org.biomage.QuantitationType
Class StandardQuantitationType

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
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasChannel, HasConfidenceIndicators, HasDataType, HasDescriptions, HasPropertySets, HasQuantitationTypeMaps, HasScale, HasSecurity
Direct Known Subclasses:
ConfidenceIndicator, DerivedSignal, Failed, MeasuredSignal, PresentAbsent, Ratio

public abstract class StandardQuantitationType
extends QuantitationType
implements java.io.Serializable

Superclass for the named quantitation type. Useful for mapping to those languages that can use a fly-weight for processing the subclasses.

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
 
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
StandardQuantitationType()
          Default constructor.
StandardQuantitationType(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 java.lang.String getModelClassName()
           
 void setAttributes(org.xml.sax.Attributes atts)
           
 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
 

Constructor Detail

StandardQuantitationType

public StandardQuantitationType()
Default constructor.


StandardQuantitationType

public StandardQuantitationType(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 QuantitationType

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 QuantitationType
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 QuantitationType
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 QuantitationType
Throws:
java.io.IOException

getModelClassName

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