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

---

org.biomage.BioAssayData
Class Transformation  

java.lang.Object
  org.biomage.Common.Extendable
      org.biomage.Common.Describable
          org.biomage.Common.Identifiable
              org.biomage.BioEvent.BioEvent
                  org.biomage.BioAssayData.Transformation

All Implemented Interfaces:

org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasBioAssayDataSources, org.biomage.Interface.HasBioAssayMapping, org.biomage.Interface.HasDerivedBioAssayDataTarget, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasDesignElementMapping, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasProtocolApplications, org.biomage.Interface.HasQuantitationTypeMapping, org.biomage.Interface.HasSecurity, java.io.Serializable

---

public class Transformation

extends org.biomage.BioEvent.BioEvent

implements java.io.Serializable, org.biomage.Interface.HasBioAssayDataSources, org.biomage.Interface.HasBioAssayMapping, org.biomage.Interface.HasDerivedBioAssayDataTarget, org.biomage.Interface.HasQuantitationTypeMapping, org.biomage.Interface.HasDesignElementMapping

The process by which derivedBioAssays are created from measuredBioAssays and/or derivedBioAssays. It uses mappings to indicate the input and output dimensions.

---

Nested Class Summary

 

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

org.biomage.Interface.HasBioAssayDataSources.BioAssayDataSources_list

 

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

org.biomage.Interface.HasProtocolApplications.ProtocolApplications_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.HasBioAssayDataSources.BioAssayDataSources_list	bioAssayDataSources           The BioAssayData sources that the Transformation event uses to produce the target DerivedBioAssayData.
private  BioAssayMapping	bioAssayMapping           The collection of mappings for the BioAssays.
private  DerivedBioAssayData	derivedBioAssayDataTarget           The association between the DerivedBioAssayData and the Transformation event that produced it.
private  DesignElementMapping	designElementMapping           The collection of mappings for the DesignElements.
private  QuantitationTypeMapping	quantitationTypeMapping           The collection of mappings for the QuantitationTypes.

 

Fields inherited from class org.biomage.BioEvent.BioEvent

 

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

Transformation()           Default constructor.

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

 

Method Summary
void	addToBioAssayDataSources(BioAssayData bioAssayData)           Method to add BioAssayData to BioAssayDataSources_list
void	addToBioAssayDataSources(int position, BioAssayData bioAssayData)           Method to add BioAssayData at position to BioAssayDataSources_list
org.biomage.Interface.HasBioAssayDataSources.BioAssayDataSources_list	getBioAssayDataSources()           Get method for bioAssayDataSources
BioAssayMapping	getBioAssayMapping()           Get method for bioAssayMapping
DerivedBioAssayData	getDerivedBioAssayDataTarget()           Get method for derivedBioAssayDataTarget
DesignElementMapping	getDesignElementMapping()           Get method for designElementMapping
BioAssayData	getFromBioAssayDataSources(int position)           Method to get BioAssayData from BioAssayDataSources_list
QuantitationTypeMapping	getQuantitationTypeMapping()           Get method for quantitationTypeMapping
void	removeElementAtFromBioAssayDataSources(int position)           Method to remove by position from BioAssayDataSources_list
void	removeFromBioAssayDataSources(BioAssayData bioAssayData)           Method to remove first BioAssayData from BioAssayDataSources_list
void	setBioAssayDataSources(org.biomage.Interface.HasBioAssayDataSources.BioAssayDataSources_list bioAssayDataSources)           Set method for bioAssayDataSources
void	setBioAssayMapping(BioAssayMapping bioAssayMapping)           Set method for bioAssayMapping
void	setDerivedBioAssayDataTarget(DerivedBioAssayData derivedBioAssayDataTarget)           Set method for derivedBioAssayDataTarget
void	setDesignElementMapping(DesignElementMapping designElementMapping)           Set method for designElementMapping
void	setQuantitationTypeMapping(QuantitationTypeMapping quantitationTypeMapping)           Set method for quantitationTypeMapping
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.BioEvent.BioEvent

addToProtocolApplications, addToProtocolApplications, getFromProtocolApplications, getProtocolApplications, removeElementAtFromProtocolApplications, removeFromProtocolApplications, setProtocolApplications

 

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

bioAssayDataSources

private org.biomage.Interface.HasBioAssayDataSources.BioAssayDataSources_list bioAssayDataSources

The BioAssayData sources that the Transformation event uses to produce the target DerivedBioAssayData.

---

bioAssayMapping

private BioAssayMapping bioAssayMapping

The collection of mappings for the BioAssays.

---

derivedBioAssayDataTarget

private DerivedBioAssayData derivedBioAssayDataTarget

The association between the DerivedBioAssayData and the Transformation event that produced it.

---

quantitationTypeMapping

private QuantitationTypeMapping quantitationTypeMapping

The collection of mappings for the QuantitationTypes.

---

designElementMapping

private DesignElementMapping designElementMapping

The collection of mappings for the DesignElements.

Constructor Detail

Transformation

public Transformation()

Default constructor.

---

Transformation

public Transformation(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.

---

setBioAssayDataSources

public void setBioAssayDataSources(org.biomage.Interface.HasBioAssayDataSources.BioAssayDataSources_list bioAssayDataSources)

Set method for bioAssayDataSources

Specified by:

setBioAssayDataSources in interface org.biomage.Interface.HasBioAssayDataSources

---

getBioAssayDataSources

public org.biomage.Interface.HasBioAssayDataSources.BioAssayDataSources_list getBioAssayDataSources()

Get method for bioAssayDataSources

Specified by:

getBioAssayDataSources in interface org.biomage.Interface.HasBioAssayDataSources

---

addToBioAssayDataSources

public void addToBioAssayDataSources(BioAssayData bioAssayData)

Method to add BioAssayData to BioAssayDataSources_list

Specified by:

addToBioAssayDataSources in interface org.biomage.Interface.HasBioAssayDataSources

---

addToBioAssayDataSources

public void addToBioAssayDataSources(int position,
                                     BioAssayData bioAssayData)

Method to add BioAssayData at position to BioAssayDataSources_list

Specified by:

addToBioAssayDataSources in interface org.biomage.Interface.HasBioAssayDataSources

---

getFromBioAssayDataSources

public BioAssayData getFromBioAssayDataSources(int position)

Method to get BioAssayData from BioAssayDataSources_list

Specified by:

getFromBioAssayDataSources in interface org.biomage.Interface.HasBioAssayDataSources

---

removeElementAtFromBioAssayDataSources

public void removeElementAtFromBioAssayDataSources(int position)

Method to remove by position from BioAssayDataSources_list

Specified by:

removeElementAtFromBioAssayDataSources in interface org.biomage.Interface.HasBioAssayDataSources

---

removeFromBioAssayDataSources

public void removeFromBioAssayDataSources(BioAssayData bioAssayData)

Method to remove first BioAssayData from BioAssayDataSources_list

Specified by:

removeFromBioAssayDataSources in interface org.biomage.Interface.HasBioAssayDataSources

---

setBioAssayMapping

public void setBioAssayMapping(BioAssayMapping bioAssayMapping)

Set method for bioAssayMapping

Specified by:

setBioAssayMapping in interface org.biomage.Interface.HasBioAssayMapping

---

getBioAssayMapping

public BioAssayMapping getBioAssayMapping()

Get method for bioAssayMapping

Specified by:

getBioAssayMapping in interface org.biomage.Interface.HasBioAssayMapping

---

setDerivedBioAssayDataTarget

public void setDerivedBioAssayDataTarget(DerivedBioAssayData derivedBioAssayDataTarget)

Set method for derivedBioAssayDataTarget

Specified by:

setDerivedBioAssayDataTarget in interface org.biomage.Interface.HasDerivedBioAssayDataTarget

---

getDerivedBioAssayDataTarget

public DerivedBioAssayData getDerivedBioAssayDataTarget()

Get method for derivedBioAssayDataTarget

Specified by:

getDerivedBioAssayDataTarget in interface org.biomage.Interface.HasDerivedBioAssayDataTarget

---

setQuantitationTypeMapping

public void setQuantitationTypeMapping(QuantitationTypeMapping quantitationTypeMapping)

Set method for quantitationTypeMapping

Specified by:

setQuantitationTypeMapping in interface org.biomage.Interface.HasQuantitationTypeMapping

---

getQuantitationTypeMapping

public QuantitationTypeMapping getQuantitationTypeMapping()

Get method for quantitationTypeMapping

Specified by:

getQuantitationTypeMapping in interface org.biomage.Interface.HasQuantitationTypeMapping

---

setDesignElementMapping

public void setDesignElementMapping(DesignElementMapping designElementMapping)

Set method for designElementMapping

Specified by:

setDesignElementMapping in interface org.biomage.Interface.HasDesignElementMapping

---

getDesignElementMapping

public DesignElementMapping getDesignElementMapping()

Get method for designElementMapping

Specified by:

getDesignElementMapping in interface org.biomage.Interface.HasDesignElementMapping

---

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

---