org.biomage.Protocol
Class Software

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

All Implemented Interfaces:

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

public class Software

extends Parameterizable

implements java.io.Serializable, HasSoftwareManufacturers, HasHardware, HasSoftwares, HasType

Software represents the software used. Examples of Software include: feature extraction software, clustering software, etc...

See Also:

Serialized Form

Nested Class Summary

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

HasSoftwareManufacturers.SoftwareManufacturers_list

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

HasSoftwares.Softwares_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 Hardware	hardware Associates Hardware and Software together.
protected HasSoftwareManufacturers.SoftwareManufacturers_list	softwareManufacturers Contact for information on the software.
protected HasSoftwares.Softwares_list	softwares Software packages this software uses, i.e.
protected OntologyEntry	type The type of a piece of Software.

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

Software()
Default constructor.

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

Method Summary

void	addToSoftwareManufacturers(Contact contact) Method to add Contact to SoftwareManufacturers_list
void	addToSoftwareManufacturers(int position, Contact contact) Method to add Contact at position to SoftwareManufacturers_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
Contact	getFromSoftwareManufacturers(int position) Method to get Contact from SoftwareManufacturers_list
Software	getFromSoftwares(int position) Method to get Software from Softwares_list
Hardware	getHardware() Get method for hardware
HasSoftwareManufacturers.SoftwareManufacturers_list	getSoftwareManufacturers() Get method for softwareManufacturers
HasSoftwares.Softwares_list	getSoftwares() Get method for softwares
OntologyEntry	getType() Get method for type
void	removeElementAtFromSoftwareManufacturers(int position) Method to remove by position from SoftwareManufacturers_list
void	removeElementAtFromSoftwares(int position) Method to remove by position from Softwares_list
void	removeFromSoftwareManufacturers(Contact contact) Method to remove first Contact from SoftwareManufacturers_list
void	removeFromSoftwares(Software software) Method to remove first Software from Softwares_list
void	setHardware(Hardware hardware) Set method for hardware
void	setSoftwareManufacturers(HasSoftwareManufacturers.SoftwareManufacturers_list softwareManufacturers) Set method for softwareManufacturers
void	setSoftwares(HasSoftwares.Softwares_list softwares) Set method for softwares
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 piece of Software. Examples include: feature extractor...

hardware

protected Hardware hardware

Associates Hardware and Software together.

softwares

protected HasSoftwares.Softwares_list softwares

Software packages this software uses, i.e. operating system, 3rd party software packages, etc.

softwareManufacturers

protected HasSoftwareManufacturers.SoftwareManufacturers_list softwareManufacturers

Contact for information on the software.

Constructor Detail

Software

public Software()

Default constructor.

Software

public Software(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

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

setHardware

public void setHardware(Hardware hardware)

Set method for hardware

Specified by:

setHardware in interface HasHardware

getHardware

public Hardware getHardware()

Get method for hardware

Specified by:

getHardware in interface HasHardware

Returns:

value of the attribute

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

setSoftwareManufacturers

public void setSoftwareManufacturers(HasSoftwareManufacturers.SoftwareManufacturers_list softwareManufacturers)

Set method for softwareManufacturers

Specified by:

setSoftwareManufacturers in interface HasSoftwareManufacturers

getSoftwareManufacturers

public HasSoftwareManufacturers.SoftwareManufacturers_list getSoftwareManufacturers()

Get method for softwareManufacturers

Specified by:

getSoftwareManufacturers in interface HasSoftwareManufacturers

Returns:

value of the attribute

addToSoftwareManufacturers

public void addToSoftwareManufacturers(Contact contact)

Method to add Contact to SoftwareManufacturers_list

Specified by:

addToSoftwareManufacturers in interface HasSoftwareManufacturers

addToSoftwareManufacturers

public void addToSoftwareManufacturers(int position,
                                       Contact contact)

Method to add Contact at position to SoftwareManufacturers_list

Specified by:

addToSoftwareManufacturers in interface HasSoftwareManufacturers

getFromSoftwareManufacturers

public Contact getFromSoftwareManufacturers(int position)

Method to get Contact from SoftwareManufacturers_list

Specified by:

getFromSoftwareManufacturers in interface HasSoftwareManufacturers

removeElementAtFromSoftwareManufacturers

public void removeElementAtFromSoftwareManufacturers(int position)

Method to remove by position from SoftwareManufacturers_list

Specified by:

removeElementAtFromSoftwareManufacturers in interface HasSoftwareManufacturers

removeFromSoftwareManufacturers

public void removeFromSoftwareManufacturers(Contact contact)

Method to remove first Contact from SoftwareManufacturers_list

Specified by:

removeFromSoftwareManufacturers in interface HasSoftwareManufacturers