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org.biomage.ArrayDesign
Class PhysicalArrayDesign  view PhysicalArrayDesign download PhysicalArrayDesign.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.ArrayDesign.ArrayDesign
                  extended byorg.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

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.


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.


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.


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

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

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

setZoneGroups

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

Specified by:
setZoneGroups in interface org.biomage.Interface.HasZoneGroups

getZoneGroups

public org.biomage.Interface.HasZoneGroups.ZoneGroups_list getZoneGroups()
Get method for zoneGroups

Specified by:
getZoneGroups in interface org.biomage.Interface.HasZoneGroups

addToZoneGroups

public void addToZoneGroups(ZoneGroup zoneGroup)
Method to add ZoneGroup to ZoneGroups_list

Specified by:
addToZoneGroups in interface org.biomage.Interface.HasZoneGroups

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

getFromZoneGroups

public ZoneGroup getFromZoneGroups(int position)
Method to get ZoneGroup from ZoneGroups_list

Specified by:
getFromZoneGroups in interface org.biomage.Interface.HasZoneGroups

removeElementAtFromZoneGroups

public void removeElementAtFromZoneGroups(int position)
Method to remove by position from ZoneGroups_list

Specified by:
removeElementAtFromZoneGroups in interface org.biomage.Interface.HasZoneGroups

removeFromZoneGroups

public void removeFromZoneGroups(ZoneGroup zoneGroup)
Method to remove first ZoneGroup from ZoneGroups_list

Specified by:
removeFromZoneGroups in interface org.biomage.Interface.HasZoneGroups

setSurfaceType

public void setSurfaceType(org.biomage.Description.OntologyEntry surfaceType)
Set method for surfaceType

Specified by:
setSurfaceType in interface org.biomage.Interface.HasSurfaceType

getSurfaceType

public org.biomage.Description.OntologyEntry getSurfaceType()
Get method for surfaceType

Specified by:
getSurfaceType in interface org.biomage.Interface.HasSurfaceType