org.biomage.QuantitationType
Class QuantitationType

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
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasChannel, HasConfidenceIndicators, HasDataType, HasDescriptions, HasPropertySets, HasQuantitationTypeMaps, HasScale, HasSecurity
Direct Known Subclasses:
SpecializedQuantitationType, StandardQuantitationType

public abstract class QuantitationType
extends Identifiable
implements java.io.Serializable, HasChannel, HasQuantitationTypeMaps, HasDataType, HasScale, HasConfidenceIndicators

A method for calculating a single datum of the matrix (e.g. raw intensity, background, error).

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  Channel channel
          The optional channel associated with the QuantitationType.
protected  java.util.List confidenceIndicators
          The association between a ConfidenceIndicator and the QuantitationType its is an indicator for.
protected  OntologyEntry dataType
          The specific type for the quantitations.
protected  java.lang.String ojbConcreteClass
           
protected  java.util.List quantitationTypeMaps
          The QuantitationType whose value will be produced from the values of the source QuantitationType according to the Protocol.
protected  OntologyEntry scale
          Indication of how to interpret the value.
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
QuantitationType()
          Default constructor.
QuantitationType(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToConfidenceIndicators(ConfidenceIndicator confidenceIndicator)
          Method to add ConfidenceIndicator to ConfidenceIndicators_list
 void addToConfidenceIndicators(int position, ConfidenceIndicator confidenceIndicator)
          Method to add ConfidenceIndicator at position to ConfidenceIndicators_list
 void addToQuantitationTypeMaps(int position, QuantitationTypeMap quantitationTypeMap)
          Method to add QuantitationTypeMap at position to QuantitationTypeMaps_list
 void addToQuantitationTypeMaps(QuantitationTypeMap quantitationTypeMap)
          Method to add QuantitationTypeMap to QuantitationTypeMaps_list
 Channel getChannel()
          Get method for channel
 HasConfidenceIndicators.ConfidenceIndicators_list getConfidenceIndicators()
          Get method for confidenceIndicators
 OntologyEntry getDataType()
          Get method for dataType
 ConfidenceIndicator getFromConfidenceIndicators(int position)
          Method to get ConfidenceIndicator from ConfidenceIndicators_list
 QuantitationTypeMap getFromQuantitationTypeMaps(int position)
          Method to get QuantitationTypeMap from QuantitationTypeMaps_list
 java.lang.Boolean getIsBackground()
          Get method for isBackground
 java.lang.String getModelClassName()
           
 HasQuantitationTypeMaps.QuantitationTypeMaps_list getQuantitationTypeMaps()
          Get method for quantitationTypeMaps
 OntologyEntry getScale()
          Get method for scale
 void removeElementAtFromConfidenceIndicators(int position)
          Method to remove by position from ConfidenceIndicators_list
 void removeElementAtFromQuantitationTypeMaps(int position)
          Method to remove by position from QuantitationTypeMaps_list
 void removeFromConfidenceIndicators(ConfidenceIndicator confidenceIndicator)
          Method to remove first ConfidenceIndicator from ConfidenceIndicators_list
 void removeFromQuantitationTypeMaps(QuantitationTypeMap quantitationTypeMap)
          Method to remove first QuantitationTypeMap from QuantitationTypeMaps_list
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setChannel(Channel channel)
          Set method for channel
 void setConfidenceIndicators(HasConfidenceIndicators.ConfidenceIndicators_list confidenceIndicators)
          Set method for confidenceIndicators
 void setDataType(OntologyEntry dataType)
          Set method for dataType
 void setIsBackground(java.lang.Boolean isBackground)
          Set method for isBackground
 void setQuantitationTypeMaps(HasQuantitationTypeMaps.QuantitationTypeMaps_list quantitationTypeMaps)
          Set method for quantitationTypeMaps
 void setScale(OntologyEntry scale)
          Set method for scale
 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.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

ojbConcreteClass

protected java.lang.String ojbConcreteClass

channel

protected Channel channel
The optional channel associated with the QuantitationType.


scale

protected OntologyEntry scale
Indication of how to interpret the value. From a suggested vocabulary of {LINEAR | LN | LOG2 |LOG10 | FOLD_CHANGE | OTHER}


dataType

protected OntologyEntry dataType
The specific type for the quantitations. From a controlled vocabulary of {float, int, boolean, etc.}


confidenceIndicators

protected java.util.List confidenceIndicators
The association between a ConfidenceIndicator and the QuantitationType its is an indicator for.


quantitationTypeMaps

protected java.util.List quantitationTypeMaps
The QuantitationType whose value will be produced from the values of the source QuantitationType according to the Protocol.

Constructor Detail

QuantitationType

public QuantitationType()
Default constructor.


QuantitationType

public QuantitationType(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 Identifiable

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 Identifiable
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 Identifiable
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 Identifiable
Throws:
java.io.IOException

setIsBackground

public void setIsBackground(java.lang.Boolean isBackground)
Set method for isBackground

Parameters:
value - to set

getIsBackground

public java.lang.Boolean getIsBackground()
Get method for isBackground

Returns:
value of the attribute

getModelClassName

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

setChannel

public void setChannel(Channel channel)
Set method for channel

Specified by:
setChannel in interface HasChannel
Parameters:
value - to set

getChannel

public Channel getChannel()
Get method for channel

Specified by:
getChannel in interface HasChannel
Returns:
value of the attribute

setScale

public void setScale(OntologyEntry scale)
Set method for scale

Specified by:
setScale in interface HasScale
Parameters:
value - to set

getScale

public OntologyEntry getScale()
Get method for scale

Specified by:
getScale in interface HasScale
Returns:
value of the attribute

setDataType

public void setDataType(OntologyEntry dataType)
Set method for dataType

Specified by:
setDataType in interface HasDataType
Parameters:
value - to set

getDataType

public OntologyEntry getDataType()
Get method for dataType

Specified by:
getDataType in interface HasDataType
Returns:
value of the attribute

setConfidenceIndicators

public void setConfidenceIndicators(HasConfidenceIndicators.ConfidenceIndicators_list confidenceIndicators)
Set method for confidenceIndicators

Specified by:
setConfidenceIndicators in interface HasConfidenceIndicators
Parameters:
value - to set

getConfidenceIndicators

public HasConfidenceIndicators.ConfidenceIndicators_list getConfidenceIndicators()
Get method for confidenceIndicators

Specified by:
getConfidenceIndicators in interface HasConfidenceIndicators
Returns:
value of the attribute

addToConfidenceIndicators

public void addToConfidenceIndicators(ConfidenceIndicator confidenceIndicator)
Method to add ConfidenceIndicator to ConfidenceIndicators_list

Specified by:
addToConfidenceIndicators in interface HasConfidenceIndicators

addToConfidenceIndicators

public void addToConfidenceIndicators(int position,
                                      ConfidenceIndicator confidenceIndicator)
Method to add ConfidenceIndicator at position to ConfidenceIndicators_list

Specified by:
addToConfidenceIndicators in interface HasConfidenceIndicators

getFromConfidenceIndicators

public ConfidenceIndicator getFromConfidenceIndicators(int position)
Method to get ConfidenceIndicator from ConfidenceIndicators_list

Specified by:
getFromConfidenceIndicators in interface HasConfidenceIndicators

removeElementAtFromConfidenceIndicators

public void removeElementAtFromConfidenceIndicators(int position)
Method to remove by position from ConfidenceIndicators_list

Specified by:
removeElementAtFromConfidenceIndicators in interface HasConfidenceIndicators

removeFromConfidenceIndicators

public void removeFromConfidenceIndicators(ConfidenceIndicator confidenceIndicator)
Method to remove first ConfidenceIndicator from ConfidenceIndicators_list

Specified by:
removeFromConfidenceIndicators in interface HasConfidenceIndicators

setQuantitationTypeMaps

public void setQuantitationTypeMaps(HasQuantitationTypeMaps.QuantitationTypeMaps_list quantitationTypeMaps)
Set method for quantitationTypeMaps

Specified by:
setQuantitationTypeMaps in interface HasQuantitationTypeMaps
Parameters:
value - to set

getQuantitationTypeMaps

public HasQuantitationTypeMaps.QuantitationTypeMaps_list getQuantitationTypeMaps()
Get method for quantitationTypeMaps

Specified by:
getQuantitationTypeMaps in interface HasQuantitationTypeMaps
Returns:
value of the attribute

addToQuantitationTypeMaps

public void addToQuantitationTypeMaps(QuantitationTypeMap quantitationTypeMap)
Method to add QuantitationTypeMap to QuantitationTypeMaps_list

Specified by:
addToQuantitationTypeMaps in interface HasQuantitationTypeMaps

addToQuantitationTypeMaps

public void addToQuantitationTypeMaps(int position,
                                      QuantitationTypeMap quantitationTypeMap)
Method to add QuantitationTypeMap at position to QuantitationTypeMaps_list

Specified by:
addToQuantitationTypeMaps in interface HasQuantitationTypeMaps

getFromQuantitationTypeMaps

public QuantitationTypeMap getFromQuantitationTypeMaps(int position)
Method to get QuantitationTypeMap from QuantitationTypeMaps_list

Specified by:
getFromQuantitationTypeMaps in interface HasQuantitationTypeMaps

removeElementAtFromQuantitationTypeMaps

public void removeElementAtFromQuantitationTypeMaps(int position)
Method to remove by position from QuantitationTypeMaps_list

Specified by:
removeElementAtFromQuantitationTypeMaps in interface HasQuantitationTypeMaps

removeFromQuantitationTypeMaps

public void removeFromQuantitationTypeMaps(QuantitationTypeMap quantitationTypeMap)
Method to remove first QuantitationTypeMap from QuantitationTypeMaps_list

Specified by:
removeFromQuantitationTypeMaps in interface HasQuantitationTypeMaps