org.biomage.DesignElement
Class ReporterCompositeMap

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.ReporterCompositeMap
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasCompositeSequence, HasDescriptions, HasPropertySets, HasProtocolApplications, HasReporterPositionSources, HasSecurity

public class ReporterCompositeMap
extends DesignElementMap
implements java.io.Serializable, HasReporterPositionSources, HasCompositeSequence

A ReporterCompositeMap is the description of how source Reporters are transformed into a target CompositeSequences. For instance, several reporters that tile across a section of a chromosome could be mapped to a CompositeSequence.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasReporterPositionSources
HasReporterPositionSources.ReporterPositionSources_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  CompositeSequence compositeSequence
          A map to the reporters 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
ReporterCompositeMap()
          Default constructor.
ReporterCompositeMap(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToReporterPositionSources(int position, ReporterPosition reporterPosition)
          Method to add ReporterPosition at position to ReporterPositionSources_list
 void addToReporterPositionSources(ReporterPosition reporterPosition)
          Method to add ReporterPosition to ReporterPositionSources_list
 boolean emptyMAGEobject()
           
 CompositeSequence getCompositeSequence()
          Get method for compositeSequence
 ReporterPosition getFromReporterPositionSources(int position)
          Method to get ReporterPosition from ReporterPositionSources_list
 java.lang.String getModelClassName()
           
 HasReporterPositionSources.ReporterPositionSources_list getReporterPositionSources()
          Get method for reporterPositionSources
 void removeElementAtFromReporterPositionSources(int position)
          Method to remove by position from ReporterPositionSources_list
 void removeFromReporterPositionSources(ReporterPosition reporterPosition)
          Method to remove first ReporterPosition from ReporterPositionSources_list
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setCompositeSequence(CompositeSequence compositeSequence)
          Set method for compositeSequence
 void setReporterPositionSources(HasReporterPositionSources.ReporterPositionSources_list reporterPositionSources)
          Set method for reporterPositionSources
 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 reporters that compose this CompositeSequence.

Constructor Detail

ReporterCompositeMap

public ReporterCompositeMap()
Default constructor.


ReporterCompositeMap

public ReporterCompositeMap(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

setReporterPositionSources

public void setReporterPositionSources(HasReporterPositionSources.ReporterPositionSources_list reporterPositionSources)
Set method for reporterPositionSources

Specified by:
setReporterPositionSources in interface HasReporterPositionSources
Parameters:
value - to set

getReporterPositionSources

public HasReporterPositionSources.ReporterPositionSources_list getReporterPositionSources()
Get method for reporterPositionSources

Specified by:
getReporterPositionSources in interface HasReporterPositionSources
Returns:
value of the attribute

addToReporterPositionSources

public void addToReporterPositionSources(ReporterPosition reporterPosition)
Method to add ReporterPosition to ReporterPositionSources_list

Specified by:
addToReporterPositionSources in interface HasReporterPositionSources

addToReporterPositionSources

public void addToReporterPositionSources(int position,
                                         ReporterPosition reporterPosition)
Method to add ReporterPosition at position to ReporterPositionSources_list

Specified by:
addToReporterPositionSources in interface HasReporterPositionSources

getFromReporterPositionSources

public ReporterPosition getFromReporterPositionSources(int position)
Method to get ReporterPosition from ReporterPositionSources_list

Specified by:
getFromReporterPositionSources in interface HasReporterPositionSources

removeElementAtFromReporterPositionSources

public void removeElementAtFromReporterPositionSources(int position)
Method to remove by position from ReporterPositionSources_list

Specified by:
removeElementAtFromReporterPositionSources in interface HasReporterPositionSources

removeFromReporterPositionSources

public void removeFromReporterPositionSources(ReporterPosition reporterPosition)
Method to remove first ReporterPosition from ReporterPositionSources_list

Specified by:
removeFromReporterPositionSources in interface HasReporterPositionSources