org.biomage.DesignElement
Class FeatureReporterMap

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.DesignElementMap
                                      |
                                      +--org.biomage.DesignElement.FeatureReporterMap

All Implemented Interfaces:

HasAuditTrail, HasDescriptions, HasFeatureInformationSources, HasPropertySets, HasProtocolApplications, HasReporter, HasSecurity, java.io.Serializable

public class FeatureReporterMap

extends DesignElementMap

implements java.io.Serializable, HasReporter, HasFeatureInformationSources

A FeatureReporterMap is the description of how source features are transformed into a target reporter. These would map replicate features for a reporter to the reporter.

See Also:

Serialized Form

Nested Class Summary

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

HasFeatureInformationSources.FeatureInformationSources_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 HasFeatureInformationSources.FeatureInformationSources_list	featureInformationSources Typically, the features on an array that are manufactured with this reporter's BioSequence.
protected Reporter	reporter Associates features with their reporter.

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

FeatureReporterMap()
Default constructor.

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

Method Summary

void	addToFeatureInformationSources(FeatureInformation featureInformation) Method to add FeatureInformation to FeatureInformationSources_list
void	addToFeatureInformationSources(int position, FeatureInformation featureInformation) Method to add FeatureInformation at position to FeatureInformationSources_list
HasFeatureInformationSources.FeatureInformationSources_list	getFeatureInformationSources() Get method for featureInformationSources
FeatureInformation	getFromFeatureInformationSources(int position) Method to get FeatureInformation from FeatureInformationSources_list
Reporter	getReporter() Get method for reporter
void	removeElementAtFromFeatureInformationSources(int position) Method to remove by position from FeatureInformationSources_list
void	removeFromFeatureInformationSources(FeatureInformation featureInformation) Method to remove first FeatureInformation from FeatureInformationSources_list
void	setFeatureInformationSources(HasFeatureInformationSources.FeatureInformationSources_list featureInformationSources) Set method for featureInformationSources
void	setReporter(Reporter reporter) Set method for reporter
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

reporter

protected Reporter reporter

Associates features with their reporter.

featureInformationSources

protected HasFeatureInformationSources.FeatureInformationSources_list featureInformationSources

Typically, the features on an array that are manufactured with this reporter's BioSequence.

Constructor Detail

FeatureReporterMap

public FeatureReporterMap()

Default constructor.

FeatureReporterMap

public FeatureReporterMap(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 DesignElementMap

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 DesignElementMap

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 DesignElementMap

java.io.IOException

setReporter

public void setReporter(Reporter reporter)

Set method for reporter

Specified by:

setReporter in interface HasReporter

getReporter

public Reporter getReporter()

Get method for reporter

Specified by:

getReporter in interface HasReporter

Returns:

value of the attribute

setFeatureInformationSources

public void setFeatureInformationSources(HasFeatureInformationSources.FeatureInformationSources_list featureInformationSources)

Set method for featureInformationSources

Specified by:

setFeatureInformationSources in interface HasFeatureInformationSources

getFeatureInformationSources

public HasFeatureInformationSources.FeatureInformationSources_list getFeatureInformationSources()

Get method for featureInformationSources

Specified by:

getFeatureInformationSources in interface HasFeatureInformationSources

Returns:

value of the attribute

addToFeatureInformationSources

public void addToFeatureInformationSources(FeatureInformation featureInformation)

Method to add FeatureInformation to FeatureInformationSources_list

Specified by:

addToFeatureInformationSources in interface HasFeatureInformationSources

addToFeatureInformationSources

public void addToFeatureInformationSources(int position,
                                           FeatureInformation featureInformation)

Method to add FeatureInformation at position to FeatureInformationSources_list

Specified by:

addToFeatureInformationSources in interface HasFeatureInformationSources

getFromFeatureInformationSources

public FeatureInformation getFromFeatureInformationSources(int position)

Method to get FeatureInformation from FeatureInformationSources_list

Specified by:

getFromFeatureInformationSources in interface HasFeatureInformationSources

removeElementAtFromFeatureInformationSources

public void removeElementAtFromFeatureInformationSources(int position)

Method to remove by position from FeatureInformationSources_list

Specified by:

removeElementAtFromFeatureInformationSources in interface HasFeatureInformationSources

removeFromFeatureInformationSources

public void removeFromFeatureInformationSources(FeatureInformation featureInformation)

Method to remove first FeatureInformation from FeatureInformationSources_list

Specified by:

removeFromFeatureInformationSources in interface HasFeatureInformationSources