org.biomage.QuantitationType
Class ConfidenceIndicator

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.QuantitationType.QuantitationType
                          |
                          +--org.biomage.QuantitationType.StandardQuantitationType
                                |
                                +--org.biomage.QuantitationType.ConfidenceIndicator

All Implemented Interfaces:

HasAuditTrail, HasChannel, HasConfidenceIndicators, HasDataType, HasDescriptions, HasPropertySets, HasScale, HasSecurity, HasTargetQuantitationType, java.io.Serializable

Direct Known Subclasses:

Error, ExpectedValue, PValue

public abstract class ConfidenceIndicator

extends StandardQuantitationType

implements java.io.Serializable, HasTargetQuantitationType

Indication of some measure of confidence for a standard quantitation type.

See Also:

Serialized Form

Nested Class Summary

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

HasConfidenceIndicators.ConfidenceIndicators_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 QuantitationType

targetQuantitationType The association between a ConfidenceIndicator and the QuantitationType its is an indicator for.

Fields inherited from class org.biomage.QuantitationType.QuantitationType

channel, confidenceIndicators, dataType, scale

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

ConfidenceIndicator()
Default constructor.

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

Method Summary

QuantitationType	getTargetQuantitationType() Get method for targetQuantitationType
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.QuantitationType.QuantitationType

addToConfidenceIndicators, addToConfidenceIndicators, getChannel, getConfidenceIndicators, getDataType, getFromConfidenceIndicators, getIsBackground, getScale, removeElementAtFromConfidenceIndicators, removeFromConfidenceIndicators, setChannel, setConfidenceIndicators, setDataType, setIsBackground, setScale

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 association between a ConfidenceIndicator and the QuantitationType its is an indicator for.

Constructor Detail

ConfidenceIndicator

public ConfidenceIndicator()

Default constructor.

ConfidenceIndicator

public ConfidenceIndicator(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 StandardQuantitationType

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 StandardQuantitationType

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 StandardQuantitationType

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