org.biomage.ArrayDesign
Class PhysicalArrayDesign

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Common.Describable
          extended by org.biomage.Common.Identifiable
              extended by org.biomage.ArrayDesign.ArrayDesign
                  extended by org.biomage.ArrayDesign.PhysicalArrayDesign
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasCompositeGroups, HasDescriptions, HasDesignProviders, HasFeatureGroups, HasPropertySets, HasProtocolApplications, HasReporterGroups, HasSecurity, HasSurfaceType, HasZoneGroups

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/interfaces inherited from interface org.biomage.Interface.HasZoneGroups
HasZoneGroups.ZoneGroups_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasProtocolApplications
HasProtocolApplications.ProtocolApplications_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasCompositeGroups
HasCompositeGroups.CompositeGroups_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDesignProviders
HasDesignProviders.DesignProviders_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasReporterGroups
HasReporterGroups.ReporterGroups_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasFeatureGroups
HasFeatureGroups.FeatureGroups_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail
HasAuditTrail.AuditTrail_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions
HasDescriptions.Descriptions_list
 
Nested classes/interfaces inherited from interface 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  java.util.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
additionalReporterFileLocation, compositeGroups, deleted, designProviderRoles, featureGroups, protocolApplications, reporterFileLocation, reporterFileType, reporterGroups
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
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
 boolean emptyMAGEobject()
           
 ZoneGroup getFromZoneGroups(int position)
          Method to get ZoneGroup from ZoneGroups_list
 java.lang.String getModelClassName()
           
 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 setAttributes(org.xml.sax.Attributes atts)
           
 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, addToDesignProviderRoles, addToDesignProviderRoles, addToDesignProviders, addToDesignProviders, addToFeatureGroups, addToFeatureGroups, addToProtocolApplications, addToProtocolApplications, addToProviderRoles, addToReporterGroups, addToReporterGroups, getAdditionalReporterFileLocation, getCompositeGroups, getDesignProviderRoles, getDesignProviders, getFeatureGroups, getFromCompositeGroups, getFromDesignProviderRoles, getFromDesignProviders, getFromFeatureGroups, getFromProtocolApplications, getFromReporterGroups, getNumberOfFeatures, getProtocolApplications, getReporterFileLocation, getReporterFileType, getReporterGroups, getVersion, isDeleted, removeElementAtFromCompositeGroups, removeElementAtFromDesignProviderRoles, removeElementAtFromDesignProviders, removeElementAtFromFeatureGroups, removeElementAtFromProtocolApplications, removeElementAtFromReporterGroups, removeFromCompositeGroups, removeFromDesignProviderRoles, removeFromDesignProviders, removeFromFeatureGroups, removeFromProtocolApplications, removeFromReporterGroups, setAdditionalReporterFileLocation, setCompositeGroups, setDeleted, setDesignProviderRoles, setDesignProviders, setFeatureGroups, setNumberOfFeatures, setProtocolApplications, setReporterFileLocation, setReporterFileType, setReporterGroups, setVersion
 
Methods inherited from class org.biomage.Common.Identifiable
getIdentifier, getName, setIdentifier, setName, toString
 
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, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, 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 java.util.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

Parameters:
atts: - the attribute list.
Method Detail

setAttributes

public void setAttributes(org.xml.sax.Attributes atts)
Overrides:
setAttributes in class ArrayDesign

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
Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()
Overrides:
emptyMAGEobject 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
Throws:
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
Throws:
java.io.IOException

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class ArrayDesign

setSurfaceType

public void setSurfaceType(OntologyEntry surfaceType)
Set method for surfaceType

Specified by:
setSurfaceType in interface HasSurfaceType
Parameters:
value - to set

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
Parameters:
value - to set

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