org.biomage.ArrayDesign
Class PhysicalArrayDesign

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

All Implemented Interfaces:

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

public class PhysicalArrayDesign

extends ArrayDesign

implements java.io.Serializable, HasZoneGroups, HasSurfaceType

A design that is expected to be used to manufacture physical arrays.

See Also:

Serialized Form

Nested Class Summary

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

HasZoneGroups.ZoneGroups_list

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 OntologyEntry	surfaceType The type of surface from a controlled vocabulary that would include terms such as non-absorptive, absorptive, etc.
protected HasZoneGroups.ZoneGroups_list	zoneGroups In the case where the array design is specified by one or more zones, allows specifying where those zones are located.

Fields inherited from class org.biomage.ArrayDesign.ArrayDesign

compositeGroups, designProviders, featureGroups, protocolApplications, reporterGroups

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

PhysicalArrayDesign()
Default constructor.

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

Method Summary

void	addToZoneGroups(int position, ZoneGroup zoneGroup) Method to add ZoneGroup at position to ZoneGroups_list
void	addToZoneGroups(ZoneGroup zoneGroup) Method to add ZoneGroup to ZoneGroups_list
ZoneGroup	getFromZoneGroups(int position) Method to get ZoneGroup from ZoneGroups_list
OntologyEntry	getSurfaceType() Get method for surfaceType
HasZoneGroups.ZoneGroups_list	getZoneGroups() Get method for zoneGroups
void	removeElementAtFromZoneGroups(int position) Method to remove by position from ZoneGroups_list
void	removeFromZoneGroups(ZoneGroup zoneGroup) Method to remove first ZoneGroup from ZoneGroups_list
void	setSurfaceType(OntologyEntry surfaceType) Set method for surfaceType
void	setZoneGroups(HasZoneGroups.ZoneGroups_list zoneGroups) Set method for zoneGroups
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.ArrayDesign.ArrayDesign

addToCompositeGroups, addToCompositeGroups, addToDesignProviders, addToDesignProviders, addToFeatureGroups, addToFeatureGroups, addToProtocolApplications, addToProtocolApplications, addToReporterGroups, addToReporterGroups, getCompositeGroups, getDesignProviders, getFeatureGroups, getFromCompositeGroups, getFromDesignProviders, getFromFeatureGroups, getFromProtocolApplications, getFromReporterGroups, getNumberOfFeatures, getProtocolApplications, getReporterGroups, getVersion, removeElementAtFromCompositeGroups, removeElementAtFromDesignProviders, removeElementAtFromFeatureGroups, removeElementAtFromProtocolApplications, removeElementAtFromReporterGroups, removeFromCompositeGroups, removeFromDesignProviders, removeFromFeatureGroups, removeFromProtocolApplications, removeFromReporterGroups, setCompositeGroups, setDesignProviders, setFeatureGroups, setNumberOfFeatures, setProtocolApplications, setReporterGroups, setVersion

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

surfaceType

protected OntologyEntry surfaceType

The type of surface from a controlled vocabulary that would include terms such as non-absorptive, absorptive, etc.

zoneGroups

protected HasZoneGroups.ZoneGroups_list zoneGroups

In the case where the array design is specified by one or more zones, allows specifying where those zones are located.

Constructor Detail

PhysicalArrayDesign

public PhysicalArrayDesign()

Default constructor.

PhysicalArrayDesign

public PhysicalArrayDesign(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 ArrayDesign

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 ArrayDesign

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 ArrayDesign

java.io.IOException

setSurfaceType

public void setSurfaceType(OntologyEntry surfaceType)

Set method for surfaceType

Specified by:

setSurfaceType in interface HasSurfaceType

getSurfaceType

public OntologyEntry getSurfaceType()

Get method for surfaceType

Specified by:

getSurfaceType in interface HasSurfaceType

Returns:

value of the attribute

setZoneGroups

public void setZoneGroups(HasZoneGroups.ZoneGroups_list zoneGroups)

Set method for zoneGroups

Specified by:

setZoneGroups in interface HasZoneGroups

getZoneGroups

public HasZoneGroups.ZoneGroups_list getZoneGroups()

Get method for zoneGroups

Specified by:

getZoneGroups in interface HasZoneGroups

Returns:

value of the attribute

addToZoneGroups

public void addToZoneGroups(ZoneGroup zoneGroup)

Method to add ZoneGroup to ZoneGroups_list

Specified by:

addToZoneGroups in interface HasZoneGroups

addToZoneGroups

public void addToZoneGroups(int position,
                            ZoneGroup zoneGroup)

Method to add ZoneGroup at position to ZoneGroups_list

Specified by:

addToZoneGroups in interface HasZoneGroups

getFromZoneGroups

public ZoneGroup getFromZoneGroups(int position)

Method to get ZoneGroup from ZoneGroups_list

Specified by:

getFromZoneGroups in interface HasZoneGroups

removeElementAtFromZoneGroups

public void removeElementAtFromZoneGroups(int position)

Method to remove by position from ZoneGroups_list

Specified by:

removeElementAtFromZoneGroups in interface HasZoneGroups

removeFromZoneGroups

public void removeFromZoneGroups(ZoneGroup zoneGroup)

Method to remove first ZoneGroup from ZoneGroups_list

Specified by:

removeFromZoneGroups in interface HasZoneGroups