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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:

org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasSecurity, org.biomage.Interface.HasSpecies, org.biomage.Interface.HasTypes, java.io.Serializable

Direct Known Subclasses:

CompositeGroup, FeatureGroup, ReporterGroup

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public abstract class DesignElementGroup

extends org.biomage.Common.Identifiable

implements java.io.Serializable, org.biomage.Interface.HasSpecies, org.biomage.Interface.HasTypes

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

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Nested Class Summary

 

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

org.biomage.Interface.HasTypes.Types_list

 

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	species           The organism from which the biosequences of this group are from.
private  org.biomage.Interface.HasTypes.Types_list	types           The specific type of a feature, reporter, or composite.

 

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

DesignElementGroup()           Default constructor.

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

 

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

species

private org.biomage.Description.OntologyEntry species

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

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types

private org.biomage.Interface.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.

Constructor Detail

DesignElementGroup

public DesignElementGroup()

Default constructor.

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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.

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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.

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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.

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setSpecies

public void setSpecies(org.biomage.Description.OntologyEntry species)

Set method for species

Specified by:

setSpecies in interface org.biomage.Interface.HasSpecies

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getSpecies

public org.biomage.Description.OntologyEntry getSpecies()

Get method for species

Specified by:

getSpecies in interface org.biomage.Interface.HasSpecies

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setTypes

public void setTypes(org.biomage.Interface.HasTypes.Types_list types)

Set method for types

Specified by:

setTypes in interface org.biomage.Interface.HasTypes

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getTypes

public org.biomage.Interface.HasTypes.Types_list getTypes()

Get method for types

Specified by:

getTypes in interface org.biomage.Interface.HasTypes

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addToTypes

public void addToTypes(org.biomage.Description.OntologyEntry ontologyEntry)

Method to add OntologyEntry to Types_list

Specified by:

addToTypes in interface org.biomage.Interface.HasTypes

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addToTypes

public void addToTypes(int position,
                       org.biomage.Description.OntologyEntry ontologyEntry)

Method to add OntologyEntry at position to Types_list

Specified by:

addToTypes in interface org.biomage.Interface.HasTypes

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getFromTypes

public org.biomage.Description.OntologyEntry getFromTypes(int position)

Method to get OntologyEntry from Types_list

Specified by:

getFromTypes in interface org.biomage.Interface.HasTypes

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removeElementAtFromTypes

public void removeElementAtFromTypes(int position)

Method to remove by position from Types_list

Specified by:

removeElementAtFromTypes in interface org.biomage.Interface.HasTypes

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removeFromTypes

public void removeFromTypes(org.biomage.Description.OntologyEntry ontologyEntry)

Method to remove first OntologyEntry from Types_list

Specified by:

removeFromTypes in interface org.biomage.Interface.HasTypes

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Home >> All >> org >> biomage >> [ ArrayDesign overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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