org.biomage.DesignElement
Class ReporterCompositeMap

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.ReporterCompositeMap

All Implemented Interfaces:

HasAuditTrail, HasCompositeSequence, HasDescriptions, HasPropertySets, HasProtocolApplications, HasReporterPositionSources, HasSecurity, java.io.Serializable

public class ReporterCompositeMap

extends DesignElementMap

implements java.io.Serializable, HasReporterPositionSources, HasCompositeSequence

A ReporterCompositeMap is the description of how source Reporters are transformed into a target CompositeSequences. For instance, several reporters that tile across a section of a chromosome could be mapped to a CompositeSequence.

See Also:

Serialized Form

Nested Class Summary

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

HasReporterPositionSources.ReporterPositionSources_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 CompositeSequence	compositeSequence A map to the reporters that compose this CompositeSequence.
protected HasReporterPositionSources.ReporterPositionSources_list	reporterPositionSources Association to the reporters that compose this CompositeSequence and where those reporters occur.

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

ReporterCompositeMap()
Default constructor.

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

Method Summary

void	addToReporterPositionSources(int position, ReporterPosition reporterPosition) Method to add ReporterPosition at position to ReporterPositionSources_list
void	addToReporterPositionSources(ReporterPosition reporterPosition) Method to add ReporterPosition to ReporterPositionSources_list
CompositeSequence	getCompositeSequence() Get method for compositeSequence
ReporterPosition	getFromReporterPositionSources(int position) Method to get ReporterPosition from ReporterPositionSources_list
HasReporterPositionSources.ReporterPositionSources_list	getReporterPositionSources() Get method for reporterPositionSources
void	removeElementAtFromReporterPositionSources(int position) Method to remove by position from ReporterPositionSources_list
void	removeFromReporterPositionSources(ReporterPosition reporterPosition) Method to remove first ReporterPosition from ReporterPositionSources_list
void	setCompositeSequence(CompositeSequence compositeSequence) Set method for compositeSequence
void	setReporterPositionSources(HasReporterPositionSources.ReporterPositionSources_list reporterPositionSources) Set method for reporterPositionSources
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

compositeSequence

protected CompositeSequence compositeSequence

A map to the reporters that compose this CompositeSequence.

reporterPositionSources

protected HasReporterPositionSources.ReporterPositionSources_list reporterPositionSources

Association to the reporters that compose this CompositeSequence and where those reporters occur.

Constructor Detail

ReporterCompositeMap

public ReporterCompositeMap()

Default constructor.

ReporterCompositeMap

public ReporterCompositeMap(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

setCompositeSequence

public void setCompositeSequence(CompositeSequence compositeSequence)

Set method for compositeSequence

Specified by:

setCompositeSequence in interface HasCompositeSequence

getCompositeSequence

public CompositeSequence getCompositeSequence()

Get method for compositeSequence

Specified by:

getCompositeSequence in interface HasCompositeSequence

Returns:

value of the attribute

setReporterPositionSources

public void setReporterPositionSources(HasReporterPositionSources.ReporterPositionSources_list reporterPositionSources)

Set method for reporterPositionSources

Specified by:

setReporterPositionSources in interface HasReporterPositionSources

getReporterPositionSources

public HasReporterPositionSources.ReporterPositionSources_list getReporterPositionSources()

Get method for reporterPositionSources

Specified by:

getReporterPositionSources in interface HasReporterPositionSources

Returns:

value of the attribute

addToReporterPositionSources

public void addToReporterPositionSources(ReporterPosition reporterPosition)

Method to add ReporterPosition to ReporterPositionSources_list

Specified by:

addToReporterPositionSources in interface HasReporterPositionSources

addToReporterPositionSources

public void addToReporterPositionSources(int position,
                                         ReporterPosition reporterPosition)

Method to add ReporterPosition at position to ReporterPositionSources_list

Specified by:

addToReporterPositionSources in interface HasReporterPositionSources

getFromReporterPositionSources

public ReporterPosition getFromReporterPositionSources(int position)

Method to get ReporterPosition from ReporterPositionSources_list

Specified by:

getFromReporterPositionSources in interface HasReporterPositionSources

removeElementAtFromReporterPositionSources

public void removeElementAtFromReporterPositionSources(int position)

Method to remove by position from ReporterPositionSources_list

Specified by:

removeElementAtFromReporterPositionSources in interface HasReporterPositionSources

removeFromReporterPositionSources

public void removeFromReporterPositionSources(ReporterPosition reporterPosition)

Method to remove first ReporterPosition from ReporterPositionSources_list

Specified by:

removeFromReporterPositionSources in interface HasReporterPositionSources