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org.biomage.BioAssayData
Class BioAssayMap  

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

All Implemented Interfaces:

org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasBioAssayMapTarget, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasProtocolApplications, org.biomage.Interface.HasSecurity, org.biomage.Interface.HasSourceBioAssays, java.io.Serializable

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public class BioAssayMap

extends org.biomage.BioEvent.Map

implements java.io.Serializable, org.biomage.Interface.HasBioAssayMapTarget, org.biomage.Interface.HasSourceBioAssays

The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays.

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Nested Class Summary

 

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

org.biomage.Interface.HasSourceBioAssays.SourceBioAssays_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.BioAssay.DerivedBioAssay	bioAssayMapTarget           The DerivedBioAssay that is produced by the sources of the BioAssayMap.
private  org.biomage.Interface.HasSourceBioAssays.SourceBioAssays_list	sourceBioAssays           The sources of the BioAssayMap that are used to produce a target DerivedBioAssay.

 

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

BioAssayMap()           Default constructor.

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

 

Method Summary
void	addToSourceBioAssays(org.biomage.BioAssay.BioAssay bioAssay)           Method to add BioAssay to SourceBioAssays_list
void	addToSourceBioAssays(int position, org.biomage.BioAssay.BioAssay bioAssay)           Method to add BioAssay at position to SourceBioAssays_list
org.biomage.BioAssay.DerivedBioAssay	getBioAssayMapTarget()           Get method for bioAssayMapTarget
org.biomage.BioAssay.BioAssay	getFromSourceBioAssays(int position)           Method to get BioAssay from SourceBioAssays_list
org.biomage.Interface.HasSourceBioAssays.SourceBioAssays_list	getSourceBioAssays()           Get method for sourceBioAssays
void	removeElementAtFromSourceBioAssays(int position)           Method to remove by position from SourceBioAssays_list
void	removeFromSourceBioAssays(org.biomage.BioAssay.BioAssay bioAssay)           Method to remove first BioAssay from SourceBioAssays_list
void	setBioAssayMapTarget(org.biomage.BioAssay.DerivedBioAssay bioAssayMapTarget)           Set method for bioAssayMapTarget
void	setSourceBioAssays(org.biomage.Interface.HasSourceBioAssays.SourceBioAssays_list sourceBioAssays)           Set method for sourceBioAssays
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

bioAssayMapTarget

private org.biomage.BioAssay.DerivedBioAssay bioAssayMapTarget

The DerivedBioAssay that is produced by the sources of the BioAssayMap.

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sourceBioAssays

private org.biomage.Interface.HasSourceBioAssays.SourceBioAssays_list sourceBioAssays

The sources of the BioAssayMap that are used to produce a target DerivedBioAssay.

Constructor Detail

BioAssayMap

public BioAssayMap()

Default constructor.

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BioAssayMap

public BioAssayMap(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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setBioAssayMapTarget

public void setBioAssayMapTarget(org.biomage.BioAssay.DerivedBioAssay bioAssayMapTarget)

Set method for bioAssayMapTarget

Specified by:

setBioAssayMapTarget in interface org.biomage.Interface.HasBioAssayMapTarget

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getBioAssayMapTarget

public org.biomage.BioAssay.DerivedBioAssay getBioAssayMapTarget()

Get method for bioAssayMapTarget

Specified by:

getBioAssayMapTarget in interface org.biomage.Interface.HasBioAssayMapTarget

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setSourceBioAssays

public void setSourceBioAssays(org.biomage.Interface.HasSourceBioAssays.SourceBioAssays_list sourceBioAssays)

Set method for sourceBioAssays

Specified by:

setSourceBioAssays in interface org.biomage.Interface.HasSourceBioAssays

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getSourceBioAssays

public org.biomage.Interface.HasSourceBioAssays.SourceBioAssays_list getSourceBioAssays()

Get method for sourceBioAssays

Specified by:

getSourceBioAssays in interface org.biomage.Interface.HasSourceBioAssays

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addToSourceBioAssays

public void addToSourceBioAssays(org.biomage.BioAssay.BioAssay bioAssay)

Method to add BioAssay to SourceBioAssays_list

Specified by:

addToSourceBioAssays in interface org.biomage.Interface.HasSourceBioAssays

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addToSourceBioAssays

public void addToSourceBioAssays(int position,
                                 org.biomage.BioAssay.BioAssay bioAssay)

Method to add BioAssay at position to SourceBioAssays_list

Specified by:

addToSourceBioAssays in interface org.biomage.Interface.HasSourceBioAssays

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getFromSourceBioAssays

public org.biomage.BioAssay.BioAssay getFromSourceBioAssays(int position)

Method to get BioAssay from SourceBioAssays_list

Specified by:

getFromSourceBioAssays in interface org.biomage.Interface.HasSourceBioAssays

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removeElementAtFromSourceBioAssays

public void removeElementAtFromSourceBioAssays(int position)

Method to remove by position from SourceBioAssays_list

Specified by:

removeElementAtFromSourceBioAssays in interface org.biomage.Interface.HasSourceBioAssays

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removeFromSourceBioAssays

public void removeFromSourceBioAssays(org.biomage.BioAssay.BioAssay bioAssay)

Method to remove first BioAssay from SourceBioAssays_list

Specified by:

removeFromSourceBioAssays in interface org.biomage.Interface.HasSourceBioAssays

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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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