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:

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

public class BioAssayMap

extends Map

implements java.io.Serializable, HasBioAssayMapTarget, HasSourceBioAssays

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

See Also:

Serialized Form

Nested Class Summary

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

HasSourceBioAssays.SourceBioAssays_list

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

HasProtocolApplications.ProtocolApplications_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 DerivedBioAssay	bioAssayMapTarget The DerivedBioAssay that is produced by the sources of the BioAssayMap.
protected 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

protocolApplications

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

BioAssayMap()
Default constructor.

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

Method Summary

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

protected DerivedBioAssay bioAssayMapTarget

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

sourceBioAssays

protected HasSourceBioAssays.SourceBioAssays_list sourceBioAssays

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

Constructor Detail

BioAssayMap

public BioAssayMap()

Default constructor.

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.

Overrides:

writeMAGEML in class Map

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 Map

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 Map

java.io.IOException

setBioAssayMapTarget

public void setBioAssayMapTarget(DerivedBioAssay bioAssayMapTarget)

Set method for bioAssayMapTarget

Specified by:

setBioAssayMapTarget in interface HasBioAssayMapTarget

getBioAssayMapTarget

public DerivedBioAssay getBioAssayMapTarget()

Get method for bioAssayMapTarget

Specified by:

getBioAssayMapTarget in interface HasBioAssayMapTarget

Returns:

value of the attribute

setSourceBioAssays

public void setSourceBioAssays(HasSourceBioAssays.SourceBioAssays_list sourceBioAssays)

Set method for sourceBioAssays

Specified by:

setSourceBioAssays in interface HasSourceBioAssays

getSourceBioAssays

public HasSourceBioAssays.SourceBioAssays_list getSourceBioAssays()

Get method for sourceBioAssays

Specified by:

getSourceBioAssays in interface HasSourceBioAssays

Returns:

value of the attribute

addToSourceBioAssays

public void addToSourceBioAssays(BioAssay bioAssay)

Method to add BioAssay to SourceBioAssays_list

Specified by:

addToSourceBioAssays in interface HasSourceBioAssays

addToSourceBioAssays

public void addToSourceBioAssays(int position,
                                 BioAssay bioAssay)

Method to add BioAssay at position to SourceBioAssays_list

Specified by:

addToSourceBioAssays in interface HasSourceBioAssays

getFromSourceBioAssays

public BioAssay getFromSourceBioAssays(int position)

Method to get BioAssay from SourceBioAssays_list

Specified by:

getFromSourceBioAssays in interface HasSourceBioAssays

removeElementAtFromSourceBioAssays

public void removeElementAtFromSourceBioAssays(int position)

Method to remove by position from SourceBioAssays_list

Specified by:

removeElementAtFromSourceBioAssays in interface HasSourceBioAssays

removeFromSourceBioAssays

public void removeFromSourceBioAssays(BioAssay bioAssay)

Method to remove first BioAssay from SourceBioAssays_list

Specified by:

removeFromSourceBioAssays in interface HasSourceBioAssays