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org.biomage.BioAssayData
Class BioAssayData  view BioAssayData download BioAssayData.java

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

public abstract class BioAssayData
extends org.biomage.Common.Identifiable
implements java.io.Serializable, org.biomage.Interface.HasBioAssayDimension, org.biomage.Interface.HasDesignElementDimension, org.biomage.Interface.HasQuantitationTypeDimension, org.biomage.Interface.HasSummaryStatistics, org.biomage.Interface.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.


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasSummaryStatistics
org.biomage.Interface.HasSummaryStatistics.SummaryStatistics_list
 
Nested classes inherited from class org.biomage.Interface.HasAuditTrail
org.biomage.Interface.HasAuditTrail.AuditTrail_list
 
Nested classes inherited from class org.biomage.Interface.HasDescriptions
org.biomage.Interface.HasDescriptions.Descriptions_list
 
Nested classes inherited from class org.biomage.Interface.HasPropertySets
org.biomage.Interface.HasPropertySets.PropertySets_list
 
Field Summary
private  BioAssayDimension bioAssayDimension
          The BioAssays of the BioAssayData.
private  BioDataValues bioDataValues
          The data values of the BioAssayData.
private  DesignElementDimension designElementDimension
          The DesignElements of the BioAssayData.
private  QuantitationTypeDimension quantitationTypeDimension
          The QuantitationTypes of the BioAssayData.
private  org.biomage.Interface.HasSummaryStatistics.SummaryStatistics_list summaryStatistics
          Statistics on the Quality of the BioAssayData.
 
Fields inherited from class org.biomage.Common.Identifiable
 
Fields inherited from class org.biomage.Common.Describable
 
Fields inherited from class org.biomage.Common.Extendable
 
Constructor Summary
BioAssayData()
          Default constructor.
BioAssayData(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToSummaryStatistics(int position, org.biomage.Common.NameValueType nameValueType)
          Method to add NameValueType at position to SummaryStatistics_list
 void addToSummaryStatistics(org.biomage.Common.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
 org.biomage.Common.NameValueType getFromSummaryStatistics(int position)
          Method to get NameValueType from SummaryStatistics_list
 QuantitationTypeDimension getQuantitationTypeDimension()
          Get method for quantitationTypeDimension
 org.biomage.Interface.HasSummaryStatistics.SummaryStatistics_list getSummaryStatistics()
          Get method for summaryStatistics
 void removeElementAtFromSummaryStatistics(int position)
          Method to remove by position from SummaryStatistics_list
 void removeFromSummaryStatistics(org.biomage.Common.NameValueType nameValueType)
          Method to remove first NameValueType from SummaryStatistics_list
 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(org.biomage.Interface.HasSummaryStatistics.SummaryStatistics_list summaryStatistics)
          Set method for summaryStatistics
 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 org.biomage.Common.Identifiable
getIdentifier, getName, setIdentifier, setName
 
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, getFromPropertySets, getPropertySets, removeElementAtFromPropertySets, removeFromPropertySets, setPropertySets
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

bioAssayDimension

private BioAssayDimension bioAssayDimension
The BioAssays of the BioAssayData.


designElementDimension

private DesignElementDimension designElementDimension
The DesignElements of the BioAssayData.


quantitationTypeDimension

private QuantitationTypeDimension quantitationTypeDimension
The QuantitationTypes of the BioAssayData.


summaryStatistics

private org.biomage.Interface.HasSummaryStatistics.SummaryStatistics_list summaryStatistics
Statistics on the Quality of the BioAssayData.


bioDataValues

private 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

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.


setBioAssayDimension

public void setBioAssayDimension(BioAssayDimension bioAssayDimension)
Set method for bioAssayDimension

Specified by:
setBioAssayDimension in interface org.biomage.Interface.HasBioAssayDimension

getBioAssayDimension

public BioAssayDimension getBioAssayDimension()
Get method for bioAssayDimension

Specified by:
getBioAssayDimension in interface org.biomage.Interface.HasBioAssayDimension

setDesignElementDimension

public void setDesignElementDimension(DesignElementDimension designElementDimension)
Set method for designElementDimension

Specified by:
setDesignElementDimension in interface org.biomage.Interface.HasDesignElementDimension

getDesignElementDimension

public DesignElementDimension getDesignElementDimension()
Get method for designElementDimension

Specified by:
getDesignElementDimension in interface org.biomage.Interface.HasDesignElementDimension

setQuantitationTypeDimension

public void setQuantitationTypeDimension(QuantitationTypeDimension quantitationTypeDimension)
Set method for quantitationTypeDimension

Specified by:
setQuantitationTypeDimension in interface org.biomage.Interface.HasQuantitationTypeDimension

getQuantitationTypeDimension

public QuantitationTypeDimension getQuantitationTypeDimension()
Get method for quantitationTypeDimension

Specified by:
getQuantitationTypeDimension in interface org.biomage.Interface.HasQuantitationTypeDimension

setSummaryStatistics

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

Specified by:
setSummaryStatistics in interface org.biomage.Interface.HasSummaryStatistics

getSummaryStatistics

public org.biomage.Interface.HasSummaryStatistics.SummaryStatistics_list getSummaryStatistics()
Get method for summaryStatistics

Specified by:
getSummaryStatistics in interface org.biomage.Interface.HasSummaryStatistics

addToSummaryStatistics

public void addToSummaryStatistics(org.biomage.Common.NameValueType nameValueType)
Method to add NameValueType to SummaryStatistics_list

Specified by:
addToSummaryStatistics in interface org.biomage.Interface.HasSummaryStatistics

addToSummaryStatistics

public void addToSummaryStatistics(int position,
                                   org.biomage.Common.NameValueType nameValueType)
Method to add NameValueType at position to SummaryStatistics_list

Specified by:
addToSummaryStatistics in interface org.biomage.Interface.HasSummaryStatistics

getFromSummaryStatistics

public org.biomage.Common.NameValueType getFromSummaryStatistics(int position)
Method to get NameValueType from SummaryStatistics_list

Specified by:
getFromSummaryStatistics in interface org.biomage.Interface.HasSummaryStatistics

removeElementAtFromSummaryStatistics

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

Specified by:
removeElementAtFromSummaryStatistics in interface org.biomage.Interface.HasSummaryStatistics

removeFromSummaryStatistics

public void removeFromSummaryStatistics(org.biomage.Common.NameValueType nameValueType)
Method to remove first NameValueType from SummaryStatistics_list

Specified by:
removeFromSummaryStatistics in interface org.biomage.Interface.HasSummaryStatistics

setBioDataValues

public void setBioDataValues(BioDataValues bioDataValues)
Set method for bioDataValues

Specified by:
setBioDataValues in interface org.biomage.Interface.HasBioDataValues

getBioDataValues

public BioDataValues getBioDataValues()
Get method for bioDataValues

Specified by:
getBioDataValues in interface org.biomage.Interface.HasBioDataValues