org.biomage.Protocol
Class ProtocolApplication

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Common.Describable
          extended by org.biomage.Protocol.ParameterizableApplication
              extended by org.biomage.Protocol.ProtocolApplication
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasDescriptions, HasHardwareApplications, HasParameterValues, HasPerformers, HasPropertySets, HasProtocol, HasSecurity, HasSoftwareApplications

public class ProtocolApplication
extends ParameterizableApplication
implements java.io.Serializable, HasPerformers, HasProtocol, HasSoftwareApplications, HasHardwareApplications

The use of a protocol with the requisite Parameters and ParameterValues.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPerformers
HasPerformers.Performers_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasSoftwareApplications
HasSoftwareApplications.SoftwareApplications_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasHardwareApplications
HasHardwareApplications.HardwareApplications_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasParameterValues
HasParameterValues.ParameterValues_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 hardwareApplications
          The use of hardware for the application of the protocol.
protected  java.util.List performers
          The people who performed the protocol.
protected  Protocol protocol
          The protocol that is being used.
protected  java.util.List softwareApplications
          The use of software for the application of the protocol.
 
Fields inherited from class org.biomage.Protocol.ParameterizableApplication
parameterValues
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
ProtocolApplication()
          Default constructor.
ProtocolApplication(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToHardwareApplications(HardwareApplication hardwareApplication)
          Method to add HardwareApplication to HardwareApplications_list
 void addToHardwareApplications(int position, HardwareApplication hardwareApplication)
          Method to add HardwareApplication at position to HardwareApplications_list
 void addToPerformers(int position, Person person)
          Method to add Person at position to Performers_list
 void addToPerformers(Person person)
          Method to add Person to Performers_list
 void addToSoftwareApplications(int position, SoftwareApplication softwareApplication)
          Method to add SoftwareApplication at position to SoftwareApplications_list
 void addToSoftwareApplications(SoftwareApplication softwareApplication)
          Method to add SoftwareApplication to SoftwareApplications_list
 boolean emptyMAGEobject()
           
 java.util.Date getActivityDate()
          Get method for activityDate
 HardwareApplication getFromHardwareApplications(int position)
          Method to get HardwareApplication from HardwareApplications_list
 Person getFromPerformers(int position)
          Method to get Person from Performers_list
 SoftwareApplication getFromSoftwareApplications(int position)
          Method to get SoftwareApplication from SoftwareApplications_list
 HasHardwareApplications.HardwareApplications_list getHardwareApplications()
          Get method for hardwareApplications
 java.lang.String getModelClassName()
           
 HasPerformers.Performers_list getPerformers()
          Get method for performers
 Protocol getProtocol()
          Get method for protocol
 HasSoftwareApplications.SoftwareApplications_list getSoftwareApplications()
          Get method for softwareApplications
 void removeElementAtFromHardwareApplications(int position)
          Method to remove by position from HardwareApplications_list
 void removeElementAtFromPerformers(int position)
          Method to remove by position from Performers_list
 void removeElementAtFromSoftwareApplications(int position)
          Method to remove by position from SoftwareApplications_list
 void removeFromHardwareApplications(HardwareApplication hardwareApplication)
          Method to remove first HardwareApplication from HardwareApplications_list
 void removeFromPerformers(Person person)
          Method to remove first Person from Performers_list
 void removeFromSoftwareApplications(SoftwareApplication softwareApplication)
          Method to remove first SoftwareApplication from SoftwareApplications_list
 void setActivityDate(java.util.Date activityDate)
          Set method for activityDate
 void setHardwareApplications(HasHardwareApplications.HardwareApplications_list hardwareApplications)
          Set method for hardwareApplications
 void setPerformers(HasPerformers.Performers_list performers)
          Set method for performers
 void setProtocol(Protocol protocol)
          Set method for protocol
 void setSoftwareApplications(HasSoftwareApplications.SoftwareApplications_list softwareApplications)
          Set method for softwareApplications
 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.ParameterizableApplication
addToParameterValues, addToParameterValues, getFromParameterValues, getParameterValues, removeElementAtFromParameterValues, removeFromParameterValues, setParameterValues
 
Methods inherited from class org.biomage.Common.Describable
addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAttributes, 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, toString
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

hardwareApplications

protected java.util.List hardwareApplications
The use of hardware for the application of the protocol.


softwareApplications

protected java.util.List softwareApplications
The use of software for the application of the protocol.


performers

protected java.util.List performers
The people who performed the protocol.


protocol

protected Protocol protocol
The protocol that is being used.

Constructor Detail

ProtocolApplication

public ProtocolApplication()
Default constructor.


ProtocolApplication

public ProtocolApplication(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

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 ParameterizableApplication
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 ParameterizableApplication
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 ParameterizableApplication
Throws:
java.io.IOException

setActivityDate

public void setActivityDate(java.util.Date activityDate)
Set method for activityDate

Parameters:
value - to set

getActivityDate

public java.util.Date getActivityDate()
Get method for activityDate

Returns:
value of the attribute

getModelClassName

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

setHardwareApplications

public void setHardwareApplications(HasHardwareApplications.HardwareApplications_list hardwareApplications)
Set method for hardwareApplications

Specified by:
setHardwareApplications in interface HasHardwareApplications
Parameters:
value - to set

getHardwareApplications

public HasHardwareApplications.HardwareApplications_list getHardwareApplications()
Get method for hardwareApplications

Specified by:
getHardwareApplications in interface HasHardwareApplications
Returns:
value of the attribute

addToHardwareApplications

public void addToHardwareApplications(HardwareApplication hardwareApplication)
Method to add HardwareApplication to HardwareApplications_list

Specified by:
addToHardwareApplications in interface HasHardwareApplications

addToHardwareApplications

public void addToHardwareApplications(int position,
                                      HardwareApplication hardwareApplication)
Method to add HardwareApplication at position to HardwareApplications_list

Specified by:
addToHardwareApplications in interface HasHardwareApplications

getFromHardwareApplications

public HardwareApplication getFromHardwareApplications(int position)
Method to get HardwareApplication from HardwareApplications_list

Specified by:
getFromHardwareApplications in interface HasHardwareApplications

removeElementAtFromHardwareApplications

public void removeElementAtFromHardwareApplications(int position)
Method to remove by position from HardwareApplications_list

Specified by:
removeElementAtFromHardwareApplications in interface HasHardwareApplications

removeFromHardwareApplications

public void removeFromHardwareApplications(HardwareApplication hardwareApplication)
Method to remove first HardwareApplication from HardwareApplications_list

Specified by:
removeFromHardwareApplications in interface HasHardwareApplications

setSoftwareApplications

public void setSoftwareApplications(HasSoftwareApplications.SoftwareApplications_list softwareApplications)
Set method for softwareApplications

Specified by:
setSoftwareApplications in interface HasSoftwareApplications
Parameters:
value - to set

getSoftwareApplications

public HasSoftwareApplications.SoftwareApplications_list getSoftwareApplications()
Get method for softwareApplications

Specified by:
getSoftwareApplications in interface HasSoftwareApplications
Returns:
value of the attribute

addToSoftwareApplications

public void addToSoftwareApplications(SoftwareApplication softwareApplication)
Method to add SoftwareApplication to SoftwareApplications_list

Specified by:
addToSoftwareApplications in interface HasSoftwareApplications

addToSoftwareApplications

public void addToSoftwareApplications(int position,
                                      SoftwareApplication softwareApplication)
Method to add SoftwareApplication at position to SoftwareApplications_list

Specified by:
addToSoftwareApplications in interface HasSoftwareApplications

getFromSoftwareApplications

public SoftwareApplication getFromSoftwareApplications(int position)
Method to get SoftwareApplication from SoftwareApplications_list

Specified by:
getFromSoftwareApplications in interface HasSoftwareApplications

removeElementAtFromSoftwareApplications

public void removeElementAtFromSoftwareApplications(int position)
Method to remove by position from SoftwareApplications_list

Specified by:
removeElementAtFromSoftwareApplications in interface HasSoftwareApplications

removeFromSoftwareApplications

public void removeFromSoftwareApplications(SoftwareApplication softwareApplication)
Method to remove first SoftwareApplication from SoftwareApplications_list

Specified by:
removeFromSoftwareApplications in interface HasSoftwareApplications

setPerformers

public void setPerformers(HasPerformers.Performers_list performers)
Set method for performers

Specified by:
setPerformers in interface HasPerformers
Parameters:
value - to set

getPerformers

public HasPerformers.Performers_list getPerformers()
Get method for performers

Specified by:
getPerformers in interface HasPerformers
Returns:
value of the attribute

addToPerformers

public void addToPerformers(Person person)
Method to add Person to Performers_list

Specified by:
addToPerformers in interface HasPerformers

addToPerformers

public void addToPerformers(int position,
                            Person person)
Method to add Person at position to Performers_list

Specified by:
addToPerformers in interface HasPerformers

getFromPerformers

public Person getFromPerformers(int position)
Method to get Person from Performers_list

Specified by:
getFromPerformers in interface HasPerformers

removeElementAtFromPerformers

public void removeElementAtFromPerformers(int position)
Method to remove by position from Performers_list

Specified by:
removeElementAtFromPerformers in interface HasPerformers

removeFromPerformers

public void removeFromPerformers(Person person)
Method to remove first Person from Performers_list

Specified by:
removeFromPerformers in interface HasPerformers

setProtocol

public void setProtocol(Protocol protocol)
Set method for protocol

Specified by:
setProtocol in interface HasProtocol
Parameters:
value - to set

getProtocol

public Protocol getProtocol()
Get method for protocol

Specified by:
getProtocol in interface HasProtocol
Returns:
value of the attribute