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:

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

public class CompositeCompositeMap

extends DesignElementMap

implements java.io.Serializable, HasCompositePositionSources, 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.

See Also:

Serialized Form

Nested Class Summary

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

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

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

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
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(HasCompositePositionSources.CompositePositionSources_list compositePositionSources) Set method for compositePositionSources
void	setCompositeSequence(CompositeSequence compositeSequence) Set method for compositeSequence
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 compositeSequences that compose this CompositeSequence.

compositePositionSources

protected HasCompositePositionSources.CompositePositionSources_list compositePositionSources

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

Constructor Detail

CompositeCompositeMap

public CompositeCompositeMap()

Default constructor.

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.

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

setCompositePositionSources

public void setCompositePositionSources(HasCompositePositionSources.CompositePositionSources_list compositePositionSources)

Set method for compositePositionSources

Specified by:

setCompositePositionSources in interface HasCompositePositionSources

getCompositePositionSources

public HasCompositePositionSources.CompositePositionSources_list getCompositePositionSources()

Get method for compositePositionSources

Specified by:

getCompositePositionSources in interface HasCompositePositionSources

Returns:

value of the attribute

addToCompositePositionSources

public void addToCompositePositionSources(CompositePosition compositePosition)

Method to add CompositePosition to CompositePositionSources_list

Specified by:

addToCompositePositionSources in interface HasCompositePositionSources

addToCompositePositionSources

public void addToCompositePositionSources(int position,
                                          CompositePosition compositePosition)

Method to add CompositePosition at position to CompositePositionSources_list

Specified by:

addToCompositePositionSources in interface HasCompositePositionSources

getFromCompositePositionSources

public CompositePosition getFromCompositePositionSources(int position)

Method to get CompositePosition from CompositePositionSources_list

Specified by:

getFromCompositePositionSources in interface HasCompositePositionSources

removeElementAtFromCompositePositionSources

public void removeElementAtFromCompositePositionSources(int position)

Method to remove by position from CompositePositionSources_list

Specified by:

removeElementAtFromCompositePositionSources in interface HasCompositePositionSources

removeFromCompositePositionSources

public void removeFromCompositePositionSources(CompositePosition compositePosition)

Method to remove first CompositePosition from CompositePositionSources_list

Specified by:

removeFromCompositePositionSources in interface HasCompositePositionSources