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

java.lang.Object
  extended byorg.biomage.BioAssay.BioAssay_package
All Implemented Interfaces:
java.io.Serializable

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.


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).


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.


bioAssay_list

public BioAssay_package.BioAssay_list bioAssay_list
An abstract class which represents both physical and computational groupings of arrays and biomaterials.


channel_list

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


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.


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.


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.


setPhysicalBioAssay_list

public void setPhysicalBioAssay_list(BioAssay_package.PhysicalBioAssay_list physicalBioAssay_list)
Set method for physicalBioAssay_list


getPhysicalBioAssay_list

public BioAssay_package.PhysicalBioAssay_list getPhysicalBioAssay_list()
Get method for physicalBioAssay_list


addToPhysicalBioAssay_list

public void addToPhysicalBioAssay_list(PhysicalBioAssay physicalBioAssay)
Method to add PhysicalBioAssay to PhysicalBioAssay_list


addToPhysicalBioAssay_list

public void addToPhysicalBioAssay_list(int position,
                                       PhysicalBioAssay physicalBioAssay)
Method to add PhysicalBioAssay at position to PhysicalBioAssay_list


getFromPhysicalBioAssay_list

public PhysicalBioAssay getFromPhysicalBioAssay_list(int position)
Method to get PhysicalBioAssay from PhysicalBioAssay_list


removeElementAtFromPhysicalBioAssay_list

public void removeElementAtFromPhysicalBioAssay_list(int position)
Method to remove by position from PhysicalBioAssay_list


removeFromPhysicalBioAssay_list

public void removeFromPhysicalBioAssay_list(PhysicalBioAssay physicalBioAssay)
Method to remove first PhysicalBioAssay from PhysicalBioAssay_list


setDerivedBioAssay_list

public void setDerivedBioAssay_list(BioAssay_package.DerivedBioAssay_list derivedBioAssay_list)
Set method for derivedBioAssay_list


getDerivedBioAssay_list

public BioAssay_package.DerivedBioAssay_list getDerivedBioAssay_list()
Get method for derivedBioAssay_list


addToDerivedBioAssay_list

public void addToDerivedBioAssay_list(DerivedBioAssay derivedBioAssay)
Method to add DerivedBioAssay to DerivedBioAssay_list


addToDerivedBioAssay_list

public void addToDerivedBioAssay_list(int position,
                                      DerivedBioAssay derivedBioAssay)
Method to add DerivedBioAssay at position to DerivedBioAssay_list


getFromDerivedBioAssay_list

public DerivedBioAssay getFromDerivedBioAssay_list(int position)
Method to get DerivedBioAssay from DerivedBioAssay_list


removeElementAtFromDerivedBioAssay_list

public void removeElementAtFromDerivedBioAssay_list(int position)
Method to remove by position from DerivedBioAssay_list


removeFromDerivedBioAssay_list

public void removeFromDerivedBioAssay_list(DerivedBioAssay derivedBioAssay)
Method to remove first DerivedBioAssay from DerivedBioAssay_list


setBioAssay_list

public void setBioAssay_list(BioAssay_package.BioAssay_list bioAssay_list)
Set method for bioAssay_list


getBioAssay_list

public BioAssay_package.BioAssay_list getBioAssay_list()
Get method for bioAssay_list


addToBioAssay_list

public void addToBioAssay_list(BioAssay bioAssay)
Method to add BioAssay to BioAssay_list


addToBioAssay_list

public void addToBioAssay_list(int position,
                               BioAssay bioAssay)
Method to add BioAssay at position to BioAssay_list


getFromBioAssay_list

public BioAssay getFromBioAssay_list(int position)
Method to get BioAssay from BioAssay_list


removeElementAtFromBioAssay_list

public void removeElementAtFromBioAssay_list(int position)
Method to remove by position from BioAssay_list


removeFromBioAssay_list

public void removeFromBioAssay_list(BioAssay bioAssay)
Method to remove first BioAssay from BioAssay_list


setChannel_list

public void setChannel_list(BioAssay_package.Channel_list channel_list)
Set method for channel_list


getChannel_list

public BioAssay_package.Channel_list getChannel_list()
Get method for channel_list


addToChannel_list

public void addToChannel_list(Channel channel)
Method to add Channel to Channel_list


addToChannel_list

public void addToChannel_list(int position,
                              Channel channel)
Method to add Channel at position to Channel_list


getFromChannel_list

public Channel getFromChannel_list(int position)
Method to get Channel from Channel_list


removeElementAtFromChannel_list

public void removeElementAtFromChannel_list(int position)
Method to remove by position from Channel_list


removeFromChannel_list

public void removeFromChannel_list(Channel channel)
Method to remove first Channel from Channel_list


setMeasuredBioAssay_list

public void setMeasuredBioAssay_list(BioAssay_package.MeasuredBioAssay_list measuredBioAssay_list)
Set method for measuredBioAssay_list


getMeasuredBioAssay_list

public BioAssay_package.MeasuredBioAssay_list getMeasuredBioAssay_list()
Get method for measuredBioAssay_list


addToMeasuredBioAssay_list

public void addToMeasuredBioAssay_list(MeasuredBioAssay measuredBioAssay)
Method to add MeasuredBioAssay to MeasuredBioAssay_list


addToMeasuredBioAssay_list

public void addToMeasuredBioAssay_list(int position,
                                       MeasuredBioAssay measuredBioAssay)
Method to add MeasuredBioAssay at position to MeasuredBioAssay_list


getFromMeasuredBioAssay_list

public MeasuredBioAssay getFromMeasuredBioAssay_list(int position)
Method to get MeasuredBioAssay from MeasuredBioAssay_list


removeElementAtFromMeasuredBioAssay_list

public void removeElementAtFromMeasuredBioAssay_list(int position)
Method to remove by position from MeasuredBioAssay_list


removeFromMeasuredBioAssay_list

public void removeFromMeasuredBioAssay_list(MeasuredBioAssay measuredBioAssay)
Method to remove first MeasuredBioAssay from MeasuredBioAssay_list