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org.biomage.DesignElement
Class CompositeCompositeMap  view CompositeCompositeMap download CompositeCompositeMap.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.BioEvent.BioEvent
                  extended byorg.biomage.BioEvent.Map
                      extended byorg.biomage.BioAssayData.DesignElementMap
                          extended byorg.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

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.


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.


compositeSequence

private CompositeSequence compositeSequence
A map to the compositeSequences that compose this CompositeSequence.

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.


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.


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.


setCompositePositionSources

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

Specified by:
setCompositePositionSources in interface org.biomage.Interface.HasCompositePositionSources

getCompositePositionSources

public org.biomage.Interface.HasCompositePositionSources.CompositePositionSources_list getCompositePositionSources()
Get method for compositePositionSources

Specified by:
getCompositePositionSources in interface org.biomage.Interface.HasCompositePositionSources

addToCompositePositionSources

public void addToCompositePositionSources(CompositePosition compositePosition)
Method to add CompositePosition to CompositePositionSources_list

Specified by:
addToCompositePositionSources in interface org.biomage.Interface.HasCompositePositionSources

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

getFromCompositePositionSources

public CompositePosition getFromCompositePositionSources(int position)
Method to get CompositePosition from CompositePositionSources_list

Specified by:
getFromCompositePositionSources in interface org.biomage.Interface.HasCompositePositionSources

removeElementAtFromCompositePositionSources

public void removeElementAtFromCompositePositionSources(int position)
Method to remove by position from CompositePositionSources_list

Specified by:
removeElementAtFromCompositePositionSources in interface org.biomage.Interface.HasCompositePositionSources

removeFromCompositePositionSources

public void removeFromCompositePositionSources(CompositePosition compositePosition)
Method to remove first CompositePosition from CompositePositionSources_list

Specified by:
removeFromCompositePositionSources in interface org.biomage.Interface.HasCompositePositionSources

setCompositeSequence

public void setCompositeSequence(CompositeSequence compositeSequence)
Set method for compositeSequence

Specified by:
setCompositeSequence in interface org.biomage.Interface.HasCompositeSequence

getCompositeSequence

public CompositeSequence getCompositeSequence()
Get method for compositeSequence

Specified by:
getCompositeSequence in interface org.biomage.Interface.HasCompositeSequence