org.biomage.BioAssayData
Class BioAssayData

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.BioAssayData.BioAssayData

All Implemented Interfaces:

HasAuditTrail, HasBioAssayDimension, HasBioDataValues, HasDescriptions, HasDesignElementDimension, HasPropertySets, HasQuantitationTypeDimension, HasSecurity, HasSummaryStatistics, java.io.Serializable

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 inherited from class org.biomage.Interface.HasSummaryStatistics

HasSummaryStatistics.SummaryStatistics_list

Nested classes inherited from class org.biomage.Interface.HasAuditTrail

HasAuditTrail.AuditTrail_list

Nested classes inherited from class org.biomage.Interface.HasDescriptions

HasDescriptions.Descriptions_list

Nested classes inherited from class 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 HasSummaryStatistics.SummaryStatistics_list	summaryStatistics Statistics on the Quality of the BioAssayData.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

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
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	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

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

summaryStatistics

protected HasSummaryStatistics.SummaryStatistics_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

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.

Overrides:

writeMAGEML in class Identifiable

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

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

java.io.IOException

setSummaryStatistics

public void setSummaryStatistics(HasSummaryStatistics.SummaryStatistics_list summaryStatistics)

Set method for summaryStatistics

Specified by:

setSummaryStatistics in interface HasSummaryStatistics

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

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

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

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

getBioDataValues

public BioDataValues getBioDataValues()

Get method for bioDataValues

Specified by:

getBioDataValues in interface HasBioDataValues

Returns:

value of the attribute