org.biomage.Protocol
Class Software

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.Software
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasDescriptions, HasHardware, HasParameterTypes, HasPropertySets, HasSecurity, HasSoftwareManufacturers, HasSoftwares, HasType

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/interfaces inherited from interface org.biomage.Interface.HasSoftwareManufacturers
HasSoftwareManufacturers.SoftwareManufacturers_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasSoftwares
HasSoftwares.Softwares_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  Hardware hardware
          Associates Hardware and Software together.
protected  java.util.List softwareManufacturers
          Contact for information on the software.
protected  java.util.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
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
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
 boolean emptyMAGEobject()
           
 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
 java.lang.String getModelClassName()
           
 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 setAttributes(org.xml.sax.Attributes atts)
           
 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, 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 piece of Software. Examples include: feature extractor...


hardware

protected Hardware hardware
Associates Hardware and Software together.


softwares

protected java.util.List softwares
Software packages this software uses, i.e. operating system, 3rd party software packages, etc.


softwareManufacturers

protected java.util.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

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

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

setHardware

public void setHardware(Hardware hardware)
Set method for hardware

Specified by:
setHardware in interface HasHardware
Parameters:
value - to set

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
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

setSoftwareManufacturers

public void setSoftwareManufacturers(HasSoftwareManufacturers.SoftwareManufacturers_list softwareManufacturers)
Set method for softwareManufacturers

Specified by:
setSoftwareManufacturers in interface HasSoftwareManufacturers
Parameters:
value - to set

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