org.biomage.BioAssay
Class BioAssay_package

java.lang.Object
  extended by org.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.

See Also:
Serialized Form

Nested Class Summary
 class BioAssay_package.BioAssay_list
          Inner list class for holding multiple entries for attribute bioAssay.
 class BioAssay_package.Channel_list
          Inner list class for holding multiple entries for attribute channel.
 
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.
 
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
 boolean emptyMAGEobject()
           
 BioAssay_package.BioAssay_list getBioAssay_list()
          Get method for bioAssay_list
 BioAssay_package.Channel_list getChannel_list()
          Get method for channel_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
 java.lang.String getModelClassName()
           
 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 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 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 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 java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

channel_list

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


bioAssay_list

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

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

Parameters:
atts: - the attribute list.
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.

Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

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.

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.

Throws:
java.io.IOException

getModelClassName

public java.lang.String getModelClassName()

setChannel_list

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

Parameters:
value - to set

getChannel_list

public BioAssay_package.Channel_list getChannel_list()
Get method for channel_list

Returns:
value of the attribute

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


setBioAssay_list

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

Parameters:
value - to set

getBioAssay_list

public BioAssay_package.BioAssay_list getBioAssay_list()
Get method for bioAssay_list

Returns:
value of the attribute

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