org.biomage.BioAssayData
Class BioAssayDimension

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.BioAssayData.BioAssayDimension
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasBioAssays, HasDescriptions, HasPropertySets, HasSecurity

public class BioAssayDimension
extends Identifiable
implements java.io.Serializable, HasBioAssays

An ordered list of bioAssays.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasBioAssays
HasBioAssays.BioAssays_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 bioAssays
          The BioAssays for this Dimension
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
BioAssayDimension()
          Default constructor.
BioAssayDimension(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToBioAssays(BioAssay bioAssay)
          Method to add BioAssay to BioAssays_list
 void addToBioAssays(int position, BioAssay bioAssay)
          Method to add BioAssay at position to BioAssays_list
 boolean emptyMAGEobject()
           
 HasBioAssays.BioAssays_list getBioAssays()
          Get method for bioAssays
 BioAssay getFromBioAssays(int position)
          Method to get BioAssay from BioAssays_list
 java.lang.String getModelClassName()
           
 void removeElementAtFromBioAssays(int position)
          Method to remove by position from BioAssays_list
 void removeFromBioAssays(BioAssay bioAssay)
          Method to remove first BioAssay from BioAssays_list
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setBioAssays(HasBioAssays.BioAssays_list bioAssays)
          Set method for bioAssays
 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

bioAssays

protected java.util.List bioAssays
The BioAssays for this Dimension

Constructor Detail

BioAssayDimension

public BioAssayDimension()
Default constructor.


BioAssayDimension

public BioAssayDimension(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

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 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

getModelClassName

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

setBioAssays

public void setBioAssays(HasBioAssays.BioAssays_list bioAssays)
Set method for bioAssays

Specified by:
setBioAssays in interface HasBioAssays
Parameters:
value - to set

getBioAssays

public HasBioAssays.BioAssays_list getBioAssays()
Get method for bioAssays

Specified by:
getBioAssays in interface HasBioAssays
Returns:
value of the attribute

addToBioAssays

public void addToBioAssays(BioAssay bioAssay)
Method to add BioAssay to BioAssays_list

Specified by:
addToBioAssays in interface HasBioAssays

addToBioAssays

public void addToBioAssays(int position,
                           BioAssay bioAssay)
Method to add BioAssay at position to BioAssays_list

Specified by:
addToBioAssays in interface HasBioAssays

getFromBioAssays

public BioAssay getFromBioAssays(int position)
Method to get BioAssay from BioAssays_list

Specified by:
getFromBioAssays in interface HasBioAssays

removeElementAtFromBioAssays

public void removeElementAtFromBioAssays(int position)
Method to remove by position from BioAssays_list

Specified by:
removeElementAtFromBioAssays in interface HasBioAssays

removeFromBioAssays

public void removeFromBioAssays(BioAssay bioAssay)
Method to remove first BioAssay from BioAssays_list

Specified by:
removeFromBioAssays in interface HasBioAssays