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org.biomage.BioAssayData
Class BioAssayDimension  view BioAssayDimension download BioAssayDimension.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.BioAssayData.BioAssayDimension
All Implemented Interfaces:
org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasBioAssays, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasSecurity, java.io.Serializable

public class BioAssayDimension
extends org.biomage.Common.Identifiable
implements java.io.Serializable, org.biomage.Interface.HasBioAssays

An ordered list of bioAssays.


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasBioAssays
org.biomage.Interface.HasBioAssays.BioAssays_list
 
Nested classes inherited from class org.biomage.Interface.HasAuditTrail
org.biomage.Interface.HasAuditTrail.AuditTrail_list
 
Nested classes inherited from class org.biomage.Interface.HasDescriptions
org.biomage.Interface.HasDescriptions.Descriptions_list
 
Nested classes inherited from class org.biomage.Interface.HasPropertySets
org.biomage.Interface.HasPropertySets.PropertySets_list
 
Field Summary
private  org.biomage.Interface.HasBioAssays.BioAssays_list bioAssays
          The BioAssays for this Dimension
 
Fields inherited from class org.biomage.Common.Identifiable
 
Fields inherited from class org.biomage.Common.Describable
 
Fields inherited from class org.biomage.Common.Extendable
 
Constructor Summary
BioAssayDimension()
          Default constructor.
BioAssayDimension(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToBioAssays(org.biomage.BioAssay.BioAssay bioAssay)
          Method to add BioAssay to BioAssays_list
 void addToBioAssays(int position, org.biomage.BioAssay.BioAssay bioAssay)
          Method to add BioAssay at position to BioAssays_list
 org.biomage.Interface.HasBioAssays.BioAssays_list getBioAssays()
          Get method for bioAssays
 org.biomage.BioAssay.BioAssay getFromBioAssays(int position)
          Method to get BioAssay from BioAssays_list
 void removeElementAtFromBioAssays(int position)
          Method to remove by position from BioAssays_list
 void removeFromBioAssays(org.biomage.BioAssay.BioAssay bioAssay)
          Method to remove first BioAssay from BioAssays_list
 void setBioAssays(org.biomage.Interface.HasBioAssays.BioAssays_list bioAssays)
          Set method for bioAssays
 void writeAssociations(java.io.Writer out)
          writeAssociations
 void writeAttributes(java.io.Writer out)
          writeAttributes
 void writeMAGEML(java.io.Writer out)
          writeMAGEML
 
Methods inherited from class org.biomage.Common.Identifiable
getIdentifier, getName, setIdentifier, setName
 
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, getFromPropertySets, getPropertySets, removeElementAtFromPropertySets, removeFromPropertySets, setPropertySets
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

bioAssays

private org.biomage.Interface.HasBioAssays.BioAssays_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

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.


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.


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.


setBioAssays

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

Specified by:
setBioAssays in interface org.biomage.Interface.HasBioAssays

getBioAssays

public org.biomage.Interface.HasBioAssays.BioAssays_list getBioAssays()
Get method for bioAssays

Specified by:
getBioAssays in interface org.biomage.Interface.HasBioAssays

addToBioAssays

public void addToBioAssays(org.biomage.BioAssay.BioAssay bioAssay)
Method to add BioAssay to BioAssays_list

Specified by:
addToBioAssays in interface org.biomage.Interface.HasBioAssays

addToBioAssays

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

Specified by:
addToBioAssays in interface org.biomage.Interface.HasBioAssays

getFromBioAssays

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

Specified by:
getFromBioAssays in interface org.biomage.Interface.HasBioAssays

removeElementAtFromBioAssays

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

Specified by:
removeElementAtFromBioAssays in interface org.biomage.Interface.HasBioAssays

removeFromBioAssays

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

Specified by:
removeFromBioAssays in interface org.biomage.Interface.HasBioAssays