface.HasSoftwares.Softwares_list	getSoftwares()           Get method for softwares
java.lang.String	getText()           Get method for text
java.lang.String	getTitle()           Get method for title
org.biomage.Description.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(org.biomage.Interface.HasHardwares.Hardwares_list hardwares)           Set method for hardwares
void	setSoftwares(org.biomage.Interface.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(org.biomage.Description.OntologyEntry type)           Set method for type
void	writeAssociations(java.io.Writer out)           writeAssociations
void	writeAttributes(java.io.Writer out)           writeAttributes
void	writeMAGEML(java.io.Writer out)           writeMAGEML

 

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

text

java.lang.String text

The text description of the Protocol.

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title

java.lang.String title

The title of the Protocol

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softwares

private org.biomage.Interface.HasSoftwares.Softwares_list softwares

Software used by this Protocol.

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hardwares

private org.biomage.Interface.HasHardwares.Hardwares_list hardwares

Hardware used by this protocol.

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type

private org.biomage.Description.OntologyEntry type

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

Constructor Detail

Protocol

public Protocol()

Default constructor.

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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

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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

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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

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setText

public void setText(java.lang.String text)

Set method for text

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getText

public java.lang.String getText()

Get method for text

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setTitle

public void setTitle(java.lang.String title)

Set method for title

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getTitle

public java.lang.String getTitle()

Get method for title

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setSoftwares

public void setSoftwares(org.biomage.Interface.HasSoftwares.Softwares_list softwares)

Set method for softwares

Specified by:

setSoftwares in interface org.biomage.Interface.HasSoftwares

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getSoftwares

public org.biomage.Interface.HasSoftwares.Softwares_list getSoftwares()

Get method for softwares

Specified by:

getSoftwares in interface org.biomage.Interface.HasSoftwares

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addToSoftwares

public void addToSoftwares(Software software)

Method to add Software to Softwares_list

Specified by:

addToSoftwares in interface org.biomage.Interface.HasSoftwares

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addToSoftwares

public void addToSoftwares(int position,
                           Software software)

Method to add Software at position to Softwares_list

Specified by:

addToSoftwares in interface org.biomage.Interface.HasSoftwares

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getFromSoftwares

public Software getFromSoftwares(int position)

Method to get Software from Softwares_list

Specified by:

getFromSoftwares in interface org.biomage.Interface.HasSoftwares

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removeElementAtFromSoftwares

public void removeElementAtFromSoftwares(int position)

Method to remove by position from Softwares_list

Specified by:

removeElementAtFromSoftwares in interface org.biomage.Interface.HasSoftwares

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removeFromSoftwares

public void removeFromSoftwares(Software software)

Method to remove first Software from Softwares_list

Specified by:

removeFromSoftwares in interface org.biomage.Interface.HasSoftwares

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setHardwares

public void setHardwares(org.biomage.Interface.HasHardwares.Hardwares_list hardwares)

Set method for hardwares

Specified by:

setHardwares in interface org.biomage.Interface.HasHardwares

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getHardwares

public org.biomage.Interface.HasHardwares.Hardwares_list getHardwares()

Get method for hardwares

Specified by:

getHardwares in interface org.biomage.Interface.HasHardwares

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addToHardwares

public void addToHardwares(Hardware hardware)

Method to add Hardware to Hardwares_list

Specified by:

addToHardwares in interface org.biomage.Interface.HasHardwares

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addToHardwares

public void addToHardwares(int position,
                           Hardware hardware)

Method to add Hardware at position to Hardwares_list

Specified by:

addToHardwares in interface org.biomage.Interface.HasHardwares

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getFromHardwares

public Hardware getFromHardwares(int position)

Method to get Hardware from Hardwares_list

Specified by:

getFromHardwares in interface org.biomage.Interface.HasHardwares

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removeElementAtFromHardwares

public void removeElementAtFromHardwares(int position)

Method to remove by position from Hardwares_list

Specified by:

removeElementAtFromHardwares in interface org.biomage.Interface.HasHardwares

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removeFromHardwares

public void removeFromHardwares(Hardware hardware)

Method to remove first Hardware from Hardwares_list

Specified by:

removeFromHardwares in interface org.biomage.Interface.HasHardwares

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setType

public void setType(org.biomage.Description.OntologyEntry type)

Set method for type

Specified by:

setType in interface org.biomage.Interface.HasType

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getType

public org.biomage.Description.OntologyEntry getType()

Get method for type

Specified by:

getType in interface org.biomage.Interface.HasType

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ Protocol overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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