org.biomage.ArrayDesign
Class ArrayDesign

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

All Implemented Interfaces:

HasAuditTrail, HasCompositeGroups, HasDescriptions, HasDesignProviders, HasFeatureGroups, HasPropertySets, HasProtocolApplications, HasReporterGroups, HasSecurity, java.io.Serializable

Direct Known Subclasses:

PhysicalArrayDesign

public class ArrayDesign

extends Identifiable

implements java.io.Serializable, HasProtocolApplications, HasCompositeGroups, HasDesignProviders, HasReporterGroups, HasFeatureGroups

Describes the design of an gene expression layout. In some cases this might be virtual and, for instance, represent the output from analysis software at the composite level without reporters or features.

See Also:

Serialized Form

Nested Class Summary

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

HasProtocolApplications.ProtocolApplications_list

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

HasCompositeGroups.CompositeGroups_list

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

HasDesignProviders.DesignProviders_list

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

HasReporterGroups.ReporterGroups_list

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

HasFeatureGroups.FeatureGroups_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 HasCompositeGroups.CompositeGroups_list	compositeGroups The grouping of like CompositeSequence together.
protected HasDesignProviders.DesignProviders_list	designProviders The primary contact for information on the array design
protected HasFeatureGroups.FeatureGroups_list	featureGroups The grouping of like Features together.
protected HasProtocolApplications.ProtocolApplications_list	protocolApplications Describes the application of any protocols, such as the methodology used to pick oligos, in the design of the array.
protected HasReporterGroups.ReporterGroups_list	reporterGroups The grouping of like Reporter together.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

ArrayDesign()
Default constructor.

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

Method Summary

void	addToCompositeGroups(CompositeGroup compositeGroup) Method to add CompositeGroup to CompositeGroups_list
void	addToCompositeGroups(int position, CompositeGroup compositeGroup) Method to add CompositeGroup at position to CompositeGroups_list
void	addToDesignProviders(Contact contact) Method to add Contact to DesignProviders_list
void	addToDesignProviders(int position, Contact contact) Method to add Contact at position to DesignProviders_list
void	addToFeatureGroups(FeatureGroup featureGroup) Method to add FeatureGroup to FeatureGroups_list
void	addToFeatureGroups(int position, FeatureGroup featureGroup) Method to add FeatureGroup at position to FeatureGroups_list
void	addToProtocolApplications(int position, ProtocolApplication protocolApplication) Method to add ProtocolApplication at position to ProtocolApplications_list
void	addToProtocolApplications(ProtocolApplication protocolApplication) Method to add ProtocolApplication to ProtocolApplications_list
void	addToReporterGroups(int position, ReporterGroup reporterGroup) Method to add ReporterGroup at position to ReporterGroups_list
void	addToReporterGroups(ReporterGroup reporterGroup) Method to add ReporterGroup to ReporterGroups_list
HasCompositeGroups.CompositeGroups_list	getCompositeGroups() Get method for compositeGroups
HasDesignProviders.DesignProviders_list	getDesignProviders() Get method for designProviders
HasFeatureGroups.FeatureGroups_list	getFeatureGroups() Get method for featureGroups
CompositeGroup	getFromCompositeGroups(int position) Method to get CompositeGroup from CompositeGroups_list
Contact	getFromDesignProviders(int position) Method to get Contact from DesignProviders_list
FeatureGroup	getFromFeatureGroups(int position) Method to get FeatureGroup from FeatureGroups_list
ProtocolApplication	getFromProtocolApplications(int position) Method to get ProtocolApplication from ProtocolApplications_list
ReporterGroup	getFromReporterGroups(int position) Method to get ReporterGroup from ReporterGroups_list
int	getNumberOfFeatures() Get method for numberOfFeatures
HasProtocolApplications.ProtocolApplications_list	getProtocolApplications() Get method for protocolApplications
HasReporterGroups.ReporterGroups_list	getReporterGroups() Get method for reporterGroups
java.lang.String	getVersion() Get method for version
void	removeElementAtFromCompositeGroups(int position) Method to remove by position from CompositeGroups_list
void	removeElementAtFromDesignProviders(int position) Method to remove by position from DesignProviders_list
void	removeElementAtFromFeatureGroups(int position) Method to remove by position from FeatureGroups_list
void	removeElementAtFromProtocolApplications(int position) Method to remove by position from ProtocolApplications_list
void	removeElementAtFromReporterGroups(int position) Method to remove by position from ReporterGroups_list
void	removeFromCompositeGroups(CompositeGroup compositeGroup) Method to remove first CompositeGroup from CompositeGroups_list
void	removeFromDesignProviders(Contact contact) Method to remove first Contact from DesignProviders_list
void	removeFromFeatureGroups(FeatureGroup featureGroup) Method to remove first FeatureGroup from FeatureGroups_list
void	removeFromProtocolApplications(ProtocolApplication protocolApplication) Method to remove first ProtocolApplication from ProtocolApplications_list
void	removeFromReporterGroups(ReporterGroup reporterGroup) Method to remove first ReporterGroup from ReporterGroups_list
void	setCompositeGroups(HasCompositeGroups.CompositeGroups_list compositeGroups) Set method for compositeGroups
void	setDesignProviders(HasDesignProviders.DesignProviders_list designProviders) Set method for designProviders
void	setFeatureGroups(HasFeatureGroups.FeatureGroups_list featureGroups) Set method for featureGroups
void	setNumberOfFeatures(int numberOfFeatures) Set method for numberOfFeatures
void	setProtocolApplications(HasProtocolApplications.ProtocolApplications_list protocolApplications) Set method for protocolApplications
void	setReporterGroups(HasReporterGroups.ReporterGroups_list reporterGroups) Set method for reporterGroups
void	setVersion(java.lang.String version) Set method for version
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

protocolApplications

protected HasProtocolApplications.ProtocolApplications_list protocolApplications

Describes the application of any protocols, such as the methodology used to pick oligos, in the design of the array.

featureGroups

protected HasFeatureGroups.FeatureGroups_list featureGroups

The grouping of like Features together. Typically for a physical array design, this will be a single grouping of features whose type might be PCR Product or Oligo. If more than one technology type occurs on the array, such as the mixing of Cloned BioMaterial and Oligos, then there would be multiple FeatureGroups to segregate the technology types.

reporterGroups

protected HasReporterGroups.ReporterGroups_list reporterGroups

The grouping of like Reporter together. If more than one technology type occurs on the array, such as the mixing of Cloned BioMaterial and Oligos, then there would be multiple ReporterGroups to segregate the technology types.

compositeGroups

protected HasCompositeGroups.CompositeGroups_list compositeGroups

The grouping of like CompositeSequence together. If more than one technology type occurs on the array, such as the mixing of Cloned BioMaterial and Oligos, then there would be multiple CompositeGroups to segregate the technology types.

designProviders

protected HasDesignProviders.DesignProviders_list designProviders

The primary contact for information on the array design

Constructor Detail

ArrayDesign

public ArrayDesign()

Default constructor.

ArrayDesign

public ArrayDesign(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

setVersion

public void setVersion(java.lang.String version)

Set method for version

getVersion

public java.lang.String getVersion()

Get method for version

Returns:

value of the attribute

setNumberOfFeatures

public void setNumberOfFeatures(int numberOfFeatures)

Set method for numberOfFeatures

getNumberOfFeatures

public int getNumberOfFeatures()

Get method for numberOfFeatures

Returns:

value of the attribute

setProtocolApplications

public void setProtocolApplications(HasProtocolApplications.ProtocolApplications_list protocolApplications)

Set method for protocolApplications

Specified by:

setProtocolApplications in interface HasProtocolApplications

getProtocolApplications

public HasProtocolApplications.ProtocolApplications_list getProtocolApplications()

Get method for protocolApplications

Specified by:

getProtocolApplications in interface HasProtocolApplications

Returns:

value of the attribute

addToProtocolApplications

public void addToProtocolApplications(ProtocolApplication protocolApplication)

Method to add ProtocolApplication to ProtocolApplications_list

Specified by:

addToProtocolApplications in interface HasProtocolApplications

addToProtocolApplications

public void addToProtocolApplications(int position,
                                      ProtocolApplication protocolApplication)

Method to add ProtocolApplication at position to ProtocolApplications_list

Specified by:

addToProtocolApplications in interface HasProtocolApplications

getFromProtocolApplications

public ProtocolApplication getFromProtocolApplications(int position)

Method to get ProtocolApplication from ProtocolApplications_list

Specified by:

getFromProtocolApplications in interface HasProtocolApplications

removeElementAtFromProtocolApplications

public void removeElementAtFromProtocolApplications(int position)

Method to remove by position from ProtocolApplications_list

Specified by:

removeElementAtFromProtocolApplications in interface HasProtocolApplications

removeFromProtocolApplications

public void removeFromProtocolApplications(ProtocolApplication protocolApplication)

Method to remove first ProtocolApplication from ProtocolApplications_list

Specified by:

removeFromProtocolApplications in interface HasProtocolApplications

setFeatureGroups

public void setFeatureGroups(HasFeatureGroups.FeatureGroups_list featureGroups)

Set method for featureGroups

Specified by:

setFeatureGroups in interface HasFeatureGroups

getFeatureGroups

public HasFeatureGroups.FeatureGroups_list getFeatureGroups()

Get method for featureGroups

Specified by:

getFeatureGroups in interface HasFeatureGroups

Returns:

value of the attribute

addToFeatureGroups

public void addToFeatureGroups(FeatureGroup featureGroup)

Method to add FeatureGroup to FeatureGroups_list

Specified by:

addToFeatureGroups in interface HasFeatureGroups

addToFeatureGroups

public void addToFeatureGroups(int position,
                               FeatureGroup featureGroup)

Method to add FeatureGroup at position to FeatureGroups_list

Specified by:

addToFeatureGroups in interface HasFeatureGroups

getFromFeatureGroups

public FeatureGroup getFromFeatureGroups(int position)

Method to get FeatureGroup from FeatureGroups_list

Specified by:

getFromFeatureGroups in interface HasFeatureGroups

removeElementAtFromFeatureGroups

public void removeElementAtFromFeatureGroups(int position)

Method to remove by position from FeatureGroups_list

Specified by:

removeElementAtFromFeatureGroups in interface HasFeatureGroups

removeFromFeatureGroups

public void removeFromFeatureGroups(FeatureGroup featureGroup)

Method to remove first FeatureGroup from FeatureGroups_list

Specified by:

removeFromFeatureGroups in interface HasFeatureGroups

setReporterGroups

public void setReporterGroups(HasReporterGroups.ReporterGroups_list reporterGroups)

Set method for reporterGroups

Specified by:

setReporterGroups in interface HasReporterGroups

getReporterGroups

public HasReporterGroups.ReporterGroups_list getReporterGroups()

Get method for reporterGroups

Specified by:

getReporterGroups in interface HasReporterGroups

Returns:

value of the attribute

addToReporterGroups

public void addToReporterGroups(ReporterGroup reporterGroup)

Method to add ReporterGroup to ReporterGroups_list

Specified by:

addToReporterGroups in interface HasReporterGroups

addToReporterGroups

public void addToReporterGroups(int position,
                                ReporterGroup reporterGroup)

Method to add ReporterGroup at position to ReporterGroups_list

Specified by:

addToReporterGroups in interface HasReporterGroups

getFromReporterGroups

public ReporterGroup getFromReporterGroups(int position)

Method to get ReporterGroup from ReporterGroups_list

Specified by:

getFromReporterGroups in interface HasReporterGroups

removeElementAtFromReporterGroups

public void removeElementAtFromReporterGroups(int position)

Method to remove by position from ReporterGroups_list

Specified by:

removeElementAtFromReporterGroups in interface HasReporterGroups

removeFromReporterGroups

public void removeFromReporterGroups(ReporterGroup reporterGroup)

Method to remove first ReporterGroup from ReporterGroups_list

Specified by:

removeFromReporterGroups in interface HasReporterGroups

setCompositeGroups

public void setCompositeGroups(HasCompositeGroups.CompositeGroups_list compositeGroups)

Set method for compositeGroups

Specified by:

setCompositeGroups in interface HasCompositeGroups

getCompositeGroups

public HasCompositeGroups.CompositeGroups_list getCompositeGroups()

Get method for compositeGroups

Specified by:

getCompositeGroups in interface HasCompositeGroups

Returns:

value of the attribute

addToCompositeGroups

public void addToCompositeGroups(CompositeGroup compositeGroup)

Method to add CompositeGroup to CompositeGroups_list

Specified by:

addToCompositeGroups in interface HasCompositeGroups

addToCompositeGroups

public void addToCompositeGroups(int position,
                                 CompositeGroup compositeGroup)

Method to add CompositeGroup at position to CompositeGroups_list

Specified by:

addToCompositeGroups in interface HasCompositeGroups

getFromCompositeGroups

public CompositeGroup getFromCompositeGroups(int position)

Method to get CompositeGroup from CompositeGroups_list

Specified by:

getFromCompositeGroups in interface HasCompositeGroups

removeElementAtFromCompositeGroups

public void removeElementAtFromCompositeGroups(int position)

Method to remove by position from CompositeGroups_list

Specified by:

removeElementAtFromCompositeGroups in interface HasCompositeGroups

removeFromCompositeGroups

public void removeFromCompositeGroups(CompositeGroup compositeGroup)

Method to remove first CompositeGroup from CompositeGroups_list

Specified by:

removeFromCompositeGroups in interface HasCompositeGroups

setDesignProviders

public void setDesignProviders(HasDesignProviders.DesignProviders_list designProviders)

Set method for designProviders

Specified by:

setDesignProviders in interface HasDesignProviders

getDesignProviders

public HasDesignProviders.DesignProviders_list getDesignProviders()

Get method for designProviders

Specified by:

getDesignProviders in interface HasDesignProviders

Returns:

value of the attribute

addToDesignProviders

public void addToDesignProviders(Contact contact)

Method to add Contact to DesignProviders_list

Specified by:

addToDesignProviders in interface HasDesignProviders

addToDesignProviders

public void addToDesignProviders(int position,
                                 Contact contact)

Method to add Contact at position to DesignProviders_list

Specified by:

addToDesignProviders in interface HasDesignProviders

getFromDesignProviders

public Contact getFromDesignProviders(int position)

Method to get Contact from DesignProviders_list

Specified by:

getFromDesignProviders in interface HasDesignProviders

removeElementAtFromDesignProviders

public void removeElementAtFromDesignProviders(int position)

Method to remove by position from DesignProviders_list

Specified by:

removeElementAtFromDesignProviders in interface HasDesignProviders

removeFromDesignProviders

public void removeFromDesignProviders(Contact contact)

Method to remove first Contact from DesignProviders_list

Specified by:

removeFromDesignProviders in interface HasDesignProviders