org.biomage.Protocol
Class Protocol

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.Parameterizable
                  extended by org.biomage.Protocol.Protocol
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasDescriptions, HasHardwares, HasParameterTypes, HasPropertySets, HasSecurity, HasSoftwares, HasType

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/interfaces inherited from interface org.biomage.Interface.HasSoftwares
HasSoftwares.Softwares_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasHardwares
HasHardwares.Hardwares_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasParameterTypes
HasParameterTypes.ParameterTypes_list
 
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  java.util.List hardwares
          Hardware used by this protocol.
protected  java.util.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
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
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
 boolean emptyMAGEobject()
           
 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
 java.lang.String getModelClassName()
           
 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 setAttributes(org.xml.sax.Attributes atts)
           
 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, 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

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 java.util.List hardwares
Hardware used by this protocol.


softwares

protected java.util.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

Parameters:
atts: - the attribute list.
Method Detail

setAttributes

public void setAttributes(org.xml.sax.Attributes atts)
Overrides:
setAttributes in class Parameterizable

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
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 Parameterizable
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 Parameterizable
Throws:
java.io.IOException

setText

public void setText(java.lang.String text)
Set method for text

Parameters:
value - to set

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

Parameters:
value - to set

getTitle

public java.lang.String getTitle()
Get method for title

Returns:
value of the attribute

getModelClassName

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

setType

public void setType(OntologyEntry type)
Set method for type

Specified by:
setType in interface HasType
Parameters:
value - to set

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
Parameters:
value - to set

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
Parameters:
value - to set

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