org.biomage.BioAssayData
Class BioAssayMapping

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.BioAssayData.BioAssayMapping
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasBioAssayMaps, HasPropertySets

public class BioAssayMapping
extends Extendable
implements java.io.Serializable, HasBioAssayMaps

Container of the mappings of the input BioAssay dimensions to the output BioAssay dimension.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasBioAssayMaps
HasBioAssayMaps.BioAssayMaps_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets
HasPropertySets.PropertySets_list
 
Field Summary
protected  java.util.List bioAssayMaps
          The maps for the BioAssays.
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
BioAssayMapping()
          Default constructor.
BioAssayMapping(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToBioAssayMaps(BioAssayMap bioAssayMap)
          Method to add BioAssayMap to BioAssayMaps_list
 void addToBioAssayMaps(int position, BioAssayMap bioAssayMap)
          Method to add BioAssayMap at position to BioAssayMaps_list
 boolean emptyMAGEobject()
           
 HasBioAssayMaps.BioAssayMaps_list getBioAssayMaps()
          Get method for bioAssayMaps
 BioAssayMap getFromBioAssayMaps(int position)
          Method to get BioAssayMap from BioAssayMaps_list
 java.lang.String getModelClassName()
           
 void removeElementAtFromBioAssayMaps(int position)
          Method to remove by position from BioAssayMaps_list
 void removeFromBioAssayMaps(BioAssayMap bioAssayMap)
          Method to remove first BioAssayMap from BioAssayMaps_list
 void setBioAssayMaps(HasBioAssayMaps.BioAssayMaps_list bioAssayMaps)
          Set method for bioAssayMaps
 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.Extendable
addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setAttributes, setId, setIsEditable, setPropertySets, setSecuredElementId, toString
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

bioAssayMaps

protected java.util.List bioAssayMaps
The maps for the BioAssays.

Constructor Detail

BioAssayMapping

public BioAssayMapping()
Default constructor.


BioAssayMapping

public BioAssayMapping(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

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 Extendable
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 Extendable
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 Extendable
Throws:
java.io.IOException

getModelClassName

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

setBioAssayMaps

public void setBioAssayMaps(HasBioAssayMaps.BioAssayMaps_list bioAssayMaps)
Set method for bioAssayMaps

Specified by:
setBioAssayMaps in interface HasBioAssayMaps
Parameters:
value - to set

getBioAssayMaps

public HasBioAssayMaps.BioAssayMaps_list getBioAssayMaps()
Get method for bioAssayMaps

Specified by:
getBioAssayMaps in interface HasBioAssayMaps
Returns:
value of the attribute

addToBioAssayMaps

public void addToBioAssayMaps(BioAssayMap bioAssayMap)
Method to add BioAssayMap to BioAssayMaps_list

Specified by:
addToBioAssayMaps in interface HasBioAssayMaps

addToBioAssayMaps

public void addToBioAssayMaps(int position,
                              BioAssayMap bioAssayMap)
Method to add BioAssayMap at position to BioAssayMaps_list

Specified by:
addToBioAssayMaps in interface HasBioAssayMaps

getFromBioAssayMaps

public BioAssayMap getFromBioAssayMaps(int position)
Method to get BioAssayMap from BioAssayMaps_list

Specified by:
getFromBioAssayMaps in interface HasBioAssayMaps

removeElementAtFromBioAssayMaps

public void removeElementAtFromBioAssayMaps(int position)
Method to remove by position from BioAssayMaps_list

Specified by:
removeElementAtFromBioAssayMaps in interface HasBioAssayMaps

removeFromBioAssayMaps

public void removeFromBioAssayMaps(BioAssayMap bioAssayMap)
Method to remove first BioAssayMap from BioAssayMaps_list

Specified by:
removeFromBioAssayMaps in interface HasBioAssayMaps