org.biomage.BioAssayData
Class BioAssayMap

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.BioAssayMap
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasBioAssayMapTarget, HasDescriptions, HasPropertySets, HasProtocolApplications, HasSecurity, HasSourceBioAssays

public class BioAssayMap
extends Map
implements java.io.Serializable, HasBioAssayMapTarget, HasSourceBioAssays

The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasSourceBioAssays
HasSourceBioAssays.SourceBioAssays_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  DerivedBioAssay bioAssayMapTarget
          The DerivedBioAssay that is produced by the sources of the BioAssayMap.
protected  java.util.List sourceBioAssays
          The sources of the BioAssayMap that are used to produce a target DerivedBioAssay.
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
BioAssayMap()
          Default constructor.
BioAssayMap(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToSourceBioAssays(BioAssay bioAssay)
          Method to add BioAssay to SourceBioAssays_list
 void addToSourceBioAssays(int position, BioAssay bioAssay)
          Method to add BioAssay at position to SourceBioAssays_list
 boolean emptyMAGEobject()
           
 DerivedBioAssay getBioAssayMapTarget()
          Get method for bioAssayMapTarget
 BioAssay getFromSourceBioAssays(int position)
          Method to get BioAssay from SourceBioAssays_list
 java.lang.String getModelClassName()
           
 HasSourceBioAssays.SourceBioAssays_list getSourceBioAssays()
          Get method for sourceBioAssays
 void removeElementAtFromSourceBioAssays(int position)
          Method to remove by position from SourceBioAssays_list
 void removeFromSourceBioAssays(BioAssay bioAssay)
          Method to remove first BioAssay from SourceBioAssays_list
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setBioAssayMapTarget(DerivedBioAssay bioAssayMapTarget)
          Set method for bioAssayMapTarget
 void setSourceBioAssays(HasSourceBioAssays.SourceBioAssays_list sourceBioAssays)
          Set method for sourceBioAssays
 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

bioAssayMapTarget

protected DerivedBioAssay bioAssayMapTarget
The DerivedBioAssay that is produced by the sources of the BioAssayMap.


sourceBioAssays

protected java.util.List sourceBioAssays
The sources of the BioAssayMap that are used to produce a target DerivedBioAssay.

Constructor Detail

BioAssayMap

public BioAssayMap()
Default constructor.


BioAssayMap

public BioAssayMap(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

setBioAssayMapTarget

public void setBioAssayMapTarget(DerivedBioAssay bioAssayMapTarget)
Set method for bioAssayMapTarget

Specified by:
setBioAssayMapTarget in interface HasBioAssayMapTarget
Parameters:
value - to set

getBioAssayMapTarget

public DerivedBioAssay getBioAssayMapTarget()
Get method for bioAssayMapTarget

Specified by:
getBioAssayMapTarget in interface HasBioAssayMapTarget
Returns:
value of the attribute

setSourceBioAssays

public void setSourceBioAssays(HasSourceBioAssays.SourceBioAssays_list sourceBioAssays)
Set method for sourceBioAssays

Specified by:
setSourceBioAssays in interface HasSourceBioAssays
Parameters:
value - to set

getSourceBioAssays

public HasSourceBioAssays.SourceBioAssays_list getSourceBioAssays()
Get method for sourceBioAssays

Specified by:
getSourceBioAssays in interface HasSourceBioAssays
Returns:
value of the attribute

addToSourceBioAssays

public void addToSourceBioAssays(BioAssay bioAssay)
Method to add BioAssay to SourceBioAssays_list

Specified by:
addToSourceBioAssays in interface HasSourceBioAssays

addToSourceBioAssays

public void addToSourceBioAssays(int position,
                                 BioAssay bioAssay)
Method to add BioAssay at position to SourceBioAssays_list

Specified by:
addToSourceBioAssays in interface HasSourceBioAssays

getFromSourceBioAssays

public BioAssay getFromSourceBioAssays(int position)
Method to get BioAssay from SourceBioAssays_list

Specified by:
getFromSourceBioAssays in interface HasSourceBioAssays

removeElementAtFromSourceBioAssays

public void removeElementAtFromSourceBioAssays(int position)
Method to remove by position from SourceBioAssays_list

Specified by:
removeElementAtFromSourceBioAssays in interface HasSourceBioAssays

removeFromSourceBioAssays

public void removeFromSourceBioAssays(BioAssay bioAssay)
Method to remove first BioAssay from SourceBioAssays_list

Specified by:
removeFromSourceBioAssays in interface HasSourceBioAssays