org.biomage.ArrayDesign
Class DesignElementGroup

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

All Implemented Interfaces:

HasAuditTrail, HasDescriptions, HasPropertySets, HasSecurity, HasSpecies, HasTypes, java.io.Serializable

Direct Known Subclasses:

CompositeGroup, FeatureGroup, ReporterGroup

public abstract class DesignElementGroup

extends Identifiable

implements java.io.Serializable, HasSpecies, HasTypes

The DesignElementGroup holds information on either features, reporters, or compositeSequences, particularly that information that is common between all of the DesignElements contained.

See Also:

Serialized Form

Nested Class Summary

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

HasTypes.Types_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 OntologyEntry	species The organism from which the biosequences of this group are from.
protected HasTypes.Types_list	types The specific type of a feature, reporter, or composite.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

DesignElementGroup()
Default constructor.

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

Method Summary

void	addToTypes(int position, OntologyEntry ontologyEntry) Method to add OntologyEntry at position to Types_list
void	addToTypes(OntologyEntry ontologyEntry) Method to add OntologyEntry to Types_list
OntologyEntry	getFromTypes(int position) Method to get OntologyEntry from Types_list
OntologyEntry	getSpecies() Get method for species
HasTypes.Types_list	getTypes() Get method for types
void	removeElementAtFromTypes(int position) Method to remove by position from Types_list
void	removeFromTypes(OntologyEntry ontologyEntry) Method to remove first OntologyEntry from Types_list
void	setSpecies(OntologyEntry species) Set method for species
void	setTypes(HasTypes.Types_list types) Set method for types
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

types

protected HasTypes.Types_list types

The specific type of a feature, reporter, or composite. A composite type might be a gene while a reporter type might be a cDNA clone or an oligo.

species

protected OntologyEntry species

The organism from which the biosequences of this group are from.

Constructor Detail

DesignElementGroup

public DesignElementGroup()

Default constructor.

DesignElementGroup

public DesignElementGroup(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

setTypes

public void setTypes(HasTypes.Types_list types)

Set method for types

Specified by:

setTypes in interface HasTypes

getTypes

public HasTypes.Types_list getTypes()

Get method for types

Specified by:

getTypes in interface HasTypes

Returns:

value of the attribute

addToTypes

public void addToTypes(OntologyEntry ontologyEntry)

Method to add OntologyEntry to Types_list

Specified by:

addToTypes in interface HasTypes

addToTypes

public void addToTypes(int position,
                       OntologyEntry ontologyEntry)

Method to add OntologyEntry at position to Types_list

Specified by:

addToTypes in interface HasTypes

getFromTypes

public OntologyEntry getFromTypes(int position)

Method to get OntologyEntry from Types_list

Specified by:

getFromTypes in interface HasTypes

removeElementAtFromTypes

public void removeElementAtFromTypes(int position)

Method to remove by position from Types_list

Specified by:

removeElementAtFromTypes in interface HasTypes

removeFromTypes

public void removeFromTypes(OntologyEntry ontologyEntry)

Method to remove first OntologyEntry from Types_list

Specified by:

removeFromTypes in interface HasTypes

setSpecies

public void setSpecies(OntologyEntry species)

Set method for species

Specified by:

setSpecies in interface HasSpecies

getSpecies

public OntologyEntry getSpecies()

Get method for species

Specified by:

getSpecies in interface HasSpecies

Returns:

value of the attribute