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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:

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

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public class PhysicalArrayDesign

extends ArrayDesign

implements java.io.Serializable, org.biomage.Interface.HasZoneGroups, org.biomage.Interface.HasSurfaceType

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

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Nested Class Summary

 

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

org.biomage.Interface.HasZoneGroups.ZoneGroups_list

 

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

org.biomage.Interface.HasProtocolApplications.ProtocolApplications_list

 

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

org.biomage.Interface.HasCompositeGroups.CompositeGroups_list

 

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

org.biomage.Interface.HasDesignProviders.DesignProviders_list

 

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

org.biomage.Interface.HasReporterGroups.ReporterGroups_list

 

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

org.biomage.Interface.HasFeatureGroups.FeatureGroups_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	surfaceType           The type of surface from a controlled vocabulary that would include terms such as non-absorptive, absorptive, etc.
private  org.biomage.Interface.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

numberOfFeatures, version

 

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

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
org.biomage.Description.OntologyEntry	getSurfaceType()           Get method for surfaceType
org.biomage.Interface.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(org.biomage.Description.OntologyEntry surfaceType)           Set method for surfaceType
void	setZoneGroups(org.biomage.Interface.HasZoneGroups.ZoneGroups_list zoneGroups)           Set method for zoneGroups
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.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

zoneGroups

private org.biomage.Interface.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.

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surfaceType

private org.biomage.Description.OntologyEntry surfaceType

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

Constructor Detail

PhysicalArrayDesign

public PhysicalArrayDesign()

Default constructor.

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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

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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.

Overrides:

writeAttributes in class ArrayDesign

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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.

Overrides:

writeAssociations in class ArrayDesign

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setZoneGroups

public void setZoneGroups(org.biomage.Interface.HasZoneGroups.ZoneGroups_list zoneGroups)

Set method for zoneGroups

Specified by:

setZoneGroups in interface org.biomage.Interface.HasZoneGroups

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getZoneGroups

public org.biomage.Interface.HasZoneGroups.ZoneGroups_list getZoneGroups()

Get method for zoneGroups

Specified by:

getZoneGroups in interface org.biomage.Interface.HasZoneGroups

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addToZoneGroups

public void addToZoneGroups(ZoneGroup zoneGroup)

Method to add ZoneGroup to ZoneGroups_list

Specified by:

addToZoneGroups in interface org.biomage.Interface.HasZoneGroups

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addToZoneGroups

public void addToZoneGroups(int position,
                            ZoneGroup zoneGroup)

Method to add ZoneGroup at position to ZoneGroups_list

Specified by:

addToZoneGroups in interface org.biomage.Interface.HasZoneGroups

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getFromZoneGroups

public ZoneGroup getFromZoneGroups(int position)

Method to get ZoneGroup from ZoneGroups_list

Specified by:

getFromZoneGroups in interface org.biomage.Interface.HasZoneGroups

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removeElementAtFromZoneGroups

public void removeElementAtFromZoneGroups(int position)

Method to remove by position from ZoneGroups_list

Specified by:

removeElementAtFromZoneGroups in interface org.biomage.Interface.HasZoneGroups

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removeFromZoneGroups

public void removeFromZoneGroups(ZoneGroup zoneGroup)

Method to remove first ZoneGroup from ZoneGroups_list

Specified by:

removeFromZoneGroups in interface org.biomage.Interface.HasZoneGroups

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setSurfaceType

public void setSurfaceType(org.biomage.Description.OntologyEntry surfaceType)

Set method for surfaceType

Specified by:

setSurfaceType in interface org.biomage.Interface.HasSurfaceType

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getSurfaceType

public org.biomage.Description.OntologyEntry getSurfaceType()

Get method for surfaceType

Specified by:

getSurfaceType in interface org.biomage.Interface.HasSurfaceType

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Overview  Package   Class  Use  Deprecated  Index
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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