org.biomage.BioAssayData
Class BioAssayData

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Common.Describable
          extended by org.biomage.Common.Identifiable
              extended by org.biomage.BioAssayData.BioAssayData
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasBioAssayDimension, HasBioDataValues, HasDescriptions, HasDesignElementDimension, HasPropertySets, HasQuantitationTypeDimension, HasSecurity, HasSummaryStatistics
Direct Known Subclasses:
DerivedBioAssayData, MeasuredBioAssayData

public abstract class BioAssayData
extends Identifiable
implements java.io.Serializable, HasBioAssayDimension, HasDesignElementDimension, HasQuantitationTypeDimension, HasSummaryStatistics, HasBioDataValues

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.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasSummaryStatistics
HasSummaryStatistics.SummaryStatistics_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail
HasAuditTrail.AuditTrail_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions
HasDescriptions.Descriptions_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets
HasPropertySets.PropertySets_list
 
Field Summary
protected  BioAssayDimension bioAssayDimension
          The BioAssays of the BioAssayData.
protected  BioDataValues bioDataValues
          The data values of the BioAssayData.
protected  DesignElementDimension designElementDimension
          The DesignElements of the BioAssayData.
protected  QuantitationTypeDimension quantitationTypeDimension
          The QuantitationTypes of the BioAssayData.
protected  java.util.List summaryStatistics
          Statistics on the Quality of the BioAssayData.
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
BioAssayData()
          Default constructor.
BioAssayData(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToSummaryStatistics(int position, NameValueType nameValueType)
          Method to add NameValueType at position to SummaryStatistics_list
 void addToSummaryStatistics(NameValueType nameValueType)
          Method to add NameValueType to SummaryStatistics_list
 BioAssayDimension getBioAssayDimension()
          Get method for bioAssayDimension
 BioDataValues getBioDataValues()
          Get method for bioDataValues
 DesignElementDimension getDesignElementDimension()
          Get method for designElementDimension
 NameValueType getFromSummaryStatistics(int position)
          Method to get NameValueType from SummaryStatistics_list
 java.lang.String getModelClassName()
           
 QuantitationTypeDimension getQuantitationTypeDimension()
          Get method for quantitationTypeDimension
 HasSummaryStatistics.SummaryStatistics_list getSummaryStatistics()
          Get method for summaryStatistics
 void removeElementAtFromSummaryStatistics(int position)
          Method to remove by position from SummaryStatistics_list
 void removeFromSummaryStatistics(NameValueType nameValueType)
          Method to remove first NameValueType from SummaryStatistics_list
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setBioAssayDimension(BioAssayDimension bioAssayDimension)
          Set method for bioAssayDimension
 void setBioDataValues(BioDataValues bioDataValues)
          Set method for bioDataValues
 void setDesignElementDimension(DesignElementDimension designElementDimension)
          Set method for designElementDimension
 void setQuantitationTypeDimension(QuantitationTypeDimension quantitationTypeDimension)
          Set method for quantitationTypeDimension
 void setSummaryStatistics(HasSummaryStatistics.SummaryStatistics_list summaryStatistics)
          Set method for summaryStatistics
 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 org.biomage.Common.Identifiable
getIdentifier, getName, setIdentifier, setName, toString
 
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, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

summaryStatistics

protected java.util.List summaryStatistics
Statistics on the Quality of the BioAssayData.


bioAssayDimension

protected BioAssayDimension bioAssayDimension
The BioAssays of the BioAssayData.


designElementDimension

protected DesignElementDimension designElementDimension
The DesignElements of the BioAssayData.


quantitationTypeDimension

protected QuantitationTypeDimension quantitationTypeDimension
The QuantitationTypes of the BioAssayData.


bioDataValues

protected BioDataValues bioDataValues
The data values of the BioAssayData.

Constructor Detail

BioAssayData

public BioAssayData()
Default constructor.


BioAssayData

public BioAssayData(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

setAttributes

public void setAttributes(org.xml.sax.Attributes atts)
Overrides:
setAttributes in class Identifiable

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.

Overrides:
writeMAGEML in class Identifiable
Throws:
java.io.IOException

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.

Overrides:
writeAttributes in class Identifiable
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.

Overrides:
writeAssociations in class Identifiable
Throws:
java.io.IOException

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class Identifiable

setSummaryStatistics

public void setSummaryStatistics(HasSummaryStatistics.SummaryStatistics_list summaryStatistics)
Set method for summaryStatistics

Specified by:
setSummaryStatistics in interface HasSummaryStatistics
Parameters:
value - to set

getSummaryStatistics

public HasSummaryStatistics.SummaryStatistics_list getSummaryStatistics()
Get method for summaryStatistics

Specified by:
getSummaryStatistics in interface HasSummaryStatistics
Returns:
value of the attribute

addToSummaryStatistics

public void addToSummaryStatistics(NameValueType nameValueType)
Method to add NameValueType to SummaryStatistics_list

Specified by:
addToSummaryStatistics in interface HasSummaryStatistics

addToSummaryStatistics

public void addToSummaryStatistics(int position,
                                   NameValueType nameValueType)
Method to add NameValueType at position to SummaryStatistics_list

Specified by:
addToSummaryStatistics in interface HasSummaryStatistics

getFromSummaryStatistics

public NameValueType getFromSummaryStatistics(int position)
Method to get NameValueType from SummaryStatistics_list

Specified by:
getFromSummaryStatistics in interface HasSummaryStatistics

removeElementAtFromSummaryStatistics

public void removeElementAtFromSummaryStatistics(int position)
Method to remove by position from SummaryStatistics_list

Specified by:
removeElementAtFromSummaryStatistics in interface HasSummaryStatistics

removeFromSummaryStatistics

public void removeFromSummaryStatistics(NameValueType nameValueType)
Method to remove first NameValueType from SummaryStatistics_list

Specified by:
removeFromSummaryStatistics in interface HasSummaryStatistics

setBioAssayDimension

public void setBioAssayDimension(BioAssayDimension bioAssayDimension)
Set method for bioAssayDimension

Specified by:
setBioAssayDimension in interface HasBioAssayDimension
Parameters:
value - to set

getBioAssayDimension

public BioAssayDimension getBioAssayDimension()
Get method for bioAssayDimension

Specified by:
getBioAssayDimension in interface HasBioAssayDimension
Returns:
value of the attribute

setDesignElementDimension

public void setDesignElementDimension(DesignElementDimension designElementDimension)
Set method for designElementDimension

Specified by:
setDesignElementDimension in interface HasDesignElementDimension
Parameters:
value - to set

getDesignElementDimension

public DesignElementDimension getDesignElementDimension()
Get method for designElementDimension

Specified by:
getDesignElementDimension in interface HasDesignElementDimension
Returns:
value of the attribute

setQuantitationTypeDimension

public void setQuantitationTypeDimension(QuantitationTypeDimension quantitationTypeDimension)
Set method for quantitationTypeDimension

Specified by:
setQuantitationTypeDimension in interface HasQuantitationTypeDimension
Parameters:
value - to set

getQuantitationTypeDimension

public QuantitationTypeDimension getQuantitationTypeDimension()
Get method for quantitationTypeDimension

Specified by:
getQuantitationTypeDimension in interface HasQuantitationTypeDimension
Returns:
value of the attribute

setBioDataValues

public void setBioDataValues(BioDataValues bioDataValues)
Set method for bioDataValues

Specified by:
setBioDataValues in interface HasBioDataValues
Parameters:
value - to set

getBioDataValues

public BioDataValues getBioDataValues()
Get method for bioDataValues

Specified by:
getBioDataValues in interface HasBioDataValues
Returns:
value of the attribute