org.biomage.DesignElement
Class CompositeSequence

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.DesignElement.DesignElement
                  extended by org.biomage.DesignElement.CompositeSequence
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasBiologicalCharacteristics, HasCompositeCompositeMaps, HasControlType, HasDescriptions, HasPropertySets, HasReporterCompositeMaps, HasSecurity

public class CompositeSequence
extends DesignElement
implements java.io.Serializable, HasBiologicalCharacteristics, HasReporterCompositeMaps, HasCompositeCompositeMaps

A collection of Reporter or CompositeSequence Design Elements, annotated through the association to BioSequence.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasBiologicalCharacteristics
HasBiologicalCharacteristics.BiologicalCharacteristics_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasReporterCompositeMaps
HasReporterCompositeMaps.ReporterCompositeMaps_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasCompositeCompositeMaps
HasCompositeCompositeMaps.CompositeCompositeMaps_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
 
Fields inherited from class org.biomage.DesignElement.DesignElement
controlType
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
CompositeSequence()
          Default constructor.
CompositeSequence(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToBiologicalCharacteristics(BioSequence bioSequence)
          Method to add BioSequence to BiologicalCharacteristics_list
 void addToBiologicalCharacteristics(int position, BioSequence bioSequence)
          Method to add BioSequence at position to BiologicalCharacteristics_list
 void addToCompositeCompositeMaps(CompositeCompositeMap compositeCompositeMap)
          Method to add CompositeCompositeMap to CompositeCompositeMaps_list
 void addToCompositeCompositeMaps(int position, CompositeCompositeMap compositeCompositeMap)
          Method to add CompositeCompositeMap at position to CompositeCompositeMaps_list
 void addToReporterCompositeMaps(int position, ReporterCompositeMap reporterCompositeMap)
          Method to add ReporterCompositeMap at position to ReporterCompositeMaps_list
 void addToReporterCompositeMaps(ReporterCompositeMap reporterCompositeMap)
          Method to add ReporterCompositeMap to ReporterCompositeMaps_list
 boolean emptyMAGEobject()
           
 HasBiologicalCharacteristics.BiologicalCharacteristics_list getBiologicalCharacteristics()
          Get method for biologicalCharacteristics
 HasCompositeCompositeMaps.CompositeCompositeMaps_list getCompositeCompositeMaps()
          Get method for compositeCompositeMaps
 BioSequence getFromBiologicalCharacteristics(int position)
          Method to get BioSequence from BiologicalCharacteristics_list
 CompositeCompositeMap getFromCompositeCompositeMaps(int position)
          Method to get CompositeCompositeMap from CompositeCompositeMaps_list
 ReporterCompositeMap getFromReporterCompositeMaps(int position)
          Method to get ReporterCompositeMap from ReporterCompositeMaps_list
 java.lang.String getModelClassName()
           
 HasReporterCompositeMaps.ReporterCompositeMaps_list getReporterCompositeMaps()
          Get method for reporterCompositeMaps
 void removeElementAtFromBiologicalCharacteristics(int position)
          Method to remove by position from BiologicalCharacteristics_list
 void removeElementAtFromCompositeCompositeMaps(int position)
          Method to remove by position from CompositeCompositeMaps_list
 void removeElementAtFromReporterCompositeMaps(int position)
          Method to remove by position from ReporterCompositeMaps_list
 void removeFromBiologicalCharacteristics(BioSequence bioSequence)
          Method to remove first BioSequence from BiologicalCharacteristics_list
 void removeFromCompositeCompositeMaps(CompositeCompositeMap compositeCompositeMap)
          Method to remove first CompositeCompositeMap from CompositeCompositeMaps_list
 void removeFromReporterCompositeMaps(ReporterCompositeMap reporterCompositeMap)
          Method to remove first ReporterCompositeMap from ReporterCompositeMaps_list
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setBiologicalCharacteristics(HasBiologicalCharacteristics.BiologicalCharacteristics_list biologicalCharacteristics)
          Set method for biologicalCharacteristics
 void setCompositeCompositeMaps(HasCompositeCompositeMaps.CompositeCompositeMaps_list compositeCompositeMaps)
          Set method for compositeCompositeMaps
 void setReporterCompositeMaps(HasReporterCompositeMaps.ReporterCompositeMaps_list reporterCompositeMaps)
          Set method for reporterCompositeMaps
 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.DesignElement.DesignElement
getControlType, setControlType
 
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
 

Constructor Detail

CompositeSequence

public CompositeSequence()
Default constructor.


CompositeSequence

public CompositeSequence(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 DesignElement

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 DesignElement
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 DesignElement
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 DesignElement
Throws:
java.io.IOException

getModelClassName

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

setBiologicalCharacteristics

public void setBiologicalCharacteristics(HasBiologicalCharacteristics.BiologicalCharacteristics_list biologicalCharacteristics)
Set method for biologicalCharacteristics

Specified by:
setBiologicalCharacteristics in interface HasBiologicalCharacteristics
Parameters:
value - to set

getBiologicalCharacteristics

public HasBiologicalCharacteristics.BiologicalCharacteristics_list getBiologicalCharacteristics()
Get method for biologicalCharacteristics

Specified by:
getBiologicalCharacteristics in interface HasBiologicalCharacteristics
Returns:
value of the attribute

addToBiologicalCharacteristics

public void addToBiologicalCharacteristics(BioSequence bioSequence)
Method to add BioSequence to BiologicalCharacteristics_list

Specified by:
addToBiologicalCharacteristics in interface HasBiologicalCharacteristics

addToBiologicalCharacteristics

public void addToBiologicalCharacteristics(int position,
                                           BioSequence bioSequence)
Method to add BioSequence at position to BiologicalCharacteristics_list

Specified by:
addToBiologicalCharacteristics in interface HasBiologicalCharacteristics

getFromBiologicalCharacteristics

public BioSequence getFromBiologicalCharacteristics(int position)
Method to get BioSequence from BiologicalCharacteristics_list

Specified by:
getFromBiologicalCharacteristics in interface HasBiologicalCharacteristics

removeElementAtFromBiologicalCharacteristics

public void removeElementAtFromBiologicalCharacteristics(int position)
Method to remove by position from BiologicalCharacteristics_list

Specified by:
removeElementAtFromBiologicalCharacteristics in interface HasBiologicalCharacteristics

removeFromBiologicalCharacteristics

public void removeFromBiologicalCharacteristics(BioSequence bioSequence)
Method to remove first BioSequence from BiologicalCharacteristics_list

Specified by:
removeFromBiologicalCharacteristics in interface HasBiologicalCharacteristics

setReporterCompositeMaps

public void setReporterCompositeMaps(HasReporterCompositeMaps.ReporterCompositeMaps_list reporterCompositeMaps)
Set method for reporterCompositeMaps

Specified by:
setReporterCompositeMaps in interface HasReporterCompositeMaps
Parameters:
value - to set

getReporterCompositeMaps

public HasReporterCompositeMaps.ReporterCompositeMaps_list getReporterCompositeMaps()
Get method for reporterCompositeMaps

Specified by:
getReporterCompositeMaps in interface HasReporterCompositeMaps
Returns:
value of the attribute

addToReporterCompositeMaps

public void addToReporterCompositeMaps(ReporterCompositeMap reporterCompositeMap)
Method to add ReporterCompositeMap to ReporterCompositeMaps_list

Specified by:
addToReporterCompositeMaps in interface HasReporterCompositeMaps

addToReporterCompositeMaps

public void addToReporterCompositeMaps(int position,
                                       ReporterCompositeMap reporterCompositeMap)
Method to add ReporterCompositeMap at position to ReporterCompositeMaps_list

Specified by:
addToReporterCompositeMaps in interface HasReporterCompositeMaps

getFromReporterCompositeMaps

public ReporterCompositeMap getFromReporterCompositeMaps(int position)
Method to get ReporterCompositeMap from ReporterCompositeMaps_list

Specified by:
getFromReporterCompositeMaps in interface HasReporterCompositeMaps

removeElementAtFromReporterCompositeMaps

public void removeElementAtFromReporterCompositeMaps(int position)
Method to remove by position from ReporterCompositeMaps_list

Specified by:
removeElementAtFromReporterCompositeMaps in interface HasReporterCompositeMaps

removeFromReporterCompositeMaps

public void removeFromReporterCompositeMaps(ReporterCompositeMap reporterCompositeMap)
Method to remove first ReporterCompositeMap from ReporterCompositeMaps_list

Specified by:
removeFromReporterCompositeMaps in interface HasReporterCompositeMaps

setCompositeCompositeMaps

public void setCompositeCompositeMaps(HasCompositeCompositeMaps.CompositeCompositeMaps_list compositeCompositeMaps)
Set method for compositeCompositeMaps

Specified by:
setCompositeCompositeMaps in interface HasCompositeCompositeMaps
Parameters:
value - to set

getCompositeCompositeMaps

public HasCompositeCompositeMaps.CompositeCompositeMaps_list getCompositeCompositeMaps()
Get method for compositeCompositeMaps

Specified by:
getCompositeCompositeMaps in interface HasCompositeCompositeMaps
Returns:
value of the attribute

addToCompositeCompositeMaps

public void addToCompositeCompositeMaps(CompositeCompositeMap compositeCompositeMap)
Method to add CompositeCompositeMap to CompositeCompositeMaps_list

Specified by:
addToCompositeCompositeMaps in interface HasCompositeCompositeMaps

addToCompositeCompositeMaps

public void addToCompositeCompositeMaps(int position,
                                        CompositeCompositeMap compositeCompositeMap)
Method to add CompositeCompositeMap at position to CompositeCompositeMaps_list

Specified by:
addToCompositeCompositeMaps in interface HasCompositeCompositeMaps

getFromCompositeCompositeMaps

public CompositeCompositeMap getFromCompositeCompositeMaps(int position)
Method to get CompositeCompositeMap from CompositeCompositeMaps_list

Specified by:
getFromCompositeCompositeMaps in interface HasCompositeCompositeMaps

removeElementAtFromCompositeCompositeMaps

public void removeElementAtFromCompositeCompositeMaps(int position)
Method to remove by position from CompositeCompositeMaps_list

Specified by:
removeElementAtFromCompositeCompositeMaps in interface HasCompositeCompositeMaps

removeFromCompositeCompositeMaps

public void removeFromCompositeCompositeMaps(CompositeCompositeMap compositeCompositeMap)
Method to remove first CompositeCompositeMap from CompositeCompositeMaps_list

Specified by:
removeFromCompositeCompositeMaps in interface HasCompositeCompositeMaps