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org.biomage.ArrayDesign
Class CompositeGroup  view CompositeGroup download CompositeGroup.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.ArrayDesign.DesignElementGroup
                  extended byorg.biomage.ArrayDesign.CompositeGroup
All Implemented Interfaces:
org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasCompositeSequences, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasSecurity, org.biomage.Interface.HasSpecies, org.biomage.Interface.HasTypes, java.io.Serializable

public class CompositeGroup
extends DesignElementGroup
implements java.io.Serializable, org.biomage.Interface.HasCompositeSequences

Allows specification of the type of Composite Design Element.


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasCompositeSequences
org.biomage.Interface.HasCompositeSequences.CompositeSequences_list
 
Nested classes inherited from class org.biomage.Interface.HasTypes
org.biomage.Interface.HasTypes.Types_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.HasCompositeSequences.CompositeSequences_list compositeSequences
          The compositeSequences that belong to this group.
 
Fields inherited from class org.biomage.ArrayDesign.DesignElementGroup
 
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
CompositeGroup()
          Default constructor.
CompositeGroup(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToCompositeSequences(org.biomage.DesignElement.CompositeSequence compositeSequence)
          Method to add CompositeSequence to CompositeSequences_list
 void addToCompositeSequences(int position, org.biomage.DesignElement.CompositeSequence compositeSequence)
          Method to add CompositeSequence at position to CompositeSequences_list
 org.biomage.Interface.HasCompositeSequences.CompositeSequences_list getCompositeSequences()
          Get method for compositeSequences
 org.biomage.DesignElement.CompositeSequence getFromCompositeSequences(int position)
          Method to get CompositeSequence from CompositeSequences_list
 void removeElementAtFromCompositeSequences(int position)
          Method to remove by position from CompositeSequences_list
 void removeFromCompositeSequences(org.biomage.DesignElement.CompositeSequence compositeSequence)
          Method to remove first CompositeSequence from CompositeSequences_list
 void setCompositeSequences(org.biomage.Interface.HasCompositeSequences.CompositeSequences_list compositeSequences)
          Set method for compositeSequences
 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.ArrayDesign.DesignElementGroup
addToTypes, addToTypes, getFromTypes, getSpecies, getTypes, removeElementAtFromTypes, removeFromTypes, setSpecies, setTypes
 
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

compositeSequences

private org.biomage.Interface.HasCompositeSequences.CompositeSequences_list compositeSequences
The compositeSequences that belong to this group.

Constructor Detail

CompositeGroup

public CompositeGroup()
Default constructor.


CompositeGroup

public CompositeGroup(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 DesignElementGroup

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 DesignElementGroup

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 DesignElementGroup

setCompositeSequences

public void setCompositeSequences(org.biomage.Interface.HasCompositeSequences.CompositeSequences_list compositeSequences)
Set method for compositeSequences

Specified by:
setCompositeSequences in interface org.biomage.Interface.HasCompositeSequences

getCompositeSequences

public org.biomage.Interface.HasCompositeSequences.CompositeSequences_list getCompositeSequences()
Get method for compositeSequences

Specified by:
getCompositeSequences in interface org.biomage.Interface.HasCompositeSequences

addToCompositeSequences

public void addToCompositeSequences(org.biomage.DesignElement.CompositeSequence compositeSequence)
Method to add CompositeSequence to CompositeSequences_list

Specified by:
addToCompositeSequences in interface org.biomage.Interface.HasCompositeSequences

addToCompositeSequences

public void addToCompositeSequences(int position,
                                    org.biomage.DesignElement.CompositeSequence compositeSequence)
Method to add CompositeSequence at position to CompositeSequences_list

Specified by:
addToCompositeSequences in interface org.biomage.Interface.HasCompositeSequences

getFromCompositeSequences

public org.biomage.DesignElement.CompositeSequence getFromCompositeSequences(int position)
Method to get CompositeSequence from CompositeSequences_list

Specified by:
getFromCompositeSequences in interface org.biomage.Interface.HasCompositeSequences

removeElementAtFromCompositeSequences

public void removeElementAtFromCompositeSequences(int position)
Method to remove by position from CompositeSequences_list

Specified by:
removeElementAtFromCompositeSequences in interface org.biomage.Interface.HasCompositeSequences

removeFromCompositeSequences

public void removeFromCompositeSequences(org.biomage.DesignElement.CompositeSequence compositeSequence)
Method to remove first CompositeSequence from CompositeSequences_list

Specified by:
removeFromCompositeSequences in interface org.biomage.Interface.HasCompositeSequences