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:

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

public class CompositeSequence

extends DesignElement

implements java.io.Serializable, HasBiologicalCharacteristics, HasReporterCompositeMaps, HasCompositeCompositeMaps

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

See Also:

Serialized Form

Nested Class Summary

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

HasBiologicalCharacteristics.BiologicalCharacteristics_list

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

HasReporterCompositeMaps.ReporterCompositeMaps_list

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

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

Fields inherited from class org.biomage.DesignElement.DesignElement

controlType

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

CompositeSequence()
Default constructor.

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

Method Summary

void	addToBiologicalCharacteristics(BioSequence bioSequence) Method to add BioSequence to BiologicalCharacteristics_list
void	addToBiologicalCharacteristics(int position, 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
HasBiologicalCharacteristics.BiologicalCharacteristics_list	getBiologicalCharacteristics() Get method for biologicalCharacteristics
HasCompositeCompositeMaps.CompositeCompositeMaps_list	getCompositeCompositeMaps() Get method for compositeCompositeMaps
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
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(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(HasBiologicalCharacteristics.BiologicalCharacteristics_list biologicalCharacteristics) Set method for biologicalCharacteristics
void	setCompositeCompositeMaps(HasCompositeCompositeMaps.CompositeCompositeMaps_list compositeCompositeMaps) Set method for compositeCompositeMaps
void	setReporterCompositeMaps(HasReporterCompositeMaps.ReporterCompositeMaps_list reporterCompositeMaps) Set method for reporterCompositeMaps
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.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

protected HasBiologicalCharacteristics.BiologicalCharacteristics_list biologicalCharacteristics

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

reporterCompositeMaps

protected HasReporterCompositeMaps.ReporterCompositeMaps_list reporterCompositeMaps

A map to the reporters that compose this CompositeSequence.

compositeCompositeMaps

protected HasCompositeCompositeMaps.CompositeCompositeMaps_list compositeCompositeMaps

A map to the compositeSequences that compose this CompositeSequence.

Constructor Detail

CompositeSequence

public CompositeSequence()

Default constructor.

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

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 DesignElement

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 DesignElement

java.io.IOException

setBiologicalCharacteristics

public void setBiologicalCharacteristics(HasBiologicalCharacteristics.BiologicalCharacteristics_list biologicalCharacteristics)

Set method for biologicalCharacteristics

Specified by:

setBiologicalCharacteristics in interface HasBiologicalCharacteristics

getBiologicalCharacteristics

public HasBiologicalCharacteristics.BiologicalCharacteristics_list getBiologicalCharacteristics()

Get method for biologicalCharacteristics

Specified by:

getBiologicalCharacteristics in interface HasBiologicalCharacteristics

Returns:

value of the attribute

addToBiologicalCharacteristics

public void addToBiologicalCharacteristics(BioSequence bioSequence)

Method to add BioSequence to BiologicalCharacteristics_list

Specified by:

addToBiologicalCharacteristics in interface HasBiologicalCharacteristics

addToBiologicalCharacteristics

public void addToBiologicalCharacteristics(int position,
                                           BioSequence bioSequence)

Method to add BioSequence at position to BiologicalCharacteristics_list

Specified by:

addToBiologicalCharacteristics in interface HasBiologicalCharacteristics

getFromBiologicalCharacteristics

public BioSequence getFromBiologicalCharacteristics(int position)

Method to get BioSequence from BiologicalCharacteristics_list

Specified by:

getFromBiologicalCharacteristics in interface HasBiologicalCharacteristics

removeElementAtFromBiologicalCharacteristics

public void removeElementAtFromBiologicalCharacteristics(int position)

Method to remove by position from BiologicalCharacteristics_list

Specified by:

removeElementAtFromBiologicalCharacteristics in interface HasBiologicalCharacteristics

removeFromBiologicalCharacteristics

public void removeFromBiologicalCharacteristics(BioSequence bioSequence)

Method to remove first BioSequence from BiologicalCharacteristics_list

Specified by:

removeFromBiologicalCharacteristics in interface HasBiologicalCharacteristics

setReporterCompositeMaps

public void setReporterCompositeMaps(HasReporterCompositeMaps.ReporterCompositeMaps_list reporterCompositeMaps)

Set method for reporterCompositeMaps

Specified by:

setReporterCompositeMaps in interface HasReporterCompositeMaps

getReporterCompositeMaps

public HasReporterCompositeMaps.ReporterCompositeMaps_list getReporterCompositeMaps()

Get method for reporterCompositeMaps

Specified by:

getReporterCompositeMaps in interface HasReporterCompositeMaps

Returns:

value of the attribute

addToReporterCompositeMaps

public void addToReporterCompositeMaps(ReporterCompositeMap reporterCompositeMap)

Method to add ReporterCompositeMap to ReporterCompositeMaps_list

Specified by:

addToReporterCompositeMaps in interface HasReporterCompositeMaps

addToReporterCompositeMaps

public void addToReporterCompositeMaps(int position,
                                       ReporterCompositeMap reporterCompositeMap)

Method to add ReporterCompositeMap at position to ReporterCompositeMaps_list

Specified by:

addToReporterCompositeMaps in interface HasReporterCompositeMaps

getFromReporterCompositeMaps

public ReporterCompositeMap getFromReporterCompositeMaps(int position)

Method to get ReporterCompositeMap from ReporterCompositeMaps_list

Specified by:

getFromReporterCompositeMaps in interface HasReporterCompositeMaps

removeElementAtFromReporterCompositeMaps

public void removeElementAtFromReporterCompositeMaps(int position)

Method to remove by position from ReporterCompositeMaps_list

Specified by:

removeElementAtFromReporterCompositeMaps in interface HasReporterCompositeMaps

removeFromReporterCompositeMaps

public void removeFromReporterCompositeMaps(ReporterCompositeMap reporterCompositeMap)

Method to remove first ReporterCompositeMap from ReporterCompositeMaps_list

Specified by:

removeFromReporterCompositeMaps in interface HasReporterCompositeMaps

setCompositeCompositeMaps

public void setCompositeCompositeMaps(HasCompositeCompositeMaps.CompositeCompositeMaps_list compositeCompositeMaps)

Set method for compositeCompositeMaps

Specified by:

setCompositeCompositeMaps in interface HasCompositeCompositeMaps

getCompositeCompositeMaps

public HasCompositeCompositeMaps.CompositeCompositeMaps_list getCompositeCompositeMaps()

Get method for compositeCompositeMaps

Specified by:

getCompositeCompositeMaps in interface HasCompositeCompositeMaps

Returns:

value of the attribute

addToCompositeCompositeMaps

public void addToCompositeCompositeMaps(CompositeCompositeMap compositeCompositeMap)

Method to add CompositeCompositeMap to CompositeCompositeMaps_list

Specified by:

addToCompositeCompositeMaps in interface HasCompositeCompositeMaps

addToCompositeCompositeMaps

public void addToCompositeCompositeMaps(int position,
                                        CompositeCompositeMap compositeCompositeMap)

Method to add CompositeCompositeMap at position to CompositeCompositeMaps_list

Specified by:

addToCompositeCompositeMaps in interface HasCompositeCompositeMaps

getFromCompositeCompositeMaps

public CompositeCompositeMap getFromCompositeCompositeMaps(int position)

Method to get CompositeCompositeMap from CompositeCompositeMaps_list

Specified by:

getFromCompositeCompositeMaps in interface HasCompositeCompositeMaps

removeElementAtFromCompositeCompositeMaps

public void removeElementAtFromCompositeCompositeMaps(int position)

Method to remove by position from CompositeCompositeMaps_list

Specified by:

removeElementAtFromCompositeCompositeMaps in interface HasCompositeCompositeMaps

removeFromCompositeCompositeMaps

public void removeFromCompositeCompositeMaps(CompositeCompositeMap compositeCompositeMap)

Method to remove first CompositeCompositeMap from CompositeCompositeMaps_list

Specified by:

removeFromCompositeCompositeMaps in interface HasCompositeCompositeMaps