org.biomage.BioAssayData
Class FeatureDimension

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.BioAssayData.DesignElementDimension
                          |
                          +--org.biomage.BioAssayData.FeatureDimension

All Implemented Interfaces:

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

public class FeatureDimension

extends DesignElementDimension

implements java.io.Serializable, HasContainedFeatures

Specialized DesignElementDimension to hold Features.

See Also:

Serialized Form

Nested Class Summary

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

HasContainedFeatures.ContainedFeatures_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 HasContainedFeatures.ContainedFeatures_list

containedFeatures The features for this dimension.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

FeatureDimension()
Default constructor.

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

Method Summary

void	addToContainedFeatures(Feature feature) Method to add Feature to ContainedFeatures_list
void	addToContainedFeatures(int position, Feature feature) Method to add Feature at position to ContainedFeatures_list
HasContainedFeatures.ContainedFeatures_list	getContainedFeatures() Get method for containedFeatures
Feature	getFromContainedFeatures(int position) Method to get Feature from ContainedFeatures_list
void	removeElementAtFromContainedFeatures(int position) Method to remove by position from ContainedFeatures_list
void	removeFromContainedFeatures(Feature feature) Method to remove first Feature from ContainedFeatures_list
void	setContainedFeatures(HasContainedFeatures.ContainedFeatures_list containedFeatures) Set method for containedFeatures
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

containedFeatures

protected HasContainedFeatures.ContainedFeatures_list containedFeatures

The features for this dimension.

Constructor Detail

FeatureDimension

public FeatureDimension()

Default constructor.

FeatureDimension

public FeatureDimension(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 DesignElementDimension

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 DesignElementDimension

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 DesignElementDimension

java.io.IOException

setContainedFeatures

public void setContainedFeatures(HasContainedFeatures.ContainedFeatures_list containedFeatures)

Set method for containedFeatures

Specified by:

setContainedFeatures in interface HasContainedFeatures

getContainedFeatures

public HasContainedFeatures.ContainedFeatures_list getContainedFeatures()

Get method for containedFeatures

Specified by:

getContainedFeatures in interface HasContainedFeatures

Returns:

value of the attribute

addToContainedFeatures

public void addToContainedFeatures(Feature feature)

Method to add Feature to ContainedFeatures_list

Specified by:

addToContainedFeatures in interface HasContainedFeatures

addToContainedFeatures

public void addToContainedFeatures(int position,
                                   Feature feature)

Method to add Feature at position to ContainedFeatures_list

Specified by:

addToContainedFeatures in interface HasContainedFeatures

getFromContainedFeatures

public Feature getFromContainedFeatures(int position)

Method to get Feature from ContainedFeatures_list

Specified by:

getFromContainedFeatures in interface HasContainedFeatures

removeElementAtFromContainedFeatures

public void removeElementAtFromContainedFeatures(int position)

Method to remove by position from ContainedFeatures_list

Specified by:

removeElementAtFromContainedFeatures in interface HasContainedFeatures

removeFromContainedFeatures

public void removeFromContainedFeatures(Feature feature)

Method to remove first Feature from ContainedFeatures_list

Specified by:

removeFromContainedFeatures in interface HasContainedFeatures