org.biomage.BioAssay
Class BioAssay

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
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasBioAssayFactorValues, HasChannels, HasDescriptions, HasPropertySets, HasSecurity
Direct Known Subclasses:
DerivedBioAssay, MeasuredBioAssay, PhysicalBioAssay

public abstract class BioAssay
extends Identifiable
implements java.io.Serializable, HasChannels, HasBioAssayFactorValues

An abstract class which represents both physical and computational groupings of arrays and biomaterials.

See Also:
Serialized Form

Nested Class Summary
 
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 bioAssayFactorValues
          The values that this BioAssay is associated with for the experiment.
protected  java.util.List channels
          Channels can be non-null for all subclasses.
protected  boolean deleted
          caARRAY-specific marker for a DELETED BioAssay.
protected  java.lang.String ojbConcreteClass
           
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
BioAssay()
          Default constructor.
BioAssay(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToBioAssayFactorValues(FactorValue factorValue)
          Method to add FactorValue to BioAssayFactorValues_list
 void addToBioAssayFactorValues(int position, FactorValue factorValue)
          Method to add FactorValue at position to BioAssayFactorValues_list
 void addToChannels(Channel channel)
          Method to add Channel to Channels_list
 void addToChannels(int position, Channel channel)
          Method to add Channel at position to Channels_list
 HasBioAssayFactorValues.BioAssayFactorValues_list getBioAssayFactorValues()
          Get method for bioAssayFactorValues
 HasChannels.Channels_list getChannels()
          Get method for channels
 FactorValue getFromBioAssayFactorValues(int position)
          Method to get FactorValue from BioAssayFactorValues_list
 Channel getFromChannels(int position)
          Method to get Channel from Channels_list
 java.lang.String getModelClassName()
           
 boolean isDeleted()
           
 void removeElementAtFromBioAssayFactorValues(int position)
          Method to remove by position from BioAssayFactorValues_list
 void removeElementAtFromChannels(int position)
          Method to remove by position from Channels_list
 void removeFromBioAssayFactorValues(FactorValue factorValue)
          Method to remove first FactorValue from BioAssayFactorValues_list
 void removeFromChannels(Channel channel)
          Method to remove first Channel from Channels_list
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setBioAssayFactorValues(HasBioAssayFactorValues.BioAssayFactorValues_list bioAssayFactorValues)
          Set method for bioAssayFactorValues
 void setChannels(HasChannels.Channels_list channels)
          Set method for channels
 void setDeleted(boolean deleted)
          Marks if this BioAssay is deleted.
 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

ojbConcreteClass

protected java.lang.String ojbConcreteClass

channels

protected java.util.List channels
Channels can be non-null for all subclasses. For instance, collapsing across replicate features will create a DerivedBioAssay that will potentially reference channels.


bioAssayFactorValues

protected java.util.List bioAssayFactorValues
The values that this BioAssay is associated with for the experiment.


deleted

protected boolean deleted
caARRAY-specific marker for a DELETED BioAssay. tranp.

Constructor Detail

BioAssay

public BioAssay()
Default constructor.


BioAssay

public BioAssay(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

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

setChannels

public void setChannels(HasChannels.Channels_list channels)
Set method for channels

Specified by:
setChannels in interface HasChannels
Parameters:
value - to set

getChannels

public HasChannels.Channels_list getChannels()
Get method for channels

Specified by:
getChannels in interface HasChannels
Returns:
value of the attribute

addToChannels

public void addToChannels(Channel channel)
Method to add Channel to Channels_list

Specified by:
addToChannels in interface HasChannels

addToChannels

public void addToChannels(int position,
                          Channel channel)
Method to add Channel at position to Channels_list

Specified by:
addToChannels in interface HasChannels

getFromChannels

public Channel getFromChannels(int position)
Method to get Channel from Channels_list

Specified by:
getFromChannels in interface HasChannels

removeElementAtFromChannels

public void removeElementAtFromChannels(int position)
Method to remove by position from Channels_list

Specified by:
removeElementAtFromChannels in interface HasChannels

removeFromChannels

public void removeFromChannels(Channel channel)
Method to remove first Channel from Channels_list

Specified by:
removeFromChannels in interface HasChannels

setBioAssayFactorValues

public void setBioAssayFactorValues(HasBioAssayFactorValues.BioAssayFactorValues_list bioAssayFactorValues)
Set method for bioAssayFactorValues

Specified by:
setBioAssayFactorValues in interface HasBioAssayFactorValues
Parameters:
value - to set

getBioAssayFactorValues

public HasBioAssayFactorValues.BioAssayFactorValues_list getBioAssayFactorValues()
Get method for bioAssayFactorValues

Specified by:
getBioAssayFactorValues in interface HasBioAssayFactorValues
Returns:
value of the attribute

addToBioAssayFactorValues

public void addToBioAssayFactorValues(FactorValue factorValue)
Method to add FactorValue to BioAssayFactorValues_list

Specified by:
addToBioAssayFactorValues in interface HasBioAssayFactorValues

addToBioAssayFactorValues

public void addToBioAssayFactorValues(int position,
                                      FactorValue factorValue)
Method to add FactorValue at position to BioAssayFactorValues_list

Specified by:
addToBioAssayFactorValues in interface HasBioAssayFactorValues

getFromBioAssayFactorValues

public FactorValue getFromBioAssayFactorValues(int position)
Method to get FactorValue from BioAssayFactorValues_list

Specified by:
getFromBioAssayFactorValues in interface HasBioAssayFactorValues

removeElementAtFromBioAssayFactorValues

public void removeElementAtFromBioAssayFactorValues(int position)
Method to remove by position from BioAssayFactorValues_list

Specified by:
removeElementAtFromBioAssayFactorValues in interface HasBioAssayFactorValues

removeFromBioAssayFactorValues

public void removeFromBioAssayFactorValues(FactorValue factorValue)
Method to remove first FactorValue from BioAssayFactorValues_list

Specified by:
removeFromBioAssayFactorValues in interface HasBioAssayFactorValues

isDeleted

public boolean isDeleted()
Returns:
- True if this BioAssay has been deleted; false otherwise.

setDeleted

public void setDeleted(boolean deleted)
Marks if this BioAssay is deleted. caARRAY-specific.

Parameters:
deleted - - True if this BioAssay is deleted; false otherwise.