org.biomage.BioAssayData
Class QuantitationTypeMap

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.BioEvent.BioEvent
                          |
                          +--org.biomage.BioEvent.Map
                                |
                                +--org.biomage.BioAssayData.QuantitationTypeMap

All Implemented Interfaces:

HasAuditTrail, HasDescriptions, HasPropertySets, HasProtocolApplications, HasSecurity, HasSourcesQuantitationType, HasTargetQuantitationType, java.io.Serializable

public class QuantitationTypeMap

extends Map

implements java.io.Serializable, HasTargetQuantitationType, HasSourcesQuantitationType

A QuantitationTypeMap is the description of how source QuantitationTypes are mathematically transformed into a target QuantitationType.

See Also:

Serialized Form

Nested Class Summary

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

HasSourcesQuantitationType.SourcesQuantitationType_list

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

HasProtocolApplications.ProtocolApplications_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 HasSourcesQuantitationType.SourcesQuantitationType_list	sourcesQuantitationType The QuantitationType sources for values for the transformation.
protected QuantitationType	targetQuantitationType The QuantitationType whose value will be produced from the values of the source QuantitationType according to the Protocol.

Fields inherited from class org.biomage.BioEvent.BioEvent

protocolApplications

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

QuantitationTypeMap()
Default constructor.

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

Method Summary

void	addToSourcesQuantitationType(int position, QuantitationType quantitationType) Method to add QuantitationType at position to SourcesQuantitationType_list
void	addToSourcesQuantitationType(QuantitationType quantitationType) Method to add QuantitationType to SourcesQuantitationType_list
QuantitationType	getFromSourcesQuantitationType(int position) Method to get QuantitationType from SourcesQuantitationType_list
HasSourcesQuantitationType.SourcesQuantitationType_list	getSourcesQuantitationType() Get method for sourcesQuantitationType
QuantitationType	getTargetQuantitationType() Get method for targetQuantitationType
void	removeElementAtFromSourcesQuantitationType(int position) Method to remove by position from SourcesQuantitationType_list
void	removeFromSourcesQuantitationType(QuantitationType quantitationType) Method to remove first QuantitationType from SourcesQuantitationType_list
void	setSourcesQuantitationType(HasSourcesQuantitationType.SourcesQuantitationType_list sourcesQuantitationType) Set method for sourcesQuantitationType
void	setTargetQuantitationType(QuantitationType targetQuantitationType) Set method for targetQuantitationType
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.BioEvent.BioEvent

addToProtocolApplications, addToProtocolApplications, getFromProtocolApplications, getProtocolApplications, removeElementAtFromProtocolApplications, removeFromProtocolApplications, setProtocolApplications

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

targetQuantitationType

protected QuantitationType targetQuantitationType

The QuantitationType whose value will be produced from the values of the source QuantitationType according to the Protocol.

sourcesQuantitationType

protected HasSourcesQuantitationType.SourcesQuantitationType_list sourcesQuantitationType

The QuantitationType sources for values for the transformation.

Constructor Detail

QuantitationTypeMap

public QuantitationTypeMap()

Default constructor.

QuantitationTypeMap

public QuantitationTypeMap(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 Map

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 Map

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 Map

java.io.IOException

setTargetQuantitationType

public void setTargetQuantitationType(QuantitationType targetQuantitationType)

Set method for targetQuantitationType

Specified by:

setTargetQuantitationType in interface HasTargetQuantitationType

getTargetQuantitationType

public QuantitationType getTargetQuantitationType()

Get method for targetQuantitationType

Specified by:

getTargetQuantitationType in interface HasTargetQuantitationType

Returns:

value of the attribute

setSourcesQuantitationType

public void setSourcesQuantitationType(HasSourcesQuantitationType.SourcesQuantitationType_list sourcesQuantitationType)

Set method for sourcesQuantitationType

Specified by:

setSourcesQuantitationType in interface HasSourcesQuantitationType

getSourcesQuantitationType

public HasSourcesQuantitationType.SourcesQuantitationType_list getSourcesQuantitationType()

Get method for sourcesQuantitationType

Specified by:

getSourcesQuantitationType in interface HasSourcesQuantitationType

Returns:

value of the attribute

addToSourcesQuantitationType

public void addToSourcesQuantitationType(QuantitationType quantitationType)

Method to add QuantitationType to SourcesQuantitationType_list

Specified by:

addToSourcesQuantitationType in interface HasSourcesQuantitationType

addToSourcesQuantitationType

public void addToSourcesQuantitationType(int position,
                                         QuantitationType quantitationType)

Method to add QuantitationType at position to SourcesQuantitationType_list

Specified by:

addToSourcesQuantitationType in interface HasSourcesQuantitationType

getFromSourcesQuantitationType

public QuantitationType getFromSourcesQuantitationType(int position)

Method to get QuantitationType from SourcesQuantitationType_list

Specified by:

getFromSourcesQuantitationType in interface HasSourcesQuantitationType

removeElementAtFromSourcesQuantitationType

public void removeElementAtFromSourcesQuantitationType(int position)

Method to remove by position from SourcesQuantitationType_list

Specified by:

removeElementAtFromSourcesQuantitationType in interface HasSourcesQuantitationType

removeFromSourcesQuantitationType

public void removeFromSourcesQuantitationType(QuantitationType quantitationType)

Method to remove first QuantitationType from SourcesQuantitationType_list

Specified by:

removeFromSourcesQuantitationType in interface HasSourcesQuantitationType