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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:

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

Direct Known Subclasses:

SpecializedQuantitationType, StandardQuantitationType

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public abstract class QuantitationType

extends org.biomage.Common.Identifiable

implements java.io.Serializable, org.biomage.Interface.HasChannel, org.biomage.Interface.HasDataType, org.biomage.Interface.HasScale, org.biomage.Interface.HasConfidenceIndicators

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

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Nested Class Summary

 

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

org.biomage.Interface.HasConfidenceIndicators.ConfidenceIndicators_list

 

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

org.biomage.Interface.HasAuditTrail.AuditTrail_list

 

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

org.biomage.Interface.HasDescriptions.Descriptions_list

 

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

org.biomage.Interface.HasPropertySets.PropertySets_list

 

Field Summary
private  org.biomage.BioAssay.Channel	channel           The optional channel associated with the QuantitationType.
private  org.biomage.Interface.HasConfidenceIndicators.ConfidenceIndicators_list	confidenceIndicators           The association between a ConfidenceIndicator and the QuantitationType its is an indicator for.
private  org.biomage.Description.OntologyEntry	dataType           The specific type for the quantitations.
(package private)  boolean	isBackground           Indicates whether the quantitation has been measured from the background or from the feature itself.
private  org.biomage.Description.OntologyEntry	scale           Indication of how to interpret the value.

 

Fields inherited from class org.biomage.Common.Identifiable

 

Fields inherited from class org.biomage.Common.Describable

 

Fields inherited from class org.biomage.Common.Extendable

 

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
org.biomage.BioAssay.Channel	getChannel()           Get method for channel
org.biomage.Interface.HasConfidenceIndicators.ConfidenceIndicators_list	getConfidenceIndicators()           Get method for confidenceIndicators
org.biomage.Description.OntologyEntry	getDataType()           Get method for dataType
ConfidenceIndicator	getFromConfidenceIndicators(int position)           Method to get ConfidenceIndicator from ConfidenceIndicators_list
boolean	getIsBackground()           Get method for isBackground
org.biomage.Description.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(org.biomage.BioAssay.Channel channel)           Set method for channel
void	setConfidenceIndicators(org.biomage.Interface.HasConfidenceIndicators.ConfidenceIndicators_list confidenceIndicators)           Set method for confidenceIndicators
void	setDataType(org.biomage.Description.OntologyEntry dataType)           Set method for dataType
void	setIsBackground(boolean isBackground)           Set method for isBackground
void	setScale(org.biomage.Description.OntologyEntry scale)           Set method for scale
void	writeAssociations(java.io.Writer out)           writeAssociations
void	writeAttributes(java.io.Writer out)           writeAttributes
void	writeMAGEML(java.io.Writer out)           writeMAGEML

 

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

isBackground

boolean isBackground

Indicates whether the quantitation has been measured from the background or from the feature itself.

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channel

private org.biomage.BioAssay.Channel channel

The optional channel associated with the QuantitationType.

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dataType

private org.biomage.Description.OntologyEntry dataType

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

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scale

private org.biomage.Description.OntologyEntry scale

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

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confidenceIndicators

private org.biomage.Interface.HasConfidenceIndicators.ConfidenceIndicators_list confidenceIndicators

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

Constructor Detail

QuantitationType

public QuantitationType()

Default constructor.

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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.

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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.

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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.

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setIsBackground

public void setIsBackground(boolean isBackground)

Set method for isBackground

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getIsBackground

public boolean getIsBackground()

Get method for isBackground

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setChannel

public void setChannel(org.biomage.BioAssay.Channel channel)

Set method for channel

Specified by:

setChannel in interface org.biomage.Interface.HasChannel

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getChannel

public org.biomage.BioAssay.Channel getChannel()

Get method for channel

Specified by:

getChannel in interface org.biomage.Interface.HasChannel

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setDataType

public void setDataType(org.biomage.Description.OntologyEntry dataType)

Set method for dataType

Specified by:

setDataType in interface org.biomage.Interface.HasDataType

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getDataType

public org.biomage.Description.OntologyEntry getDataType()

Get method for dataType

Specified by:

getDataType in interface org.biomage.Interface.HasDataType

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setScale

public void setScale(org.biomage.Description.OntologyEntry scale)

Set method for scale

Specified by:

setScale in interface org.biomage.Interface.HasScale

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getScale

public org.biomage.Description.OntologyEntry getScale()

Get method for scale

Specified by:

getScale in interface org.biomage.Interface.HasScale

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setConfidenceIndicators

public void setConfidenceIndicators(org.biomage.Interface.HasConfidenceIndicators.ConfidenceIndicators_list confidenceIndicators)

Set method for confidenceIndicators

Specified by:

setConfidenceIndicators in interface org.biomage.Interface.HasConfidenceIndicators

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getConfidenceIndicators

public org.biomage.Interface.HasConfidenceIndicators.ConfidenceIndicators_list getConfidenceIndicators()

Get method for confidenceIndicators

Specified by:

getConfidenceIndicators in interface org.biomage.Interface.HasConfidenceIndicators

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addToConfidenceIndicators

public void addToConfidenceIndicators(ConfidenceIndicator confidenceIndicator)

Method to add ConfidenceIndicator to ConfidenceIndicators_list

Specified by:

addToConfidenceIndicators in interface org.biomage.Interface.HasConfidenceIndicators

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addToConfidenceIndicators

public void addToConfidenceIndicators(int position,
                                      ConfidenceIndicator confidenceIndicator)

Method to add ConfidenceIndicator at position to ConfidenceIndicators_list

Specified by:

addToConfidenceIndicators in interface org.biomage.Interface.HasConfidenceIndicators

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getFromConfidenceIndicators

public ConfidenceIndicator getFromConfidenceIndicators(int position)

Method to get ConfidenceIndicator from ConfidenceIndicators_list

Specified by:

getFromConfidenceIndicators in interface org.biomage.Interface.HasConfidenceIndicators

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removeElementAtFromConfidenceIndicators

public void removeElementAtFromConfidenceIndicators(int position)

Method to remove by position from ConfidenceIndicators_list

Specified by:

removeElementAtFromConfidenceIndicators in interface org.biomage.Interface.HasConfidenceIndicators

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removeFromConfidenceIndicators

public void removeFromConfidenceIndicators(ConfidenceIndicator confidenceIndicator)

Method to remove first ConfidenceIndicator from ConfidenceIndicators_list

Specified by:

removeFromConfidenceIndicators in interface org.biomage.Interface.HasConfidenceIndicators

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ QuantitationType overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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