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org.biomage.BioAssayData
Class QuantitationTypeMap  view QuantitationTypeMap download QuantitationTypeMap.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.BioEvent.BioEvent
                  extended byorg.biomage.BioEvent.Map
                      extended byorg.biomage.BioAssayData.QuantitationTypeMap
All Implemented Interfaces:
org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasProtocolApplications, org.biomage.Interface.HasSecurity, org.biomage.Interface.HasSourcesQuantitationType, org.biomage.Interface.HasTargetQuantitationType, java.io.Serializable

public class QuantitationTypeMap
extends org.biomage.BioEvent.Map
implements java.io.Serializable, org.biomage.Interface.HasTargetQuantitationType, org.biomage.Interface.HasSourcesQuantitationType

A QuantitationTypeMap is the description of how source QuantitationTypes are mathematically transformed into a target QuantitationType.


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasSourcesQuantitationType
org.biomage.Interface.HasSourcesQuantitationType.SourcesQuantitationType_list
 
Nested classes inherited from class org.biomage.Interface.HasProtocolApplications
org.biomage.Interface.HasProtocolApplications.ProtocolApplications_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.Interface.HasSourcesQuantitationType.SourcesQuantitationType_list sourcesQuantitationType
          The QuantitationType sources for values for the transformation.
private  org.biomage.QuantitationType.QuantitationType targetQuantitationType
          The QuantitationType whose value will be produced from the values of the source QuantitationType according to the Protocol.
 
Fields inherited from class org.biomage.BioEvent.BioEvent
 
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
QuantitationTypeMap()
          Default constructor.
QuantitationTypeMap(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToSourcesQuantitationType(int position, org.biomage.QuantitationType.QuantitationType quantitationType)
          Method to add QuantitationType at position to SourcesQuantitationType_list
 void addToSourcesQuantitationType(org.biomage.QuantitationType.QuantitationType quantitationType)
          Method to add QuantitationType to SourcesQuantitationType_list
 org.biomage.QuantitationType.QuantitationType getFromSourcesQuantitationType(int position)
          Method to get QuantitationType from SourcesQuantitationType_list
 org.biomage.Interface.HasSourcesQuantitationType.SourcesQuantitationType_list getSourcesQuantitationType()
          Get method for sourcesQuantitationType
 org.biomage.QuantitationType.QuantitationType getTargetQuantitationType()
          Get method for targetQuantitationType
 void removeElementAtFromSourcesQuantitationType(int position)
          Method to remove by position from SourcesQuantitationType_list
 void removeFromSourcesQuantitationType(org.biomage.QuantitationType.QuantitationType quantitationType)
          Method to remove first QuantitationType from SourcesQuantitationType_list
 void setSourcesQuantitationType(org.biomage.Interface.HasSourcesQuantitationType.SourcesQuantitationType_list sourcesQuantitationType)
          Set method for sourcesQuantitationType
 void setTargetQuantitationType(org.biomage.QuantitationType.QuantitationType targetQuantitationType)
          Set method for targetQuantitationType
 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.BioEvent.BioEvent
addToProtocolApplications, addToProtocolApplications, getFromProtocolApplications, getProtocolApplications, removeElementAtFromProtocolApplications, removeFromProtocolApplications, setProtocolApplications
 
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

targetQuantitationType

private org.biomage.QuantitationType.QuantitationType targetQuantitationType
The QuantitationType whose value will be produced from the values of the source QuantitationType according to the Protocol.


sourcesQuantitationType

private org.biomage.Interface.HasSourcesQuantitationType.SourcesQuantitationType_list sourcesQuantitationType
The QuantitationType sources for values for the transformation.

Constructor Detail

QuantitationTypeMap

public QuantitationTypeMap()
Default constructor.


QuantitationTypeMap

public QuantitationTypeMap(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.


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.


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.


setTargetQuantitationType

public void setTargetQuantitationType(org.biomage.QuantitationType.QuantitationType targetQuantitationType)
Set method for targetQuantitationType

Specified by:
setTargetQuantitationType in interface org.biomage.Interface.HasTargetQuantitationType

getTargetQuantitationType

public org.biomage.QuantitationType.QuantitationType getTargetQuantitationType()
Get method for targetQuantitationType

Specified by:
getTargetQuantitationType in interface org.biomage.Interface.HasTargetQuantitationType

setSourcesQuantitationType

public void setSourcesQuantitationType(org.biomage.Interface.HasSourcesQuantitationType.SourcesQuantitationType_list sourcesQuantitationType)
Set method for sourcesQuantitationType

Specified by:
setSourcesQuantitationType in interface org.biomage.Interface.HasSourcesQuantitationType

getSourcesQuantitationType

public org.biomage.Interface.HasSourcesQuantitationType.SourcesQuantitationType_list getSourcesQuantitationType()
Get method for sourcesQuantitationType

Specified by:
getSourcesQuantitationType in interface org.biomage.Interface.HasSourcesQuantitationType

addToSourcesQuantitationType

public void addToSourcesQuantitationType(org.biomage.QuantitationType.QuantitationType quantitationType)
Method to add QuantitationType to SourcesQuantitationType_list

Specified by:
addToSourcesQuantitationType in interface org.biomage.Interface.HasSourcesQuantitationType

addToSourcesQuantitationType

public void addToSourcesQuantitationType(int position,
                                         org.biomage.QuantitationType.QuantitationType quantitationType)
Method to add QuantitationType at position to SourcesQuantitationType_list

Specified by:
addToSourcesQuantitationType in interface org.biomage.Interface.HasSourcesQuantitationType

getFromSourcesQuantitationType

public org.biomage.QuantitationType.QuantitationType getFromSourcesQuantitationType(int position)
Method to get QuantitationType from SourcesQuantitationType_list

Specified by:
getFromSourcesQuantitationType in interface org.biomage.Interface.HasSourcesQuantitationType

removeElementAtFromSourcesQuantitationType

public void removeElementAtFromSourcesQuantitationType(int position)
Method to remove by position from SourcesQuantitationType_list

Specified by:
removeElementAtFromSourcesQuantitationType in interface org.biomage.Interface.HasSourcesQuantitationType

removeFromSourcesQuantitationType

public void removeFromSourcesQuantitationType(org.biomage.QuantitationType.QuantitationType quantitationType)
Method to remove first QuantitationType from SourcesQuantitationType_list

Specified by:
removeFromSourcesQuantitationType in interface org.biomage.Interface.HasSourcesQuantitationType