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org.biomage.BioAssay
Class BioAssay  view BioAssay download BioAssay.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.BioAssay.BioAssay
All Implemented Interfaces:
org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasBioAssayFactorValues, org.biomage.Interface.HasChannels, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasSecurity, java.io.Serializable
Direct Known Subclasses:
DerivedBioAssay, MeasuredBioAssay, PhysicalBioAssay

public abstract class BioAssay
extends org.biomage.Common.Identifiable
implements java.io.Serializable, org.biomage.Interface.HasChannels, org.biomage.Interface.HasBioAssayFactorValues

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


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasChannels
org.biomage.Interface.HasChannels.Channels_list
 
Nested classes inherited from class org.biomage.Interface.HasBioAssayFactorValues
org.biomage.Interface.HasBioAssayFactorValues.BioAssayFactorValues_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.HasBioAssayFactorValues.BioAssayFactorValues_list bioAssayFactorValues
          The values that this BioAssay is associated with for the experiment.
private  org.biomage.Interface.HasChannels.Channels_list channels
          Channels can be non-null for all subclasses.
 
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
BioAssay()
          Default constructor.
BioAssay(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToBioAssayFactorValues(org.biomage.Experiment.FactorValue factorValue)
          Method to add FactorValue to BioAssayFactorValues_list
 void addToBioAssayFactorValues(int position, org.biomage.Experiment.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
 org.biomage.Interface.HasBioAssayFactorValues.BioAssayFactorValues_list getBioAssayFactorValues()
          Get method for bioAssayFactorValues
 org.biomage.Interface.HasChannels.Channels_list getChannels()
          Get method for channels
 org.biomage.Experiment.FactorValue getFromBioAssayFactorValues(int position)
          Method to get FactorValue from BioAssayFactorValues_list
 Channel getFromChannels(int position)
          Method to get Channel from Channels_list
 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(org.biomage.Experiment.FactorValue factorValue)
          Method to remove first FactorValue from BioAssayFactorValues_list
 void removeFromChannels(Channel channel)
          Method to remove first Channel from Channels_list
 void setBioAssayFactorValues(org.biomage.Interface.HasBioAssayFactorValues.BioAssayFactorValues_list bioAssayFactorValues)
          Set method for bioAssayFactorValues
 void setChannels(org.biomage.Interface.HasChannels.Channels_list channels)
          Set method for channels
 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

channels

private org.biomage.Interface.HasChannels.Channels_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

private org.biomage.Interface.HasBioAssayFactorValues.BioAssayFactorValues_list bioAssayFactorValues
The values that this BioAssay is associated with for the experiment.

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

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.


setChannels

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

Specified by:
setChannels in interface org.biomage.Interface.HasChannels

getChannels

public org.biomage.Interface.HasChannels.Channels_list getChannels()
Get method for channels

Specified by:
getChannels in interface org.biomage.Interface.HasChannels

addToChannels

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

Specified by:
addToChannels in interface org.biomage.Interface.HasChannels

addToChannels

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

Specified by:
addToChannels in interface org.biomage.Interface.HasChannels

getFromChannels

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

Specified by:
getFromChannels in interface org.biomage.Interface.HasChannels

removeElementAtFromChannels

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

Specified by:
removeElementAtFromChannels in interface org.biomage.Interface.HasChannels

removeFromChannels

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

Specified by:
removeFromChannels in interface org.biomage.Interface.HasChannels

setBioAssayFactorValues

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

Specified by:
setBioAssayFactorValues in interface org.biomage.Interface.HasBioAssayFactorValues

getBioAssayFactorValues

public org.biomage.Interface.HasBioAssayFactorValues.BioAssayFactorValues_list getBioAssayFactorValues()
Get method for bioAssayFactorValues

Specified by:
getBioAssayFactorValues in interface org.biomage.Interface.HasBioAssayFactorValues

addToBioAssayFactorValues

public void addToBioAssayFactorValues(org.biomage.Experiment.FactorValue factorValue)
Method to add FactorValue to BioAssayFactorValues_list

Specified by:
addToBioAssayFactorValues in interface org.biomage.Interface.HasBioAssayFactorValues

addToBioAssayFactorValues

public void addToBioAssayFactorValues(int position,
                                      org.biomage.Experiment.FactorValue factorValue)
Method to add FactorValue at position to BioAssayFactorValues_list

Specified by:
addToBioAssayFactorValues in interface org.biomage.Interface.HasBioAssayFactorValues

getFromBioAssayFactorValues

public org.biomage.Experiment.FactorValue getFromBioAssayFactorValues(int position)
Method to get FactorValue from BioAssayFactorValues_list

Specified by:
getFromBioAssayFactorValues in interface org.biomage.Interface.HasBioAssayFactorValues

removeElementAtFromBioAssayFactorValues

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

Specified by:
removeElementAtFromBioAssayFactorValues in interface org.biomage.Interface.HasBioAssayFactorValues

removeFromBioAssayFactorValues

public void removeFromBioAssayFactorValues(org.biomage.Experiment.FactorValue factorValue)
Method to remove first FactorValue from BioAssayFactorValues_list

Specified by:
removeFromBioAssayFactorValues in interface org.biomage.Interface.HasBioAssayFactorValues