org.biomage.QuantitationType
Class ConfidenceIndicator

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Common.Describable
          extended by org.biomage.Common.Identifiable
              extended by org.biomage.QuantitationType.QuantitationType
                  extended by org.biomage.QuantitationType.StandardQuantitationType
                      extended by org.biomage.QuantitationType.ConfidenceIndicator
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasChannel, HasConfidenceIndicators, HasDataType, HasDescriptions, HasPropertySets, HasQuantitationTypeMaps, HasScale, HasSecurity, HasTargetQuantitationType
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/interfaces inherited from interface org.biomage.Interface.HasQuantitationTypeMaps
HasQuantitationTypeMaps.QuantitationTypeMaps_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasConfidenceIndicators
HasConfidenceIndicators.ConfidenceIndicators_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail
HasAuditTrail.AuditTrail_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions
HasDescriptions.Descriptions_list
 
Nested classes/interfaces inherited from interface 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, ojbConcreteClass, quantitationTypeMaps, scale
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
ConfidenceIndicator()
          Default constructor.
ConfidenceIndicator(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 java.lang.String getModelClassName()
           
 QuantitationType getTargetQuantitationType()
          Get method for targetQuantitationType
 void setAttributes(org.xml.sax.Attributes atts)
           
 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, addToQuantitationTypeMaps, addToQuantitationTypeMaps, getChannel, getConfidenceIndicators, getDataType, getFromConfidenceIndicators, getFromQuantitationTypeMaps, getIsBackground, getQuantitationTypeMaps, getScale, removeElementAtFromConfidenceIndicators, removeElementAtFromQuantitationTypeMaps, removeFromConfidenceIndicators, removeFromQuantitationTypeMaps, setChannel, setConfidenceIndicators, setDataType, setIsBackground, setQuantitationTypeMaps, setScale
 
Methods inherited from class org.biomage.Common.Identifiable
getIdentifier, getName, setIdentifier, setName, toString
 
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, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, 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

Parameters:
atts: - the attribute list.
Method Detail

setAttributes

public void setAttributes(org.xml.sax.Attributes atts)
Overrides:
setAttributes in class StandardQuantitationType

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
Throws:
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
Throws:
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
Throws:
java.io.IOException

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class StandardQuantitationType

setTargetQuantitationType

public void setTargetQuantitationType(QuantitationType targetQuantitationType)
Set method for targetQuantitationType

Specified by:
setTargetQuantitationType in interface HasTargetQuantitationType
Parameters:
value - to set

getTargetQuantitationType

public QuantitationType getTargetQuantitationType()
Get method for targetQuantitationType

Specified by:
getTargetQuantitationType in interface HasTargetQuantitationType
Returns:
value of the attribute