org.biomage.ArrayDesign
Class ArrayDesign

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
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasCompositeGroups, HasDescriptions, HasDesignProviders, HasFeatureGroups, HasPropertySets, HasProtocolApplications, HasReporterGroups, HasSecurity
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/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  java.lang.String additionalReporterFileLocation
           
protected  java.util.List compositeGroups
          The grouping of like CompositeSequence together.
protected  boolean deleted
           
protected  java.util.List designProviderRoles
          The providers of the ArrayDesign that have a role which describes how he/she contributes the ArrayDesign, e.g.
protected  java.util.List featureGroups
          The grouping of like Features together.
protected  java.util.List protocolApplications
          Describes the application of any protocols, such as the methodology used to pick oligos, in the design of the array.
protected  java.lang.String reporterFileLocation
           
protected  java.lang.String reporterFileType
           
protected  java.util.List reporterGroups
          The grouping of like Reporter together.
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
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 addToDesignProviderRoles(DesignProviderRole providerRole)
          Method to add Contact to DesignProviders_list
 void addToDesignProviderRoles(int position, DesignProviderRole providerRole)
          Adds a provider of this experiment that has a role
 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 addToProviderRoles(DesignProviderRole providerRole)
          Adds a provider of this experiment that has a role
 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
 boolean emptyMAGEobject()
           
 java.lang.String getAdditionalReporterFileLocation()
           
 HasCompositeGroups.CompositeGroups_list getCompositeGroups()
          Get method for compositeGroups
 java.util.ArrayList getDesignProviderRoles()
           
 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
 DesignProviderRole getFromDesignProviderRoles(int position)
           
 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
 java.lang.String getModelClassName()
           
 java.lang.Integer getNumberOfFeatures()
          Get method for numberOfFeatures
 HasProtocolApplications.ProtocolApplications_list getProtocolApplications()
          Get method for protocolApplications
 java.lang.String getReporterFileLocation()
           
 java.lang.String getReporterFileType()
           
 HasReporterGroups.ReporterGroups_list getReporterGroups()
          Get method for reporterGroups
 java.lang.String getVersion()
          Get method for version
 boolean isDeleted()
           
 void removeElementAtFromCompositeGroups(int position)
          Method to remove by position from CompositeGroups_list
 void removeElementAtFromDesignProviderRoles(int position)
           
 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 removeFromDesignProviderRoles(DesignProviderRole providerRole)
           
 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 setAdditionalReporterFileLocation(java.lang.String string)
           
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setCompositeGroups(HasCompositeGroups.CompositeGroups_list compositeGroups)
          Set method for compositeGroups
 void setDeleted(boolean deleted)
          Mark this ArrayDesign as deleted.
 void setDesignProviderRoles(java.util.ArrayList providerRoles)
          The specified providerRoles must be instantiable List subclass for creation by reflection to work.
 void setDesignProviders(HasDesignProviders.DesignProviders_list designProviders)
          Set method for designProviders
 void setFeatureGroups(HasFeatureGroups.FeatureGroups_list featureGroups)
          Set method for featureGroups
 void setNumberOfFeatures(java.lang.Integer numberOfFeatures)
          Set method for numberOfFeatures
 void setProtocolApplications(HasProtocolApplications.ProtocolApplications_list protocolApplications)
          Set method for protocolApplications
 void setReporterFileLocation(java.lang.String string)
           
 void setReporterFileType(java.lang.String string)
           
 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, 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

reporterFileLocation

protected java.lang.String reporterFileLocation

reporterFileType

protected java.lang.String reporterFileType

additionalReporterFileLocation

protected java.lang.String additionalReporterFileLocation

deleted

protected boolean deleted

protocolApplications

protected java.util.List protocolApplications
Describes the application of any protocols, such as the methodology used to pick oligos, in the design of the array.


featureGroups

protected java.util.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 java.util.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 java.util.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.


designProviderRoles

protected java.util.List designProviderRoles
The providers of the ArrayDesign that have a role which describes how he/she contributes the ArrayDesign, e.g. investigator, primary contact, etc.

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

Parameters:
atts: - the attribute list.
Method Detail

setAttributes

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

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
Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

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
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 Identifiable
Throws:
java.io.IOException

setVersion

public void setVersion(java.lang.String version)
Set method for version

Parameters:
value - to set

getVersion

public java.lang.String getVersion()
Get method for version

Returns:
value of the attribute

setNumberOfFeatures

public void setNumberOfFeatures(java.lang.Integer numberOfFeatures)
Set method for numberOfFeatures

Parameters:
value - to set

getNumberOfFeatures

public java.lang.Integer getNumberOfFeatures()
Get method for numberOfFeatures

Returns:
value of the attribute

getModelClassName

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

setProtocolApplications

public void setProtocolApplications(HasProtocolApplications.ProtocolApplications_list protocolApplications)
Set method for protocolApplications

Specified by:
setProtocolApplications in interface HasProtocolApplications
Parameters:
value - to set

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
Parameters:
value - to set

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
Parameters:
value - to set

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
Parameters:
value - to set

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
Parameters:
value - to set

setDesignProviderRoles

public void setDesignProviderRoles(java.util.ArrayList providerRoles)
The specified providerRoles must be instantiable List subclass for creation by reflection to work. tranp (caARRAY) 8/4/04

Parameters:
providerRoles -

getDesignProviders

public HasDesignProviders.DesignProviders_list getDesignProviders()
Get method for designProviders

Specified by:
getDesignProviders in interface HasDesignProviders
Returns:
value of the attribute

getDesignProviderRoles

public java.util.ArrayList getDesignProviderRoles()

addToDesignProviders

public void addToDesignProviders(Contact contact)
Method to add Contact to DesignProviders_list

Specified by:
addToDesignProviders in interface HasDesignProviders

addToDesignProviderRoles

public void addToDesignProviderRoles(DesignProviderRole providerRole)
Method to add Contact to DesignProviders_list


addToProviderRoles

public void addToProviderRoles(DesignProviderRole providerRole)
Adds a provider of this experiment that has a role

Parameters:
providerRole - - A provider who has a role such as investigator, primary contact, etc.

addToDesignProviders

public void addToDesignProviders(int position,
                                 Contact contact)
Method to add Contact at position to DesignProviders_list

Specified by:
addToDesignProviders in interface HasDesignProviders

addToDesignProviderRoles

public void addToDesignProviderRoles(int position,
                                     DesignProviderRole providerRole)
Adds a provider of this experiment that has a role


getFromDesignProviders

public Contact getFromDesignProviders(int position)
Method to get Contact from DesignProviders_list

Specified by:
getFromDesignProviders in interface HasDesignProviders

getFromDesignProviderRoles

public DesignProviderRole getFromDesignProviderRoles(int position)

removeElementAtFromDesignProviders

public void removeElementAtFromDesignProviders(int position)
Method to remove by position from DesignProviders_list

Specified by:
removeElementAtFromDesignProviders in interface HasDesignProviders

removeElementAtFromDesignProviderRoles

public void removeElementAtFromDesignProviderRoles(int position)

removeFromDesignProviders

public void removeFromDesignProviders(Contact contact)
Method to remove first Contact from DesignProviders_list

Specified by:
removeFromDesignProviders in interface HasDesignProviders

removeFromDesignProviderRoles

public void removeFromDesignProviderRoles(DesignProviderRole providerRole)

getReporterFileLocation

public java.lang.String getReporterFileLocation()
Returns:

getReporterFileType

public java.lang.String getReporterFileType()
Returns:

setReporterFileLocation

public void setReporterFileLocation(java.lang.String string)
Parameters:
string -

setReporterFileType

public void setReporterFileType(java.lang.String string)
Parameters:
string -

getAdditionalReporterFileLocation

public java.lang.String getAdditionalReporterFileLocation()
Returns:

setAdditionalReporterFileLocation

public void setAdditionalReporterFileLocation(java.lang.String string)
Parameters:
string -

isDeleted

public boolean isDeleted()
Returns:

setDeleted

public void setDeleted(boolean deleted)
Mark this ArrayDesign as deleted. tranp.

Parameters:
b -