org.biomage.QuantitationType
Class QuantitationType

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

All Implemented Interfaces:

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

Direct Known Subclasses:

SpecializedQuantitationType, StandardQuantitationType

public abstract class QuantitationType

extends Identifiable

implements java.io.Serializable, HasChannel, HasDataType, HasScale, HasConfidenceIndicators

A method for calculating a single datum of the matrix (e.g. raw intensity, background, error).

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 Channel	channel The optional channel associated with the QuantitationType.
protected HasConfidenceIndicators.ConfidenceIndicators_list	confidenceIndicators The association between a ConfidenceIndicator and the QuantitationType its is an indicator for.
protected OntologyEntry	dataType The specific type for the quantitations.
protected OntologyEntry	scale Indication of how to interpret the value.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

QuantitationType()
Default constructor.

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

Method Summary

void	addToConfidenceIndicators(ConfidenceIndicator confidenceIndicator) Method to add ConfidenceIndicator to ConfidenceIndicators_list
void	addToConfidenceIndicators(int position, ConfidenceIndicator confidenceIndicator) Method to add ConfidenceIndicator at position to ConfidenceIndicators_list
Channel	getChannel() Get method for channel
HasConfidenceIndicators.ConfidenceIndicators_list	getConfidenceIndicators() Get method for confidenceIndicators
OntologyEntry	getDataType() Get method for dataType
ConfidenceIndicator	getFromConfidenceIndicators(int position) Method to get ConfidenceIndicator from ConfidenceIndicators_list
boolean	getIsBackground() Get method for isBackground
OntologyEntry	getScale() Get method for scale
void	removeElementAtFromConfidenceIndicators(int position) Method to remove by position from ConfidenceIndicators_list
void	removeFromConfidenceIndicators(ConfidenceIndicator confidenceIndicator) Method to remove first ConfidenceIndicator from ConfidenceIndicators_list
void	setChannel(Channel channel) Set method for channel
void	setConfidenceIndicators(HasConfidenceIndicators.ConfidenceIndicators_list confidenceIndicators) Set method for confidenceIndicators
void	setDataType(OntologyEntry dataType) Set method for dataType
void	setIsBackground(boolean isBackground) Set method for isBackground
void	setScale(OntologyEntry scale) Set method for scale
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.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

channel

protected Channel channel

The optional channel associated with the QuantitationType.

scale

protected OntologyEntry scale

Indication of how to interpret the value. From a suggested vocabulary of {LINEAR | LN | LOG2 |LOG10 | FOLD_CHANGE | OTHER}

dataType

protected OntologyEntry dataType

The specific type for the quantitations. From a controlled vocabulary of {float, int, boolean, etc.}

confidenceIndicators

protected HasConfidenceIndicators.ConfidenceIndicators_list confidenceIndicators

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

Constructor Detail

QuantitationType

public QuantitationType()

Default constructor.

QuantitationType

public QuantitationType(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 Identifiable

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 Identifiable

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 Identifiable

java.io.IOException

setIsBackground

public void setIsBackground(boolean isBackground)

Set method for isBackground

getIsBackground

public boolean getIsBackground()

Get method for isBackground

Returns:

value of the attribute

setChannel

public void setChannel(Channel channel)

Set method for channel

Specified by:

setChannel in interface HasChannel

getChannel

public Channel getChannel()

Get method for channel

Specified by:

getChannel in interface HasChannel

Returns:

value of the attribute

setScale

public void setScale(OntologyEntry scale)

Set method for scale

Specified by:

setScale in interface HasScale

getScale

public OntologyEntry getScale()

Get method for scale

Specified by:

getScale in interface HasScale

Returns:

value of the attribute

setDataType

public void setDataType(OntologyEntry dataType)

Set method for dataType

Specified by:

setDataType in interface HasDataType

getDataType

public OntologyEntry getDataType()

Get method for dataType

Specified by:

getDataType in interface HasDataType

Returns:

value of the attribute

setConfidenceIndicators

public void setConfidenceIndicators(HasConfidenceIndicators.ConfidenceIndicators_list confidenceIndicators)

Set method for confidenceIndicators

Specified by:

setConfidenceIndicators in interface HasConfidenceIndicators

getConfidenceIndicators

public HasConfidenceIndicators.ConfidenceIndicators_list getConfidenceIndicators()

Get method for confidenceIndicators

Specified by:

getConfidenceIndicators in interface HasConfidenceIndicators

Returns:

value of the attribute

addToConfidenceIndicators

public void addToConfidenceIndicators(ConfidenceIndicator confidenceIndicator)

Method to add ConfidenceIndicator to ConfidenceIndicators_list

Specified by:

addToConfidenceIndicators in interface HasConfidenceIndicators

addToConfidenceIndicators

public void addToConfidenceIndicators(int position,
                                      ConfidenceIndicator confidenceIndicator)

Method to add ConfidenceIndicator at position to ConfidenceIndicators_list

Specified by:

addToConfidenceIndicators in interface HasConfidenceIndicators

getFromConfidenceIndicators

public ConfidenceIndicator getFromConfidenceIndicators(int position)

Method to get ConfidenceIndicator from ConfidenceIndicators_list

Specified by:

getFromConfidenceIndicators in interface HasConfidenceIndicators

removeElementAtFromConfidenceIndicators

public void removeElementAtFromConfidenceIndicators(int position)

Method to remove by position from ConfidenceIndicators_list

Specified by:

removeElementAtFromConfidenceIndicators in interface HasConfidenceIndicators

removeFromConfidenceIndicators

public void removeFromConfidenceIndicators(ConfidenceIndicator confidenceIndicator)

Method to remove first ConfidenceIndicator from ConfidenceIndicators_list

Specified by:

removeFromConfidenceIndicators in interface HasConfidenceIndicators