org.biomage.BioAssayData
Class BioAssayData_package

java.lang.Object
  extended by org.biomage.BioAssayData.BioAssayData_package
All Implemented Interfaces:
java.io.Serializable

public class BioAssayData_package
extends java.lang.Object
implements java.io.Serializable

The classes defined here provide data and the information and annotation on the derivation of that data. Some of the scenarios that might occur are the following. FeatureExtraction of a single PhysicalBioAssay produces MeasuredBioAssayData that has a single BioAssay on the BioAssayDimension, typically the Features described in the ArrayDesign on the DesignElementDimension, and the Quantitations associated with the application of a FeatureExtraction protocol on the QuantitationDimension. An error model transformation might be applied that doesn't change the BioAssayDimension or the DesignElementDimension but likely changes the QuantitationDimension. A transformation on replicate Reporters or CompositeSequences might be applied on the single BioAssay that would change the DesignElementDimension and the QuantitationDimension both. Replicate and Control BioAssays might be added to the BioAssayDimension and a transformation could change the BioAssayDimension and the QuantitationDimension but not change the DesignElementDimension to produce a new DerivedBioAssayData. Or some combination of the above transformations could be performed at once to change all three dimensions. Because the classes derive from Describable, the Experimenter can provide as much detail at each level of the class hierarchy as desired.

See Also:
Serialized Form

Nested Class Summary
 class BioAssayData_package.BioAssayData_list
          Inner list class for holding multiple entries for attribute bioAssayData.
 class BioAssayData_package.BioAssayDimension_list
          Inner list class for holding multiple entries for attribute bioAssayDimension.
 class BioAssayData_package.BioAssayMap_list
          Inner list class for holding multiple entries for attribute bioAssayMap.
 class BioAssayData_package.DesignElementDimension_list
          Inner list class for holding multiple entries for attribute designElementDimension.
 class BioAssayData_package.QuantitationTypeDimension_list
          Inner list class for holding multiple entries for attribute quantitationTypeDimension.
 class BioAssayData_package.QuantitationTypeMap_list
          Inner list class for holding multiple entries for attribute quantitationTypeMap.
 
Field Summary
 BioAssayData_package.BioAssayData_list bioAssayData_list
          Represents the dataset created when the BioAssays are created.
 BioAssayData_package.BioAssayDimension_list bioAssayDimension_list
          An ordered list of bioAssays.
 BioAssayData_package.BioAssayMap_list bioAssayMap_list
          The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays.
 BioAssayData_package.DesignElementDimension_list designElementDimension_list
          An ordered list of designElements.
 BioAssayData_package.QuantitationTypeDimension_list quantitationTypeDimension_list
          An ordered list of quantitationTypes.
 BioAssayData_package.QuantitationTypeMap_list quantitationTypeMap_list
          A QuantitationTypeMap is the description of how source QuantitationTypes are mathematically transformed into a target QuantitationType.
 
Constructor Summary
BioAssayData_package()
          Default constructor.
BioAssayData_package(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToBioAssayData_list(BioAssayData bioAssayData)
          Method to add BioAssayData to BioAssayData_list
 void addToBioAssayData_list(int position, BioAssayData bioAssayData)
          Method to add BioAssayData at position to BioAssayData_list
 void addToBioAssayDimension_list(BioAssayDimension bioAssayDimension)
          Method to add BioAssayDimension to BioAssayDimension_list
 void addToBioAssayDimension_list(int position, BioAssayDimension bioAssayDimension)
          Method to add BioAssayDimension at position to BioAssayDimension_list
 void addToBioAssayMap_list(BioAssayMap bioAssayMap)
          Method to add BioAssayMap to BioAssayMap_list
 void addToBioAssayMap_list(int position, BioAssayMap bioAssayMap)
          Method to add BioAssayMap at position to BioAssayMap_list
 void addToDesignElementDimension_list(DesignElementDimension designElementDimension)
          Method to add DesignElementDimension to DesignElementDimension_list
 void addToDesignElementDimension_list(int position, DesignElementDimension designElementDimension)
          Method to add DesignElementDimension at position to DesignElementDimension_list
 void addToQuantitationTypeDimension_list(int position, QuantitationTypeDimension quantitationTypeDimension)
          Method to add QuantitationTypeDimension at position to QuantitationTypeDimension_list
 void addToQuantitationTypeDimension_list(QuantitationTypeDimension quantitationTypeDimension)
          Method to add QuantitationTypeDimension to QuantitationTypeDimension_list
 void addToQuantitationTypeMap_list(int position, QuantitationTypeMap quantitationTypeMap)
          Method to add QuantitationTypeMap at position to QuantitationTypeMap_list
 void addToQuantitationTypeMap_list(QuantitationTypeMap quantitationTypeMap)
          Method to add QuantitationTypeMap to QuantitationTypeMap_list
 boolean emptyMAGEobject()
           
 BioAssayData_package.BioAssayData_list getBioAssayData_list()
          Get method for bioAssayData_list
 BioAssayData_package.BioAssayDimension_list getBioAssayDimension_list()
          Get method for bioAssayDimension_list
 BioAssayData_package.BioAssayMap_list getBioAssayMap_list()
          Get method for bioAssayMap_list
 BioAssayData_package.DesignElementDimension_list getDesignElementDimension_list()
          Get method for designElementDimension_list
 BioAssayData getFromBioAssayData_list(int position)
          Method to get BioAssayData from BioAssayData_list
 BioAssayDimension getFromBioAssayDimension_list(int position)
          Method to get BioAssayDimension from BioAssayDimension_list
 BioAssayMap getFromBioAssayMap_list(int position)
          Method to get BioAssayMap from BioAssayMap_list
 DesignElementDimension getFromDesignElementDimension_list(int position)
          Method to get DesignElementDimension from DesignElementDimension_list
 QuantitationTypeDimension getFromQuantitationTypeDimension_list(int position)
          Method to get QuantitationTypeDimension from QuantitationTypeDimension_list
 QuantitationTypeMap getFromQuantitationTypeMap_list(int position)
          Method to get QuantitationTypeMap from QuantitationTypeMap_list
 java.lang.String getModelClassName()
           
 BioAssayData_package.QuantitationTypeDimension_list getQuantitationTypeDimension_list()
          Get method for quantitationTypeDimension_list
 BioAssayData_package.QuantitationTypeMap_list getQuantitationTypeMap_list()
          Get method for quantitationTypeMap_list
 void removeElementAtFromBioAssayData_list(int position)
          Method to remove by position from BioAssayData_list
 void removeElementAtFromBioAssayDimension_list(int position)
          Method to remove by position from BioAssayDimension_list
 void removeElementAtFromBioAssayMap_list(int position)
          Method to remove by position from BioAssayMap_list
 void removeElementAtFromDesignElementDimension_list(int position)
          Method to remove by position from DesignElementDimension_list
 void removeElementAtFromQuantitationTypeDimension_list(int position)
          Method to remove by position from QuantitationTypeDimension_list
 void removeElementAtFromQuantitationTypeMap_list(int position)
          Method to remove by position from QuantitationTypeMap_list
 void removeFromBioAssayData_list(BioAssayData bioAssayData)
          Method to remove first BioAssayData from BioAssayData_list
 void removeFromBioAssayDimension_list(BioAssayDimension bioAssayDimension)
          Method to remove first BioAssayDimension from BioAssayDimension_list
 void removeFromBioAssayMap_list(BioAssayMap bioAssayMap)
          Method to remove first BioAssayMap from BioAssayMap_list
 void removeFromDesignElementDimension_list(DesignElementDimension designElementDimension)
          Method to remove first DesignElementDimension from DesignElementDimension_list
 void removeFromQuantitationTypeDimension_list(QuantitationTypeDimension quantitationTypeDimension)
          Method to remove first QuantitationTypeDimension from QuantitationTypeDimension_list
 void removeFromQuantitationTypeMap_list(QuantitationTypeMap quantitationTypeMap)
          Method to remove first QuantitationTypeMap from QuantitationTypeMap_list
 void setBioAssayData_list(BioAssayData_package.BioAssayData_list bioAssayData_list)
          Set method for bioAssayData_list
 void setBioAssayDimension_list(BioAssayData_package.BioAssayDimension_list bioAssayDimension_list)
          Set method for bioAssayDimension_list
 void setBioAssayMap_list(BioAssayData_package.BioAssayMap_list bioAssayMap_list)
          Set method for bioAssayMap_list
 void setDesignElementDimension_list(BioAssayData_package.DesignElementDimension_list designElementDimension_list)
          Set method for designElementDimension_list
 void setQuantitationTypeDimension_list(BioAssayData_package.QuantitationTypeDimension_list quantitationTypeDimension_list)
          Set method for quantitationTypeDimension_list
 void setQuantitationTypeMap_list(BioAssayData_package.QuantitationTypeMap_list quantitationTypeMap_list)
          Set method for quantitationTypeMap_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

bioAssayDimension_list

public BioAssayData_package.BioAssayDimension_list bioAssayDimension_list
An ordered list of bioAssays.


designElementDimension_list

public BioAssayData_package.DesignElementDimension_list designElementDimension_list
An ordered list of designElements. It will be realized as one of its three subclasses.


quantitationTypeDimension_list

public BioAssayData_package.QuantitationTypeDimension_list quantitationTypeDimension_list
An ordered list of quantitationTypes.


bioAssayMap_list

public BioAssayData_package.BioAssayMap_list bioAssayMap_list
The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays.


quantitationTypeMap_list

public BioAssayData_package.QuantitationTypeMap_list quantitationTypeMap_list
A QuantitationTypeMap is the description of how source QuantitationTypes are mathematically transformed into a target QuantitationType.


bioAssayData_list

public BioAssayData_package.BioAssayData_list bioAssayData_list
Represents the dataset created when the BioAssays are created. BioAssayData is the entry point to the values. Because the actual values are represented by a different object, BioDataValues, which can be memory intensive, the annotation of the transformation can be gotten separate from the data.

Constructor Detail

BioAssayData_package

public BioAssayData_package()
Default constructor.


BioAssayData_package

public BioAssayData_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()

setBioAssayDimension_list

public void setBioAssayDimension_list(BioAssayData_package.BioAssayDimension_list bioAssayDimension_list)
Set method for bioAssayDimension_list

Parameters:
value - to set

getBioAssayDimension_list

public BioAssayData_package.BioAssayDimension_list getBioAssayDimension_list()
Get method for bioAssayDimension_list

Returns:
value of the attribute

addToBioAssayDimension_list

public void addToBioAssayDimension_list(BioAssayDimension bioAssayDimension)
Method to add BioAssayDimension to BioAssayDimension_list


addToBioAssayDimension_list

public void addToBioAssayDimension_list(int position,
                                        BioAssayDimension bioAssayDimension)
Method to add BioAssayDimension at position to BioAssayDimension_list


getFromBioAssayDimension_list

public BioAssayDimension getFromBioAssayDimension_list(int position)
Method to get BioAssayDimension from BioAssayDimension_list


removeElementAtFromBioAssayDimension_list

public void removeElementAtFromBioAssayDimension_list(int position)
Method to remove by position from BioAssayDimension_list


removeFromBioAssayDimension_list

public void removeFromBioAssayDimension_list(BioAssayDimension bioAssayDimension)
Method to remove first BioAssayDimension from BioAssayDimension_list


setDesignElementDimension_list

public void setDesignElementDimension_list(BioAssayData_package.DesignElementDimension_list designElementDimension_list)
Set method for designElementDimension_list

Parameters:
value - to set

getDesignElementDimension_list

public BioAssayData_package.DesignElementDimension_list getDesignElementDimension_list()
Get method for designElementDimension_list

Returns:
value of the attribute

addToDesignElementDimension_list

public void addToDesignElementDimension_list(DesignElementDimension designElementDimension)
Method to add DesignElementDimension to DesignElementDimension_list


addToDesignElementDimension_list

public void addToDesignElementDimension_list(int position,
                                             DesignElementDimension designElementDimension)
Method to add DesignElementDimension at position to DesignElementDimension_list


getFromDesignElementDimension_list

public DesignElementDimension getFromDesignElementDimension_list(int position)
Method to get DesignElementDimension from DesignElementDimension_list


removeElementAtFromDesignElementDimension_list

public void removeElementAtFromDesignElementDimension_list(int position)
Method to remove by position from DesignElementDimension_list


removeFromDesignElementDimension_list

public void removeFromDesignElementDimension_list(DesignElementDimension designElementDimension)
Method to remove first DesignElementDimension from DesignElementDimension_list


setQuantitationTypeDimension_list

public void setQuantitationTypeDimension_list(BioAssayData_package.QuantitationTypeDimension_list quantitationTypeDimension_list)
Set method for quantitationTypeDimension_list

Parameters:
value - to set

getQuantitationTypeDimension_list

public BioAssayData_package.QuantitationTypeDimension_list getQuantitationTypeDimension_list()
Get method for quantitationTypeDimension_list

Returns:
value of the attribute

addToQuantitationTypeDimension_list

public void addToQuantitationTypeDimension_list(QuantitationTypeDimension quantitationTypeDimension)
Method to add QuantitationTypeDimension to QuantitationTypeDimension_list


addToQuantitationTypeDimension_list

public void addToQuantitationTypeDimension_list(int position,
                                                QuantitationTypeDimension quantitationTypeDimension)
Method to add QuantitationTypeDimension at position to QuantitationTypeDimension_list


getFromQuantitationTypeDimension_list

public QuantitationTypeDimension getFromQuantitationTypeDimension_list(int position)
Method to get QuantitationTypeDimension from QuantitationTypeDimension_list


removeElementAtFromQuantitationTypeDimension_list

public void removeElementAtFromQuantitationTypeDimension_list(int position)
Method to remove by position from QuantitationTypeDimension_list


removeFromQuantitationTypeDimension_list

public void removeFromQuantitationTypeDimension_list(QuantitationTypeDimension quantitationTypeDimension)
Method to remove first QuantitationTypeDimension from QuantitationTypeDimension_list


setBioAssayMap_list

public void setBioAssayMap_list(BioAssayData_package.BioAssayMap_list bioAssayMap_list)
Set method for bioAssayMap_list

Parameters:
value - to set

getBioAssayMap_list

public BioAssayData_package.BioAssayMap_list getBioAssayMap_list()
Get method for bioAssayMap_list

Returns:
value of the attribute

addToBioAssayMap_list

public void addToBioAssayMap_list(BioAssayMap bioAssayMap)
Method to add BioAssayMap to BioAssayMap_list


addToBioAssayMap_list

public void addToBioAssayMap_list(int position,
                                  BioAssayMap bioAssayMap)
Method to add BioAssayMap at position to BioAssayMap_list


getFromBioAssayMap_list

public BioAssayMap getFromBioAssayMap_list(int position)
Method to get BioAssayMap from BioAssayMap_list


removeElementAtFromBioAssayMap_list

public void removeElementAtFromBioAssayMap_list(int position)
Method to remove by position from BioAssayMap_list


removeFromBioAssayMap_list

public void removeFromBioAssayMap_list(BioAssayMap bioAssayMap)
Method to remove first BioAssayMap from BioAssayMap_list


setQuantitationTypeMap_list

public void setQuantitationTypeMap_list(BioAssayData_package.QuantitationTypeMap_list quantitationTypeMap_list)
Set method for quantitationTypeMap_list

Parameters:
value - to set

getQuantitationTypeMap_list

public BioAssayData_package.QuantitationTypeMap_list getQuantitationTypeMap_list()
Get method for quantitationTypeMap_list

Returns:
value of the attribute

addToQuantitationTypeMap_list

public void addToQuantitationTypeMap_list(QuantitationTypeMap quantitationTypeMap)
Method to add QuantitationTypeMap to QuantitationTypeMap_list


addToQuantitationTypeMap_list

public void addToQuantitationTypeMap_list(int position,
                                          QuantitationTypeMap quantitationTypeMap)
Method to add QuantitationTypeMap at position to QuantitationTypeMap_list


getFromQuantitationTypeMap_list

public QuantitationTypeMap getFromQuantitationTypeMap_list(int position)
Method to get QuantitationTypeMap from QuantitationTypeMap_list


removeElementAtFromQuantitationTypeMap_list

public void removeElementAtFromQuantitationTypeMap_list(int position)
Method to remove by position from QuantitationTypeMap_list


removeFromQuantitationTypeMap_list

public void removeFromQuantitationTypeMap_list(QuantitationTypeMap quantitationTypeMap)
Method to remove first QuantitationTypeMap from QuantitationTypeMap_list


setBioAssayData_list

public void setBioAssayData_list(BioAssayData_package.BioAssayData_list bioAssayData_list)
Set method for bioAssayData_list

Parameters:
value - to set

getBioAssayData_list

public BioAssayData_package.BioAssayData_list getBioAssayData_list()
Get method for bioAssayData_list

Returns:
value of the attribute

addToBioAssayData_list

public void addToBioAssayData_list(BioAssayData bioAssayData)
Method to add BioAssayData to BioAssayData_list


addToBioAssayData_list

public void addToBioAssayData_list(int position,
                                   BioAssayData bioAssayData)
Method to add BioAssayData at position to BioAssayData_list


getFromBioAssayData_list

public BioAssayData getFromBioAssayData_list(int position)
Method to get BioAssayData from BioAssayData_list


removeElementAtFromBioAssayData_list

public void removeElementAtFromBioAssayData_list(int position)
Method to remove by position from BioAssayData_list


removeFromBioAssayData_list

public void removeFromBioAssayData_list(BioAssayData bioAssayData)
Method to remove first BioAssayData from BioAssayData_list