org.biomage.BioAssayData
Class QuantitationTypeMap

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.BioEvent.BioEvent
                  extended by org.biomage.BioEvent.Map
                      extended by org.biomage.BioAssayData.QuantitationTypeMap
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasDescriptions, HasPropertySets, HasProtocolApplications, HasSecurity, HasSourcesQuantitationType, HasTargetQuantitationType

public class QuantitationTypeMap
extends Map
implements java.io.Serializable, HasTargetQuantitationType, HasSourcesQuantitationType

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

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasSourcesQuantitationType
HasSourcesQuantitationType.SourcesQuantitationType_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasProtocolApplications
HasProtocolApplications.ProtocolApplications_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  java.util.List sourcesQuantitationType
          The QuantitationType sources for values for the transformation.
protected  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.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
QuantitationTypeMap()
          Default constructor.
QuantitationTypeMap(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToSourcesQuantitationType(int position, QuantitationType quantitationType)
          Method to add QuantitationType at position to SourcesQuantitationType_list
 void addToSourcesQuantitationType(QuantitationType quantitationType)
          Method to add QuantitationType to SourcesQuantitationType_list
 boolean emptyMAGEobject()
           
 QuantitationType getFromSourcesQuantitationType(int position)
          Method to get QuantitationType from SourcesQuantitationType_list
 java.lang.String getModelClassName()
           
 HasSourcesQuantitationType.SourcesQuantitationType_list getSourcesQuantitationType()
          Get method for sourcesQuantitationType
 QuantitationType getTargetQuantitationType()
          Get method for targetQuantitationType
 void removeElementAtFromSourcesQuantitationType(int position)
          Method to remove by position from SourcesQuantitationType_list
 void removeFromSourcesQuantitationType(QuantitationType quantitationType)
          Method to remove first QuantitationType from SourcesQuantitationType_list
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setSourcesQuantitationType(HasSourcesQuantitationType.SourcesQuantitationType_list sourcesQuantitationType)
          Set method for sourcesQuantitationType
 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.BioEvent.BioEvent
addToProtocolApplications, addToProtocolApplications, getFromProtocolApplications, getProtocolApplications, removeElementAtFromProtocolApplications, removeFromProtocolApplications, setProtocolApplications
 
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 QuantitationType whose value will be produced from the values of the source QuantitationType according to the Protocol.


sourcesQuantitationType

protected java.util.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

Parameters:
atts: - the attribute list.
Method Detail

setAttributes

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

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 Map
Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

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 Map
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 Map
Throws:
java.io.IOException

getModelClassName

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

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

setSourcesQuantitationType

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

Specified by:
setSourcesQuantitationType in interface HasSourcesQuantitationType
Parameters:
value - to set

getSourcesQuantitationType

public HasSourcesQuantitationType.SourcesQuantitationType_list getSourcesQuantitationType()
Get method for sourcesQuantitationType

Specified by:
getSourcesQuantitationType in interface HasSourcesQuantitationType
Returns:
value of the attribute

addToSourcesQuantitationType

public void addToSourcesQuantitationType(QuantitationType quantitationType)
Method to add QuantitationType to SourcesQuantitationType_list

Specified by:
addToSourcesQuantitationType in interface HasSourcesQuantitationType

addToSourcesQuantitationType

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

Specified by:
addToSourcesQuantitationType in interface HasSourcesQuantitationType

getFromSourcesQuantitationType

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

Specified by:
getFromSourcesQuantitationType in interface HasSourcesQuantitationType

removeElementAtFromSourcesQuantitationType

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

Specified by:
removeElementAtFromSourcesQuantitationType in interface HasSourcesQuantitationType

removeFromSourcesQuantitationType

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

Specified by:
removeFromSourcesQuantitationType in interface HasSourcesQuantitationType