org.biomage.BioAssay
Class DerivedBioAssay

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.BioAssay.BioAssay
                  extended by org.biomage.BioAssay.DerivedBioAssay
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasBioAssayFactorValues, HasChannels, HasDerivedBioAssayData, HasDerivedBioAssayMap, HasDescriptions, HasPropertySets, HasSecurity, HasType

public class DerivedBioAssay
extends BioAssay
implements java.io.Serializable, HasDerivedBioAssayData, HasType, HasDerivedBioAssayMap

A BioAssay that is created by the Transformation BioEvent from one or more MeasuredBioAssays or DerivedBioAssays.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDerivedBioAssayData
HasDerivedBioAssayData.DerivedBioAssayData_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDerivedBioAssayMap
HasDerivedBioAssayMap.DerivedBioAssayMap_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasChannels
HasChannels.Channels_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasBioAssayFactorValues
HasBioAssayFactorValues.BioAssayFactorValues_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 derivedBioAssayData
          The data associated with the DerivedBioAssay.
protected  java.util.List derivedBioAssayMap
          The DerivedBioAssay that is produced by the sources of the BioAssayMap.
protected  OntologyEntry type
          The derivation type, for instance collapsed spot replicate, ratio, averaged intensity, bioassay replicates, etc.
 
Fields inherited from class org.biomage.BioAssay.BioAssay
bioAssayFactorValues, channels, deleted, ojbConcreteClass
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
DerivedBioAssay()
          Default constructor.
DerivedBioAssay(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToDerivedBioAssayData(DerivedBioAssayData derivedBioAssayData)
          Method to add DerivedBioAssayData to DerivedBioAssayData_list
 void addToDerivedBioAssayData(int position, DerivedBioAssayData derivedBioAssayData)
          Method to add DerivedBioAssayData at position to DerivedBioAssayData_list
 void addToDerivedBioAssayMap(BioAssayMap bioAssayMap)
          Method to add BioAssayMap to DerivedBioAssayMap_list
 void addToDerivedBioAssayMap(int position, BioAssayMap bioAssayMap)
          Method to add BioAssayMap at position to DerivedBioAssayMap_list
 boolean emptyMAGEobject()
           
 HasDerivedBioAssayData.DerivedBioAssayData_list getDerivedBioAssayData()
          Get method for derivedBioAssayData
 HasDerivedBioAssayMap.DerivedBioAssayMap_list getDerivedBioAssayMap()
          Get method for derivedBioAssayMap
 DerivedBioAssayData getFromDerivedBioAssayData(int position)
          Method to get DerivedBioAssayData from DerivedBioAssayData_list
 BioAssayMap getFromDerivedBioAssayMap(int position)
          Method to get BioAssayMap from DerivedBioAssayMap_list
 java.lang.String getModelClassName()
           
 OntologyEntry getType()
          Get method for type
 void removeElementAtFromDerivedBioAssayData(int position)
          Method to remove by position from DerivedBioAssayData_list
 void removeElementAtFromDerivedBioAssayMap(int position)
          Method to remove by position from DerivedBioAssayMap_list
 void removeFromDerivedBioAssayData(DerivedBioAssayData derivedBioAssayData)
          Method to remove first DerivedBioAssayData from DerivedBioAssayData_list
 void removeFromDerivedBioAssayMap(BioAssayMap bioAssayMap)
          Method to remove first BioAssayMap from DerivedBioAssayMap_list
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setDerivedBioAssayData(HasDerivedBioAssayData.DerivedBioAssayData_list derivedBioAssayData)
          Set method for derivedBioAssayData
 void setDerivedBioAssayMap(HasDerivedBioAssayMap.DerivedBioAssayMap_list derivedBioAssayMap)
          Set method for derivedBioAssayMap
 void setType(OntologyEntry type)
          Set method for type
 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.BioAssay.BioAssay
addToBioAssayFactorValues, addToBioAssayFactorValues, addToChannels, addToChannels, getBioAssayFactorValues, getChannels, getFromBioAssayFactorValues, getFromChannels, isDeleted, removeElementAtFromBioAssayFactorValues, removeElementAtFromChannels, removeFromBioAssayFactorValues, removeFromChannels, setBioAssayFactorValues, setChannels, setDeleted
 
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

type

protected OntologyEntry type
The derivation type, for instance collapsed spot replicate, ratio, averaged intensity, bioassay replicates, etc.


derivedBioAssayData

protected java.util.List derivedBioAssayData
The data associated with the DerivedBioAssay.


derivedBioAssayMap

protected java.util.List derivedBioAssayMap
The DerivedBioAssay that is produced by the sources of the BioAssayMap.

Constructor Detail

DerivedBioAssay

public DerivedBioAssay()
Default constructor.


DerivedBioAssay

public DerivedBioAssay(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 BioAssay

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 BioAssay
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 BioAssay
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 BioAssay
Throws:
java.io.IOException

getModelClassName

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

setType

public void setType(OntologyEntry type)
Set method for type

Specified by:
setType in interface HasType
Parameters:
value - to set

getType

public OntologyEntry getType()
Get method for type

Specified by:
getType in interface HasType
Returns:
value of the attribute

setDerivedBioAssayData

public void setDerivedBioAssayData(HasDerivedBioAssayData.DerivedBioAssayData_list derivedBioAssayData)
Set method for derivedBioAssayData

Specified by:
setDerivedBioAssayData in interface HasDerivedBioAssayData
Parameters:
value - to set

getDerivedBioAssayData

public HasDerivedBioAssayData.DerivedBioAssayData_list getDerivedBioAssayData()
Get method for derivedBioAssayData

Specified by:
getDerivedBioAssayData in interface HasDerivedBioAssayData
Returns:
value of the attribute

addToDerivedBioAssayData

public void addToDerivedBioAssayData(DerivedBioAssayData derivedBioAssayData)
Method to add DerivedBioAssayData to DerivedBioAssayData_list

Specified by:
addToDerivedBioAssayData in interface HasDerivedBioAssayData

addToDerivedBioAssayData

public void addToDerivedBioAssayData(int position,
                                     DerivedBioAssayData derivedBioAssayData)
Method to add DerivedBioAssayData at position to DerivedBioAssayData_list

Specified by:
addToDerivedBioAssayData in interface HasDerivedBioAssayData

getFromDerivedBioAssayData

public DerivedBioAssayData getFromDerivedBioAssayData(int position)
Method to get DerivedBioAssayData from DerivedBioAssayData_list

Specified by:
getFromDerivedBioAssayData in interface HasDerivedBioAssayData

removeElementAtFromDerivedBioAssayData

public void removeElementAtFromDerivedBioAssayData(int position)
Method to remove by position from DerivedBioAssayData_list

Specified by:
removeElementAtFromDerivedBioAssayData in interface HasDerivedBioAssayData

removeFromDerivedBioAssayData

public void removeFromDerivedBioAssayData(DerivedBioAssayData derivedBioAssayData)
Method to remove first DerivedBioAssayData from DerivedBioAssayData_list

Specified by:
removeFromDerivedBioAssayData in interface HasDerivedBioAssayData

setDerivedBioAssayMap

public void setDerivedBioAssayMap(HasDerivedBioAssayMap.DerivedBioAssayMap_list derivedBioAssayMap)
Set method for derivedBioAssayMap

Specified by:
setDerivedBioAssayMap in interface HasDerivedBioAssayMap
Parameters:
value - to set

getDerivedBioAssayMap

public HasDerivedBioAssayMap.DerivedBioAssayMap_list getDerivedBioAssayMap()
Get method for derivedBioAssayMap

Specified by:
getDerivedBioAssayMap in interface HasDerivedBioAssayMap
Returns:
value of the attribute

addToDerivedBioAssayMap

public void addToDerivedBioAssayMap(BioAssayMap bioAssayMap)
Method to add BioAssayMap to DerivedBioAssayMap_list

Specified by:
addToDerivedBioAssayMap in interface HasDerivedBioAssayMap

addToDerivedBioAssayMap

public void addToDerivedBioAssayMap(int position,
                                    BioAssayMap bioAssayMap)
Method to add BioAssayMap at position to DerivedBioAssayMap_list

Specified by:
addToDerivedBioAssayMap in interface HasDerivedBioAssayMap

getFromDerivedBioAssayMap

public BioAssayMap getFromDerivedBioAssayMap(int position)
Method to get BioAssayMap from DerivedBioAssayMap_list

Specified by:
getFromDerivedBioAssayMap in interface HasDerivedBioAssayMap

removeElementAtFromDerivedBioAssayMap

public void removeElementAtFromDerivedBioAssayMap(int position)
Method to remove by position from DerivedBioAssayMap_list

Specified by:
removeElementAtFromDerivedBioAssayMap in interface HasDerivedBioAssayMap

removeFromDerivedBioAssayMap

public void removeFromDerivedBioAssayMap(BioAssayMap bioAssayMap)
Method to remove first BioAssayMap from DerivedBioAssayMap_list

Specified by:
removeFromDerivedBioAssayMap in interface HasDerivedBioAssayMap