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org.biomage.QuantitationType
Class PresentAbsent  view PresentAbsent download PresentAbsent.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.QuantitationType.QuantitationType
                  extended byorg.biomage.QuantitationType.StandardQuantitationType
                      extended byorg.biomage.QuantitationType.PresentAbsent
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

public class PresentAbsent
extends StandardQuantitationType
implements java.io.Serializable

Indicates relative presence or absence. From the enumeration AbsoluteCallTypeEnum {Present | Absent | Marginal | No call} or ComparisonCallTypeEnum {Increase I Marginal Increase | Decrease | Marginal Decrease | No change | No Call | Unknown }, as specified by the dataType.


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
 
Fields inherited from class org.biomage.QuantitationType.QuantitationType
isBackground
 
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
PresentAbsent()
          Default constructor.
PresentAbsent(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 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.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
 

Constructor Detail

PresentAbsent

public PresentAbsent()
Default constructor.


PresentAbsent

public PresentAbsent(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

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

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