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

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.ArrayDesign.ArrayDesign
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, java.io.Serializable
Direct Known Subclasses:
PhysicalArrayDesign

public class ArrayDesign
extends org.biomage.Common.Identifiable
implements java.io.Serializable, org.biomage.Interface.HasProtocolApplications, org.biomage.Interface.HasCompositeGroups, org.biomage.Interface.HasDesignProviders, org.biomage.Interface.HasReporterGroups, org.biomage.Interface.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.


Nested Class Summary
 
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.Interface.HasCompositeGroups.CompositeGroups_list compositeGroups
          The grouping of like CompositeSequence together.
private  org.biomage.Interface.HasDesignProviders.DesignProviders_list designProviders
          The primary contact for information on the array design
private  org.biomage.Interface.HasFeatureGroups.FeatureGroups_list featureGroups
          The grouping of like Features together.
(package private)  int numberOfFeatures
          The number of features for this array
private  org.biomage.Interface.HasProtocolApplications.ProtocolApplications_list protocolApplications
          Describes the application of any protocols, such as the methodology used to pick oligos, in the design of the array.
private  org.biomage.Interface.HasReporterGroups.ReporterGroups_list reporterGroups
          The grouping of like Reporter together.
(package private)  java.lang.String version
          The version of this design.
 
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
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 addToDesignProviders(org.biomage.AuditAndSecurity.Contact contact)
          Method to add Contact to DesignProviders_list
 void addToDesignProviders(int position, org.biomage.AuditAndSecurity.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, org.biomage.Protocol.ProtocolApplication protocolApplication)
          Method to add ProtocolApplication at position to ProtocolApplications_list
 void addToProtocolApplications(org.biomage.Protocol.ProtocolApplication protocolApplication)
          Method to add ProtocolApplication to ProtocolApplications_list
 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
 org.biomage.Interface.HasCompositeGroups.CompositeGroups_list getCompositeGroups()
          Get method for compositeGroups
 org.biomage.Interface.HasDesignProviders.DesignProviders_list getDesignProviders()
          Get method for designProviders
 org.biomage.Interface.HasFeatureGroups.FeatureGroups_list getFeatureGroups()
          Get method for featureGroups
 CompositeGroup getFromCompositeGroups(int position)
          Method to get CompositeGroup from CompositeGroups_list
 org.biomage.AuditAndSecurity.Contact getFromDesignProviders(int position)
          Method to get Contact from DesignProviders_list
 FeatureGroup getFromFeatureGroups(int position)
          Method to get FeatureGroup from FeatureGroups_list
 org.biomage.Protocol.ProtocolApplication getFromProtocolApplications(int position)
          Method to get ProtocolApplication from ProtocolApplications_list
 ReporterGroup getFromReporterGroups(int position)
          Method to get ReporterGroup from ReporterGroups_list
 int getNumberOfFeatures()
          Get method for numberOfFeatures
 org.biomage.Interface.HasProtocolApplications.ProtocolApplications_list getProtocolApplications()
          Get method for protocolApplications
 org.biomage.Interface.HasReporterGroups.ReporterGroups_list getReporterGroups()
          Get method for reporterGroups
 java.lang.String getVersion()
          Get method for version
 void removeElementAtFromCompositeGroups(int position)
          Method to remove by position from CompositeGroups_list
 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 removeFromDesignProviders(org.biomage.AuditAndSecurity.Contact contact)
          Method to remove first Contact from DesignProviders_list
 void removeFromFeatureGroups(FeatureGroup featureGroup)
          Method to remove first FeatureGroup from FeatureGroups_list
 void removeFromProtocolApplications(org.biomage.Protocol.ProtocolApplication protocolApplication)
          Method to remove first ProtocolApplication from ProtocolApplications_list
 void removeFromReporterGroups(ReporterGroup reporterGroup)
          Method to remove first ReporterGroup from ReporterGroups_list
 void setCompositeGroups(org.biomage.Interface.HasCompositeGroups.CompositeGroups_list compositeGroups)
          Set method for compositeGroups
 void setDesignProviders(org.biomage.Interface.HasDesignProviders.DesignProviders_list designProviders)
          Set method for designProviders
 void setFeatureGroups(org.biomage.Interface.HasFeatureGroups.FeatureGroups_list featureGroups)
          Set method for featureGroups
 void setNumberOfFeatures(int numberOfFeatures)
          Set method for numberOfFeatures
 void setProtocolApplications(org.biomage.Interface.HasProtocolApplications.ProtocolApplications_list protocolApplications)
          Set method for protocolApplications
 void setReporterGroups(org.biomage.Interface.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
 void writeAttributes(java.io.Writer out)
          writeAttributes
 void writeMAGEML(java.io.Writer out)
          writeMAGEML
 
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

version

java.lang.String version
The version of this design.


numberOfFeatures

int numberOfFeatures
The number of features for this array


protocolApplications

private org.biomage.Interface.HasProtocolApplications.ProtocolApplications_list protocolApplications
Describes the application of any protocols, such as the methodology used to pick oligos, in the design of the array.


compositeGroups

private org.biomage.Interface.HasCompositeGroups.CompositeGroups_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.


designProviders

private org.biomage.Interface.HasDesignProviders.DesignProviders_list designProviders
The primary contact for information on the array design


reporterGroups

private org.biomage.Interface.HasReporterGroups.ReporterGroups_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.


featureGroups

private org.biomage.Interface.HasFeatureGroups.FeatureGroups_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.

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

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.


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.


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.


setVersion

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


getVersion

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


setNumberOfFeatures

public void setNumberOfFeatures(int numberOfFeatures)
Set method for numberOfFeatures


getNumberOfFeatures

public int getNumberOfFeatures()
Get method for numberOfFeatures


setProtocolApplications

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

Specified by:
setProtocolApplications in interface org.biomage.Interface.HasProtocolApplications

getProtocolApplications

public org.biomage.Interface.HasProtocolApplications.ProtocolApplications_list getProtocolApplications()
Get method for protocolApplications

Specified by:
getProtocolApplications in interface org.biomage.Interface.HasProtocolApplications

addToProtocolApplications

public void addToProtocolApplications(org.biomage.Protocol.ProtocolApplication protocolApplication)
Method to add ProtocolApplication to ProtocolApplications_list

Specified by:
addToProtocolApplications in interface org.biomage.Interface.HasProtocolApplications

addToProtocolApplications

public void addToProtocolApplications(int position,
                                      org.biomage.Protocol.ProtocolApplication protocolApplication)
Method to add ProtocolApplication at position to ProtocolApplications_list

Specified by:
addToProtocolApplications in interface org.biomage.Interface.HasProtocolApplications

getFromProtocolApplications

public org.biomage.Protocol.ProtocolApplication getFromProtocolApplications(int position)
Method to get ProtocolApplication from ProtocolApplications_list

Specified by:
getFromProtocolApplications in interface org.biomage.Interface.HasProtocolApplications

removeElementAtFromProtocolApplications

public void removeElementAtFromProtocolApplications(int position)
Method to remove by position from ProtocolApplications_list

Specified by:
removeElementAtFromProtocolApplications in interface org.biomage.Interface.HasProtocolApplications

removeFromProtocolApplications

public void removeFromProtocolApplications(org.biomage.Protocol.ProtocolApplication protocolApplication)
Method to remove first ProtocolApplication from ProtocolApplications_list

Specified by:
removeFromProtocolApplications in interface org.biomage.Interface.HasProtocolApplications

setCompositeGroups

public void setCompositeGroups(org.biomage.Interface.HasCompositeGroups.CompositeGroups_list compositeGroups)
Set method for compositeGroups

Specified by:
setCompositeGroups in interface org.biomage.Interface.HasCompositeGroups

getCompositeGroups

public org.biomage.Interface.HasCompositeGroups.CompositeGroups_list getCompositeGroups()
Get method for compositeGroups

Specified by:
getCompositeGroups in interface org.biomage.Interface.HasCompositeGroups

addToCompositeGroups

public void addToCompositeGroups(CompositeGroup compositeGroup)
Method to add CompositeGroup to CompositeGroups_list

Specified by:
addToCompositeGroups in interface org.biomage.Interface.HasCompositeGroups

addToCompositeGroups

public void addToCompositeGroups(int position,
                                 CompositeGroup compositeGroup)
Method to add CompositeGroup at position to CompositeGroups_list

Specified by:
addToCompositeGroups in interface org.biomage.Interface.HasCompositeGroups

getFromCompositeGroups

public CompositeGroup getFromCompositeGroups(int position)
Method to get CompositeGroup from CompositeGroups_list

Specified by:
getFromCompositeGroups in interface org.biomage.Interface.HasCompositeGroups

removeElementAtFromCompositeGroups

public void removeElementAtFromCompositeGroups(int position)
Method to remove by position from CompositeGroups_list

Specified by:
removeElementAtFromCompositeGroups in interface org.biomage.Interface.HasCompositeGroups

removeFromCompositeGroups

public void removeFromCompositeGroups(CompositeGroup compositeGroup)
Method to remove first CompositeGroup from CompositeGroups_list

Specified by:
removeFromCompositeGroups in interface org.biomage.Interface.HasCompositeGroups

setDesignProviders

public void setDesignProviders(org.biomage.Interface.HasDesignProviders.DesignProviders_list designProviders)
Set method for designProviders

Specified by:
setDesignProviders in interface org.biomage.Interface.HasDesignProviders

getDesignProviders

public org.biomage.Interface.HasDesignProviders.DesignProviders_list getDesignProviders()
Get method for designProviders

Specified by:
getDesignProviders in interface org.biomage.Interface.HasDesignProviders

addToDesignProviders

public void addToDesignProviders(org.biomage.AuditAndSecurity.Contact contact)
Method to add Contact to DesignProviders_list

Specified by:
addToDesignProviders in interface org.biomage.Interface.HasDesignProviders

addToDesignProviders

public void addToDesignProviders(int position,
                                 org.biomage.AuditAndSecurity.Contact contact)
Method to add Contact at position to DesignProviders_list

Specified by:
addToDesignProviders in interface org.biomage.Interface.HasDesignProviders

getFromDesignProviders

public org.biomage.AuditAndSecurity.Contact getFromDesignProviders(int position)
Method to get Contact from DesignProviders_list

Specified by:
getFromDesignProviders in interface org.biomage.Interface.HasDesignProviders

removeElementAtFromDesignProviders

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

Specified by:
removeElementAtFromDesignProviders in interface org.biomage.Interface.HasDesignProviders

removeFromDesignProviders

public void removeFromDesignProviders(org.biomage.AuditAndSecurity.Contact contact)
Method to remove first Contact from DesignProviders_list

Specified by:
removeFromDesignProviders in interface org.biomage.Interface.HasDesignProviders

setReporterGroups

public void setReporterGroups(org.biomage.Interface.HasReporterGroups.ReporterGroups_list reporterGroups)
Set method for reporterGroups

Specified by:
setReporterGroups in interface org.biomage.Interface.HasReporterGroups

getReporterGroups

public org.biomage.Interface.HasReporterGroups.ReporterGroups_list getReporterGroups()
Get method for reporterGroups

Specified by:
getReporterGroups in interface org.biomage.Interface.HasReporterGroups

addToReporterGroups

public void addToReporterGroups(ReporterGroup reporterGroup)
Method to add ReporterGroup to ReporterGroups_list

Specified by:
addToReporterGroups in interface org.biomage.Interface.HasReporterGroups

addToReporterGroups

public void addToReporterGroups(int position,
                                ReporterGroup reporterGroup)
Method to add ReporterGroup at position to ReporterGroups_list

Specified by:
addToReporterGroups in interface org.biomage.Interface.HasReporterGroups

getFromReporterGroups

public ReporterGroup getFromReporterGroups(int position)
Method to get ReporterGroup from ReporterGroups_list

Specified by:
getFromReporterGroups in interface org.biomage.Interface.HasReporterGroups

removeElementAtFromReporterGroups

public void removeElementAtFromReporterGroups(int position)
Method to remove by position from ReporterGroups_list

Specified by:
removeElementAtFromReporterGroups in interface org.biomage.Interface.HasReporterGroups

removeFromReporterGroups

public void removeFromReporterGroups(ReporterGroup reporterGroup)
Method to remove first ReporterGroup from ReporterGroups_list

Specified by:
removeFromReporterGroups in interface org.biomage.Interface.HasReporterGroups

setFeatureGroups

public void setFeatureGroups(org.biomage.Interface.HasFeatureGroups.FeatureGroups_list featureGroups)
Set method for featureGroups

Specified by:
setFeatureGroups in interface org.biomage.Interface.HasFeatureGroups

getFeatureGroups

public org.biomage.Interface.HasFeatureGroups.FeatureGroups_list getFeatureGroups()
Get method for featureGroups

Specified by:
getFeatureGroups in interface org.biomage.Interface.HasFeatureGroups

addToFeatureGroups

public void addToFeatureGroups(FeatureGroup featureGroup)
Method to add FeatureGroup to FeatureGroups_list

Specified by:
addToFeatureGroups in interface org.biomage.Interface.HasFeatureGroups

addToFeatureGroups

public void addToFeatureGroups(int position,
                               FeatureGroup featureGroup)
Method to add FeatureGroup at position to FeatureGroups_list

Specified by:
addToFeatureGroups in interface org.biomage.Interface.HasFeatureGroups

getFromFeatureGroups

public FeatureGroup getFromFeatureGroups(int position)
Method to get FeatureGroup from FeatureGroups_list

Specified by:
getFromFeatureGroups in interface org.biomage.Interface.HasFeatureGroups

removeElementAtFromFeatureGroups

public void removeElementAtFromFeatureGroups(int position)
Method to remove by position from FeatureGroups_list

Specified by:
removeElementAtFromFeatureGroups in interface org.biomage.Interface.HasFeatureGroups

removeFromFeatureGroups

public void removeFromFeatureGroups(FeatureGroup featureGroup)
Method to remove first FeatureGroup from FeatureGroups_list

Specified by:
removeFromFeatureGroups in interface org.biomage.Interface.HasFeatureGroups