org.biomage.DesignElement
Class CompositeCompositeMap

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Common.Describable
          extended by org.biomage.Common.Identifiable
              extended by org.biomage.BioEvent.BioEvent
                  extended by org.biomage.BioEvent.Map
                      extended by org.biomage.BioAssayData.DesignElementMap
                          extended by org.biomage.DesignElement.CompositeCompositeMap
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasCompositePositionSources, HasCompositeSequence, HasDescriptions, HasPropertySets, HasProtocolApplications, HasSecurity

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/interfaces inherited from interface org.biomage.Interface.HasCompositePositionSources
HasCompositePositionSources.CompositePositionSources_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasProtocolApplications
HasProtocolApplications.ProtocolApplications_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail
HasAuditTrail.AuditTrail_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions
HasDescriptions.Descriptions_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets
HasPropertySets.PropertySets_list
 
Field Summary
protected  java.util.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.BioAssayData.DesignElementMap
ojbConcreteClass
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
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
 boolean emptyMAGEobject()
           
 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
 java.lang.String getModelClassName()
           
 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 setAttributes(org.xml.sax.Attributes atts)
           
 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, toString
 
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, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

compositeSequence

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


compositePositionSources

protected java.util.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

Parameters:
atts: - the attribute list.
Method Detail

setAttributes

public void setAttributes(org.xml.sax.Attributes atts)
Overrides:
setAttributes in class DesignElementMap

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
Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

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
Throws:
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
Throws:
java.io.IOException

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class DesignElementMap

setCompositeSequence

public void setCompositeSequence(CompositeSequence compositeSequence)
Set method for compositeSequence

Specified by:
setCompositeSequence in interface HasCompositeSequence
Parameters:
value - to set

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
Parameters:
value - to set

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