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org.biomage.BioAssay
Class BioAssay_package  

java.lang.Object
  org.biomage.BioAssay.BioAssay_package

All Implemented Interfaces:

java.io.Serializable

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public class BioAssay_package

extends java.lang.Object

implements java.io.Serializable

Provides classes that contain information and annotation on the event of joining an Array with a BioMaterial preparation, the acquisition of images and the extraction of data on a per feature basis from those images. The derived classes of BioAssay represent the base PhysicalBioAssays which lead to the production of Images, the MeasuredBioAssay which is associated with the set of quantitations produced by FeatureExtraction, and DerivedBioAssay (see BioAssayData package) which groups together BioAssays that have been analyzed together to produce further refinement of the quantitations. The design of this package and the related BioAssayData package was driven by the following query considerations and the desire to return as little data as necessary to satisfy a query. Often, the first set of queries for experiments below the Experiment level will want to discover the why of an experiment and this is captured in the BioAssay class through its FactorValue, BioEvent and Description associations. This separates it from the data but allows an overview of the experiment hierarchy. The BioAssayData class association to BioDataValues is optional only to allow queries on them to discover the how of the experiment through the association to the transformation and mappings of the three BioAssayData dimensions and the protocols used. Once a researcher, for instance, has narrowed down the experiments of interest then the actual data, represented by the BioDataValues, can be downloaded. Because these data can be in the hundreds of megabytes to gigabytes range, it was considered desirable to be able to return information and annotation on the experiment without the data.

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Nested Class Summary
class	BioAssay_package.BioAssay_list           Inner list class for holding multiple entries for attribute bioAssay_list.
class	BioAssay_package.Channel_list           Inner list class for holding multiple entries for attribute channel_list.
class	BioAssay_package.DerivedBioAssay_list           Inner list class for holding multiple entries for attribute derivedBioAssay_list.
class	BioAssay_package.MeasuredBioAssay_list           Inner list class for holding multiple entries for attribute measuredBioAssay_list.
class	BioAssay_package.PhysicalBioAssay_list           Inner list class for holding multiple entries for attribute physicalBioAssay_list.

 

Field Summary
BioAssay_package.BioAssay_list	bioAssay_list           An abstract class which represents both physical and computational groupings of arrays and biomaterials.
BioAssay_package.Channel_list	channel_list           A channel represents an independent acquisition scheme for the ImageAcquisition event, typically a wavelength.
BioAssay_package.DerivedBioAssay_list	derivedBioAssay_list           A BioAssay that is created by the Transformation BioEvent from one or more MeasuredBioAssays or DerivedBioAssays.
BioAssay_package.MeasuredBioAssay_list	measuredBioAssay_list           A measured bioAssay is the direct processing of information in a physical bioAssay by the featureExtraction event.
BioAssay_package.PhysicalBioAssay_list	physicalBioAssay_list           A bioAssay created by the bioAssayCreation event (e.g.

 

Constructor Summary

BioAssay_package()           Default constructor.

BioAssay_package(org.xml.sax.Attributes atts)           Attribute constructor.

 

Method Summary
void	addToBioAssay_list(BioAssay bioAssay)           Method to add BioAssay to BioAssay_list
void	addToBioAssay_list(int position, BioAssay bioAssay)           Method to add BioAssay at position to BioAssay_list
void	addToChannel_list(Channel channel)           Method to add Channel to Channel_list
void	addToChannel_list(int position, Channel channel)           Method to add Channel at position to Channel_list
void	addToDerivedBioAssay_list(DerivedBioAssay derivedBioAssay)           Method to add DerivedBioAssay to DerivedBioAssay_list
void	addToDerivedBioAssay_list(int position, DerivedBioAssay derivedBioAssay)           Method to add DerivedBioAssay at position to DerivedBioAssay_list
void	addToMeasuredBioAssay_list(int position, MeasuredBioAssay measuredBioAssay)           Method to add MeasuredBioAssay at position to MeasuredBioAssay_list
void	addToMeasuredBioAssay_list(MeasuredBioAssay measuredBioAssay)           Method to add MeasuredBioAssay to MeasuredBioAssay_list
void	addToPhysicalBioAssay_list(int position, PhysicalBioAssay physicalBioAssay)           Method to add PhysicalBioAssay at position to PhysicalBioAssay_list
void	addToPhysicalBioAssay_list(PhysicalBioAssay physicalBioAssay)           Method to add PhysicalBioAssay to PhysicalBioAssay_list
BioAssay_package.BioAssay_list	getBioAssay_list()           Get method for bioAssay_list
BioAssay_package.Channel_list	getChannel_list()           Get method for channel_list
BioAssay_package.DerivedBioAssay_list	getDerivedBioAssay_list()           Get method for derivedBioAssay_list
BioAssay	getFromBioAssay_list(int position)           Method to get BioAssay from BioAssay_list
Channel	getFromChannel_list(int position)           Method to get Channel from Channel_list
DerivedBioAssay	getFromDerivedBioAssay_list(int position)           Method to get DerivedBioAssay from DerivedBioAssay_list
MeasuredBioAssay	getFromMeasuredBioAssay_list(int position)           Method to get MeasuredBioAssay from MeasuredBioAssay_list
PhysicalBioAssay	getFromPhysicalBioAssay_list(int position)           Method to get PhysicalBioAssay from PhysicalBioAssay_list
BioAssay_package.MeasuredBioAssay_list	getMeasuredBioAssay_list()           Get method for measuredBioAssay_list
BioAssay_package.PhysicalBioAssay_list	getPhysicalBioAssay_list()           Get method for physicalBioAssay_list
void	removeElementAtFromBioAssay_list(int position)           Method to remove by position from BioAssay_list
void	removeElementAtFromChannel_list(int position)           Method to remove by position from Channel_list
void	removeElementAtFromDerivedBioAssay_list(int position)           Method to remove by position from DerivedBioAssay_list
void	removeElementAtFromMeasuredBioAssay_list(int position)           Method to remove by position from MeasuredBioAssay_list
void	removeElementAtFromPhysicalBioAssay_list(int position)           Method to remove by position from PhysicalBioAssay_list
void	removeFromBioAssay_list(BioAssay bioAssay)           Method to remove first BioAssay from BioAssay_list
void	removeFromChannel_list(Channel channel)           Method to remove first Channel from Channel_list
void	removeFromDerivedBioAssay_list(DerivedBioAssay derivedBioAssay)           Method to remove first DerivedBioAssay from DerivedBioAssay_list
void	removeFromMeasuredBioAssay_list(MeasuredBioAssay measuredBioAssay)           Method to remove first MeasuredBioAssay from MeasuredBioAssay_list
void	removeFromPhysicalBioAssay_list(PhysicalBioAssay physicalBioAssay)           Method to remove first PhysicalBioAssay from PhysicalBioAssay_list
void	setBioAssay_list(BioAssay_package.BioAssay_list bioAssay_list)           Set method for bioAssay_list
void	setChannel_list(BioAssay_package.Channel_list channel_list)           Set method for channel_list
void	setDerivedBioAssay_list(BioAssay_package.DerivedBioAssay_list derivedBioAssay_list)           Set method for derivedBioAssay_list
void	setMeasuredBioAssay_list(BioAssay_package.MeasuredBioAssay_list measuredBioAssay_list)           Set method for measuredBioAssay_list
void	setPhysicalBioAssay_list(BioAssay_package.PhysicalBioAssay_list physicalBioAssay_list)           Set method for physicalBioAssay_list
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 java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

 

Field Detail

physicalBioAssay_list

public BioAssay_package.PhysicalBioAssay_list physicalBioAssay_list

A bioAssay created by the bioAssayCreation event (e.g. in gene expression analysis this event is represented by the hybridization event).

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derivedBioAssay_list

public BioAssay_package.DerivedBioAssay_list derivedBioAssay_list

A BioAssay that is created by the Transformation BioEvent from one or more MeasuredBioAssays or DerivedBioAssays.

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bioAssay_list

public BioAssay_package.BioAssay_list bioAssay_list

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

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channel_list

public BioAssay_package.Channel_list channel_list

A channel represents an independent acquisition scheme for the ImageAcquisition event, typically a wavelength.

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measuredBioAssay_list

public BioAssay_package.MeasuredBioAssay_list measuredBioAssay_list

A measured bioAssay is the direct processing of information in a physical bioAssay by the featureExtraction event. Often uses images which are referenced through the physical bioAssay.

Constructor Detail

BioAssay_package

public BioAssay_package()

Default constructor.

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BioAssay_package

public BioAssay_package(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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setPhysicalBioAssay_list

public void setPhysicalBioAssay_list(BioAssay_package.PhysicalBioAssay_list physicalBioAssay_list)

Set method for physicalBioAssay_list

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getPhysicalBioAssay_list

public BioAssay_package.PhysicalBioAssay_list getPhysicalBioAssay_list()

Get method for physicalBioAssay_list

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addToPhysicalBioAssay_list

public void addToPhysicalBioAssay_list(PhysicalBioAssay physicalBioAssay)

Method to add PhysicalBioAssay to PhysicalBioAssay_list

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addToPhysicalBioAssay_list

public void addToPhysicalBioAssay_list(int position,
                                       PhysicalBioAssay physicalBioAssay)

Method to add PhysicalBioAssay at position to PhysicalBioAssay_list

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getFromPhysicalBioAssay_list

public PhysicalBioAssay getFromPhysicalBioAssay_list(int position)

Method to get PhysicalBioAssay from PhysicalBioAssay_list

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removeElementAtFromPhysicalBioAssay_list

public void removeElementAtFromPhysicalBioAssay_list(int position)

Method to remove by position from PhysicalBioAssay_list

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removeFromPhysicalBioAssay_list

public void removeFromPhysicalBioAssay_list(PhysicalBioAssay physicalBioAssay)

Method to remove first PhysicalBioAssay from PhysicalBioAssay_list

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setDerivedBioAssay_list

public void setDerivedBioAssay_list(BioAssay_package.DerivedBioAssay_list derivedBioAssay_list)

Set method for derivedBioAssay_list

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getDerivedBioAssay_list

public BioAssay_package.DerivedBioAssay_list getDerivedBioAssay_list()

Get method for derivedBioAssay_list

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addToDerivedBioAssay_list

public void addToDerivedBioAssay_list(DerivedBioAssay derivedBioAssay)

Method to add DerivedBioAssay to DerivedBioAssay_list

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addToDerivedBioAssay_list

public void addToDerivedBioAssay_list(int position,
                                      DerivedBioAssay derivedBioAssay)

Method to add DerivedBioAssay at position to DerivedBioAssay_list

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getFromDerivedBioAssay_list

public DerivedBioAssay getFromDerivedBioAssay_list(int position)

Method to get DerivedBioAssay from DerivedBioAssay_list

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removeElementAtFromDerivedBioAssay_list

public void removeElementAtFromDerivedBioAssay_list(int position)

Method to remove by position from DerivedBioAssay_list

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removeFromDerivedBioAssay_list

public void removeFromDerivedBioAssay_list(DerivedBioAssay derivedBioAssay)

Method to remove first DerivedBioAssay from DerivedBioAssay_list

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setBioAssay_list

public void setBioAssay_list(BioAssay_package.BioAssay_list bioAssay_list)

Set method for bioAssay_list

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getBioAssay_list

public BioAssay_package.BioAssay_list getBioAssay_list()

Get method for bioAssay_list

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addToBioAssay_list

public void addToBioAssay_list(BioAssay bioAssay)

Method to add BioAssay to BioAssay_list

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addToBioAssay_list

public void addToBioAssay_list(int position,
                               BioAssay bioAssay)

Method to add BioAssay at position to BioAssay_list

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getFromBioAssay_list

public BioAssay getFromBioAssay_list(int position)

Method to get BioAssay from BioAssay_list

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removeElementAtFromBioAssay_list

public void removeElementAtFromBioAssay_list(int position)

Method to remove by position from BioAssay_list

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removeFromBioAssay_list

public void removeFromBioAssay_list(BioAssay bioAssay)

Method to remove first BioAssay from BioAssay_list

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setChannel_list

public void setChannel_list(BioAssay_package.Channel_list channel_list)

Set method for channel_list

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getChannel_list

public BioAssay_package.Channel_list getChannel_list()

Get method for channel_list

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addToChannel_list

public void addToChannel_list(Channel channel)

Method to add Channel to Channel_list

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addToChannel_list

public void addToChannel_list(int position,
                              Channel channel)

Method to add Channel at position to Channel_list

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getFromChannel_list

public Channel getFromChannel_list(int position)

Method to get Channel from Channel_list

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removeElementAtFromChannel_list

public void removeElementAtFromChannel_list(int position)

Method to remove by position from Channel_list

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removeFromChannel_list

public void removeFromChannel_list(Channel channel)

Method to remove first Channel from Channel_list

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setMeasuredBioAssay_list

public void setMeasuredBioAssay_list(BioAssay_package.MeasuredBioAssay_list measuredBioAssay_list)

Set method for measuredBioAssay_list

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getMeasuredBioAssay_list

public BioAssay_package.MeasuredBioAssay_list getMeasuredBioAssay_list()

Get method for measuredBioAssay_list

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addToMeasuredBioAssay_list

public void addToMeasuredBioAssay_list(MeasuredBioAssay measuredBioAssay)

Method to add MeasuredBioAssay to MeasuredBioAssay_list

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addToMeasuredBioAssay_list

public void addToMeasuredBioAssay_list(int position,
                                       MeasuredBioAssay measuredBioAssay)

Method to add MeasuredBioAssay at position to MeasuredBioAssay_list

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getFromMeasuredBioAssay_list

public MeasuredBioAssay getFromMeasuredBioAssay_list(int position)

Method to get MeasuredBioAssay from MeasuredBioAssay_list

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removeElementAtFromMeasuredBioAssay_list

public void removeElementAtFromMeasuredBioAssay_list(int position)

Method to remove by position from MeasuredBioAssay_list

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removeFromMeasuredBioAssay_list

public void removeFromMeasuredBioAssay_list(MeasuredBioAssay measuredBioAssay)

Method to remove first MeasuredBioAssay from MeasuredBioAssay_list

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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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