SBOLDocument

java.lang.Object
- org.sbolstandard.core2.SBOLDocument

```
public class SBOLDocument
extends Object
```
Represents the SBOL document where all top-level instances can be created and manipulated.

Version:

2.1

Author:

Zhen Zhang, Nicholas Roehner, Chris Myers

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`FASTAformat` Constant representing FASTA file format
`static String`	`GENBANK` Constant representing GenBank file format
`static String`	`JSON` Constant representing JSON file format
`static String`	`RDF` Constant representing RDF file format
`static String`	`RDFV1` Constant representing the format of an SBOL version 1.1 output file as being RDF format
`static String`	`SNAPGENE` Constant representing SnapGene file format
`static String`	`TURTLE` Constant representing TURTLE file format

Constructor Summary

Constructors
Constructor and Description
`SBOLDocument()` Creates a new SBOLDocument instance with one empty list for the namespaces and one for each top-level instance, and then adds the following namespaces: `Sbol2Terms.sbol2`, `Sbol1Terms.rdf`, `Sbol2Terms.dc`, and `Sbol2Terms.prov`.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addNamespace(QName qName)` Adds the given namespace QName to this SBOL document.
`void`	`addNamespace(URI nameSpaceURI, String prefix)` Adds the given namespace URI and its prefix to this SBOL document.
`SynBioHubFrontend`	`addRegistry(String registryURL)` Adds the given registry to this SBOL document.
`SynBioHubFrontend`	`addRegistry(String registryURL, String uriPrefix)` Adds the given registry to this SBOL document.
`SBOLDocument`	`changeURIPrefixVersion(String URIPrefix, String version, String defaultVersion)` Copy all objects to an a new SBOL Document and change the URI prefix/version of each object
`void`	`clearActivitys()` Removes all entries in the list of activities owned by this SBOL document.
`void`	`clearAgents()` Removes all entries in the list of agents owned by this SBOL document.
`void`	`clearAttachments()` Removes all entries in the list of attachments owned by this SBOL document.
`void`	`clearCollections()` Removes all entries in the list of collections owned by this SBOL document.
`void`	`clearCombinatorialDerivations()` Removes all entries in the list of combinatorial derivations owned by this SBOL document.
`void`	`clearComponentDefinitions()` Removes all entries in the list of component definitions owned by this SBOL document.
`void`	`clearExperimentalData()` Removes all entries in the list of experimentalData owned by this SBOL document.
`void`	`clearExperiments()` Removes all entries in the list of experiments owned by this SBOL document.
`void`	`clearGenericTopLevels()` Removes all entries in the list of generic top-levels owned by this SBOL document.
`void`	`clearImplementations()` Removes all entries in the list of implementations owned by this SBOL document.
`void`	`clearModels()` Removes all entries in the list of models owned by this SBOL document.
`void`	`clearModuleDefinitions()` Removes all entries in the list of module definitions owned by this SBOL document.
`void`	`clearNamespaces()` Removes all non-required namespaces from this SBOL document.
`void`	`clearPlans()` Removes all entries in the list of plans owned by this SBOL document.
`void`	`clearRegistries()` Removes all registries from this SBOL document.
`void`	`clearSequences()` Removes all entries in the list of sequences owned by this SBOL document.
`Activity`	`createActivity(String displayId)` Creates an activity, and then adds it to this SBOL document's list of activities.
`Activity`	`createActivity(String displayId, String version)` Creates an activity, and then adds it to this SBOL document's list of activities.
`Activity`	`createActivity(String URIprefix, String displayId, String version)` Creates an activity, and then adds it to this SBOL document's list of activities.
`Agent`	`createAgent(String displayId)` Creates an agent, and then adds it to this SBOL document's list of agents.
`Agent`	`createAgent(String displayId, String version)` Creates an agent, and then adds it to this SBOL document's list of agents.
`Agent`	`createAgent(String URIprefix, String displayId, String version)` Creates an agent, and then adds it to this SBOL document's list of agents.
`Attachment`	`createAttachment(String URIprefix, String displayId, String version, URI source)` Creates an attachment, and then adds it to this SBOL document's list of attachments.
`Attachment`	`createAttachment(String displayId, String version, URI source)` Creates an attachment, and then adds it to this SBOL document's list of attachments.
`Attachment`	`createAttachment(String displayId, URI source)` Creates an attachment, and then adds it to this SBOL document's list of attachments.
`Collection`	`createCollection(String displayId)` Creates a collection first, and then adds to this SBOL document's list of collections.
`Collection`	`createCollection(String displayId, String version)` Creates a collection first, and then adds to this SBOL document's list of collections.
`Collection`	`createCollection(String URIprefix, String displayId, String version)` Creates a collection first, and then adds to this SBOL document's list of collections.
`CombinatorialDerivation`	`createCombinatorialDerivation(String displayId, String version, String templateDisplayId, String templateVersion)` Creates a combinatorial derivation, and then adds it to this SBOL document's list of combinatorial derivations.
`CombinatorialDerivation`	`createCombinatorialDerivation(String URIprefix, String displayId, String version, URI template)` Creates a combinatorial derivation, and then adds it to this SBOL document's list of combinatorial derivations.
`CombinatorialDerivation`	`createCombinatorialDerivation(String displayId, String version, URI template)` Creates a combinatorial derivation, and then adds it to this SBOL document's list of combinatorial derivations.
`CombinatorialDerivation`	`createCombinatorialDerivation(String displayId, URI template)` Creates a combinatorial derivation, and then adds it to this SBOL document's list of combinatorial derivations.
`ComponentDefinition`	`createComponentDefinition(String displayId, Set<URI> types)` Creates a component definition, and then adds it to this SBOL document's list of component definitions.
`ComponentDefinition`	`createComponentDefinition(String displayId, String version, Set<URI> types)` Creates a component definition, and then adds it to this SBOL document's list of component definitions.
`ComponentDefinition`	`createComponentDefinition(String URIprefix, String displayId, String version, Set<URI> types)` Creates a component definition, and then adds it to this SBOL document's list of component definitions.
`ComponentDefinition`	`createComponentDefinition(String URIprefix, String displayId, String version, URI type)` Creates a component definition, and then adds it to this SBOL document's list of component definitions.
`ComponentDefinition`	`createComponentDefinition(String displayId, String version, URI type)` Creates a component definition, and then adds it to this SBOL document's list of component definitions.
`ComponentDefinition`	`createComponentDefinition(String displayId, URI type)` Creates a component definition, and then adds it to this SBOL document's list of component definitions.
`void`	`createCopy(SBOLDocument document)` Creates an identical copy of each top-level element of a document, and then adds the created top-level to the corresponding list of top-levels in this SBOL document.
`TopLevel`	`createCopy(TopLevel topLevel)` Creates an identical copy of the given top-level, and then adds the created top-level to the corresponding list of top-levels in this SBOL document.
`TopLevel`	`createCopy(TopLevel topLevel, String displayId)` Creates a copy of the given top-level with the given display ID, and then adds the created top-level to the corresponding list of top-levels in this SBOL document.
`TopLevel`	`createCopy(TopLevel topLevel, String displayId, String version)` Creates a copy of the given top-level with the given display ID and version, and then adds the created top-level to the corresponding list of top-levels in this SBOL document.
`TopLevel`	`createCopy(TopLevel topLevel, String URIprefix, String displayId, String version)` Creates a copy of the given top-level with the given URI prefix, display ID and version, and then adds the created top-level to the corresponding list of top-levels in this SBOL document.
`Experiment`	`createExperiment(String displayId)` Creates a experiment first, and then adds to this SBOL document's list of experiments.
`Experiment`	`createExperiment(String displayId, String version)` Creates a experiment first, and then adds to this SBOL document's list of experiments.
`Experiment`	`createExperiment(String URIprefix, String displayId, String version)` Creates a experiment first, and then adds to this SBOL document's list of experiments.
`ExperimentalData`	`createExperimentalData(String displayId)` Creates a experimentalData first, and then adds to this SBOL document's list of experimentalDatas.
`ExperimentalData`	`createExperimentalData(String displayId, String version)` Creates a experimentalData first, and then adds to this SBOL document's list of experimentalDatas.
`ExperimentalData`	`createExperimentalData(String URIprefix, String displayId, String version)` Creates a experimentalData first, and then adds to this SBOL document's list of experimentalDatas.
`GenericTopLevel`	`createGenericTopLevel(String displayId, QName rdfType)` Creates a generic top-level, and then adds it to this SBOL document's list of generic top-levels.
`GenericTopLevel`	`createGenericTopLevel(String displayId, String version, QName rdfType)` Creates a generic top-level, and then adds it to this SBOL document's list of generic top-levels.
`GenericTopLevel`	`createGenericTopLevel(String URIprefix, String displayId, String version, QName rdfType)` Creates a generic top-level, and then adds it to this SBOL document's list of generic top-levels.
`Implementation`	`createImplementation(String displayId)` Creates an implementation, and then adds it to this SBOL document's list of implementations.
`Implementation`	`createImplementation(String displayId, String version)` Creates an implementation, and then adds it to this SBOL document's list of implementations.
`Implementation`	`createImplementation(String URIprefix, String displayId, String version)` Creates an implementation, and then adds it to this SBOL document's list of implementations.
`Model`	`createModel(String URIprefix, String displayId, String version, URI source, URI language, URI framework)` Creates a model, and then adds it to this SBOL document's list of models.
`Model`	`createModel(String displayId, String version, URI source, URI language, URI framework)` Creates a model, and then adds it to this SBOL document's list of models.
`Model`	`createModel(String displayId, URI source, URI language, URI framework)` Creates a model, and then adds it to this SBOL document's list of models.
`ModuleDefinition`	`createModuleDefinition(String displayId)` Creates a module definition, and then adds it to this SBOL document's list of module definitions.
`ModuleDefinition`	`createModuleDefinition(String displayId, String version)` Creates a module definition, and then adds it to this SBOL document's list of module definitions.
`ModuleDefinition`	`createModuleDefinition(String URIprefix, String displayId, String version)` Creates a module definition with the given arguments, and then adds it to this SBOL document's list of module definitions.
`Plan`	`createPlan(String displayId)` Creates an plan, and then adds it to this SBOL document's list of plans.
`Plan`	`createPlan(String displayId, String version)` Creates an plan, and then adds it to this SBOL document's list of plans.
`Plan`	`createPlan(String URIprefix, String displayId, String version)` Creates an plan, and then adds it to this SBOL document's list of plans.
`void`	`createRecursiveCopy(SBOLDocument document, TopLevel topLevel)`
`SBOLDocument`	`createRecursiveCopy(TopLevel topLevel)` Creates an identical copy of the given top-level and returns it in a new SBOLDocument.
`Sequence`	`createSequence(String URIprefix, String displayId, String version, String elements, URI encoding)` Creates a Sequence instance with the given arguments, and then adds it to this SBOLDocument object's list of Sequence instances.
`Sequence`	`createSequence(String displayId, String version, String elements, URI encoding)` Creates a Sequence instance with this SBOL document's `defaultURIprefix` and the given arguments, and then adds it to this SBOL document's list of Sequence instances.
`Sequence`	`createSequence(String displayId, String elements, URI encoding)` Creates a Sequence instance with this SBOL document's `defaultURIprefix`, the given arguments, and an empty version string, and then adds it to this SBOL document's list of Sequence instances.
`boolean`	`equals(Object obj)`
`Set<Activity>`	`getActivities()` Returns the set of activities owned by this SBOL document.
`Activity`	`getActivity(String displayId, String version)` Returns the activity matching the given display ID and version from this SBOL document's list of activities.
`Activity`	`getActivity(URI activityURI)` Returns the activity matching the given display identity URI from this SBOL document's list of activities.
`Agent`	`getAgent(String displayId, String version)` Returns the agent matching the given display ID and version from this SBOL document's list of agents.
`Agent`	`getAgent(URI agentURI)` Returns the agent matching the given display identity URI from this SBOL document's list of agents.
`Set<Agent>`	`getAgents()` Returns the set of agents owned by this SBOL document.
`Attachment`	`getAttachment(String displayId, String version)` Returns the attachment matching the given display ID and version from this SBOL document's list of attachments.
`Attachment`	`getAttachment(URI attachmentURI)` Returns the attachment matching the given identity URI from this SBOL document's list of attachments.
`Set<Attachment>`	`getAttachments()` Returns the set of attachments owned by this SBOL document.
`Set<TopLevel>`	`getByWasDerivedFrom(URI wasDerivedFrom)` Retrieves a set of top-levels in this SBOL document whose `wasDerivedFrom` field matches the given one.
`Collection`	`getCollection(String displayId, String version)` Returns the collection matching the given display ID and version from this SBOL document's list of collections.
`Collection`	`getCollection(URI collectionURI)` Returns the collection matching the given identity URI from this SBOL document's list of collections.
`Set<Collection>`	`getCollections()` Returns the set of `Collection` instances owned by this SBOL document.
`CombinatorialDerivation`	`getCombinatorialDerivation(String displayId, String version)` Returns the combinatorial derivation matching the given display ID and version from this SBOL document's list of combinatorial derivations.
`CombinatorialDerivation`	`getCombinatorialDerivation(URI combinatorialDerivationURI)` Returns the combinatorial derivation matching the given identity URI from this SBOL document's list of combinatorial derivations.
`Set<CombinatorialDerivation>`	`getCombinatorialDerivations()` Returns the set of combinatorial derivations owned by this SBOL document.
`ComponentDefinition`	`getComponentDefinition(String displayId, String version)` Returns the component definition matching the given display ID and version from this SBOL document's list of component definitions.
`ComponentDefinition`	`getComponentDefinition(URI componentDefinitionURI)` Returns the component definition matching the given identity URI from this SBOL document's list of component definitions.
`Set<ComponentDefinition>`	`getComponentDefinitions()` Returns the set of component definitions owned by this SBOL document.
`String`	`getDefaultURIprefix()` Returns the default URI prefix of this SBOL document.
`Experiment`	`getExperiment(String displayId, String version)` Returns the experiment matching the given display ID and version from this SBOL document's list of experiments.
`Experiment`	`getExperiment(URI experimentURI)` Returns the experiment matching the given identity URI from this SBOL document's list of experiments.
`Set<ExperimentalData>`	`getExperimentalData()` Returns the set of `ExperimentalData` instances owned by this SBOL document.
`ExperimentalData`	`getExperimentalData(String displayId, String version)` Returns the experimentalData matching the given display ID and version from this SBOL document's list of experimentalData.
`ExperimentalData`	`getExperimentalData(URI experimentalDataURI)` Returns the experimentalData matching the given identity URI from this SBOL document's list of experimentalDatas.
`Set<Experiment>`	`getExperiments()` Returns the set of `Experiment` instances owned by this SBOL document.
`GenericTopLevel`	`getGenericTopLevel(String displayId, String version)` Returns the generic top-level matching the given display ID and version from this SBOL document's list of generic top-levels.
`GenericTopLevel`	`getGenericTopLevel(URI genericTopLevelURI)` Returns the generic top-level matching the given display identity URI from this SBOL document's list of generic top-levels.
`Set<GenericTopLevel>`	`getGenericTopLevels()` Returns the set of generic top-levels owned by this SBOL document.
`Implementation`	`getImplementation(String displayId, String version)` Returns the implementation matching the given display ID and version from this SBOL document's list of implementations.
`Implementation`	`getImplementation(URI implementationURI)` Returns the implementation matching the given identity URI from this SBOL document's list of implementations.
`Set<Implementation>`	`getImplementations()` Returns the set of implementations owned by this SBOL document.
`Model`	`getModel(String displayId, String version)` Returns the model matching the given display ID and version from this SBOL document's list of models.
`Model`	`getModel(URI modelURI)` Returns the model matching the given identity URI from this SBOL document's list of models.
`Set<Model>`	`getModels()` Returns the set of models owned by this SBOL document.
`ModuleDefinition`	`getModuleDefinition(String displayId, String version)` Returns the module definition matching the given display ID and version from this SBOLDocument object's list of module definitions.
`ModuleDefinition`	`getModuleDefinition(URI moduleDefinitionURI)` Returns the module definition matching the given identity URI from this SBOL document object's list of module definitions.
`Set<ModuleDefinition>`	`getModuleDefinitions()` Returns the set of module definitions owned by this SBOLDocument object.
`QName`	`getNamespace(String namespacePrefix)` Returns the QName matching the given namespace prefix from this SBOL document's list of QNames.
`QName`	`getNamespace(URI namespaceURI)` Returns the QName matching the given namespace URI from this SBOL document's list of QNames.
`List<QName>`	`getNamespaces()` Returns the list of namespaces owned by this SBOL document.
`Plan`	`getPlan(String displayId, String version)` Returns the plan matching the given display ID and version from this SBOL document's list of plans.
`Plan`	`getPlan(URI planURI)` Returns the plan matching the given display identity URI from this SBOL document's list of plans.
`Set<Plan>`	`getPlans()` Returns the set of plans owned by this SBOL document.
`List<SynBioHubFrontend>`	`getRegistries()` Returns the list of registries used by this SBOL document.
`SynBioHubFrontend`	`getRegistry(String registryURL)` Returns the StackFrontend for the registry specified by its URL
`Set<ComponentDefinition>`	`getRootComponentDefinitions()` Returns the set of root component definitions.
`Set<ModuleDefinition>`	`getRootModuleDefinitions()` Returns the set of root module definitions.
`Sequence`	`getSequence(String displayId, String version)` Returns the sequence matching the given display ID and version from this SBOL document's list of sequences.
`Sequence`	`getSequence(URI sequenceURI)` Returns the sequence matching the given `modelURI` from this SBOL document's list of sequences.
`Set<Sequence>`	`getSequences()` Returns the set of sequences owned by this SBOL document.
`TopLevel`	`getTopLevel(URI topLevelURI)` Returns the top-level matching the given identity URI from this SBOL document's lists of top-levels.
`Set<TopLevel>`	`getTopLevels()` Returns the set of all top-levels owned by this SBOL document.
`int`	`hashCode()`
`boolean`	`isComplete()` Returns the value of the complete flag for this SBOL document.
`boolean`	`isCompliant()` Returns the value of the compliant flag in this SBOL document.
`boolean`	`isCreateDefaults()` Returns the value of the createDefaults flag in this SBOL document.
`boolean`	`isTypesInURIs()` Returns the value of the typesInURI flag in this SBOL document.
`void`	`read(File file)` Takes in a given RDF file and adds the data read to this SBOL document.
`void`	`read(InputStream in)` Takes in a given RDF input stream and adds the data read to this SBOL document.
`void`	`read(String fileName)` Takes in a given RDF file name and adds the data read to this SBOLDocument.
`boolean`	`removeActivity(Activity activity)` Removes the given activity from this SBOL document's list of activities.
`boolean`	`removeAgent(Agent agent)` Removes the given agent from this SBOL document's list of agents.
`boolean`	`removeAttachment(Attachment attachment)` Removes the given attachment from this SBOL document's list of attachments.
`boolean`	`removeCollection(Collection collection)` Removes the given collection from this SBOL document's list of collections.
`boolean`	`removeCombinatorialDerivation(CombinatorialDerivation combinatorialDerivation)` Removes the given combinatorial derivation from this SBOL document's list of combinatorial derivations.
`boolean`	`removeComponentDefinition(ComponentDefinition componentDefinition)` Removes the given component definition from this SBOL document's list of component definitions.
`boolean`	`removeExperiment(Experiment experiment)` Removes the given experiment from this SBOL document's list of experiments.
`boolean`	`removeExperimentalData(ExperimentalData experimentalDatum)` Removes the given experimentalData from this SBOL document's list of experimentalData.
`boolean`	`removeGenericTopLevel(GenericTopLevel genericTopLevel)` Removes the given generic top-level from this SBOL document's list of generic top-levels.
`boolean`	`removeImplementation(Implementation implementation)` Removes the given implementation from this SBOL document's list of implementations.
`boolean`	`removeModel(Model model)` Removes the given model from this SBOL document's list of models.
`boolean`	`removeModuleDefinition(ModuleDefinition moduleDefinition)` Removes the given module definition from this SBOL document's list of module definitions.
`void`	`removeNamespace(URI namespaceURI)` Removes the given namespace URI from this SBOL document's list of namespaces.
`boolean`	`removePlan(Plan plan)` Removes the given plan from this SBOL document's list of plans.
`void`	`removeRegistry(String registryId)` Removes the given registry id from this SBOL document's list of registries.
`boolean`	`removeSequence(Sequence sequence)` Removes the given sequence from this SBOL document's list of sequences.
`void`	`removeTopLevel(TopLevel topLevel)` Method to remove a TopLevel object
`TopLevel`	`rename(TopLevel topLevel, String displayId)` Renames the given top-level's display ID with the given one.
`TopLevel`	`rename(TopLevel topLevel, String displayId, String version)` Renames the given top-level's display ID and version with the given ones.
`TopLevel`	`rename(TopLevel topLevel, String URIprefix, String displayId, String version)` Renames the given top-level's URI prefix, display ID, and version with the given ones.
`void`	`setComplete(boolean complete)` Sets the complete flag to the given value.
`void`	`setCreateDefaults(boolean createDefaults)` Sets the createDefaults flag to the given value.
`void`	`setDefaultURIprefix(String defaultURIprefix)` Sets the default URI prefix of this SBOL document to the given one.
`void`	`setTypesInURIs(boolean typesInURIs)` Sets the typesInURIs flag to the given value.
`String`	`toString()`
`void`	`write(File file)` Outputs this SBOL document's data from the RDF/XML serialization to the given file.
`void`	`write(File file, String fileType)` Outputs this SBOL document's data from the serialization in the given serialization format to the given file.
`void`	`write(OutputStream out)` Outputs this SBOL document's data from the RDF/XML serialization to the given output stream.
`void`	`write(OutputStream out, String fileType)` Outputs this SBOL document's data from the serialization in the given serialization format to the given output stream.
`void`	`write(String filename)` Outputs this SBOL document's data from the RDF/XML serialization to a new file with the given file name.
`void`	`write(String filename, String fileType)` Outputs this SBOL document's data from serialization in the given serialization format to a new file with the given file name.

Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait

- Field Detail
  - TURTLE
```
public static final String TURTLE
```
    Constant representing TURTLE file format
    
    See Also:
    
    Constant Field Values
  - JSON
```
public static final String JSON
```
    Constant representing JSON file format
    
    See Also:
    
    Constant Field Values
  - RDFV1
```
public static final String RDFV1
```
    Constant representing the format of an SBOL version 1.1 output file as being RDF format
    
    See Also:
    
    Constant Field Values
  - RDF
```
public static final String RDF
```
    Constant representing RDF file format
    
    See Also:
    
    Constant Field Values
  - FASTAformat
```
public static final String FASTAformat
```
    Constant representing FASTA file format
    
    See Also:
    
    Constant Field Values
  - GENBANK
```
public static final String GENBANK
```
    Constant representing GenBank file format
    
    See Also:
    
    Constant Field Values
  - SNAPGENE
```
public static final String SNAPGENE
```
    Constant representing SnapGene file format
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - SBOLDocument
```
public SBOLDocument()
```
    Creates a new SBOLDocument instance with one empty list for the namespaces and one for each top-level instance, and then adds the following namespaces: Sbol2Terms.sbol2, Sbol1Terms.rdf, Sbol2Terms.dc, and Sbol2Terms.prov.
- Method Detail
  - createModuleDefinition
```
public ModuleDefinition createModuleDefinition(String displayId)
                                        throws SBOLValidationException
```
    Creates a module definition, and then adds it to this SBOL document's list of module definitions.
    This method calls createModuleDefinition(String, String, String) with the default URI prefix of this SBOL document, the given module definition display ID, and an empty version string.
    
    Parameters:
    
    displayId - the display ID of the module definition to be created
    
    Returns:
    
    the created module definition
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule was violated in createModuleDefinition(String, String, String) .
  - createModuleDefinition
```
public ModuleDefinition createModuleDefinition(String displayId,
                                               String version)
                                        throws SBOLValidationException
```
    Creates a module definition, and then adds it to this SBOL document's list of module definitions.
    This method calls createModuleDefinition(String, String, String) with the default URI prefix of this SBOL document, the given module definition display ID and version.
    
    Parameters:
    
    displayId - the display ID of the module definition to be created
    
    version - the version of the module definition to be created
    
    Returns:
    
    the created module definition
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule was violated in createModuleDefinition(String, String, String) .
  - createModuleDefinition
```
public ModuleDefinition createModuleDefinition(String URIprefix,
                                               String displayId,
                                               String version)
                                        throws SBOLValidationException
```
    Creates a module definition with the given arguments, and then adds it to this SBOL document's list of module definitions.
    This method first creates a compliant URI for the module definition to be retrieved. It starts with the given URI prefix after its been successfully validated, optionally followed by its type, namely TopLevel.MODULE_DEFINITION, followed by the given display ID, and ends with the given version.
    
    Parameters:
    
    URIprefix - the URI prefix used to construct the compliant URI for the module definition to be created
    
    displayId - the display ID of the module definition to be created
    
    version - the version of the module definition to be created
    
    Returns:
    
    the created module definition
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 10220.
  - removeModuleDefinition
```
public boolean removeModuleDefinition(ModuleDefinition moduleDefinition)
                               throws SBOLValidationException
```
    Removes the given module definition from this SBOL document's list of module definitions.
    
    Parameters:
    
    moduleDefinition - The moduleDefinition to be removed
    
    Returns:
    
    true if the given moduleDefinition is successfully removed, false otherwise.
    
    Throws:
    
    SBOLValidationException - if either of the following SBOL validation rules was violated: 11703, 12103.
  - getModuleDefinition
```
public ModuleDefinition getModuleDefinition(String displayId,
                                            String version)
```
    Returns the module definition matching the given display ID and version from this SBOLDocument object's list of module definitions.
    This method first creates a compliant URI for the module definition to be retrieved. It starts with the given URI prefix after its been successfully validated, optionally followed by its type, namely TopLevel.MODULE_DEFINITION, followed by the given display ID, and ends with the given version. This URI is used to look up the module definition in this SBOL document.
    
    Parameters:
    
    displayId - the display ID of the module definition to be retrieved
    
    version - the version of the module definition to be retrieved
    
    Returns:
    
    the matching module definition if present, or null otherwise
  - getModuleDefinition
```
public ModuleDefinition getModuleDefinition(URI moduleDefinitionURI)
```
    Returns the module definition matching the given identity URI from this SBOL document object's list of module definitions.
    
    Parameters:
    
    moduleDefinitionURI - the give identity URI of the module definition to be retrieved
    
    Returns:
    
    the matching module definition if present, or null otherwise
  - getModuleDefinitions
```
public Set<ModuleDefinition> getModuleDefinitions()
```
    Returns the set of module definitions owned by this SBOLDocument object.
    
    Returns:
    
    the set of module definitions owned by this SBOLDocument object.
  - clearModuleDefinitions
```
public void clearModuleDefinitions()
                            throws SBOLValidationException
```
    Removes all entries in the list of module definitions owned by this SBOL document. The list will be empty after this call returns.
    This method calls removeModuleDefinition(ModuleDefinition) to iteratively remove each module definition.
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in removeModuleDefinition(ModuleDefinition).
  - createCollection
```
public Collection createCollection(String displayId)
                            throws SBOLValidationException
```
    Creates a collection first, and then adds to this SBOL document's list of collections.
    This method calls createCollection(String, String, String) with the default URI prefix for this SOBL document, the given display ID of the collection to be created, and an empty version string.
    
    Parameters:
    
    displayId - the display ID of the collection to be created
    
    Returns:
    
    the created collection
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createCollection(String, String, String).
  - createCollection
```
public Collection createCollection(String displayId,
                                   String version)
                            throws SBOLValidationException
```
    Creates a collection first, and then adds to this SBOL document's list of collections.
    This method calls createCollection(String, String, String) with the default URI prefix for this SOBL document, the given display ID and version of the collection to be created.
    
    Parameters:
    
    displayId - the display ID of the collection to be created
    
    version - the version of the collection to be created
    
    Returns:
    
    the created collection
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createCollection(String, String, String).
  - createCollection
```
public Collection createCollection(String URIprefix,
                                   String displayId,
                                   String version)
                            throws SBOLValidationException
```
    Creates a collection first, and then adds to this SBOL document's list of collections.
    This method creates a compliant URI for the collection to be created first. It starts with the given URI prefix after its been successfully validated, followed by the given display ID, and ends with the given version.
    
    Parameters:
    
    URIprefix - the URI prefix for the collection to be created
    
    displayId - the display ID of the collection to be created
    
    version - the version of the collection to be created
    
    Returns:
    
    the created collection
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10204, 10206.
  - removeCollection
```
public boolean removeCollection(Collection collection)
                         throws SBOLValidationException
```
    Removes the given collection from this SBOL document's list of collections.
    
    Parameters:
    
    collection - the given collection to be removed
    
    Returns:
    
    true if the given collection was successfully removed, false otherwise
    
    Throws:
    
    SBOLValidationException - if the following SBOL validation rule was violated: 12103.
  - getCollection
```
public Collection getCollection(String displayId,
                                String version)
```
    Returns the collection matching the given display ID and version from this SBOL document's list of collections.
    A compliant Collection URI is created first. It starts with the given URI prefix after its been successfully validated, optionally followed by its type, namely TopLevel.COLLECTION, followed by the given display ID, and ends with the given version. This URI is used to look up the module definition in this SBOL document.
    
    Parameters:
    
    displayId - the display ID of the collection to be retrieved
    
    version - the version of the collection to be retrieved
    
    Returns:
    
    the matching collection if present, or null otherwise
  - getCollection
```
public Collection getCollection(URI collectionURI)
```
    Returns the collection matching the given identity URI from this SBOL document's list of collections.
    
    Parameters:
    
    collectionURI - the given identity URI of the collection to be retrieved
    
    Returns:
    
    the matching collection if present, or null otherwise
  - getCollections
```
public Set<Collection> getCollections()
```
    Returns the set of Collection instances owned by this SBOL document.
    
    Returns:
    
    the set of Collection instances owned by this SBOL document.
  - clearCollections
```
public void clearCollections()
                      throws SBOLValidationException
```
    Removes all entries in the list of collections owned by this SBOL document. The list will be empty after this call returns.
    This method calls removeCollection(Collection) to iteratively remove each collection.
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in removeCollection(Collection).
  - createExperiment
```
public Experiment createExperiment(String displayId)
                            throws SBOLValidationException
```
    Creates a experiment first, and then adds to this SBOL document's list of experiments.
    This method calls createExperiment(String, String, String) with the default URI prefix for this SOBL document, the given display ID of the experiment to be created, and an empty version string.
    
    Parameters:
    
    displayId - the display ID of the experiment to be created
    
    Returns:
    
    the created experiment
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createExperiment(String, String, String).
  - createExperiment
```
public Experiment createExperiment(String displayId,
                                   String version)
                            throws SBOLValidationException
```
    Creates a experiment first, and then adds to this SBOL document's list of experiments.
    This method calls createExperiment(String, String, String) with the default URI prefix for this SOBL document, the given display ID and version of the experiment to be created.
    
    Parameters:
    
    displayId - the display ID of the experiment to be created
    
    version - the version of the experiment to be created
    
    Returns:
    
    the created experiment
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createExperiment(String, String, String).
  - createExperiment
```
public Experiment createExperiment(String URIprefix,
                                   String displayId,
                                   String version)
                            throws SBOLValidationException
```
    Creates a experiment first, and then adds to this SBOL document's list of experiments.
    This method creates a compliant URI for the experiment to be created first. It starts with the given URI prefix after its been successfully validated, followed by the given display ID, and ends with the given version.
    
    Parameters:
    
    URIprefix - the URI prefix for the experiment to be created
    
    displayId - the display ID of the experiment to be created
    
    version - the version of the experiment to be created
    
    Returns:
    
    the created experiment
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10204, 10206.
  - removeExperiment
```
public boolean removeExperiment(Experiment experiment)
                         throws SBOLValidationException
```
    Removes the given experiment from this SBOL document's list of experiments.
    
    Parameters:
    
    experiment - the given experiment to be removed
    
    Returns:
    
    true if the given experiment was successfully removed, false otherwise
    
    Throws:
    
    SBOLValidationException - if the following SBOL validation rule was violated: 12103.
  - getExperiment
```
public Experiment getExperiment(String displayId,
                                String version)
```
    Returns the experiment matching the given display ID and version from this SBOL document's list of experiments.
    A compliant Experiment URI is created first. It starts with the given URI prefix after its been successfully validated, optionally followed by its type, namely TopLevel.EXPERIMENT, followed by the given display ID, and ends with the given version. This URI is used to look up the module definition in this SBOL document.
    
    Parameters:
    
    displayId - the display ID of the experiment to be retrieved
    
    version - the version of the experiment to be retrieved
    
    Returns:
    
    the matching experiment if present, or null otherwise
  - getExperiment
```
public Experiment getExperiment(URI experimentURI)
```
    Returns the experiment matching the given identity URI from this SBOL document's list of experiments.
    
    Parameters:
    
    experimentURI - the given identity URI of the experiment to be retrieved
    
    Returns:
    
    the matching experiment if present, or null otherwise
  - getExperiments
```
public Set<Experiment> getExperiments()
```
    Returns the set of Experiment instances owned by this SBOL document.
    
    Returns:
    
    the set of Experiment instances owned by this SBOL document.
  - clearExperiments
```
public void clearExperiments()
                      throws SBOLValidationException
```
    Removes all entries in the list of experiments owned by this SBOL document. The list will be empty after this call returns.
    This method calls removeExperiment(Experiment) to iteratively remove each experiment.
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in removeExperiment(Experiment).
  - createExperimentalData
```
public ExperimentalData createExperimentalData(String displayId)
                                        throws SBOLValidationException
```
    Creates a experimentalData first, and then adds to this SBOL document's list of experimentalDatas.
    This method calls createExperimentalData(String, String, String) with the default URI prefix for this SOBL document, the given display ID of the experimentalData to be created, and an empty version string.
    
    Parameters:
    
    displayId - the display ID of the experimentalData to be created
    
    Returns:
    
    the created experimentalData
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createExperimentalData(String, String, String).
  - createExperimentalData
```
public ExperimentalData createExperimentalData(String displayId,
                                               String version)
                                        throws SBOLValidationException
```
    Creates a experimentalData first, and then adds to this SBOL document's list of experimentalDatas.
    This method calls createExperimentalData(String, String, String) with the default URI prefix for this SOBL document, the given display ID and version of the experimentalData to be created.
    
    Parameters:
    
    displayId - the display ID of the experimentalData to be created
    
    version - the version of the experimentalData to be created
    
    Returns:
    
    the created experimentalData
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createExperimentalData(String, String, String).
  - createExperimentalData
```
public ExperimentalData createExperimentalData(String URIprefix,
                                               String displayId,
                                               String version)
                                        throws SBOLValidationException
```
    Creates a experimentalData first, and then adds to this SBOL document's list of experimentalDatas.
    This method creates a compliant URI for the experimentalData to be created first. It starts with the given URI prefix after its been successfully validated, followed by the given display ID, and ends with the given version.
    
    Parameters:
    
    URIprefix - the URI prefix for the experimentalData to be created
    
    displayId - the display ID of the experimentalData to be created
    
    version - the version of the experimentalData to be created
    
    Returns:
    
    the created experimentalData
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10204, 10206.
  - removeExperimentalData
```
public boolean removeExperimentalData(ExperimentalData experimentalDatum)
                               throws SBOLValidationException
```
    Removes the given experimentalData from this SBOL document's list of experimentalData.
    
    Parameters:
    
    experimentalDatum - the given experimentalData to be removed
    
    Returns:
    
    true if the given experimentalData was successfully removed, false otherwise
    
    Throws:
    
    SBOLValidationException - if the following SBOL validation rule was violated: 12103.
  - getExperimentalData
```
public ExperimentalData getExperimentalData(String displayId,
                                            String version)
```
    Returns the experimentalData matching the given display ID and version from this SBOL document's list of experimentalData.
    A compliant ExperimentalData URI is created first. It starts with the given URI prefix after its been successfully validated, optionally followed by its type, namely TopLevel.EXPERIMENTAL_DATA, followed by the given display ID, and ends with the given version. This URI is used to look up the module definition in this SBOL document.
    
    Parameters:
    
    displayId - the display ID of the experimentalData to be retrieved
    
    version - the version of the experimentalData to be retrieved
    
    Returns:
    
    the matching experimentalData if present, or null otherwise
  - getExperimentalData
```
public ExperimentalData getExperimentalData(URI experimentalDataURI)
```
    Returns the experimentalData matching the given identity URI from this SBOL document's list of experimentalDatas.
    
    Parameters:
    
    experimentalDataURI - the given identity URI of the experimentalData to be retrieved
    
    Returns:
    
    the matching experimentalData if present, or null otherwise
  - getExperimentalData
```
public Set<ExperimentalData> getExperimentalData()
```
    Returns the set of ExperimentalData instances owned by this SBOL document.
    
    Returns:
    
    the set of ExperimentalData instances owned by this SBOL document.
  - clearExperimentalData
```
public void clearExperimentalData()
                           throws SBOLValidationException
```
    Removes all entries in the list of experimentalData owned by this SBOL document. The list will be empty after this call returns.
    This method calls removeExperimentalData(ExperimentalData) to iteratively remove each experimentalData.
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in removeExperimentalData(ExperimentalData).
  - createModel
```
public Model createModel(String displayId,
                         URI source,
                         URI language,
                         URI framework)
                  throws SBOLValidationException
```
    Creates a model, and then adds it to this SBOL document's list of models.
    This method calls createModel(String, String, String, URI, URI, URI) with this SBOL document's default URI prefix, an empty version string, and all given arguments.
    
    Parameters:
    
    displayId - the display ID of the model to be created
    
    source - the source of the model to be created
    
    language - the language of the model to be created
    
    framework - the framework of the model to be created
    
    Returns:
    
    the created model
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createModel(String, String, String, URI, URI, URI);
  - createModel
```
public Model createModel(String displayId,
                         String version,
                         URI source,
                         URI language,
                         URI framework)
                  throws SBOLValidationException
```
    Creates a model, and then adds it to this SBOL document's list of models.
    This method calls createModel(String, String, String, URI, URI, URI) with this SBOL document's default URI prefix, and all given arguments.
    
    Parameters:
    
    displayId - the display ID of the model to be created
    
    version - the version of the model to be created
    
    source - the source of the model to be created
    
    language - the language of the model to be created
    
    framework - the framework of the model to be created
    
    Returns:
    
    the created model
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createModel(String, String, String, URI, URI, URI);
  - createModel
```
public Model createModel(String URIprefix,
                         String displayId,
                         String version,
                         URI source,
                         URI language,
                         URI framework)
                  throws SBOLValidationException
```
    Creates a model, and then adds it to this SBOL document's list of models.
    This method first creates a compliant URI for the model to be created. It starts with the given URI prefix, followed by the given display ID, and ends with the given version.
    
    Parameters:
    
    URIprefix - the URI prefix used to construct the compliant URI for the model to be created
    
    displayId - the display ID of the model to be created
    
    version - the version of the model to be created
    
    source - the source of the model to be created
    
    language - the language of the model to be created
    
    framework - the framework of the model to be created
    
    Returns:
    
    the created model
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 10220, 10303, 10304, 10305, 10401, 10501, 10701, 10801, 10901, 11101, 11201, 11301, 11401, 11501, 11502, 11504, 11508, 11601, 11701, 11801, 11901, 12001, 12301.
  - removeModel
```
public boolean removeModel(Model model)
                    throws SBOLValidationException
```
    Removes the given model from this SBOL document's list of models.
    
    Parameters:
    
    model - the given model to be removed
    
    Returns:
    
    true if the given model was successfully removed, false otherwise
    
    Throws:
    
    SBOLValidationException - if either of the following SBOL validation rules was violated: 11608, 12103.
  - removeAttachment
```
public boolean removeAttachment(Attachment attachment)
                         throws SBOLValidationException
```
    Removes the given attachment from this SBOL document's list of attachments.
    
    Parameters:
    
    attachment - the given attachment to be removed
    
    Returns:
    
    true if the given attachment was successfully removed, false otherwise
    
    Throws:
    
    SBOLValidationException - if either of the following SBOL validation rules was violated: 11608, 12103. // TODO
  - getModel
```
public Model getModel(String displayId,
                      String version)
```
    Returns the model matching the given display ID and version from this SBOL document's list of models.
    This method first creates a compliant URI for the model to be retrieved. It starts with the given URI prefix after its been successfully validated, optionally followed by its type, namely TopLevel.MODEL, followed by the given display ID, and ends with the given version. This URI is used to look up the model in this SBOL document.
    
    Parameters:
    
    displayId - the display ID of the model to be retrieved
    
    version - the version of the model to be retrieved
    
    Returns:
    
    the matching model if present, or null otherwise
  - getModel
```
public Model getModel(URI modelURI)
```
    Returns the model matching the given identity URI from this SBOL document's list of models.
    
    Parameters:
    
    modelURI - the identity URI of the model to be retrieved
    
    Returns:
    
    the matching model if present, or null otherwise
  - getModels
```
public Set<Model> getModels()
```
    Returns the set of models owned by this SBOL document.
    
    Returns:
    
    the set of models owned by this SBOL document.
  - clearModels
```
public void clearModels()
                 throws SBOLValidationException
```
    Removes all entries in the list of models owned by this SBOL document. The list will be empty after this call returns.
    This method calls removeModel(Model) to iteratively remove each model.
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in removeModel(Model).
  - createAttachment
```
public Attachment createAttachment(String displayId,
                                   URI source)
                            throws SBOLValidationException
```
    Creates an attachment, and then adds it to this SBOL document's list of attachments.
    This method calls createAttachment(String, String, String, URI) with this SBOL document's default URI prefix, an empty version string, and all given arguments.
    
    Parameters:
    
    displayId - the display ID of the attachment to be created
    
    source - the source of the attachment to be created
    
    Returns:
    
    the created attachment
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createAttachment(String, String, String, URI);
  - createAttachment
```
public Attachment createAttachment(String displayId,
                                   String version,
                                   URI source)
                            throws SBOLValidationException
```
    Creates an attachment, and then adds it to this SBOL document's list of attachments.
    This method calls createAttachment(String, String, String, URI) with this SBOL document's default URI prefix, and all given arguments.
    
    Parameters:
    
    displayId - the display ID of the attachment to be created
    
    version - the version of the attachment to be created
    
    source - the source of the attachment to be created
    
    Returns:
    
    the created attachment
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createAttachment(String, String, String, URI);
  - createAttachment
```
public Attachment createAttachment(String URIprefix,
                                   String displayId,
                                   String version,
                                   URI source)
                            throws SBOLValidationException
```
    Creates an attachment, and then adds it to this SBOL document's list of attachments.
    This method first creates a compliant URI for the attachment to be created. It starts with the given URI prefix, followed by the given display ID, and ends with the given version.
    
    Parameters:
    
    URIprefix - the URI prefix used to construct the compliant URI for the attachment to be created
    
    displayId - the display ID of the attachment to be created
    
    version - the version of the attachment to be created
    
    source - the source of the attachment to be created
    
    Returns:
    
    the created attachment
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 10220, 10303, 10304, 10305, 10401, 10501, 10701, 10801, 10901, 11101, 11201, 11301, 11401, 11501, 11502, 11504, 11508, 11601, 11701, 11801, 11901, 12001, 12301. // TODO
  - getAttachment
```
public Attachment getAttachment(String displayId,
                                String version)
```
    Returns the attachment matching the given display ID and version from this SBOL document's list of attachments.
    This method first creates a compliant URI for the attachment to be retrieved. It starts with the given URI prefix after its been successfully validated, optionally followed by its type, namely TopLevel.ATTACHMENT, followed by the given display ID, and ends with the given version. This URI is used to look up the attachment in this SBOL document.
    
    Parameters:
    
    displayId - the display ID of the attachment to be retrieved
    
    version - the version of the attachment to be retrieved
    
    Returns:
    
    the matching attachment if present, or null otherwise
  - getAttachment
```
public Attachment getAttachment(URI attachmentURI)
```
    Returns the attachment matching the given identity URI from this SBOL document's list of attachments.
    
    Parameters:
    
    attachmentURI - the identity URI of the attachment to be retrieved
    
    Returns:
    
    the matching attachment if present, or null otherwise
  - getAttachments
```
public Set<Attachment> getAttachments()
```
    Returns the set of attachments owned by this SBOL document.
    
    Returns:
    
    the set of attachments owned by this SBOL document.
  - clearAttachments
```
public void clearAttachments()
                      throws SBOLValidationException
```
    Removes all entries in the list of attachments owned by this SBOL document. The list will be empty after this call returns.
    This method calls removeAttachment(Attachment) to iteratively remove each attachment.
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in removeAttachment(Attachment).
  - createComponentDefinition
```
public ComponentDefinition createComponentDefinition(String displayId,
                                                     Set<URI> types)
                                              throws SBOLValidationException
```
    Creates a component definition, and then adds it to this SBOL document's list of component definitions.
    This method calls createComponentDefinition(String, String, String, Set) with the default URI prefix of this SBOL document, the given component definition display ID, and an empty version string. given types.
    
    Parameters:
    
    displayId - the display ID of the component definition to be created
    
    types - the types of the component definition to be created
    
    Returns:
    
    the created component definition
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule was violated in createComponentDefinition(String, String, String, Set).
  - createComponentDefinition
```
public ComponentDefinition createComponentDefinition(String displayId,
                                                     URI type)
                                              throws SBOLValidationException
```
    Creates a component definition, and then adds it to this SBOL document's list of component definitions.
    This method first creates an empty set of types, and then adds to this set the given type. It then calls createComponentDefinition(String, String, String, Set) with the given display ID, and version, and the created types.
    
    Parameters:
    
    displayId - the display ID of the component definition to be created
    
    type - the type to be added to the component definition to be created
    
    Returns:
    
    the created component definition
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createComponentDefinition(String, String, String, Set).
  - createComponentDefinition
```
public ComponentDefinition createComponentDefinition(String displayId,
                                                     String version,
                                                     Set<URI> types)
                                              throws SBOLValidationException
```
    Creates a component definition, and then adds it to this SBOL document's list of component definitions.
    This method calls createComponentDefinition(String, String, String, Set) with the given component definition display ID, version, and the given types.
    
    Parameters:
    
    displayId - the display ID of the component definition to be created
    
    version - the version of the component definition to be created
    
    types - the types of the component definition to be created
    
    Returns:
    
    the created component definition
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule was violated in createComponentDefinition(String, String, String, Set).
  - createComponentDefinition
```
public ComponentDefinition createComponentDefinition(String displayId,
                                                     String version,
                                                     URI type)
                                              throws SBOLValidationException
```
    Creates a component definition, and then adds it to this SBOL document's list of component definitions.
    This method first creates an empty set of types, and then adds to this set the given type. It then calls createComponentDefinition(String, String, String, Set) with the default URI prefix of this SBOL document, display ID, and version, and the created types.
    
    Parameters:
    
    displayId - the display ID of the component definition to be created
    
    version - the version of the component definition to be created
    
    type - the type to be added to the component definition to be created
    
    Returns:
    
    the created component definition
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createComponentDefinition(String, String, String, Set).
  - createComponentDefinition
```
public ComponentDefinition createComponentDefinition(String URIprefix,
                                                     String displayId,
                                                     String version,
                                                     Set<URI> types)
                                              throws SBOLValidationException
```
    Creates a component definition, and then adds it to this SBOL document's list of component definitions.
    This method creates a compliant URI for the component definition to be created first. It starts with the given URI prefix after its been successfully validated, followed by the given display ID, and ends with the given version.
    
    Parameters:
    
    URIprefix - the URI prefix used to construct the compliant URI for the component definition to be created
    
    displayId - the display ID of the component definition to be created
    
    version - the version of the component definition to be created
    
    types - the types of the component definition to be created
    
    Returns:
    
    the created component definition
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 10220, 10502, 10503.
  - createComponentDefinition
```
public ComponentDefinition createComponentDefinition(String URIprefix,
                                                     String displayId,
                                                     String version,
                                                     URI type)
                                              throws SBOLValidationException
```
    Creates a component definition, and then adds it to this SBOL document's list of component definitions.
    This method first creates an empty set of types, and then adds to this set the given type. It then calls createComponentDefinition(String, String, String, Set) with the given URI prefix, display ID, and version, and the created types.
    
    Parameters:
    
    URIprefix - the URI prefix used to construct the compliant URI for the component definition to be created
    
    displayId - the display ID of the component definition to be created
    
    version - the version of the component definition to be created
    
    type - the type to be added to the component definition to be created
    
    Returns:
    
    the created component definition
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createComponentDefinition(String, String, String, Set).
  - removeComponentDefinition
```
public boolean removeComponentDefinition(ComponentDefinition componentDefinition)
                                  throws SBOLValidationException
```
    Removes the given component definition from this SBOL document's list of component definitions.
    
    Parameters:
    
    componentDefinition - the component definition to be removed
    
    Returns:
    
    true if the given component definition was successfully removed, false otherwise
    
    Throws:
    
    SBOLValidationException - if either of the following SBOL validation rules was violated: 10604, 12103.
  - getComponentDefinition
```
public ComponentDefinition getComponentDefinition(String displayId,
                                                  String version)
```
    Returns the component definition matching the given display ID and version from this SBOL document's list of component definitions.
    A compliant ComponentDefinition URI is created first. It starts with this SBOL document's default URI prefix after its been successfully validated, optionally followed by its type, namely TopLevel.COMPONENT_DEFINITION, followed by the given display ID, and ends with the given version. This URI is used to look up the module definition in this SBOL document.
    
    Parameters:
    
    displayId - the display ID of the component definition to be retrieved
    
    version - the version of the component definition to be retrieved
    
    Returns:
    
    the matching component definition if present, or null otherwise
  - getComponentDefinition
```
public ComponentDefinition getComponentDefinition(URI componentDefinitionURI)
```
    Returns the component definition matching the given identity URI from this SBOL document's list of component definitions.
    
    Parameters:
    
    componentDefinitionURI - the given identity URI of the component definition to be retrieved
    
    Returns:
    
    the matching component definition if present, or null otherwise.
  - getCombinatorialDerivation
```
public CombinatorialDerivation getCombinatorialDerivation(String displayId,
                                                          String version)
                                                   throws SBOLValidationException
```
    Returns the combinatorial derivation matching the given display ID and version from this SBOL document's list of combinatorial derivations.
    A compliant combinatorialDerivation URI is created first. It starts with this SBOL document's default URI prefix after its been successfully validated, optionally followed by its type, namely TopLevel.COMBINATORIAL_DERIVATION, followed by the given display ID, and ends with the given version. This URI is used to look up the module definition in this SBOL document.
    
    Parameters:
    
    displayId - the display ID of the combinatorial derivation to be retrieved
    
    version - the version of the combinatorial derivation to be retrieved
    
    Returns:
    
    the matching combinatorial derivation if present, or null otherwise
    
    Throws:
    
    SBOLValidationException - validation error
  - getCombinatorialDerivation
```
public CombinatorialDerivation getCombinatorialDerivation(URI combinatorialDerivationURI)
```
    Returns the combinatorial derivation matching the given identity URI from this SBOL document's list of combinatorial derivations.
    
    Parameters:
    
    combinatorialDerivationURI - the given identity URI of the combinatorial derivation to be retrieved
    
    Returns:
    
    the matching combinatorial derivation if present, or null otherwise.
  - removeCombinatorialDerivation
```
public boolean removeCombinatorialDerivation(CombinatorialDerivation combinatorialDerivation)
                                      throws SBOLValidationException
```
    Removes the given combinatorial derivation from this SBOL document's list of combinatorial derivations.
    
    Parameters:
    
    combinatorialDerivation - the combinatorialDerivation to be removed
    
    Returns:
    
    true if the given combinatorial derivation was successfully removed, false otherwise
    
    Throws:
    
    SBOLValidationException - if either of the following SBOL validation rules was violated: TODO: 10604, 12103.
  - createCombinatorialDerivation
```
public CombinatorialDerivation createCombinatorialDerivation(String displayId,
                                                             String version,
                                                             String templateDisplayId,
                                                             String templateVersion)
                                                      throws SBOLValidationException
```
    Creates a combinatorial derivation, and then adds it to this SBOL document's list of combinatorial derivations.
    createCombinatorialDerivation(String, String, URI) with the default URI prefix of this SBOL document, display ID, and version.
    
    Parameters:
    
    displayId - the display ID of the combinatorial derivation to be created
    
    version - the version of the combinatorial derivation to be created
    
    templateDisplayId - the display ID of the template of the combinatorial derivation to be created
    
    templateVersion - the version of the template of the combinatorial derivation to be created
    
    Returns:
    
    the created combinatorial derivation
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createCombinatorialDerivation(String, String, URI).
  - createCombinatorialDerivation
```
public CombinatorialDerivation createCombinatorialDerivation(String displayId,
                                                             URI template)
                                                      throws SBOLValidationException
```
    Creates a combinatorial derivation, and then adds it to this SBOL document's list of combinatorial derivations.
    createCombinatorialDerivation(String, URI) with the default URI prefix of this SBOL document, display ID, and version.
    
    Parameters:
    
    displayId - the display ID of the combinatorial derivation to be created
    
    template - the URI of the template of the combinatorial derivation to be created
    
    Returns:
    
    the created combinatorial derivation
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createCombinatorialDerivation(String, URI).
  - createCombinatorialDerivation
```
public CombinatorialDerivation createCombinatorialDerivation(String displayId,
                                                             String version,
                                                             URI template)
                                                      throws SBOLValidationException
```
    Creates a combinatorial derivation, and then adds it to this SBOL document's list of combinatorial derivations.
    createCombinatorialDerivation(String, String, String, URI) with the default URI prefix of this SBOL document, display ID, and version.
    
    Parameters:
    
    displayId - the display ID of the combinatorial derivation to be created
    
    version - the version of the combinatorial derivation to be created
    
    template - the URI of the template of the combinatorial derivation to be created
    
    Returns:
    
    the created combinatorial derivation
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createCombinatorialDerivation(String, String, String, URI).
  - createCombinatorialDerivation
```
public CombinatorialDerivation createCombinatorialDerivation(String URIprefix,
                                                             String displayId,
                                                             String version,
                                                             URI template)
                                                      throws SBOLValidationException
```
    Creates a combinatorial derivation, and then adds it to this SBOL document's list of combinatorial derivations.
    This method creates a compliant URI for the combinatorial derivation to be created first. It starts with the given URI prefix after its been successfully validated, followed by the given display ID, and ends with the given version.
    
    Parameters:
    
    URIprefix - the URI prefix used to construct the compliant URI for the combinatorial derivation to be created
    
    displayId - the display ID of the combinatorial derivation to be created
    
    version - the version of the combinatorial derivation to be created
    
    template - the template URI of the combinatorial derivation to be created
    
    Returns:
    
    the created combinatorial derivation
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: TODO: 10201, 10202, 10204, 10206, 10220, 10502, 10503.
  - getCombinatorialDerivations
```
public Set<CombinatorialDerivation> getCombinatorialDerivations()
```
    Returns the set of combinatorial derivations owned by this SBOL document.
    
    Returns:
    
    the set of combinatorial derivation owned by this SBOL document.
  - clearCombinatorialDerivations
```
public void clearCombinatorialDerivations()
                                   throws SBOLValidationException
```
    Removes all entries in the list of combinatorial derivations owned by this SBOL document. The list will be empty after this call returns.
    This method calls removeCombinatorialDerivation(CombinatorialDerivation) to iteratively remove each combinatorialDerivation.
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in removeCombinatorialDerivation(CombinatorialDerivation).
  - getImplementation
```
public Implementation getImplementation(String displayId,
                                        String version)
                                 throws SBOLValidationException
```
    Returns the implementation matching the given display ID and version from this SBOL document's list of implementations.
    A compliant implementation URI is created first. It starts with this SBOL document's default URI prefix after its been successfully validated, optionally followed by its type, namely TopLevel.IMPLEMENTATION, followed by the given display ID, and ends with the given version. This URI is used to look up the module definition in this SBOL document.
    
    Parameters:
    
    displayId - the display ID of the implementation to be retrieved
    
    version - the version of the implementation to be retrieved
    
    Returns:
    
    the matching implementation if present, or null otherwise
    
    Throws:
    
    SBOLValidationException - validation error
  - getImplementation
```
public Implementation getImplementation(URI implementationURI)
```
    Returns the implementation matching the given identity URI from this SBOL document's list of implementations.
    
    Parameters:
    
    implementationURI - the given identity URI of the implementation to be retrieved
    
    Returns:
    
    the matching implementation if present, or null otherwise.
  - removeImplementation
```
public boolean removeImplementation(Implementation implementation)
                             throws SBOLValidationException
```
    Removes the given implementation from this SBOL document's list of implementations.
    
    Parameters:
    
    implementation - the implementation to be removed
    
    Returns:
    
    true if the given implementation was successfully removed, false otherwise
    
    Throws:
    
    SBOLValidationException - if either of the following SBOL validation rules was violated: TODO: 10604, 12103.
  - createImplementation
```
public Implementation createImplementation(String displayId)
                                    throws SBOLValidationException
```
    Creates an implementation, and then adds it to this SBOL document's list of implementations.
    createImplementation(String) with the default URI prefix of this SBOL document, display ID, and version.
    
    Parameters:
    
    displayId - the display ID of the implementation to be created
    
    Returns:
    
    the created implementation
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createImplementation(String, String, String).
  - createImplementation
```
public Implementation createImplementation(String displayId,
                                           String version)
                                    throws SBOLValidationException
```
    Creates an implementation, and then adds it to this SBOL document's list of implementations.
    createImplementation(String, String) with the default URI prefix of this SBOL document, display ID, and version.
    
    Parameters:
    
    displayId - the display ID of the implementation to be created
    
    version - the version of the implementation to be created
    
    Returns:
    
    the created implementation
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createImplementation(String, String, String).
  - createImplementation
```
public Implementation createImplementation(String URIprefix,
                                           String displayId,
                                           String version)
                                    throws SBOLValidationException
```
    Creates an implementation, and then adds it to this SBOL document's list of implementations.
    This method creates a compliant URI for the implementation to be created first. It starts with the given URI prefix after its been successfully validated, followed by the given display ID, and ends with the given version.
    
    Parameters:
    
    URIprefix - the URI prefix used to construct the compliant URI for the implementation to be created
    
    displayId - the display ID of the implementation to be created
    
    version - the version of the implementation to be created
    
    Returns:
    
    the created implementation
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: TODO: 10201, 10202, 10204, 10206, 10220, 10502, 10503.
  - getImplementations
```
public Set<Implementation> getImplementations()
```
    Returns the set of implementations owned by this SBOL document.
    
    Returns:
    
    the set of implementations owned by this SBOL document.
  - clearImplementations
```
public void clearImplementations()
                          throws SBOLValidationException
```
    Removes all entries in the list of implementations owned by this SBOL document. The list will be empty after this call returns.
    This method calls removeImplementation(Implementation) to iteratively remove each implementation.
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in removeImplementation(Implementation).
  - getComponentDefinitions
```
public Set<ComponentDefinition> getComponentDefinitions()
```
    Returns the set of component definitions owned by this SBOL document.
    
    Returns:
    
    the set of component definitions owned by this SBOL document.
  - getRootComponentDefinitions
```
public Set<ComponentDefinition> getRootComponentDefinitions()
```
    Returns the set of root component definitions. A root component definition is a component definition that is not referenced by a child component.
    
    Returns:
    
    the set of root component definitions
  - getRootModuleDefinitions
```
public Set<ModuleDefinition> getRootModuleDefinitions()
```
    Returns the set of root module definitions. A root module definition is a module definition that is not referenced by a child module.
    
    Returns:
    
    the set of root module definitions
  - clearComponentDefinitions
```
public void clearComponentDefinitions()
                               throws SBOLValidationException
```
    Removes all entries in the list of component definitions owned by this SBOL document. The list will be empty after this call returns.
    This method calls removeComponentDefinition(ComponentDefinition) to iteratively remove each component definition.
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in removeComponentDefinition(ComponentDefinition).
  - createSequence
```
public Sequence createSequence(String displayId,
                               String elements,
                               URI encoding)
                        throws SBOLValidationException
```
    Creates a Sequence instance with this SBOL document's defaultURIprefix, the given arguments, and an empty version string, and then adds it to this SBOL document's list of Sequence instances.
    This method calls createSequence(String, String, String, String, URI) to do the following validity checks and create a Sequence instance.
    If the defaultURIprefix does not end with one of the following delimiters: "/", ":", or "#", then "/" is appended to the end of it.
    This method requires the defaultURIprefix field to be set, and the given display ID is not null and is valid.
    A Sequence instance is created with a compliant URI. This URI is composed from the this SBOL document's defaultURIprefix, the optional type TopLevel.SEQUENCE, the given display ID, and an empty version string. The display ID, persistent identity, and version fields of this instance are then set accordingly.
    
    Parameters:
    
    displayId - an intermediate between name and identity that is machine-readable
    
    elements - characters that represents the constituents of a biological or chemical molecule (i.e. nucleotide bases of a molecule of DNA, the amino acid residues of a protein, or the atoms and chemical bonds of a small molecule)
    
    encoding - Indicate how the elements property of a Sequence must be formed and interpreted
    
    Returns:
    
    the created Sequence instance
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule was violated in createSequence(String, String, String, String, URI).
  - createSequence
```
public Sequence createSequence(String displayId,
                               String version,
                               String elements,
                               URI encoding)
                        throws SBOLValidationException
```
    Creates a Sequence instance with this SBOL document's defaultURIprefix and the given arguments, and then adds it to this SBOL document's list of Sequence instances.
    This method calls createSequence(String, String, String, String, URI) to do the following validity checks and create a Sequence instance.
    If the defaultURIprefix does not end with one of the following delimiters: "/", ":", or "#", then "/" is appended to the end of it.
    This method requires the defaultURIprefix field to be set, and the given display ID and version arguments are not null and are both valid.
    A Sequence instance is created with a compliant URI. This URI is composed from the this SBOL document's defaultURIprefix, the optional type TopLevel.SEQUENCE, the given display ID, and version. The display ID, persistent identity, and version fields of this instance are then set accordingly.
    
    Parameters:
    
    displayId - an intermediate between name and identity that is machine-readable
    
    version - The given version for this object
    
    elements - characters that represents the constituents of a biological or chemical molecule (i.e. nucleotide bases of a molecule of DNA, the amino acid residues of a protein, or the atoms and chemical bonds of a small molecule)
    
    encoding - Indicate how the elements property of a Sequence must be formed and interpreted
    
    Returns:
    
    the created Sequence instance
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule was violated in createSequence(String, String, String, String, URI).
  - createSequence
```
public Sequence createSequence(String URIprefix,
                               String displayId,
                               String version,
                               String elements,
                               URI encoding)
                        throws SBOLValidationException
```
    Creates a Sequence instance with the given arguments, and then adds it to this SBOLDocument object's list of Sequence instances.
    If the given URIprefix does not end with one of the following delimiters: "/", ":", or "#", then "/" is appended to the end of it.
    This method requires that the given URIprefix, display ID, and version are not null and are valid.
    A Sequence instance is created with a compliant URI. This URI is composed from the given URIprefix, the optional type TopLevel.SEQUENCE, the given display ID, and version. The display ID, persistent identity, and version fields of this instance are then set accordingly.
    
    Parameters:
    
    URIprefix - maps to a domain over which the user has control
    
    displayId - an intermediate between name and identity that is machine-readable
    
    version - The given version for this object
    
    elements - characters that represents the constituents of a biological or chemical molecule (i.e. nucleotide bases of a molecule of DNA, the amino acid residues of a protein, or the atoms and chemical bonds of a small molecule)
    
    encoding - Indicate how the elements property of a Sequence must be formed and interpreted
    
    Returns:
    
    the created Sequence instance
    
    Throws:
    
    SBOLValidationException - if if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 10220, 10402, 10403, 10405.
  - createCopy
```
public void createCopy(SBOLDocument document)
                throws SBOLValidationException
```
    Creates an identical copy of each top-level element of a document, and then adds the created top-level to the corresponding list of top-levels in this SBOL document.
    This method calls createCopy(TopLevel) for each top-level instance.
    
    Parameters:
    
    document - the document to be copied from
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createCopy(TopLevel).
  - createCopy
```
public TopLevel createCopy(TopLevel topLevel)
                    throws SBOLValidationException
```
    Creates an identical copy of the given top-level, and then adds the created top-level to the corresponding list of top-levels in this SBOL document.
    This method calls createCopy(TopLevel, String, String, String) with the given top-level instance, and null for other arguments.
    
    Parameters:
    
    topLevel - the top-level to be copied from
    
    Returns:
    
    the copied top-level instance
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createCopy(TopLevel, String, String, String).
  - createCopy
```
public TopLevel createCopy(TopLevel topLevel,
                           String displayId)
                    throws SBOLValidationException
```
    Creates a copy of the given top-level with the given display ID, and then adds the created top-level to the corresponding list of top-levels in this SBOL document.
    This method calls createCopy(TopLevel, String, String, String) with the given top-level instance, the default URI prefix for this SBOL document, the given display ID, and the empty version string.
    
    Parameters:
    
    topLevel - the top-level to be copied from
    
    displayId - the display ID of the created copy
    
    Returns:
    
    the copied top-level instance
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createCopy(TopLevel, String, String, String).
  - rename
```
public TopLevel rename(TopLevel topLevel,
                       String displayId)
                throws SBOLValidationException
```
    Renames the given top-level's display ID with the given one.
    This method first calls createCopy(TopLevel, String, String, String) to make a copy of the given top-level with this SBOL document's default URI prefix, the given display, and an empty string for version. It then removes the given top-level and then returns the newly-copied top-level.
    Parameters:
    
    topLevel - the top-level to be renamed
    
    displayId - the given display ID to be renamed to
    
    Returns:
    
    the renamed top-level
    
    Throws:
    SBOLValidationException - if either of the following conditions is satisfied:
    
    any of the following SBOL validation rules was violated: 10513, 10604, 11608, 11703, 12103; or
    
    an SBOL validation rule violation occurred in the following method: createCopy(TopLevel, String, String, String).
  - createCopy
```
public TopLevel createCopy(TopLevel topLevel,
                           String displayId,
                           String version)
                    throws SBOLValidationException
```
    Creates a copy of the given top-level with the given display ID and version, and then adds the created top-level to the corresponding list of top-levels in this SBOL document.
    This method calls createCopy(TopLevel, String, String, String) with the given top-level instance, the default URI prefix for this SBOL document, the given display ID, and the empty version string.
    
    Parameters:
    
    topLevel - the top-level to be copied from
    
    displayId - the display ID of the created copy
    
    version - the version of the created copy
    
    Returns:
    
    the copied top-level instance
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createCopy(TopLevel, String, String, String)
  - rename
```
public TopLevel rename(TopLevel topLevel,
                       String displayId,
                       String version)
                throws SBOLValidationException
```
    Renames the given top-level's display ID and version with the given ones.
    This method first calls createCopy(TopLevel, String, String, String) to make a copy of the given top-level with this SBOL document's default URI prefix, the given display ID and version. It then removes the given top-level and then returns the newly-copied top-level.
    Parameters:
    
    topLevel - the top-level to be renamed
    
    displayId - the given display ID to be renamed to
    
    version - the given version to be renamed to
    
    Returns:
    
    the renamed top-level
    
    Throws:
    SBOLValidationException - if either of the following conditions is satisfied:
    
    any of the following SBOL validation rules was violated: 10513, 10604, 11608, 11703, 12103; or
    
    an SBOL validation rule violation occurred in the following method: createCopy(TopLevel, String, String, String).
  - createCopy
```
public TopLevel createCopy(TopLevel topLevel,
                           String URIprefix,
                           String displayId,
                           String version)
                    throws SBOLValidationException
```
    Creates a copy of the given top-level with the given URI prefix, display ID and version, and then adds the created top-level to the corresponding list of top-levels in this SBOL document.
    This method creates a compliant URI for the copied top-level with the given default URI prefix, display ID, and version.
    
    Parameters:
    
    topLevel - the top-level to be copied from
    
    URIprefix - the URI prefix used to create the compliant URI for the created copy
    
    displayId - the display ID of the created copy
    
    version - the version of the created copy
    
    Returns:
    
    the copied top-level instance
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 10220, 10303, 10304, 10305, 10401, 10402, 10403, 10405, 10501, 10503, 10513, 10522, 10526, 10602, 10604, 10605, 10607, 10701, 10801, 10802, 10803, 10804, 10805, 10807, 10808, 10809, 10811, 10901, 10905, 11101, 11102, 11103, 11104, 11201, 11202, 11301, 11401, 11402, 11403, 11404, 11405, 11406, 11501, 11502, 11504, 11508, 11601, 11608, 11609, 11701, 11703, 11704, 11705, 11801, 11901, 12001, 12002, 12003, 12103, 12301, 12302.
  - createRecursiveCopy
```
public SBOLDocument createRecursiveCopy(TopLevel topLevel)
                                 throws SBOLValidationException
```
    Creates an identical copy of the given top-level and returns it in a new SBOLDocument.
    
    Parameters:
    
    topLevel - The topLevel object to be recursively copied from this SBOLDocument
    
    Returns:
    
    the created SBOLDocument with this top-level instance and all its dependencies
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 10220, 10303, 10304, 10305, 10401, 10402, 10403, 10405, 10501, 10503, 10522, 10526, 10602, 10604, 10605, 10607, 10701, 10801, 10802, 10803, 10804, 10805, 10807, 10808, 10809, 10811, 10901, 10905, 11101, 11201, 11301, 11401, 11402, 11403, 11404, 11405, 11406, 11501, 11502, 11504, 11508, 11601, 11608, 11609, 11701, 11703, 11704, 11705, 11801, 10802, 10803, 10804, 10807, 10808, 10809, 10811, 11901, 12001, 12002, 12003, 12101, 12103, 12301, 12302.
  - createRecursiveCopy
```
public void createRecursiveCopy(SBOLDocument document,
                                TopLevel topLevel)
                         throws SBOLValidationException
```
    Parameters:
    
    document - document to copy recursively into
    
    topLevel - topLevel that is being recursively copied from
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createCopy(TopLevel).
  - changeURIPrefixVersion
```
public SBOLDocument changeURIPrefixVersion(String URIPrefix,
                                           String version,
                                           String defaultVersion)
                                    throws SBOLValidationException
```
    Copy all objects to an a new SBOL Document and change the URI prefix/version of each object
    
    Parameters:
    
    URIPrefix - new URI prefix
    
    version - new version for all objects
    
    defaultVersion - if version is null, then this version is used for only for objects without a version
    
    Returns:
    
    new SBOL document with changed URI prefix
    
    Throws:
    
    SBOLValidationException - if URIprefix or version provided is invalid
  - rename
```
public TopLevel rename(TopLevel topLevel,
                       String URIprefix,
                       String displayId,
                       String version)
                throws SBOLValidationException
```
    Renames the given top-level's URI prefix, display ID, and version with the given ones.
    This method first calls createCopy(TopLevel, String, String, String) to make a copy of the given top-level with the URI prefix, display ID, and version. It then removes the given top-level and then returns the newly-copied top-level.
    Parameters:
    
    topLevel - the top-level to be renamed
    
    URIprefix - the given URI prefix to be rename to
    
    displayId - the given display ID to be renamed to
    
    version - the given version to be renamed to
    
    Returns:
    
    the renamed top-level
    
    Throws:
    SBOLValidationException - if either of the following conditions is satisfied:
    
    any of the following SBOL validation rules was violated: 10513, 10604, 11608, 11703, 12103; or
    
    an SBOL validation rule violation occurred in the following method: createCopy(TopLevel, String, String, String).
  - removeSequence
```
public boolean removeSequence(Sequence sequence)
                       throws SBOLValidationException
```
    Removes the given sequence from this SBOL document's list of sequences.
    
    Parameters:
    
    sequence - the given sequence to be removed
    
    Returns:
    
    true if the given sequence was successfully removed, false otherwise
    
    Throws:
    
    SBOLValidationException - if either of the following SBOL validation rules was violated: 10513, 12103.
  - getSequence
```
public Sequence getSequence(String displayId,
                            String version)
```
    Returns the sequence matching the given display ID and version from this SBOL document's list of sequences.
    This method first creates a compliant URI for the sequence to be retrieved. It starts with the given URI prefix after its been successfully validated, optionally followed by its type, namely TopLevel.SEQUENCE, followed by the given display ID, and ends with the given version. This URI is used to look up the sequence in this SBOL document.
    
    Parameters:
    
    displayId - an intermediate between name and identity that is machine-readable
    
    version - The given version for this object
    
    Returns:
    
    the matching sequence if present, or null otherwise.
  - getSequence
```
public Sequence getSequence(URI sequenceURI)
```
    Returns the sequence matching the given modelURI from this SBOL document's list of sequences.
    
    Parameters:
    
    sequenceURI - takes the given SequenceURI to retrieve the sequence from this SBOL document
    
    Returns:
    
    the matching sequence if present, or null otherwise.
  - getSequences
```
public Set<Sequence> getSequences()
```
    Returns the set of sequences owned by this SBOL document.
    
    Returns:
    
    the set of sequences owned by this SBOL document.
  - clearSequences
```
public void clearSequences()
                    throws SBOLValidationException
```
    Removes all entries in the list of sequences owned by this SBOL document. The list will be empty after this call returns.
    This method calls removeSequence(Sequence) to iteratively remove each sequence.
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in removeSequence(Sequence).
  - createGenericTopLevel
```
public GenericTopLevel createGenericTopLevel(String displayId,
                                             QName rdfType)
                                      throws SBOLValidationException
```
    Creates a generic top-level, and then adds it to this SBOL document's list of generic top-levels.
    This method calls createGenericTopLevel(String, String, String, QName) with the default URI prefix of this SBOL document, the given component definition display ID, an empty version string, and the given RDF type.
    
    Parameters:
    
    displayId - the display ID of the generic top-level to be created
    
    rdfType - the type of the generic top-level to be created
    
    Returns:
    
    the created generic top-level
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createGenericTopLevel(String, String, String, QName).
  - createGenericTopLevel
```
public GenericTopLevel createGenericTopLevel(String displayId,
                                             String version,
                                             QName rdfType)
                                      throws SBOLValidationException
```
    Creates a generic top-level, and then adds it to this SBOL document's list of generic top-levels.
    This method calls createGenericTopLevel(String, String, String, QName) with the default URI prefix of this SBOL document, the given component definition display ID and version, and the given RDF type.
    
    Parameters:
    
    displayId - the display ID of the generic top-level to be created
    
    version - the version of the generic top-level to be created
    
    rdfType - the type of the generic top-level to be created
    
    Returns:
    
    the created generic top-level
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createGenericTopLevel(String, String, String, QName).
  - createGenericTopLevel
```
public GenericTopLevel createGenericTopLevel(String URIprefix,
                                             String displayId,
                                             String version,
                                             QName rdfType)
                                      throws SBOLValidationException
```
    Creates a generic top-level, and then adds it to this SBOL document's list of generic top-levels.
    This method calls createGenericTopLevel(String, String, String, QName) with the default URI prefix of this SBOL document, the given component definition display ID and version, and the given RDF type.
    
    Parameters:
    
    URIprefix - the given URI prefix used to create a compliant URI for the generic top-level to be created
    
    displayId - the display ID of the generic top-level to be created
    
    version - the version of the generic top-level to be created
    
    rdfType - the type of the generic top-level to be created
    
    Returns:
    
    the created generic top-level
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rules was violated: 10201, 10202, 10204, 10206, 10220, 10303, 10304, 10305, 10401, 10501, 10701, 10801, 10901, 11101, 11201, 11301, 11401, 11501, 11601, 11701, 11801, 11901, 12001, 12301, 12302.
  - removeGenericTopLevel
```
public boolean removeGenericTopLevel(GenericTopLevel genericTopLevel)
                              throws SBOLValidationException
```
    Removes the given generic top-level from this SBOL document's list of generic top-levels.
    
    Parameters:
    
    genericTopLevel - the given generic top-level to be removed
    
    Returns:
    
    true if the given generic top-level was successfully removed, false otherwise
    
    Throws:
    
    SBOLValidationException - if the following SBOL validation rule was violated: 12103.
  - getGenericTopLevel
```
public GenericTopLevel getGenericTopLevel(String displayId,
                                          String version)
```
    Returns the generic top-level matching the given display ID and version from this SBOL document's list of generic top-levels.
    A compliant generic top-level URI is created first. It starts with this SBOL document's default URI prefix after its been successfully validated, optionally followed by its type, namely TopLevel.GENERIC_TOP_LEVEL, followed by the given display ID, and ends with the given version. This URI is used to look up the generic top-level in this SBOL document.
    
    Parameters:
    
    displayId - the display ID of the generic top-level to be retrieved
    
    version - the version of the generic top-level to be retrieved
    
    Returns:
    
    the matching generic top-level if present, or null otherwise.
  - getGenericTopLevel
```
public GenericTopLevel getGenericTopLevel(URI genericTopLevelURI)
```
    Returns the generic top-level matching the given display identity URI from this SBOL document's list of generic top-levels.
    
    Parameters:
    
    genericTopLevelURI - the identity URI of the top-level to be retrieved
    
    Returns:
    
    the matching generic top-level if present, or null otherwise.
  - getGenericTopLevels
```
public Set<GenericTopLevel> getGenericTopLevels()
```
    Returns the set of generic top-levels owned by this SBOL document.
    
    Returns:
    
    the set of generic top-levels owned by this SBOL document.
  - clearGenericTopLevels
```
public void clearGenericTopLevels()
                           throws SBOLValidationException
```
    Removes all entries in the list of generic top-levels owned by this SBOL document. The list will be empty after this call returns.
    This method calls removeGenericTopLevel(GenericTopLevel) to iteratively remove each generic top-level.
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in removeGenericTopLevel(GenericTopLevel).
  - createActivity
```
public Activity createActivity(String displayId)
                        throws SBOLValidationException
```
    Creates an activity, and then adds it to this SBOL document's list of activities.
    This method calls createActivity(String, String, String) with the default URI prefix of this SBOL document, the given display ID, and an empty version string.
    
    Parameters:
    
    displayId - the display ID of the activity to be created
    
    Returns:
    
    the created activity
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createActivity(String, String, String).
  - createActivity
```
public Activity createActivity(String displayId,
                               String version)
                        throws SBOLValidationException
```
    Creates an activity, and then adds it to this SBOL document's list of activities.
    This method calls createActivity(String, String, String) with the default URI prefix of this SBOL document, the given display ID, and version.
    
    Parameters:
    
    displayId - the display ID of the activity to be created
    
    version - the version of the activity to be created
    
    Returns:
    
    the created activity
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createActivity(String, String, String).
  - createActivity
```
public Activity createActivity(String URIprefix,
                               String displayId,
                               String version)
                        throws SBOLValidationException
```
    Creates an activity, and then adds it to this SBOL document's list of activities.
    This method calls createActivity(String, String, String) with the default URI prefix of this SBOL document, the given display ID, and version.
    
    Parameters:
    
    URIprefix - the given URI prefix used to create a compliant URI for the activity to be created
    
    displayId - the display ID of the activity to be created
    
    version - the version of the activity to be created
    
    Returns:
    
    the created activity
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rules was violated: 10201, 10202, 10204, 10206, 10220.
  - removeActivity
```
public boolean removeActivity(Activity activity)
                       throws SBOLValidationException
```
    Removes the given activity from this SBOL document's list of activities.
    
    Parameters:
    
    activity - the given activity to be removed
    
    Returns:
    
    true if the given activity was successfully removed, false otherwise
    
    Throws:
    
    SBOLValidationException - if the following SBOL validation rule was violated: ?????.
  - getActivity
```
public Activity getActivity(String displayId,
                            String version)
```
    Returns the activity matching the given display ID and version from this SBOL document's list of activities.
    A compliant activity URI is created first. It starts with this SBOL document's default URI prefix after its been successfully validated, optionally followed by its type, namely TopLevel.ACTIVITY, followed by the given display ID, and ends with the given version. This URI is used to look up the activity in this SBOL document.
    
    Parameters:
    
    displayId - the display ID of the activity to be retrieved
    
    version - the version of the activity to be retrieved
    
    Returns:
    
    the matching activity if present, or null otherwise.
  - getActivity
```
public Activity getActivity(URI activityURI)
```
    Returns the activity matching the given display identity URI from this SBOL document's list of activities.
    
    Parameters:
    
    activityURI - the identity URI of the top-level to be retrieved
    
    Returns:
    
    the matching activity if present, or null otherwise.
  - getActivities
```
public Set<Activity> getActivities()
```
    Returns the set of activities owned by this SBOL document.
    
    Returns:
    
    the set of activities owned by this SBOL document.
  - clearActivitys
```
public void clearActivitys()
                    throws SBOLValidationException
```
    Removes all entries in the list of activities owned by this SBOL document. The list will be empty after this call returns.
    This method calls removeActivity(Activity) to iteratively remove each activity.
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in removeActivity(Activity).
  - createAgent
```
public Agent createAgent(String displayId)
                  throws SBOLValidationException
```
    Creates an agent, and then adds it to this SBOL document's list of agents.
    This method calls createAgent(String, String, String) with the default URI prefix of this SBOL document, the given display ID, and an empty version string.
    
    Parameters:
    
    displayId - the display ID of the agent to be created
    
    Returns:
    
    the created agent
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createAgent(String, String, String).
  - createAgent
```
public Agent createAgent(String displayId,
                         String version)
                  throws SBOLValidationException
```
    Creates an agent, and then adds it to this SBOL document's list of agents.
    This method calls createAgent(String, String, String) with the default URI prefix of this SBOL document, the given display ID, and version.
    
    Parameters:
    
    displayId - the display ID of the agent to be created
    
    version - the version of the agent to be created
    
    Returns:
    
    the created agent
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createAgent(String, String, String).
  - createAgent
```
public Agent createAgent(String URIprefix,
                         String displayId,
                         String version)
                  throws SBOLValidationException
```
    Creates an agent, and then adds it to this SBOL document's list of agents.
    This method calls createAgent(String, String, String) with the default URI prefix of this SBOL document, the given display ID, and version.
    
    Parameters:
    
    URIprefix - the given URI prefix used to create a compliant URI for the agent to be created
    
    displayId - the display ID of the agent to be created
    
    version - the version of the agent to be created
    
    Returns:
    
    the created agent
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rules was violated: 10201, 10202, 10204, 10206, 10220.
  - removeAgent
```
public boolean removeAgent(Agent agent)
                    throws SBOLValidationException
```
    Removes the given agent from this SBOL document's list of agents.
    
    Parameters:
    
    agent - the given agent to be removed
    
    Returns:
    
    true if the given agent was successfully removed, false otherwise
    
    Throws:
    
    SBOLValidationException - if the following SBOL validation rule was violated: ?????.
  - getAgent
```
public Agent getAgent(String displayId,
                      String version)
```
    Returns the agent matching the given display ID and version from this SBOL document's list of agents.
    A compliant agent URI is created first. It starts with this SBOL document's default URI prefix after its been successfully validated, optionally followed by its type, namely TopLevel.AGENT, followed by the given display ID, and ends with the given version. This URI is used to look up the agent in this SBOL document.
    
    Parameters:
    
    displayId - the display ID of the agent to be retrieved
    
    version - the version of the agent to be retrieved
    
    Returns:
    
    the matching agent if present, or null otherwise.
  - getAgent
```
public Agent getAgent(URI agentURI)
```
    Returns the agent matching the given display identity URI from this SBOL document's list of agents.
    
    Parameters:
    
    agentURI - the identity URI of the top-level to be retrieved
    
    Returns:
    
    the matching agent if present, or null otherwise.
  - getAgents
```
public Set<Agent> getAgents()
```
    Returns the set of agents owned by this SBOL document.
    
    Returns:
    
    the set of agents owned by this SBOL document.
  - clearAgents
```
public void clearAgents()
                 throws SBOLValidationException
```
    Removes all entries in the list of agents owned by this SBOL document. The list will be empty after this call returns.
    This method calls removeAgent(Agent) to iteratively remove each agent.
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in removeAgent(Agent).
  - createPlan
```
public Plan createPlan(String displayId)
                throws SBOLValidationException
```
    Creates an plan, and then adds it to this SBOL document's list of plans.
    This method calls createPlan(String, String, String) with the default URI prefix of this SBOL document, the given display ID, and an empty version string.
    
    Parameters:
    
    displayId - the display ID of the plan to be created
    
    Returns:
    
    the created plan
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createPlan(String, String, String).
  - createPlan
```
public Plan createPlan(String displayId,
                       String version)
                throws SBOLValidationException
```
    Creates an plan, and then adds it to this SBOL document's list of plans.
    This method calls createPlan(String, String, String) with the default URI prefix of this SBOL document, the given display ID, and version.
    
    Parameters:
    
    displayId - the display ID of the plan to be created
    
    version - the version of the plan to be created
    
    Returns:
    
    the created plan
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createPlan(String, String, String).
  - createPlan
```
public Plan createPlan(String URIprefix,
                       String displayId,
                       String version)
                throws SBOLValidationException
```
    Creates an plan, and then adds it to this SBOL document's list of plans.
    This method calls createPlan(String, String, String) with the default URI prefix of this SBOL document, the given display ID, and version.
    
    Parameters:
    
    URIprefix - the given URI prefix used to create a compliant URI for the plan to be created
    
    displayId - the display ID of the plan to be created
    
    version - the version of the plan to be created
    
    Returns:
    
    the created plan
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rules was violated: 10201, 10202, 10204, 10206, 10220.
  - removePlan
```
public boolean removePlan(Plan plan)
                   throws SBOLValidationException
```
    Removes the given plan from this SBOL document's list of plans.
    
    Parameters:
    
    plan - the given plan to be removed
    
    Returns:
    
    true if the given plan was successfully removed, false otherwise
    
    Throws:
    
    SBOLValidationException - if the following SBOL validation rule was violated: ?????.
  - getPlan
```
public Plan getPlan(String displayId,
                    String version)
```
    Returns the plan matching the given display ID and version from this SBOL document's list of plans.
    A compliant plan URI is created first. It starts with this SBOL document's default URI prefix after its been successfully validated, optionally followed by its type, namely TopLevel.PLAN, followed by the given display ID, and ends with the given version. This URI is used to look up the plan in this SBOL document.
    
    Parameters:
    
    displayId - the display ID of the plan to be retrieved
    
    version - the version of the plan to be retrieved
    
    Returns:
    
    the matching plan if present, or null otherwise.
  - getPlan
```
public Plan getPlan(URI planURI)
```
    Returns the plan matching the given display identity URI from this SBOL document's list of plans.
    
    Parameters:
    
    planURI - the identity URI of the top-level to be retrieved
    
    Returns:
    
    the matching plan if present, or null otherwise.
  - getPlans
```
public Set<Plan> getPlans()
```
    Returns the set of plans owned by this SBOL document.
    
    Returns:
    
    the set of plans owned by this SBOL document.
  - clearPlans
```
public void clearPlans()
                throws SBOLValidationException
```
    Removes all entries in the list of plans owned by this SBOL document. The list will be empty after this call returns.
    This method calls removePlan(Plan) to iteratively remove each plan.
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in removePlan(Plan).
  - getTopLevel
```
public TopLevel getTopLevel(URI topLevelURI)
```
    Returns the top-level matching the given identity URI from this SBOL document's lists of top-levels.
    
    Parameters:
    
    topLevelURI - the identity URI of the top-level to be retrieved
    
    Returns:
    
    the matching top-level if present, or null otherwise.
  - getTopLevels
```
public Set<TopLevel> getTopLevels()
```
    Returns the set of all top-levels owned by this SBOL document.
    
    Returns:
    
    the set of all top-level owned by this SBOL document
  - getByWasDerivedFrom
```
public Set<TopLevel> getByWasDerivedFrom(URI wasDerivedFrom)
```
    Retrieves a set of top-levels in this SBOL document whose wasDerivedFrom field matches the given one.
    
    Parameters:
    
    wasDerivedFrom - the wasDerivedFrom field of which all matching top-levels to be retrieved
    
    Returns:
    
    a set of top-levels whose with the matching wasDerivedFrom field
  - addRegistry
```
public SynBioHubFrontend addRegistry(String registryURL)
```
    Adds the given registry to this SBOL document.
    
    Parameters:
    
    registryURL - URL of the registry to add
    
    Returns:
    
    The StackFrontend object that has been created
  - addRegistry
```
public SynBioHubFrontend addRegistry(String registryURL,
                                     String uriPrefix)
```
    Adds the given registry to this SBOL document.
    
    Parameters:
    
    registryURL - URL of the registry to add
    
    uriPrefix - URI prefix for everything stored in this repository
    
    Returns:
    
    The StackFrontend object that has been created
  - addNamespace
```
public void addNamespace(URI nameSpaceURI,
                         String prefix)
                  throws SBOLValidationException
```
    Adds the given namespace URI and its prefix to this SBOL document.
    
    Parameters:
    
    nameSpaceURI - the URI used to construct a new namespace
    
    prefix - the prefix used to construct a new namespace
    
    Throws:
    
    SBOLValidationException - if namespace URI does not end with a delimeter
  - addNamespace
```
public void addNamespace(QName qName)
                  throws SBOLValidationException
```
    Adds the given namespace QName to this SBOL document.
    
    Parameters:
    
    qName - the QName to be added
    
    Throws:
    
    SBOLValidationException - when namespace URI does not end with a delimiter
  - clearNamespaces
```
public void clearNamespaces()
```
    Removes all non-required namespaces from this SBOL document.
    This method calls removeNamespace(URI) to iteratively remove each non-required namespace.
  - clearRegistries
```
public void clearRegistries()
```
    Removes all registries from this SBOL document.
    This method calls removeRegistry(String) to iteratively remove each registry.
  - getNamespace
```
public QName getNamespace(String namespacePrefix)
```
    Returns the QName matching the given namespace prefix from this SBOL document's list of QNames.
    
    Parameters:
    
    namespacePrefix - the prefix of the namespace to be retrieved
    
    Returns:
    
    the matching QName if present, or null otherwise
  - getNamespace
```
public QName getNamespace(URI namespaceURI)
```
    Returns the QName matching the given namespace URI from this SBOL document's list of QNames.
    
    Parameters:
    
    namespaceURI - the identity URI of the namespace to be retrieved
    
    Returns:
    
    the matching QName if present, or null otherwise
  - getNamespaces
```
public List<QName> getNamespaces()
```
    Returns the list of namespaces owned by this SBOL document.
    
    Returns:
    
    the list of namespaces owned by this SBOL document
  - getRegistry
```
public SynBioHubFrontend getRegistry(String registryURL)
```
    Returns the StackFrontend for the registry specified by its URL
    
    Parameters:
    
    registryURL - URL for the registry to return
    
    Returns:
    
    a StackFrontend for the registry specified by its URL
  - getRegistries
```
public List<SynBioHubFrontend> getRegistries()
```
    Returns the list of registries used by this SBOL document.
    
    Returns:
    
    the list of registries used by this SBOL document
  - removeNamespace
```
public void removeNamespace(URI namespaceURI)
```
    Removes the given namespace URI from this SBOL document's list of namespaces.
    
    Parameters:
    
    namespaceURI - the namespaceURI to be removed
  - removeRegistry
```
public void removeRegistry(String registryId)
```
    Removes the given registry id from this SBOL document's list of registries.
    
    Parameters:
    
    registryId - the URL of the registry to be removed
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object
  - equals
```
public boolean equals(Object obj)
```
    Overrides:
    
    equals in class Object
  - removeTopLevel
```
public void removeTopLevel(TopLevel topLevel)
                    throws SBOLValidationException
```
    Method to remove a TopLevel object
    Parameters:
    
    topLevel - the TopLevel object to remove
    
    Throws:
    SBOLValidationException - if an SBOL validation rule violation occurred in any of the following methods:
    
    removeActivity(Activity),
    
    removeAgent(Agent),
    
    removePlan(Plan),
    
    removeGenericTopLevel(GenericTopLevel),
    
    removeCollection(Collection),
    
    removeExperiment(Experiment),
    
    removeExperimentalData(ExperimentalData),
    
    removeSequence(Sequence),
    
    removeComponentDefinition(ComponentDefinition),
    
    removeModel(Model), or
    
    removeModuleDefinition(ModuleDefinition).
    
    removeImplementation(Implementation).
  - setDefaultURIprefix
```
public void setDefaultURIprefix(String defaultURIprefix)
                         throws IllegalArgumentException
```
    Sets the default URI prefix of this SBOL document to the given one. This means that any SBOL instances created subsequently in this document will have the given URI prefix as the beginning of its compliant identity URI.
    
    Parameters:
    
    defaultURIprefix - the given default URI prefix
    
    Throws:
    
    IllegalArgumentException - if the given URI prefix is not compliant
  - getDefaultURIprefix
```
public String getDefaultURIprefix()
```
    Returns the default URI prefix of this SBOL document.
    
    Returns:
    
    the default URI prefix of this SBOL document
  - isComplete
```
public boolean isComplete()
```
    Returns the value of the complete flag for this SBOL document.
    A true value means that all identity URI references should be able to dereference to instances in the this document, and a false value means otherwise.
    
    Returns:
    
    the value of the complete flag for this SBOL document
  - setComplete
```
public void setComplete(boolean complete)
```
    Sets the complete flag to the given value.
    A true value indicates this SBOL document is complete: any identity URIs should be able to dereference to an instance in this document.
    
    Parameters:
    
    complete - the given boolean value for the complete flag
  - isCompliant
```
public boolean isCompliant()
```
    Returns the value of the compliant flag in this SBOL document.
    A true value means that all identity URIs in this SBOL document should be compliant, and a false value means otherwise.
    
    Returns:
    
    the value of the compliant flag in this SBOL document
  - isTypesInURIs
```
public boolean isTypesInURIs()
```
    Returns the value of the typesInURI flag in this SBOL document.
    A true value means that types will be inserted into this document's each top-level's compliant URI when it is created, and a false value means otherwise.
    
    Returns:
    
    the value of the typesInURI flag in this SBOL document
  - setTypesInURIs
```
public void setTypesInURIs(boolean typesInURIs)
```
    Sets the typesInURIs flag to the given value.
    A true value means that types are inserted into top-level identity URIs when they are created.
    
    Parameters:
    
    typesInURIs - the given boolean value for the typesInURIs flag
  - isCreateDefaults
```
public boolean isCreateDefaults()
```
    Returns the value of the createDefaults flag in this SBOL document.
    A true value means that default components and/or functional components instances should be created when not present, and a false value means otherwise.
    
    Returns:
    
    the value of the createDefaults flag in this SBOL document.
  - setCreateDefaults
```
public void setCreateDefaults(boolean createDefaults)
```
    Sets the createDefaults flag to the given value. A true value means that default component instances should be created when not present.
    
    Parameters:
    
    createDefaults - the given boolean value for the createDefaults flag
  - read
```
public void read(String fileName)
          throws SBOLValidationException,
                 IOException,
                 SBOLConversionException
```
    Takes in a given RDF file name and adds the data read to this SBOLDocument.
    
    Parameters:
    
    fileName - a given RDF file name
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in read(File).
    
    SBOLConversionException - see SBOLConversionException
    
    IOException - see IOException
  - read
```
public void read(File file)
          throws SBOLValidationException,
                 IOException,
                 SBOLConversionException
```
    Takes in a given RDF file and adds the data read to this SBOL document.
    
    Parameters:
    
    file - a given RDF file
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in read(InputStream).
    
    SBOLConversionException - see SBOLConversionException
    
    IOException - see IOException
  - read
```
public void read(InputStream in)
          throws SBOLValidationException,
                 IOException,
                 SBOLConversionException
```
    Takes in a given RDF input stream and adds the data read to this SBOL document.
    
    Parameters:
    
    in - a given RDF input stream
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10101, 10102, 10105, 10201, 10202, 10203, 10204, 10206, 10208, 10212, 10213, 10220, 10303, 10304, 10305, 10401, 10402, 10403, 10405, 10501, 10502, 10503, 10504, 10507, 10508, 10512, 10513, 10519, 10522, 10526, 10602, 10603, 10604, 10605, 10606, 10607, 10701, 10801, 10802, 10803, 10804, 10805, 10806, 10807, 10808, 10809, 10810, 10811, 10901, 10902, 10904, 10905, 11002, 11101, 11102, 11103, 11104, 11201, 11202, 11301, 11401, 11402, 11403, 11404, 11405, 11406, 11407, 11412, 11501, 11502, 11504, 11508, 11601, 11602, 11604, 11605, 11606, 11607, 11608, 11609, 11701, 11702, 11703, 11704, 11705, 11706, 11801, 11802, 11901, 11902, 11906, 12001, 12002, 12003, 12004, 12101, 12102, 12103, 12301, 12302.
    
    SBOLConversionException - see SBOLConversionException
    
    IOException - see IOException
  - write
```
public void write(String filename)
           throws IOException,
                  SBOLConversionException
```
    Outputs this SBOL document's data from the RDF/XML serialization to a new file with the given file name.
    This method calls SBOLWriter.write(SBOLDocument, File) by passing this SBOL document, and a new file with the given file name.
    
    Parameters:
    
    filename - the given output file name
    
    Throws:
    
    IOException - see IOException
    
    SBOLConversionException - see SBOLConversionException
  - write
```
public void write(String filename,
                  String fileType)
           throws IOException,
                  SBOLConversionException
```
    Outputs this SBOL document's data from serialization in the given serialization format to a new file with the given file name.
    This method calls SBOLWriter.write(SBOLDocument, File, String) by passing this SBOL document, and a new file with the given file name and type.
    
    Parameters:
    
    filename - the given output file name
    
    fileType - the serialization format
    
    Throws:
    
    IOException - see IOException
    
    SBOLConversionException - see SBOLConversionException
  - write
```
public void write(File file)
           throws IOException,
                  SBOLConversionException
```
    Outputs this SBOL document's data from the RDF/XML serialization to the given file.
    This method calls SBOLWriter.write(SBOLDocument, File).
    
    Parameters:
    
    file - the given output file
    
    Throws:
    
    IOException - see IOException
    
    SBOLConversionException - see SBOLConversionException
  - write
```
public void write(File file,
                  String fileType)
           throws IOException,
                  SBOLConversionException
```
    Outputs this SBOL document's data from the serialization in the given serialization format to the given file.
    This method calls SBOLWriter.write(SBOLDocument, OutputStream, String).
    
    Parameters:
    
    file - the given output file
    
    fileType - the given serialization format
    
    Throws:
    
    IOException - see IOException
    
    SBOLConversionException - see SBOLConversionException
  - write
```
public void write(OutputStream out)
           throws SBOLConversionException
```
    Outputs this SBOL document's data from the RDF/XML serialization to the given output stream.
    This method calls SBOLWriter.write(SBOLDocument, OutputStream) by passing this SBOL document and the given output stream.
    
    Parameters:
    
    out - the given output stream
    
    Throws:
    
    SBOLConversionException - see SBOLConversionException
  - write
```
public void write(OutputStream out,
                  String fileType)
           throws SBOLConversionException,
                  IOException
```
    Outputs this SBOL document's data from the serialization in the given serialization format to the given output stream.
    This method calls SBOLWriter.write(SBOLDocument, OutputStream, String) by passing this SBOL document, the given output stream and file type.
    
    Parameters:
    
    out - the given output stream
    
    fileType - the serialization format
    
    Throws:
    
    SBOLConversionException - see SBOLConversionException
    
    IOException - see IOException
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object

Class SBOLDocument

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

TURTLE

JSON

RDFV1

RDF

FASTAformat

GENBANK

SNAPGENE

Constructor Detail

SBOLDocument

Method Detail

createModuleDefinition

createModuleDefinition

createModuleDefinition

removeModuleDefinition

getModuleDefinition

getModuleDefinition

getModuleDefinitions

clearModuleDefinitions

createCollection

createCollection

createCollection

removeCollection

getCollection

getCollection

getCollections

clearCollections

createExperiment

createExperiment

createExperiment

removeExperiment

getExperiment

getExperiment

getExperiments

clearExperiments

createExperimentalData

createExperimentalData

createExperimentalData

removeExperimentalData

getExperimentalData

getExperimentalData

getExperimentalData

clearExperimentalData

createModel

createModel

createModel

removeModel

removeAttachment

getModel

getModel

getModels

clearModels

createAttachment

createAttachment

createAttachment

getAttachment

getAttachment

getAttachments

clearAttachments

createComponentDefinition

createComponentDefinition

createComponentDefinition

createComponentDefinition

createComponentDefinition

createComponentDefinition

removeComponentDefinition

getComponentDefinition

getComponentDefinition

getCombinatorialDerivation

getCombinatorialDerivation

removeCombinatorialDerivation

createCombinatorialDerivation

createCombinatorialDerivation

createCombinatorialDerivation

createCombinatorialDerivation