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

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.DesignElement.DesignElement
All Implemented Interfaces:
org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasControlType, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasSecurity, java.io.Serializable
Direct Known Subclasses:
CompositeSequence, Feature, Reporter

public abstract class DesignElement
extends org.biomage.Common.Identifiable
implements java.io.Serializable, org.biomage.Interface.HasControlType

An element of an array. This is generally of type feature but can be specified as reporters or compositeSequence for arrays that are abstracted from a physical array.


Nested Class Summary
 
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.Description.OntologyEntry controlType
          If the design element represents a control, the type of control it is (normalization, deletion, negative, positive, etc.)
 
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
DesignElement()
          Default constructor.
DesignElement(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 org.biomage.Description.OntologyEntry getControlType()
          Get method for controlType
 void setControlType(org.biomage.Description.OntologyEntry controlType)
          Set method for controlType
 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.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

controlType

private org.biomage.Description.OntologyEntry controlType
If the design element represents a control, the type of control it is (normalization, deletion, negative, positive, etc.)

Constructor Detail

DesignElement

public DesignElement()
Default constructor.


DesignElement

public DesignElement(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.


setControlType

public void setControlType(org.biomage.Description.OntologyEntry controlType)
Set method for controlType

Specified by:
setControlType in interface org.biomage.Interface.HasControlType

getControlType

public org.biomage.Description.OntologyEntry getControlType()
Get method for controlType

Specified by:
getControlType in interface org.biomage.Interface.HasControlType