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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:

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

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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.

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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.

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designElementDimension

private DesignElementDimension designElementDimension

The DesignElements of the BioAssayData.

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quantitationTypeDimension

private QuantitationTypeDimension quantitationTypeDimension

The QuantitationTypes of the BioAssayData.

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summaryStatistics

private org.biomage.Interface.HasSummaryStatistics.SummaryStatistics_list summaryStatistics

Statistics on the Quality of the BioAssayData.

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bioDataValues

private BioDataValues bioDataValues

The data values of the BioAssayData.

Constructor Detail

BioAssayData

public BioAssayData()

Default constructor.

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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.

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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.

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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.

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setBioAssayDimension

public void setBioAssayDimension(BioAssayDimension bioAssayDimension)

Set method for bioAssayDimension

Specified by:

setBioAssayDimension in interface org.biomage.Interface.HasBioAssayDimension

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getBioAssayDimension

public BioAssayDimension getBioAssayDimension()

Get method for bioAssayDimension

Specified by:

getBioAssayDimension in interface org.biomage.Interface.HasBioAssayDimension

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setDesignElementDimension

public void setDesignElementDimension(DesignElementDimension designElementDimension)

Set method for designElementDimension

Specified by:

setDesignElementDimension in interface org.biomage.Interface.HasDesignElementDimension

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getDesignElementDimension

public DesignElementDimension getDesignElementDimension()

Get method for designElementDimension

Specified by:

getDesignElementDimension in interface org.biomage.Interface.HasDesignElementDimension

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setQuantitationTypeDimension

public void setQuantitationTypeDimension(QuantitationTypeDimension quantitationTypeDimension)

Set method for quantitationTypeDimension

Specified by:

setQuantitationTypeDimension in interface org.biomage.Interface.HasQuantitationTypeDimension

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getQuantitationTypeDimension

public QuantitationTypeDimension getQuantitationTypeDimension()

Get method for quantitationTypeDimension

Specified by:

getQuantitationTypeDimension in interface org.biomage.Interface.HasQuantitationTypeDimension

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setSummaryStatistics

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

Set method for summaryStatistics

Specified by:

setSummaryStatistics in interface org.biomage.Interface.HasSummaryStatistics

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getSummaryStatistics

public org.biomage.Interface.HasSummaryStatistics.SummaryStatistics_list getSummaryStatistics()

Get method for summaryStatistics

Specified by:

getSummaryStatistics in interface org.biomage.Interface.HasSummaryStatistics

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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

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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

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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

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removeElementAtFromSummaryStatistics

public void removeElementAtFromSummaryStatistics(int position)

Method to remove by position from SummaryStatistics_list

Specified by:

removeElementAtFromSummaryStatistics in interface org.biomage.Interface.HasSummaryStatistics

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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

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setBioDataValues

public void setBioDataValues(BioDataValues bioDataValues)

Set method for bioDataValues

Specified by:

setBioDataValues in interface org.biomage.Interface.HasBioDataValues

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getBioDataValues

public BioDataValues getBioDataValues()

Get method for bioDataValues

Specified by:

getBioDataValues in interface org.biomage.Interface.HasBioDataValues

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ BioAssayData overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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