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org.biomage.DesignElement
Class CompositeCompositeMap  

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.CompositeCompositeMap

All Implemented Interfaces:

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

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public class CompositeCompositeMap

extends org.biomage.BioAssayData.DesignElementMap

implements java.io.Serializable, org.biomage.Interface.HasCompositePositionSources, org.biomage.Interface.HasCompositeSequence

A CompositeCompositeMap is the description of how source CompositeSequences are transformed into a target CompositeSequence. For instance, several CompositeSequences could represent different sequence regions for a Gene and could be mapped to different CompositeSequences, each representing a different splice variant for that Gene.

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Nested Class Summary

 

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

org.biomage.Interface.HasCompositePositionSources.CompositePositionSources_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  org.biomage.Interface.HasCompositePositionSources.CompositePositionSources_list	compositePositionSources           Association to the CompositeSequences that compose this CompositeSequence and where those CompositeSequences occur.
private  CompositeSequence	compositeSequence           A map to the compositeSequences that compose this CompositeSequence.

 

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

CompositeCompositeMap()           Default constructor.

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

 

Method Summary
void	addToCompositePositionSources(CompositePosition compositePosition)           Method to add CompositePosition to CompositePositionSources_list
void	addToCompositePositionSources(int position, CompositePosition compositePosition)           Method to add CompositePosition at position to CompositePositionSources_list
org.biomage.Interface.HasCompositePositionSources.CompositePositionSources_list	getCompositePositionSources()           Get method for compositePositionSources
CompositeSequence	getCompositeSequence()           Get method for compositeSequence
CompositePosition	getFromCompositePositionSources(int position)           Method to get CompositePosition from CompositePositionSources_list
void	removeElementAtFromCompositePositionSources(int position)           Method to remove by position from CompositePositionSources_list
void	removeFromCompositePositionSources(CompositePosition compositePosition)           Method to remove first CompositePosition from CompositePositionSources_list
void	setCompositePositionSources(org.biomage.Interface.HasCompositePositionSources.CompositePositionSources_list compositePositionSources)           Set method for compositePositionSources
void	setCompositeSequence(CompositeSequence compositeSequence)           Set method for compositeSequence
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

compositePositionSources

private org.biomage.Interface.HasCompositePositionSources.CompositePositionSources_list compositePositionSources

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

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compositeSequence

private CompositeSequence compositeSequence

A map to the compositeSequences that compose this CompositeSequence.

Constructor Detail

CompositeCompositeMap

public CompositeCompositeMap()

Default constructor.

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CompositeCompositeMap

public CompositeCompositeMap(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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setCompositePositionSources

public void setCompositePositionSources(org.biomage.Interface.HasCompositePositionSources.CompositePositionSources_list compositePositionSources)

Set method for compositePositionSources

Specified by:

setCompositePositionSources in interface org.biomage.Interface.HasCompositePositionSources

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getCompositePositionSources

public org.biomage.Interface.HasCompositePositionSources.CompositePositionSources_list getCompositePositionSources()

Get method for compositePositionSources

Specified by:

getCompositePositionSources in interface org.biomage.Interface.HasCompositePositionSources

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addToCompositePositionSources

public void addToCompositePositionSources(CompositePosition compositePosition)

Method to add CompositePosition to CompositePositionSources_list

Specified by:

addToCompositePositionSources in interface org.biomage.Interface.HasCompositePositionSources

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addToCompositePositionSources

public void addToCompositePositionSources(int position,
                                          CompositePosition compositePosition)

Method to add CompositePosition at position to CompositePositionSources_list

Specified by:

addToCompositePositionSources in interface org.biomage.Interface.HasCompositePositionSources

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getFromCompositePositionSources

public CompositePosition getFromCompositePositionSources(int position)

Method to get CompositePosition from CompositePositionSources_list

Specified by:

getFromCompositePositionSources in interface org.biomage.Interface.HasCompositePositionSources

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removeElementAtFromCompositePositionSources

public void removeElementAtFromCompositePositionSources(int position)

Method to remove by position from CompositePositionSources_list

Specified by:

removeElementAtFromCompositePositionSources in interface org.biomage.Interface.HasCompositePositionSources

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removeFromCompositePositionSources

public void removeFromCompositePositionSources(CompositePosition compositePosition)

Method to remove first CompositePosition from CompositePositionSources_list

Specified by:

removeFromCompositePositionSources in interface org.biomage.Interface.HasCompositePositionSources

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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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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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