org.biomage.DesignElement
Class DesignElement

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.DesignElement.DesignElement

All Implemented Interfaces:

HasAuditTrail, HasControlType, HasDescriptions, HasPropertySets, HasSecurity, java.io.Serializable

Direct Known Subclasses:

CompositeSequence, Feature, Reporter

public abstract class DesignElement

extends Identifiable

implements java.io.Serializable, 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.

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class org.biomage.Interface.HasAuditTrail

HasAuditTrail.AuditTrail_list

Nested classes inherited from class org.biomage.Interface.HasDescriptions

HasDescriptions.Descriptions_list

Nested classes inherited from class org.biomage.Interface.HasPropertySets

HasPropertySets.PropertySets_list

Field Summary

protected 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.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

DesignElement()
Default constructor.

DesignElement(org.xml.sax.Attributes atts)
Attribute constructor.

Method Summary

OntologyEntry	getControlType() Get method for controlType
void	setControlType(OntologyEntry controlType) Set method for controlType
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.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

protected 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.

Overrides:

writeMAGEML in class Identifiable

java.io.IOException

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 Identifiable

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 Identifiable

java.io.IOException

setControlType

public void setControlType(OntologyEntry controlType)

Set method for controlType

Specified by:

setControlType in interface HasControlType

getControlType

public OntologyEntry getControlType()

Get method for controlType

Specified by:

getControlType in interface HasControlType

Returns:

value of the attribute