org.biomage.Protocol
Class ProtocolApplication

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Protocol.ParameterizableApplication
                    |
                    +--org.biomage.Protocol.ProtocolApplication

All Implemented Interfaces:

HasAuditTrail, HasDescriptions, HasHardwareApplications, HasParameterValues, HasPerformers, HasPropertySets, HasProtocol, HasSecurity, HasSoftwareApplications, java.io.Serializable

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 inherited from class org.biomage.Interface.HasPerformers

HasPerformers.Performers_list

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

HasSoftwareApplications.SoftwareApplications_list

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

HasHardwareApplications.HardwareApplications_list

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

HasParameterValues.ParameterValues_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 HasHardwareApplications.HardwareApplications_list	hardwareApplications The use of hardware for the application of the protocol.
protected HasPerformers.Performers_list	performers The people who performed the protocol.
protected Protocol	protocol The protocol that is being used.
protected HasSoftwareApplications.SoftwareApplications_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

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

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
java.lang.String	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
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.lang.String 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, 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

hardwareApplications

protected HasHardwareApplications.HardwareApplications_list hardwareApplications

The use of hardware for the application of the protocol.

softwareApplications

protected HasSoftwareApplications.SoftwareApplications_list softwareApplications

The use of software for the application of the protocol.

performers

protected HasPerformers.Performers_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

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

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 ParameterizableApplication

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

java.io.IOException

setActivityDate

public void setActivityDate(java.lang.String activityDate)

Set method for activityDate

getActivityDate

public java.lang.String getActivityDate()

Get method for activityDate

Returns:

value of the attribute

setHardwareApplications

public void setHardwareApplications(HasHardwareApplications.HardwareApplications_list hardwareApplications)

Set method for hardwareApplications

Specified by:

setHardwareApplications in interface HasHardwareApplications

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

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

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

getProtocol

public Protocol getProtocol()

Get method for protocol

Specified by:

getProtocol in interface HasProtocol

Returns:

value of the attribute