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org.biomage.BioAssay
Class BioAssay  

java.lang.Object
  org.biomage.Common.Extendable
      org.biomage.Common.Describable
          org.biomage.Common.Identifiable
              org.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

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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.

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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.

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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.

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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.

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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.

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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.

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setChannels

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

Set method for channels

Specified by:

setChannels in interface org.biomage.Interface.HasChannels

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getChannels

public org.biomage.Interface.HasChannels.Channels_list getChannels()

Get method for channels

Specified by:

getChannels in interface org.biomage.Interface.HasChannels

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addToChannels

public void addToChannels(Channel channel)

Method to add Channel to Channels_list

Specified by:

addToChannels in interface org.biomage.Interface.HasChannels

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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

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getFromChannels

public Channel getFromChannels(int position)

Method to get Channel from Channels_list

Specified by:

getFromChannels in interface org.biomage.Interface.HasChannels

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removeElementAtFromChannels

public void removeElementAtFromChannels(int position)

Method to remove by position from Channels_list

Specified by:

removeElementAtFromChannels in interface org.biomage.Interface.HasChannels

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removeFromChannels

public void removeFromChannels(Channel channel)

Method to remove first Channel from Channels_list

Specified by:

removeFromChannels in interface org.biomage.Interface.HasChannels

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setBioAssayFactorValues

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

Set method for bioAssayFactorValues

Specified by:

setBioAssayFactorValues in interface org.biomage.Interface.HasBioAssayFactorValues

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getBioAssayFactorValues

public org.biomage.Interface.HasBioAssayFactorValues.BioAssayFactorValues_list getBioAssayFactorValues()

Get method for bioAssayFactorValues

Specified by:

getBioAssayFactorValues in interface org.biomage.Interface.HasBioAssayFactorValues

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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

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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

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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

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removeElementAtFromBioAssayFactorValues

public void removeElementAtFromBioAssayFactorValues(int position)

Method to remove by position from BioAssayFactorValues_list

Specified by:

removeElementAtFromBioAssayFactorValues in interface org.biomage.Interface.HasBioAssayFactorValues

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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

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ BioAssay overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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