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org.biomage.BioAssay
Class DerivedBioAssay  

java.lang.Object
  org.biomage.Common.Extendable
      org.biomage.Common.Describable
          org.biomage.Common.Identifiable
              org.biomage.BioAssay.BioAssay
                  org.biomage.BioAssay.DerivedBioAssay

All Implemented Interfaces:

org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasBioAssayFactorValues, org.biomage.Interface.HasChannels, org.biomage.Interface.HasDerivedBioAssayData, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasSecurity, org.biomage.Interface.HasType, java.io.Serializable

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public class DerivedBioAssay

extends BioAssay

implements java.io.Serializable, org.biomage.Interface.HasDerivedBioAssayData, org.biomage.Interface.HasType

A BioAssay that is created by the Transformation BioEvent from one or more MeasuredBioAssays or DerivedBioAssays.

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Nested Class Summary

 

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

org.biomage.Interface.HasDerivedBioAssayData.DerivedBioAssayData_list

 

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

org.biomage.Interface.HasChannels.Channels_list

 

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

org.biomage.Interface.HasBioAssayFactorValues.BioAssayFactorValues_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  org.biomage.Interface.HasDerivedBioAssayData.DerivedBioAssayData_list	derivedBioAssayData           The data associated with the DerivedBioAssay.
private  org.biomage.Description.OntologyEntry	type           The derivation type, for instance collapsed spot replicate, ratio, averaged intensity, bioassay replicates, etc.

 

Fields inherited from class org.biomage.BioAssay.BioAssay

 

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

DerivedBioAssay()           Default constructor.

DerivedBioAssay(org.xml.sax.Attributes atts)           Attribute constructor.

 

Method Summary
void	addToDerivedBioAssayData(org.biomage.BioAssayData.DerivedBioAssayData derivedBioAssayData)           Method to add DerivedBioAssayData to DerivedBioAssayData_list
void	addToDerivedBioAssayData(int position, org.biomage.BioAssayData.DerivedBioAssayData derivedBioAssayData)           Method to add DerivedBioAssayData at position to DerivedBioAssayData_list
org.biomage.Interface.HasDerivedBioAssayData.DerivedBioAssayData_list	getDerivedBioAssayData()           Get method for derivedBioAssayData
org.biomage.BioAssayData.DerivedBioAssayData	getFromDerivedBioAssayData(int position)           Method to get DerivedBioAssayData from DerivedBioAssayData_list
org.biomage.Description.OntologyEntry	getType()           Get method for type
void	removeElementAtFromDerivedBioAssayData(int position)           Method to remove by position from DerivedBioAssayData_list
void	removeFromDerivedBioAssayData(org.biomage.BioAssayData.DerivedBioAssayData derivedBioAssayData)           Method to remove first DerivedBioAssayData from DerivedBioAssayData_list
void	setDerivedBioAssayData(org.biomage.Interface.HasDerivedBioAssayData.DerivedBioAssayData_list derivedBioAssayData)           Set method for derivedBioAssayData
void	setType(org.biomage.Description.OntologyEntry type)           Set method for type
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.BioAssay.BioAssay

addToBioAssayFactorValues, addToBioAssayFactorValues, addToChannels, addToChannels, getBioAssayFactorValues, getChannels, getFromBioAssayFactorValues, getFromChannels, removeElementAtFromBioAssayFactorValues, removeElementAtFromChannels, removeFromBioAssayFactorValues, removeFromChannels, setBioAssayFactorValues, setChannels

 

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

derivedBioAssayData

private org.biomage.Interface.HasDerivedBioAssayData.DerivedBioAssayData_list derivedBioAssayData

The data associated with the DerivedBioAssay.

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type

private org.biomage.Description.OntologyEntry type

The derivation type, for instance collapsed spot replicate, ratio, averaged intensity, bioassay replicates, etc.

Constructor Detail

DerivedBioAssay

public DerivedBioAssay()

Default constructor.

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DerivedBioAssay

public DerivedBioAssay(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 BioAssay

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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.

Overrides:

writeAttributes in class BioAssay

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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.

Overrides:

writeAssociations in class BioAssay

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setDerivedBioAssayData

public void setDerivedBioAssayData(org.biomage.Interface.HasDerivedBioAssayData.DerivedBioAssayData_list derivedBioAssayData)

Set method for derivedBioAssayData

Specified by:

setDerivedBioAssayData in interface org.biomage.Interface.HasDerivedBioAssayData

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getDerivedBioAssayData

public org.biomage.Interface.HasDerivedBioAssayData.DerivedBioAssayData_list getDerivedBioAssayData()

Get method for derivedBioAssayData

Specified by:

getDerivedBioAssayData in interface org.biomage.Interface.HasDerivedBioAssayData

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addToDerivedBioAssayData

public void addToDerivedBioAssayData(org.biomage.BioAssayData.DerivedBioAssayData derivedBioAssayData)

Method to add DerivedBioAssayData to DerivedBioAssayData_list

Specified by:

addToDerivedBioAssayData in interface org.biomage.Interface.HasDerivedBioAssayData

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addToDerivedBioAssayData

public void addToDerivedBioAssayData(int position,
                                     org.biomage.BioAssayData.DerivedBioAssayData derivedBioAssayData)

Method to add DerivedBioAssayData at position to DerivedBioAssayData_list

Specified by:

addToDerivedBioAssayData in interface org.biomage.Interface.HasDerivedBioAssayData

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getFromDerivedBioAssayData

public org.biomage.BioAssayData.DerivedBioAssayData getFromDerivedBioAssayData(int position)

Method to get DerivedBioAssayData from DerivedBioAssayData_list

Specified by:

getFromDerivedBioAssayData in interface org.biomage.Interface.HasDerivedBioAssayData

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removeElementAtFromDerivedBioAssayData

public void removeElementAtFromDerivedBioAssayData(int position)

Method to remove by position from DerivedBioAssayData_list

Specified by:

removeElementAtFromDerivedBioAssayData in interface org.biomage.Interface.HasDerivedBioAssayData

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removeFromDerivedBioAssayData

public void removeFromDerivedBioAssayData(org.biomage.BioAssayData.DerivedBioAssayData derivedBioAssayData)

Method to remove first DerivedBioAssayData from DerivedBioAssayData_list

Specified by:

removeFromDerivedBioAssayData in interface org.biomage.Interface.HasDerivedBioAssayData

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setType

public void setType(org.biomage.Description.OntologyEntry type)

Set method for type

Specified by:

setType in interface org.biomage.Interface.HasType

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getType

public org.biomage.Description.OntologyEntry getType()

Get method for type

Specified by:

getType in interface org.biomage.Interface.HasType

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

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