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org.biomage.DesignElement
Class CompositeSequence  

java.lang.Object
  org.biomage.Common.Extendable
      org.biomage.Common.Describable
          org.biomage.Common.Identifiable
              org.biomage.DesignElement.DesignElement
                  org.biomage.DesignElement.CompositeSequence

All Implemented Interfaces:

org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasBiologicalCharacteristics, org.biomage.Interface.HasCompositeCompositeMaps, org.biomage.Interface.HasControlType, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasReporterCompositeMaps, org.biomage.Interface.HasSecurity, java.io.Serializable

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public class CompositeSequence

extends DesignElement

implements java.io.Serializable, org.biomage.Interface.HasBiologicalCharacteristics, org.biomage.Interface.HasReporterCompositeMaps, org.biomage.Interface.HasCompositeCompositeMaps

A collection of Reporter or CompositeSequence Design Elements, annotated through the association to BioSequence.

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Nested Class Summary

 

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

org.biomage.Interface.HasBiologicalCharacteristics.BiologicalCharacteristics_list

 

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

org.biomage.Interface.HasReporterCompositeMaps.ReporterCompositeMaps_list

 

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

org.biomage.Interface.HasCompositeCompositeMaps.CompositeCompositeMaps_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.Interface.HasBiologicalCharacteristics.BiologicalCharacteristics_list	biologicalCharacteristics           The annotation on the BioSequence this CompositeSequence represents.
private  org.biomage.Interface.HasCompositeCompositeMaps.CompositeCompositeMaps_list	compositeCompositeMaps           A map to the compositeSequences that compose this CompositeSequence.
private  org.biomage.Interface.HasReporterCompositeMaps.ReporterCompositeMaps_list	reporterCompositeMaps           A map to the reporters that compose this CompositeSequence.

 

Fields inherited from class org.biomage.DesignElement.DesignElement

 

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

CompositeSequence()           Default constructor.

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

 

Method Summary
void	addToBiologicalCharacteristics(org.biomage.BioSequence.BioSequence bioSequence)           Method to add BioSequence to BiologicalCharacteristics_list
void	addToBiologicalCharacteristics(int position, org.biomage.BioSequence.BioSequence bioSequence)           Method to add BioSequence at position to BiologicalCharacteristics_list
void	addToCompositeCompositeMaps(CompositeCompositeMap compositeCompositeMap)           Method to add CompositeCompositeMap to CompositeCompositeMaps_list
void	addToCompositeCompositeMaps(int position, CompositeCompositeMap compositeCompositeMap)           Method to add CompositeCompositeMap at position to CompositeCompositeMaps_list
void	addToReporterCompositeMaps(int position, ReporterCompositeMap reporterCompositeMap)           Method to add ReporterCompositeMap at position to ReporterCompositeMaps_list
void	addToReporterCompositeMaps(ReporterCompositeMap reporterCompositeMap)           Method to add ReporterCompositeMap to ReporterCompositeMaps_list
org.biomage.Interface.HasBiologicalCharacteristics.BiologicalCharacteristics_list	getBiologicalCharacteristics()           Get method for biologicalCharacteristics
org.biomage.Interface.HasCompositeCompositeMaps.CompositeCompositeMaps_list	getCompositeCompositeMaps()           Get method for compositeCompositeMaps
org.biomage.BioSequence.BioSequence	getFromBiologicalCharacteristics(int position)           Method to get BioSequence from BiologicalCharacteristics_list
CompositeCompositeMap	getFromCompositeCompositeMaps(int position)           Method to get CompositeCompositeMap from CompositeCompositeMaps_list
ReporterCompositeMap	getFromReporterCompositeMaps(int position)           Method to get ReporterCompositeMap from ReporterCompositeMaps_list
org.biomage.Interface.HasReporterCompositeMaps.ReporterCompositeMaps_list	getReporterCompositeMaps()           Get method for reporterCompositeMaps
void	removeElementAtFromBiologicalCharacteristics(int position)           Method to remove by position from BiologicalCharacteristics_list
void	removeElementAtFromCompositeCompositeMaps(int position)           Method to remove by position from CompositeCompositeMaps_list
void	removeElementAtFromReporterCompositeMaps(int position)           Method to remove by position from ReporterCompositeMaps_list
void	removeFromBiologicalCharacteristics(org.biomage.BioSequence.BioSequence bioSequence)           Method to remove first BioSequence from BiologicalCharacteristics_list
void	removeFromCompositeCompositeMaps(CompositeCompositeMap compositeCompositeMap)           Method to remove first CompositeCompositeMap from CompositeCompositeMaps_list
void	removeFromReporterCompositeMaps(ReporterCompositeMap reporterCompositeMap)           Method to remove first ReporterCompositeMap from ReporterCompositeMaps_list
void	setBiologicalCharacteristics(org.biomage.Interface.HasBiologicalCharacteristics.BiologicalCharacteristics_list biologicalCharacteristics)           Set method for biologicalCharacteristics
void	setCompositeCompositeMaps(org.biomage.Interface.HasCompositeCompositeMaps.CompositeCompositeMaps_list compositeCompositeMaps)           Set method for compositeCompositeMaps
void	setReporterCompositeMaps(org.biomage.Interface.HasReporterCompositeMaps.ReporterCompositeMaps_list reporterCompositeMaps)           Set method for reporterCompositeMaps
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.DesignElement.DesignElement

getControlType, setControlType

 

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

biologicalCharacteristics

private org.biomage.Interface.HasBiologicalCharacteristics.BiologicalCharacteristics_list biologicalCharacteristics

The annotation on the BioSequence this CompositeSequence represents. Typically the sequences will be a Genes, Exons, or SpliceVariants.

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reporterCompositeMaps

private org.biomage.Interface.HasReporterCompositeMaps.ReporterCompositeMaps_list reporterCompositeMaps

A map to the reporters that compose this CompositeSequence.

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compositeCompositeMaps

private org.biomage.Interface.HasCompositeCompositeMaps.CompositeCompositeMaps_list compositeCompositeMaps

A map to the compositeSequences that compose this CompositeSequence.

Constructor Detail

CompositeSequence

public CompositeSequence()

Default constructor.

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CompositeSequence

public CompositeSequence(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 DesignElement

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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.

Overrides:

writeAttributes in class DesignElement

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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.

Overrides:

writeAssociations in class DesignElement

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setBiologicalCharacteristics

public void setBiologicalCharacteristics(org.biomage.Interface.HasBiologicalCharacteristics.BiologicalCharacteristics_list biologicalCharacteristics)

Set method for biologicalCharacteristics

Specified by:

setBiologicalCharacteristics in interface org.biomage.Interface.HasBiologicalCharacteristics

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getBiologicalCharacteristics

public org.biomage.Interface.HasBiologicalCharacteristics.BiologicalCharacteristics_list getBiologicalCharacteristics()

Get method for biologicalCharacteristics

Specified by:

getBiologicalCharacteristics in interface org.biomage.Interface.HasBiologicalCharacteristics

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addToBiologicalCharacteristics

public void addToBiologicalCharacteristics(org.biomage.BioSequence.BioSequence bioSequence)

Method to add BioSequence to BiologicalCharacteristics_list

Specified by:

addToBiologicalCharacteristics in interface org.biomage.Interface.HasBiologicalCharacteristics

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addToBiologicalCharacteristics

public void addToBiologicalCharacteristics(int position,
                                           org.biomage.BioSequence.BioSequence bioSequence)

Method to add BioSequence at position to BiologicalCharacteristics_list

Specified by:

addToBiologicalCharacteristics in interface org.biomage.Interface.HasBiologicalCharacteristics

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getFromBiologicalCharacteristics

public org.biomage.BioSequence.BioSequence getFromBiologicalCharacteristics(int position)

Method to get BioSequence from BiologicalCharacteristics_list

Specified by:

getFromBiologicalCharacteristics in interface org.biomage.Interface.HasBiologicalCharacteristics

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removeElementAtFromBiologicalCharacteristics

public void removeElementAtFromBiologicalCharacteristics(int position)

Method to remove by position from BiologicalCharacteristics_list

Specified by:

removeElementAtFromBiologicalCharacteristics in interface org.biomage.Interface.HasBiologicalCharacteristics

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removeFromBiologicalCharacteristics

public void removeFromBiologicalCharacteristics(org.biomage.BioSequence.BioSequence bioSequence)

Method to remove first BioSequence from BiologicalCharacteristics_list

Specified by:

removeFromBiologicalCharacteristics in interface org.biomage.Interface.HasBiologicalCharacteristics

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setReporterCompositeMaps

public void setReporterCompositeMaps(org.biomage.Interface.HasReporterCompositeMaps.ReporterCompositeMaps_list reporterCompositeMaps)

Set method for reporterCompositeMaps

Specified by:

setReporterCompositeMaps in interface org.biomage.Interface.HasReporterCompositeMaps

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getReporterCompositeMaps

public org.biomage.Interface.HasReporterCompositeMaps.ReporterCompositeMaps_list getReporterCompositeMaps()

Get method for reporterCompositeMaps

Specified by:

getReporterCompositeMaps in interface org.biomage.Interface.HasReporterCompositeMaps

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addToReporterCompositeMaps

public void addToReporterCompositeMaps(ReporterCompositeMap reporterCompositeMap)

Method to add ReporterCompositeMap to ReporterCompositeMaps_list

Specified by:

addToReporterCompositeMaps in interface org.biomage.Interface.HasReporterCompositeMaps

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addToReporterCompositeMaps

public void addToReporterCompositeMaps(int position,
                                       ReporterCompositeMap reporterCompositeMap)

Method to add ReporterCompositeMap at position to ReporterCompositeMaps_list

Specified by:

addToReporterCompositeMaps in interface org.biomage.Interface.HasReporterCompositeMaps

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getFromReporterCompositeMaps

public ReporterCompositeMap getFromReporterCompositeMaps(int position)

Method to get ReporterCompositeMap from ReporterCompositeMaps_list

Specified by:

getFromReporterCompositeMaps in interface org.biomage.Interface.HasReporterCompositeMaps

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removeElementAtFromReporterCompositeMaps

public void removeElementAtFromReporterCompositeMaps(int position)

Method to remove by position from ReporterCompositeMaps_list

Specified by:

removeElementAtFromReporterCompositeMaps in interface org.biomage.Interface.HasReporterCompositeMaps

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removeFromReporterCompositeMaps

public void removeFromReporterCompositeMaps(ReporterCompositeMap reporterCompositeMap)

Method to remove first ReporterCompositeMap from ReporterCompositeMaps_list

Specified by:

removeFromReporterCompositeMaps in interface org.biomage.Interface.HasReporterCompositeMaps

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setCompositeCompositeMaps

public void setCompositeCompositeMaps(org.biomage.Interface.HasCompositeCompositeMaps.CompositeCompositeMaps_list compositeCompositeMaps)

Set method for compositeCompositeMaps

Specified by:

setCompositeCompositeMaps in interface org.biomage.Interface.HasCompositeCompositeMaps

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getCompositeCompositeMaps

public org.biomage.Interface.HasCompositeCompositeMaps.CompositeCompositeMaps_list getCompositeCompositeMaps()

Get method for compositeCompositeMaps

Specified by:

getCompositeCompositeMaps in interface org.biomage.Interface.HasCompositeCompositeMaps

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addToCompositeCompositeMaps

public void addToCompositeCompositeMaps(CompositeCompositeMap compositeCompositeMap)

Method to add CompositeCompositeMap to CompositeCompositeMaps_list

Specified by:

addToCompositeCompositeMaps in interface org.biomage.Interface.HasCompositeCompositeMaps

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addToCompositeCompositeMaps

public void addToCompositeCompositeMaps(int position,
                                        CompositeCompositeMap compositeCompositeMap)

Method to add CompositeCompositeMap at position to CompositeCompositeMaps_list

Specified by:

addToCompositeCompositeMaps in interface org.biomage.Interface.HasCompositeCompositeMaps

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getFromCompositeCompositeMaps

public CompositeCompositeMap getFromCompositeCompositeMaps(int position)

Method to get CompositeCompositeMap from CompositeCompositeMaps_list

Specified by:

getFromCompositeCompositeMaps in interface org.biomage.Interface.HasCompositeCompositeMaps

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removeElementAtFromCompositeCompositeMaps

public void removeElementAtFromCompositeCompositeMaps(int position)

Method to remove by position from CompositeCompositeMaps_list

Specified by:

removeElementAtFromCompositeCompositeMaps in interface org.biomage.Interface.HasCompositeCompositeMaps

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removeFromCompositeCompositeMaps

public void removeFromCompositeCompositeMaps(CompositeCompositeMap compositeCompositeMap)

Method to remove first CompositeCompositeMap from CompositeCompositeMaps_list

Specified by:

removeFromCompositeCompositeMaps in interface org.biomage.Interface.HasCompositeCompositeMaps

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ DesignElement overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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