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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:

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

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public class ReporterCompositeMap

extends org.biomage.BioAssayData.DesignElementMap

implements java.io.Serializable, org.biomage.Interface.HasReporterPositionSources, org.biomage.Interface.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.

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Nested Class Summary

 

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

org.biomage.Interface.HasReporterPositionSources.ReporterPositionSources_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  CompositeSequence	compositeSequence           A map to the reporters that compose this CompositeSequence.
private  org.biomage.Interface.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

 

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

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
org.biomage.Interface.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(org.biomage.Interface.HasReporterPositionSources.ReporterPositionSources_list reporterPositionSources)           Set method for reporterPositionSources
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

reporterPositionSources

private org.biomage.Interface.HasReporterPositionSources.ReporterPositionSources_list reporterPositionSources

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

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compositeSequence

private CompositeSequence compositeSequence

A map to the reporters that compose this CompositeSequence.

Constructor Detail

ReporterCompositeMap

public ReporterCompositeMap()

Default constructor.

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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.

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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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setReporterPositionSources

public void setReporterPositionSources(org.biomage.Interface.HasReporterPositionSources.ReporterPositionSources_list reporterPositionSources)

Set method for reporterPositionSources

Specified by:

setReporterPositionSources in interface org.biomage.Interface.HasReporterPositionSources

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getReporterPositionSources

public org.biomage.Interface.HasReporterPositionSources.ReporterPositionSources_list getReporterPositionSources()

Get method for reporterPositionSources

Specified by:

getReporterPositionSources in interface org.biomage.Interface.HasReporterPositionSources

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addToReporterPositionSources

public void addToReporterPositionSources(ReporterPosition reporterPosition)

Method to add ReporterPosition to ReporterPositionSources_list

Specified by:

addToReporterPositionSources in interface org.biomage.Interface.HasReporterPositionSources

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addToReporterPositionSources

public void addToReporterPositionSources(int position,
                                         ReporterPosition reporterPosition)

Method to add ReporterPosition at position to ReporterPositionSources_list

Specified by:

addToReporterPositionSources in interface org.biomage.Interface.HasReporterPositionSources

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getFromReporterPositionSources

public ReporterPosition getFromReporterPositionSources(int position)

Method to get ReporterPosition from ReporterPositionSources_list

Specified by:

getFromReporterPositionSources in interface org.biomage.Interface.HasReporterPositionSources

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removeElementAtFromReporterPositionSources

public void removeElementAtFromReporterPositionSources(int position)

Method to remove by position from ReporterPositionSources_list

Specified by:

removeElementAtFromReporterPositionSources in interface org.biomage.Interface.HasReporterPositionSources

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removeFromReporterPositionSources

public void removeFromReporterPositionSources(ReporterPosition reporterPosition)

Method to remove first ReporterPosition from ReporterPositionSources_list

Specified by:

removeFromReporterPositionSources in interface org.biomage.Interface.HasReporterPositionSources

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setCompositeSequence

public void setCompositeSequence(CompositeSequence compositeSequence)

Set method for compositeSequence

Specified by:

setCompositeSequence in interface org.biomage.Interface.HasCompositeSequence

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getCompositeSequence

public CompositeSequence getCompositeSequence()

Get method for compositeSequence

Specified by:

getCompositeSequence in interface org.biomage.Interface.HasCompositeSequence

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Home >> All >> org >> biomage >> [ DesignElement overview ]	PREV CLASS  NEXT CLASS
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