org.biomage.DesignElement
Class Feature

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

All Implemented Interfaces:

HasAuditTrail, HasControlFeatures, HasControlledFeatures, HasControlType, HasDescriptions, HasFeatureGroup, HasFeatureLocation, HasPosition, HasPropertySets, HasSecurity, HasZone, java.io.Serializable

public class Feature

extends DesignElement

implements java.io.Serializable, HasZone, HasFeatureGroup, HasPosition, HasControlledFeatures, HasControlFeatures, HasFeatureLocation

An intended position on an array.

See Also:

Serialized Form

Nested Class Summary

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

HasControlledFeatures.ControlledFeatures_list

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

HasControlFeatures.ControlFeatures_list

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 HasControlFeatures.ControlFeatures_list	controlFeatures Associates features with their control features.
protected HasControlledFeatures.ControlledFeatures_list	controlledFeatures Associates features with their control features.
protected FeatureGroup	featureGroup The features that belong to this group.
protected FeatureLocation	featureLocation Location of this feature relative to a grid.
protected Position	position The position of the feature on the array, relative to the top, left corner.
protected Zone	zone A reference to the zone this feature is in.

Fields inherited from class org.biomage.DesignElement.DesignElement

controlType

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

Feature()
Default constructor.

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

Method Summary

void	addToControlFeatures(Feature feature) Method to add Feature to ControlFeatures_list
void	addToControlFeatures(int position, Feature feature) Method to add Feature at position to ControlFeatures_list
void	addToControlledFeatures(Feature feature) Method to add Feature to ControlledFeatures_list
void	addToControlledFeatures(int position, Feature feature) Method to add Feature at position to ControlledFeatures_list
HasControlFeatures.ControlFeatures_list	getControlFeatures() Get method for controlFeatures
HasControlledFeatures.ControlledFeatures_list	getControlledFeatures() Get method for controlledFeatures
FeatureGroup	getFeatureGroup() Get method for featureGroup
FeatureLocation	getFeatureLocation() Get method for featureLocation
Feature	getFromControlFeatures(int position) Method to get Feature from ControlFeatures_list
Feature	getFromControlledFeatures(int position) Method to get Feature from ControlledFeatures_list
Position	getPosition() Get method for position
Zone	getZone() Get method for zone
void	removeElementAtFromControlFeatures(int position) Method to remove by position from ControlFeatures_list
void	removeElementAtFromControlledFeatures(int position) Method to remove by position from ControlledFeatures_list
void	removeFromControlFeatures(Feature feature) Method to remove first Feature from ControlFeatures_list
void	removeFromControlledFeatures(Feature feature) Method to remove first Feature from ControlledFeatures_list
void	setControlFeatures(HasControlFeatures.ControlFeatures_list controlFeatures) Set method for controlFeatures
void	setControlledFeatures(HasControlledFeatures.ControlledFeatures_list controlledFeatures) Set method for controlledFeatures
void	setFeatureGroup(FeatureGroup featureGroup) Set method for featureGroup
void	setFeatureLocation(FeatureLocation featureLocation) Set method for featureLocation
void	setPosition(Position position) Set method for position
void	setZone(Zone zone) Set method for zone
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

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

controlFeatures

protected HasControlFeatures.ControlFeatures_list controlFeatures

Associates features with their control features.

controlledFeatures

protected HasControlledFeatures.ControlledFeatures_list controlledFeatures

Associates features with their control features.

position

protected Position position

The position of the feature on the array, relative to the top, left corner.

zone

protected Zone zone

A reference to the zone this feature is in.

featureLocation

protected FeatureLocation featureLocation

Location of this feature relative to a grid.

featureGroup

protected FeatureGroup featureGroup

The features that belong to this group.

Constructor Detail

Feature

public Feature()

Default constructor.

Feature

public Feature(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 DesignElement

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 DesignElement

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

java.io.IOException

setControlFeatures

public void setControlFeatures(HasControlFeatures.ControlFeatures_list controlFeatures)

Set method for controlFeatures

Specified by:

setControlFeatures in interface HasControlFeatures

getControlFeatures

public HasControlFeatures.ControlFeatures_list getControlFeatures()

Get method for controlFeatures

Specified by:

getControlFeatures in interface HasControlFeatures

Returns:

value of the attribute

addToControlFeatures

public void addToControlFeatures(Feature feature)

Method to add Feature to ControlFeatures_list

Specified by:

addToControlFeatures in interface HasControlFeatures

addToControlFeatures

public void addToControlFeatures(int position,
                                 Feature feature)

Method to add Feature at position to ControlFeatures_list

Specified by:

addToControlFeatures in interface HasControlFeatures

getFromControlFeatures

public Feature getFromControlFeatures(int position)

Method to get Feature from ControlFeatures_list

Specified by:

getFromControlFeatures in interface HasControlFeatures

removeElementAtFromControlFeatures

public void removeElementAtFromControlFeatures(int position)

Method to remove by position from ControlFeatures_list

Specified by:

removeElementAtFromControlFeatures in interface HasControlFeatures

removeFromControlFeatures

public void removeFromControlFeatures(Feature feature)

Method to remove first Feature from ControlFeatures_list

Specified by:

removeFromControlFeatures in interface HasControlFeatures

setControlledFeatures

public void setControlledFeatures(HasControlledFeatures.ControlledFeatures_list controlledFeatures)

Set method for controlledFeatures

Specified by:

setControlledFeatures in interface HasControlledFeatures

getControlledFeatures

public HasControlledFeatures.ControlledFeatures_list getControlledFeatures()

Get method for controlledFeatures

Specified by:

getControlledFeatures in interface HasControlledFeatures

Returns:

value of the attribute

addToControlledFeatures

public void addToControlledFeatures(Feature feature)

Method to add Feature to ControlledFeatures_list

Specified by:

addToControlledFeatures in interface HasControlledFeatures

addToControlledFeatures

public void addToControlledFeatures(int position,
                                    Feature feature)

Method to add Feature at position to ControlledFeatures_list

Specified by:

addToControlledFeatures in interface HasControlledFeatures

getFromControlledFeatures

public Feature getFromControlledFeatures(int position)

Method to get Feature from ControlledFeatures_list

Specified by:

getFromControlledFeatures in interface HasControlledFeatures

removeElementAtFromControlledFeatures

public void removeElementAtFromControlledFeatures(int position)

Method to remove by position from ControlledFeatures_list

Specified by:

removeElementAtFromControlledFeatures in interface HasControlledFeatures

removeFromControlledFeatures

public void removeFromControlledFeatures(Feature feature)

Method to remove first Feature from ControlledFeatures_list

Specified by:

removeFromControlledFeatures in interface HasControlledFeatures

setPosition

public void setPosition(Position position)

Set method for position

Specified by:

setPosition in interface HasPosition

getPosition

public Position getPosition()

Get method for position

Specified by:

getPosition in interface HasPosition

Returns:

value of the attribute

setZone

public void setZone(Zone zone)

Set method for zone

Specified by:

setZone in interface HasZone

getZone

public Zone getZone()

Get method for zone

Specified by:

getZone in interface HasZone

Returns:

value of the attribute

setFeatureLocation

public void setFeatureLocation(FeatureLocation featureLocation)

Set method for featureLocation

Specified by:

setFeatureLocation in interface HasFeatureLocation

getFeatureLocation

public FeatureLocation getFeatureLocation()

Get method for featureLocation

Specified by:

getFeatureLocation in interface HasFeatureLocation

Returns:

value of the attribute

setFeatureGroup

public void setFeatureGroup(FeatureGroup featureGroup)

Set method for featureGroup

Specified by:

setFeatureGroup in interface HasFeatureGroup

getFeatureGroup

public FeatureGroup getFeatureGroup()

Get method for featureGroup

Specified by:

getFeatureGroup in interface HasFeatureGroup

Returns:

value of the attribute