ComponentDefinition

java.lang.Object
- org.sbolstandard.core2.Identified
- - org.sbolstandard.core2.TopLevel
  - - org.sbolstandard.core2.ComponentDefinition

```
public class ComponentDefinition
extends TopLevel
```
Represents a ComponentDefinition object in the SBOL data model.

Version:

2.1

Author:

Zhen Zhang, Nicholas Roehner, Chris Myers

Field Summary

Fields
Modifier and Type	Field and Description
`static URI`	`COMPLEX` A physical entity whose structure is comprised of other physical entities bound to each other covalently or non-covalently, at least one of which is a macromolecule (e.g.
`static URI`	`DNA` Deprecated.
`static URI`	`DNA_MOLECULE` A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic acid (DNA).
`static URI`	`DNA_REGION` A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic acid.
`static URI`	`EFFECTOR` A small molecule which increases (activator) or decreases (inhibitor) the activity of an (allosteric) enzyme by binding to the enzyme at the regulatory site (which is different from the substrate-binding catalytic site) (Effector).
`static URI`	`PROTEIN` A physical entity consisting of a sequence of amino acids; a protein monomer; a single polypeptide chain (Protein).
`static URI`	`RNA` Deprecated.
`static URI`	`RNA_MOLECULE` A physical entity consisting of a sequence of ribonucleotide monophosphates; a ribonucleic acid.
`static URI`	`RNA_REGION` A region on a RNA molecule.
`static URI`	`SMALL_MOLECULE` A small bioactive molecule (SmallMolecule).

Fields inherited from class org.sbolstandard.core2.TopLevel
ACTIVITY, AGENT, ANNOTATION, ATTACHMENT, COLLECTION, COMBINATORIAL_DERIVATION, COMPONENT_DEFINITION, EXPERIMENT, EXPERIMENTAL_DATA, GENERIC_TOP_LEVEL, IMPLEMENTATION, MODEL, MODULE_DEFINITION, PLAN, SEQUENCE

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`addRole(URI roleURI)` Adds the given role URI to this component definition's set of role URIs.
`boolean`	`addSequence(Sequence sequence)` Adds the URI of the given Sequence instance to this component definition's set of sequence URIs.
`boolean`	`addSequence(String displayId)` Constructs a compliant sequence URI using the given sequence display ID, and then adds this URI to this component definition's set of sequence URIs.
`boolean`	`addSequence(String displayId, String version)` Constructs a compliant sequence URI with the given display ID and version, and then adds this URI to this component definition's set of sequence URIs.
`boolean`	`addSequence(URI sequenceURI)` Adds the given sequence URI to this component definition's set of sequence URIs.
`boolean`	`addType(URI typeURI)` Adds the given type URI to this component definition's set of type URIs.
`void`	`clearComponents()` Removes all entries of this component definition's list of components.
`void`	`clearRoles()` Removes all entries of this component definition's set of role URIs.
`void`	`clearSequenceAnnotations()` Removes all entries of this component definition's list of sequence annotations.
`void`	`clearSequenceConstraints()` Removes all entries of this component definition's list of sequence constraints.
`void`	`clearSequences()` Removes all entries of this component definition's set of reference sequence URIs.
`boolean`	`containsRole(URI roleURI)` Checks if the given role URI is included in this component definition's set of role URIs.
`boolean`	`containsSequence(URI sequenceURI)` Checks if the given sequence URI is included in this component definition's set of sequence URIs.
`boolean`	`containsType(URI typeURI)` Checks if the given type URI is included in this component definition's set of type URIs.
`Component`	`createComponent(String displayId, AccessType access, String definitionId)` Creates a child component for this component definition with the given arguments, and then adds it to this component definition's list of components.
`Component`	`createComponent(String displayId, AccessType access, String definitionId, String version)` Creates a child component for this component definition with the given arguments, and then adds it to this component definition's list of components.
`Component`	`createComponent(String displayId, AccessType access, URI definitionURI)` Creates a child component for this component definition with the given arguments, and then adds to this component definition's list of components.
`SequenceAnnotation`	`createSequenceAnnotation(String displayId, String locationId)` Creates a child sequence annotation for this component definition with the given arguments, and then adds to this component definition's list of sequence annotations.
`SequenceAnnotation`	`createSequenceAnnotation(String displayId, String locationId, int at)` Creates a child sequence annotation for this component definition with the given arguments, and then adds to its list of sequence annotations.
`SequenceAnnotation`	`createSequenceAnnotation(String displayId, String locationId, int start, int end)` Creates a child sequence annotation for this component definition with the given arguments, and then adds to this ComponentDefinition's list of sequence annotations.
`SequenceAnnotation`	`createSequenceAnnotation(String displayId, String locationId, int start, int end, OrientationType orientation)` Creates a child sequence annotation for this ComponentDefinition instance with the given arguments, and then adds to this ComponentDefinition's list of sequence annotations.
`SequenceAnnotation`	`createSequenceAnnotation(String displayId, String locationId, int at, OrientationType orientation)` Creates a child sequence annotation for this component definition with the given arguments, and then adds to its list of sequence annotations.
`SequenceAnnotation`	`createSequenceAnnotation(String displayId, String locationId, OrientationType orientation)` Creates a child sequence annotation for this component definition with the given arguments, and then adds to this component definition's list of sequence annotations.
`SequenceConstraint`	`createSequenceConstraint(String displayId, RestrictionType restriction, String subjectId, String objectId)` Creates a child sequence constraint for this component definition with the given arguments, and then adds to this component definition's list of sequence constraints.
`SequenceConstraint`	`createSequenceConstraint(String displayId, RestrictionType restriction, URI subjectURI, URI objectURI)` Creates a child sequence constraint for this component definition with the given arguments, and then adds to this component definition's list of sequence constraints.
`boolean`	`equals(Object obj)`
`Component`	`getComponent(String displayId)` Returns the component matching the given component's display ID.
`Component`	`getComponent(URI componentURI)` Returns the instance matching the given component's identity URI.
`Set<Component>`	`getComponents()` Returns the set of components owned by this component definition.
`String`	`getImpliedNucleicAcidSequence()` Return the elements of a nucleic acid sequence implied by the hierarchically included components.
`Set<URI>`	`getRoles()` Returns the set of role URIs owned by this component definition.
`SequenceAnnotation`	`getSequenceAnnotation(Component component)` Returns the sequence annotation that references to the given component.
`SequenceAnnotation`	`getSequenceAnnotation(String displayId)` Returns the sequence annotation matching the given display ID.
`SequenceAnnotation`	`getSequenceAnnotation(URI sequenceAnnotationURI)` Returns the instance matching the given SequenceAnnotation URI from the list of sequence annotations.
`Set<SequenceAnnotation>`	`getSequenceAnnotations()` Returns the set of sequence annotations owned by this component definition.
`Sequence`	`getSequenceByEncoding(URI encoding)` Returns the first sequence referenced by this component definition that matches the given sequence encoding.
`SequenceConstraint`	`getSequenceConstraint(String displayId)` Returns the sequence constraint matching the given display ID.
`SequenceConstraint`	`getSequenceConstraint(URI sequenceConstraintURI)` Returns the sequence constraint matching the given URI.
`Set<SequenceConstraint>`	`getSequenceConstraints()` Returns the set of sequence constraints owned by this component definition.
`Set<URI>`	`getSequenceIdentities()` Returns the set of sequences identities referenced by this component definition.
`Set<Sequence>`	`getSequences()` Returns the set of sequences referenced by this component definition.
`Set<URI>`	`getSequenceURIs()` Returns the set of sequence URIs referenced by this component definition.
`List<Component>`	`getSortedComponents()` Returns a sorted list of components owned by this component definition.
`List<SequenceAnnotation>`	`getSortedSequenceAnnotations()` Returns a sorted list of sequence annotations owned by this component definition.
`Set<URI>`	`getTypes()` Returns the set of type URIs owned by this component definition.
`int`	`hashCode()`
`boolean`	`removeComponent(Component component)` Removes the given component from the list of components.
`boolean`	`removeRole(URI roleURI)` Removes the given role URI from the set of roles.
`boolean`	`removeSequence(URI sequenceURI)` Removes the given sequence URI from the set of sequence URIs.
`boolean`	`removeSequenceAnnotation(SequenceAnnotation sequenceAnnotation)` Removes the given sequence annotation from the list of sequence annotations.
`boolean`	`removeSequenceConstraint(SequenceConstraint sequenceConstraint)` Removes the given sequence constraint from the list of sequence constraints.
`boolean`	`removeType(URI typeURI)` Removes the given type URI from the set of types.
`void`	`setRoles(Set<URI> roles)` Clears the existing set of roles first, and then adds the given set of the roles to this component definition.
`void`	`setSequences(Set<URI> sequences)` Clears the existing set of sequences first, and then adds the given set of the sequences to this component definition.
`void`	`setTypes(Set<URI> types)` Clears the existing set of types first, then adds the given set of the types to this component definition.
`String`	`toString()`

Methods inherited from class org.sbolstandard.core2.TopLevel
addAttachment, addAttachment, addAttachment, clearAttachments, containsAttachment, getAttachments, getAttachmentURIs, removeAttachment, setAttachments

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

- Field Detail
  - DNA
```
@Deprecated
public static final URI DNA
```
    Deprecated.
    
    A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic acid. Usage: DNA should be used for pools of individual DNA molecules. For describing subregions on those molecules use DNARegion. Examples: a chromosome, a plasmid. A specific example is chromosome 7 of Homo sapiens. (DNA). Aspects of the state of the DNA region, including cellular location and features, are defined here, using properties inherited from PhysicalEntity. Deprecated - please use DNA_REGION instead.
  - DNA_REGION
```
public static final URI DNA_REGION
```
    A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic acid. Usage: DNA should be used for pools of individual DNA molecules. For describing subregions on those molecules use DNARegion. Examples: a chromosome, a plasmid. A specific example is chromosome 7 of Homo sapiens. (DNA). Aspects of the state of the DNA region, including cellular location and features, are defined here, using properties inherited from PhysicalEntity.
  - DNA_MOLECULE
```
public static final URI DNA_MOLECULE
```
    A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic acid (DNA). Aspects of the state of the DNA molecule, including cellular location and features, are defined here, using properties inherited from PhysicalEntity.
  - RNA
```
@Deprecated
public static final URI RNA
```
    Deprecated.
    
    A region on a RNA molecule. Usage: RNARegion is not a pool of independent molecules but a subregion on these molecules. As such, every RNARegion has a defining RNA molecule. Examples: CDS, 3'; UTR, Hairpin (RNA). Aspects of the state of the RNA region, including cellular location and features, are defined here, using properties inherited from PhysicalEntity. Deprecated - please use RNA_REGION instead.
  - RNA_REGION
```
public static final URI RNA_REGION
```
    A region on a RNA molecule. Usage: RNARegion is not a pool of independent molecules but a subregion on these molecules. As such, every RNARegion has a defining RNA molecule. Examples: CDS, 3'; UTR, Hairpin (RNA). Aspects of the state of the RNA region, including cellular location and features, are defined here, using properties inherited from PhysicalEntity.
  - RNA_MOLECULE
```
public static final URI RNA_MOLECULE
```
    A physical entity consisting of a sequence of ribonucleotide monophosphates; a ribonucleic acid. Usage: RNA should be used for pools of individual RNA molecules. For describing subregions on those molecules use RNARegion. Examples: messengerRNA, microRNA, ribosomalRNA. A specific example is the let-7 microRNA. (RNA). Aspects of the state of the RNA molecule, including cellular location and features, are defined here, using properties inherited from PhysicalEntity.
  - PROTEIN
```
public static final URI PROTEIN
```
    A physical entity consisting of a sequence of amino acids; a protein monomer; a single polypeptide chain (Protein). Aspects of the state of the protein, including cellular location and features, are defined here, using properties inherited from PhysicalEntity.
  - SMALL_MOLECULE
```
public static final URI SMALL_MOLECULE
```
    A small bioactive molecule (SmallMolecule). Small is not precisely defined, but includes all metabolites and most drugs and does not include large polymers, including complex carbohydrates. Aspects of the state of the small molecule, including cellular location and binding features, are defined here, using properties inherited from PhysicalEntity.
  - COMPLEX
```
public static final URI COMPLEX
```
    A physical entity whose structure is comprised of other physical entities bound to each other covalently or non-covalently, at least one of which is a macromolecule (e.g. protein, DNA, or RNA) and the Stoichiometry of the components are known. Comment: Complexes must be stable enough to function as a biological unit; in general, the temporary association of an enzyme with its substrate(s) should not be considered or represented as a complex. A complex is the physical product of an interaction (complexAssembly) and is not itself considered an interaction. The boundaries on the size of complexes described by this class are not defined here, although possible, elements of the cell such a mitochondria would typically not be described using this class (later versions of this ontology may include a cellularComponent class to represent these). The strength of binding cannot be described currently, but may be included in future versions of the ontology, depending on community need. Examples: Ribosome, RNA polymerase II. Other examples of this class include complexes of multiple protein monomers and complexes of proteins and small molecules.
  - EFFECTOR
```
public static final URI EFFECTOR
```
    A small molecule which increases (activator) or decreases (inhibitor) the activity of an (allosteric) enzyme by binding to the enzyme at the regulatory site (which is different from the substrate-binding catalytic site) (Effector).
- Method Detail
  - addType
```
public boolean addType(URI typeURI)
                throws SBOLValidationException
```
    Adds the given type URI to this component definition's set of type URIs.
    
    Parameters:
    
    typeURI - the given type URI
    
    Returns:
    
    true if this set did not already contain the given type URI, false otherwise.
    
    Throws:
    
    SBOLValidationException - if the following SBOL validation rule was violated: 10503.
  - removeType
```
public boolean removeType(URI typeURI)
                   throws SBOLValidationException
```
    Removes the given type URI from the set of types.
    
    Parameters:
    
    typeURI - the specified type URI
    
    Returns:
    
    true if the matching type reference was removed successfully, false otherwise.
    
    Throws:
    
    SBOLValidationException - if the following SBOL validation rule was violated: 10502.
  - setTypes
```
public void setTypes(Set<URI> types)
              throws SBOLValidationException
```
    Clears the existing set of types first, then adds the given set of the types to this component definition.
    Parameters:
    
    types - the set of types to set to
    
    Throws:
    SBOLValidationException - if either of the following condition is satisfied:
    
    if the following SBOL validation rule was violated: 10502.
    
    an SBOL validation rule violation occurred in addType(URI)
  - getTypes
```
public Set<URI> getTypes()
```
    Returns the set of type URIs owned by this component definition.
    
    Returns:
    
    the set of type URIs owned by this component definition
  - containsType
```
public boolean containsType(URI typeURI)
```
    Checks if the given type URI is included in this component definition's set of type URIs.
    
    Parameters:
    
    typeURI - the type URI to be checked
    
    Returns:
    
    true if this set contains the given type URI, false otherwise.
  - addRole
```
public boolean addRole(URI roleURI)
```
    Adds the given role URI to this component definition's set of role URIs.
    
    Parameters:
    
    roleURI - the role URI to be added
    
    Returns:
    
    true if this set did not already contain the specified role, false otherwise.
  - removeRole
```
public boolean removeRole(URI roleURI)
```
    Removes the given role URI from the set of roles.
    
    Parameters:
    
    roleURI - the given role URI to be removed
    
    Returns:
    
    true if the matching role reference was removed successfully, false otherwise.
  - setRoles
```
public void setRoles(Set<URI> roles)
```
    Clears the existing set of roles first, and then adds the given set of the roles to this component definition.
    
    Parameters:
    
    roles - the set of roles to set to
  - getRoles
```
public Set<URI> getRoles()
```
    Returns the set of role URIs owned by this component definition.
    
    Returns:
    
    the set of role URIs owned by this component definition.
  - containsRole
```
public boolean containsRole(URI roleURI)
```
    Checks if the given role URI is included in this component definition's set of role URIs.
    
    Parameters:
    
    roleURI - the role URI to be checked
    
    Returns:
    
    true if this set contains the given role URI, false otherwise.
  - clearRoles
```
public void clearRoles()
```
    Removes all entries of this component definition's set of role URIs. The set will be empty after this call returns.
  - addSequence
```
public boolean addSequence(Sequence sequence)
                    throws SBOLValidationException
```
    Adds the URI of the given Sequence instance to this component definition's set of sequence URIs. This method calls addSequence(URI) with this Sequence URI.
    
    Parameters:
    
    sequence - the Sequence instance whose identity URI to be added
    
    Returns:
    
    true if this set did not already contain the identity URI of the given Sequence, false otherwise.
    
    Throws:
    
    SBOLValidationException - if the following SBOL validation rule was violated: 10513.
  - addSequence
```
public boolean addSequence(URI sequenceURI)
                    throws SBOLValidationException
```
    Adds the given sequence URI to this component definition's set of sequence URIs.
    
    Parameters:
    
    sequenceURI - the identity URI of the sequence to be added
    
    Returns:
    
    true if this set did not already contain the given sequence's URI, false otherwise.
    
    Throws:
    
    SBOLValidationException - if the following SBOL validation rule was violated: 10513.
  - addSequence
```
public boolean addSequence(String displayId,
                           String version)
                    throws SBOLValidationException
```
    Constructs a compliant sequence URI with the given display ID and version, and then adds this URI to this component definition's set of sequence URIs.
    This method creates a compliant sequence URI with the default URI prefix, which was set in the SBOLDocument instance hosting this component definition, the given display ID and version. It then calls addSequence(URI) with this Sequence URI.
    
    Parameters:
    
    displayId - the display ID of the sequence whose identity URI is to be added
    
    version - version of the sequence whose identity URI is to be added
    
    Returns:
    
    true if this set did not already contain the given sequence's URI, false otherwise.
    
    Throws:
    
    SBOLValidationException - see addSequence(URI)
  - addSequence
```
public boolean addSequence(String displayId)
                    throws SBOLValidationException
```
    Constructs a compliant sequence URI using the given sequence display ID, and then adds this URI to this component definition's set of sequence URIs. This method calls addSequence(String, String) with the given sequence display ID and an empty string as its version.
    
    Parameters:
    
    displayId - the display ID of the sequence whose identity URI is to be added
    
    Returns:
    
    true if this set did not already contain the given sequence's URI, false otherwise.
    
    Throws:
    
    SBOLValidationException - see addSequence(String, String)
  - getSequenceURIs
```
public Set<URI> getSequenceURIs()
```
    Returns the set of sequence URIs referenced by this component definition.
    
    Returns:
    
    the set of sequence URIs referenced by this component definition
  - getSequenceIdentities
```
public Set<URI> getSequenceIdentities()
```
    Returns the set of sequences identities referenced by this component definition.
    
    Returns:
    
    the set of sequences identities referenced by this component definition
  - getSequences
```
public Set<Sequence> getSequences()
```
    Returns the set of sequences referenced by this component definition.
    
    Returns:
    
    the set of sequences referenced by this component definition
  - getSequenceByEncoding
```
public Sequence getSequenceByEncoding(URI encoding)
```
    Returns the first sequence referenced by this component definition that matches the given sequence encoding.
    
    Parameters:
    
    encoding - URI for a sequence encoding
    
    Returns:
    
    the first sequence that matches the given encoding
  - getImpliedNucleicAcidSequence
```
public String getImpliedNucleicAcidSequence()
```
    Return the elements of a nucleic acid sequence implied by the hierarchically included components.
    This method first tries to obtain the length of a nucleic acid sequence from the set of sequences referenced by this component definition that has an Sequence.IUPAC_DNA encoding. It then iterates through this component defintion's sequence annotations, and update the length with the ending locations that have a larger value than the current length. It then populates the elements with this length with unknown bases. This method iterates through this component defintion's sequence annotations to recursively search for bases implied by the hierarchically included components, and fills the elements with these known bases.
    
    Returns:
    
    the elements of a nucleic sequence implied by the hierarchically included components
  - setSequences
```
public void setSequences(Set<URI> sequences)
                  throws SBOLValidationException
```
    Clears the existing set of sequences first, and then adds the given set of the sequences to this component definition.
    
    Parameters:
    
    sequences - the given set of the sequences to set to
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in addSequence(URI)
  - removeSequence
```
public boolean removeSequence(URI sequenceURI)
```
    Removes the given sequence URI from the set of sequence URIs.
    
    Parameters:
    
    sequenceURI - the sequence URI
    
    Returns:
    
    true if the matching sequence was removed successfully, false otherwise.
  - clearSequences
```
public void clearSequences()
```
    Removes all entries of this component definition's set of reference sequence URIs. The set will be empty after this call returns.
  - containsSequence
```
public boolean containsSequence(URI sequenceURI)
```
    Checks if the given sequence URI is included in this component definition's set of sequence URIs.
    
    Parameters:
    
    sequenceURI - the sequence URI to be checked
    
    Returns:
    
    true if this set contains the given sequence URI, false otherwise.
  - createSequenceAnnotation
```
public SequenceAnnotation createSequenceAnnotation(String displayId,
                                                   String locationId)
                                            throws SBOLValidationException
```
    Creates a child sequence annotation for this component definition with the given arguments, and then adds to this component definition's list of sequence annotations.
    This method calls createSequenceAnnotation(String, String, OrientationType) with the orientation type set to null.
    
    Parameters:
    
    displayId - the display ID of the sequence annotation to be created
    
    locationId - the display ID of the location contained by sequence annotation to be created
    
    Returns:
    
    the created sequence annotation
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createSequenceAnnotation(String, String, OrientationType)
  - createSequenceAnnotation
```
public SequenceAnnotation createSequenceAnnotation(String displayId,
                                                   String locationId,
                                                   OrientationType orientation)
                                            throws SBOLValidationException
```
    Creates a child sequence annotation for this component definition with the given arguments, and then adds to this component definition's list of sequence annotations.
    This method first creates a GenericLocation instance with a compliant URI. This URI starts with this component definition's persistent identity, followed by the given sequence annotation's display ID, which is then followed by the given generic location's display ID, and ends with this component definition version.
    This method then creates a sequence annotation with a compliant URI, using this component definition's persistent identity, the given sequence annotation's display ID, and this component definition's version. It also adds the created generic location this sequence annotation.
    
    Parameters:
    
    displayId - the display ID of the sequence annotation to be created
    
    locationId - the display ID of the generic location contained by the sequence annotation to be created
    
    orientation - the orientation type of the sequence annotation to be created
    
    Returns:
    
    the created sequence annotation
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 10522, 10902, 10905.
  - createSequenceAnnotation
```
public SequenceAnnotation createSequenceAnnotation(String displayId,
                                                   String locationId,
                                                   int at)
                                            throws SBOLValidationException
```
    Creates a child sequence annotation for this component definition with the given arguments, and then adds to its list of sequence annotations.
    This method calls createSequenceAnnotation(String,String,int,OrientationType) with a null OrientationType.
    
    Parameters:
    
    displayId - the display ID of the sequence annotation to be created
    
    locationId - the display ID of the location contained by sequence annotation to be created
    
    at - the integer data field for the Cut location for the sequence annotation to be created
    
    Returns:
    
    the created sequence annotation
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createSequenceAnnotation(String, String, int, OrientationType)
  - createSequenceAnnotation
```
public SequenceAnnotation createSequenceAnnotation(String displayId,
                                                   String locationId,
                                                   int at,
                                                   OrientationType orientation)
                                            throws SBOLValidationException
```
    Creates a child sequence annotation for this component definition with the given arguments, and then adds to its list of sequence annotations.
    This method first creates a Cut instance with a compliant URI. This URI starts with this component definition's persistent identity, followed by the given sequence annotation's display ID, which is then followed by the given locationId, and ends with this component definition version.
    This method then creates a sequence annotation with the created Cut instance and a compliant URI. This URI starts with this component definition's persistent identity, followed by the given sequence annotation's display ID, and ends with this component definition's version.
    
    Parameters:
    
    displayId - the display ID of the sequence annotation to be created
    
    locationId - the display ID of the Cut location contained by sequence annotation to be created
    
    at - the integer data field for the Cut location for the sequence annotation to be created
    
    orientation - the orientation type for DNA molecules
    
    Returns:
    
    the created sequence annotation
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 10522, 10902, 10905.
  - createSequenceAnnotation
```
public SequenceAnnotation createSequenceAnnotation(String displayId,
                                                   String locationId,
                                                   int start,
                                                   int end)
                                            throws SBOLValidationException
```
    Creates a child sequence annotation for this component definition with the given arguments, and then adds to this ComponentDefinition's list of sequence annotations.
    This method calls createSequenceAnnotation(String, String, int, int, OrientationType) with a null OrientationType.
    
    Parameters:
    
    displayId - the display ID of the sequence annotation to be created
    
    locationId - the display ID of the location contained by sequence annotation to be created
    
    start - the starting position of the Range
    
    end - the ending position of the Range
    
    Returns:
    
    the created sequence annotation
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createSequenceAnnotation(String, String, int, int, OrientationType).
  - createSequenceAnnotation
```
public SequenceAnnotation createSequenceAnnotation(String displayId,
                                                   String locationId,
                                                   int start,
                                                   int end,
                                                   OrientationType orientation)
                                            throws SBOLValidationException
```
    Creates a child sequence annotation for this ComponentDefinition instance with the given arguments, and then adds to this ComponentDefinition's list of sequence annotations.
    This method first creates a Range instance with a compliant URI. This URI starts with this component definition's persistent identity, followed by the given sequence annotation's display ID, which is then followed by the given locationId, and ends with this component definition version.
    This method then creates a sequence annotation with the created Range instance and a compliant URI. This URI starts with this component definition's persistent identity, followed by the given sequence annotation's display ID, and ends with this component definition's version.
    
    Parameters:
    
    displayId - The displayId identifier for this instance
    
    locationId - Specifies a region between two discrete positions
    
    start - starting position of the Range
    
    end - ending position of the Range
    
    orientation - the orientation type for DNA molecules
    
    Returns:
    
    the created sequence annotation
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 10522, 10902, 10905.
  - removeSequenceAnnotation
```
public boolean removeSequenceAnnotation(SequenceAnnotation sequenceAnnotation)
```
    Removes the given sequence annotation from the list of sequence annotations.
    
    Parameters:
    
    sequenceAnnotation - the given sequence annotation
    
    Returns:
    
    true if the matching sequence annotation was removed successfully, false otherwise.
  - getSequenceAnnotation
```
public SequenceAnnotation getSequenceAnnotation(String displayId)
```
    Returns the sequence annotation matching the given display ID.
    
    Parameters:
    
    displayId - the display ID for the sequence annotation to be retrieved
    
    Returns:
    
    the matching sequence annotation if present, or null otherwise.
  - getSequenceAnnotation
```
public SequenceAnnotation getSequenceAnnotation(URI sequenceAnnotationURI)
```
    Returns the instance matching the given SequenceAnnotation URI from the list of sequence annotations.
    
    Parameters:
    
    sequenceAnnotationURI - the given SequenceAnnotation URI
    
    Returns:
    
    the matching sequence annotation if present, or null otherwise.
  - getSequenceAnnotation
```
public SequenceAnnotation getSequenceAnnotation(Component component)
```
    Returns the sequence annotation that references to the given component.
    
    Parameters:
    
    component - the component referenced by the sequence annotation to be retrieved
    
    Returns:
    
    the matching sequence annotation if present, or null otherwise.
  - getSequenceAnnotations
```
public Set<SequenceAnnotation> getSequenceAnnotations()
```
    Returns the set of sequence annotations owned by this component definition.
    
    Returns:
    
    the set of sequence annotations owned by this component definition.
  - getSortedComponents
```
public List<Component> getSortedComponents()
                                    throws SBOLValidationException
```
    Returns a sorted list of components owned by this component definition. The order is determined by the order of appearance of components on a DNA strand.
    
    Returns:
    
    a sorted list of components owned by this component definition
    
    Throws:
    
    SBOLValidationException - if the following SBOL validation rule was violated: 10605.
  - getSortedSequenceAnnotations
```
public List<SequenceAnnotation> getSortedSequenceAnnotations()
```
    Returns a sorted list of sequence annotations owned by this component definition. The order is determined by each sequence annotation's location.
    Priority is given to a sequence annotation whose location has a lower (starting) value. Here is an example.
    - SA1 has a range location (4, 10);
    - SA2 has a range location (3, 7);
    - SA3 has a cut location 2;
    - SA4 has a cut location 4;
    - SA5 has a cut location 6;
    - SA6 has a cut location 10; and
    - SA7 has a generic location.
    The sorted list it returns is [SA3, SA2, SA4, SA1, SA5, SA6, SA7].
    Returns:
    
    a sorted list of sequence annotations owned by this component definition.
  - clearSequenceAnnotations
```
public void clearSequenceAnnotations()
```
    Removes all entries of this component definition's list of sequence annotations. The list will be empty after this call returns.
    This method calls removeSequenceAnnotation(SequenceAnnotation) to iteratively remove each sequence annotation owned by this component definition.
  - createComponent
```
public Component createComponent(String displayId,
                                 AccessType access,
                                 String definitionId,
                                 String version)
                          throws SBOLValidationException
```
    Creates a child component for this component definition with the given arguments, and then adds it to this component definition's list of components.
    This method first creates a compliant URI for the component definition that is referenced by the child component to be created, i.e., the child component's definition property. This URI starts with the default URI prefix, which was set in the SBOLDocument instance hosting this component definition, followed by the given display ID and ends with version. It then calls createComponent(String, AccessType, URI) with this compliant component URI.
    Parameters:
    
    displayId - the display ID for the component to be created
    
    access - the access property for the component to be created
    
    definitionId - the display ID of the component definition referenced by the component to be created
    
    version - the version for the component to be created
    
    Returns:
    
    the created component
    
    Throws:
    SBOLValidationException - if either of the following condition is satisfied:
    
    if either of the following SBOL validation rules was violated: 10204, 10206; or
    
    an SBOL validation exception occurred in createComponent(String, AccessType, URI)
  - createComponent
```
public Component createComponent(String displayId,
                                 AccessType access,
                                 String definitionId)
                          throws SBOLValidationException
```
    Creates a child component for this component definition with the given arguments, and then adds it to this component definition's list of components.
    This method calls createComponent(String, AccessType, URI) with the given arguments and an empty string for version.
    
    Parameters:
    
    displayId - the display ID for the component to be created
    
    access - the access property for the component to be created
    
    definitionId - the display ID of the component definition referenced by the component to be created
    
    Returns:
    
    the created component
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in createComponent(String, AccessType, String, String)
  - createComponent
```
public Component createComponent(String displayId,
                                 AccessType access,
                                 URI definitionURI)
                          throws SBOLValidationException
```
    Creates a child component for this component definition with the given arguments, and then adds to this component definition's list of components.
    This method first creates a compliant URI for the child component to be created. This URI starts with this component definition's persistent identity, followed by the given display ID and ends with this component defintion's version.
    
    Parameters:
    
    displayId - the display ID for the component to be created
    
    access - the access property for the component to be created
    
    definitionURI - the URI of the component definition referenced by the component to be created
    
    Returns:
    
    the created component
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 10602, 10604, 10605, 10607, 10803.
  - removeComponent
```
public boolean removeComponent(Component component)
                        throws SBOLValidationException
```
    Removes the given component from the list of components.
    
    Parameters:
    
    component - the given component
    
    Returns:
    
    true if the matching component was removed successfully, false otherwise.
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules were violated: 10803, 10808, 10905, 11402, 11404,
  - getComponent
```
public Component getComponent(String displayId)
```
    Returns the component matching the given component's display ID.
    This method first creates a compliant URI for the component to be retrieved. It starts with this component definition's persistent identity, followed by the given component's display ID, and ends with this component definition's version.
    
    Parameters:
    
    displayId - the display ID of the component to be retrieved
    
    Returns:
    
    the matching component if present, or null otherwise.
  - getComponent
```
public Component getComponent(URI componentURI)
```
    Returns the instance matching the given component's identity URI.
    
    Parameters:
    
    componentURI - the identity URI of the component to be retrieved
    
    Returns:
    
    the matching component if present, or null otherwise.
  - getComponents
```
public Set<Component> getComponents()
```
    Returns the set of components owned by this component definition.
    
    Returns:
    
    the set of components owned by this component definition.
  - clearComponents
```
public void clearComponents()
                     throws SBOLValidationException
```
    Removes all entries of this component definition's list of components. The list will be empty after this call returns.
    This method calls removeComponent(Component component) to iteratively remove each component.
    
    Throws:
    
    SBOLValidationException - if an SBOL validation rule violation occurred in removeComponent(Component).
  - createSequenceConstraint
```
public SequenceConstraint createSequenceConstraint(String displayId,
                                                   RestrictionType restriction,
                                                   String subjectId,
                                                   String objectId)
                                            throws SBOLValidationException
```
    Creates a child sequence constraint for this component definition with the given arguments, and then adds to this component definition's list of sequence constraints.
    Creation of a sequence constraint requires URIs of a subject component and an object component. This method creates compliant URIs for them respectively. The subject component compliant URI is created with this component defintion's persistent identity URI, followed by the given subject component's display ID, followed by this component's version. The object component compliant URI is created similarly. This method then calls createSequenceConstraint(String, RestrictionType, URI, URI) to create the sequence constraint.
    This method automatically creates a subject component if all of the following conditions are satisfied:
    - the associated SBOLDocument, i.e., the SBOLDocument instance hosting this component definition, is not null;
    - if default components should be automatically created when not present for the associated SBOLDocument instance, i.e., SBOLDocument.isCreateDefaults() returns true; and
    - if this component definition does not already have a component with the created compliant subject component URI.
    An object component is automatically created if the similar set of conditions hold.
    Parameters:
    
    displayId - the display ID of the sequence constraint to be created
    
    restriction - the structural restriction of the subject and object components
    
    subjectId - the display ID of the subject component
    
    objectId - the display ID of the object component
    
    Returns:
    
    the created sequence constraint
    
    Throws:
    SBOLValidationException - if any of the following condition is satisfied:
    
    if any of the following SBOL validation rules was violated: 10201, 10202, 10204, 10206, 10602, 10604, 10605, 10607, 10803; or
    
    an SBOL validation rule violation occurred in createSequenceConstraint(String, RestrictionType, URI, URI).
  - createSequenceConstraint
```
public SequenceConstraint createSequenceConstraint(String displayId,
                                                   RestrictionType restriction,
                                                   URI subjectURI,
                                                   URI objectURI)
                                            throws SBOLValidationException
```
    Creates a child sequence constraint for this component definition with the given arguments, and then adds to this component definition's list of sequence constraints.
    
    Parameters:
    
    displayId - the display ID of the sequence constraint to be created
    
    restriction - the structural restriction of the subject and object components
    
    subjectURI - the display ID of the subject component
    
    objectURI - the display ID of the object component
    
    Returns:
    
    the created sequence constraint
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rule was violated: 10201, 10202, 10204, 10206, 11402, 11403, 11404, 11405, 11406, 11407, 11412.
  - removeSequenceConstraint
```
public boolean removeSequenceConstraint(SequenceConstraint sequenceConstraint)
```
    Removes the given sequence constraint from the list of sequence constraints.
    
    Parameters:
    
    sequenceConstraint - the given sequence constraint
    
    Returns:
    
    true if the matching sequence constraint was removed successfully, false otherwise.
  - getSequenceConstraint
```
public SequenceConstraint getSequenceConstraint(String displayId)
```
    Returns the sequence constraint matching the given display ID.
    
    Parameters:
    
    displayId - the display ID of the sequence constraint to be retrieved
    
    Returns:
    
    the matching sequence constraint if present, or null otherwise.
  - getSequenceConstraint
```
public SequenceConstraint getSequenceConstraint(URI sequenceConstraintURI)
```
    Returns the sequence constraint matching the given URI.
    
    Parameters:
    
    sequenceConstraintURI - the identity URI of the sequence constraint to be retrieved
    
    Returns:
    
    the matching sequence constraint if present, or null otherwise.
  - getSequenceConstraints
```
public Set<SequenceConstraint> getSequenceConstraints()
```
    Returns the set of sequence constraints owned by this component definition.
    
    Returns:
    
    the set of sequence constraints owned by this component definition
  - clearSequenceConstraints
```
public void clearSequenceConstraints()
```
    Removes all entries of this component definition's list of sequence constraints. The list will be empty after this call returns.
    This method calls removeSequenceConstraint(SequenceConstraint) to iteratively remove each sequence constraint owned by this component definition.
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class TopLevel
  - equals
```
public boolean equals(Object obj)
```
    Overrides:
    
    equals in class TopLevel
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Identified

Class ComponentDefinition

Field Summary

Fields inherited from class org.sbolstandard.core2.TopLevel

Method Summary

Methods inherited from class org.sbolstandard.core2.TopLevel

Methods inherited from class org.sbolstandard.core2.Identified

Methods inherited from class java.lang.Object

Field Detail

DNA

DNA_REGION

DNA_MOLECULE

RNA

RNA_REGION

RNA_MOLECULE

PROTEIN

SMALL_MOLECULE

COMPLEX

EFFECTOR

Method Detail

addType

removeType

setTypes

getTypes

containsType

addRole

removeRole

setRoles

getRoles

containsRole

clearRoles

addSequence

addSequence

addSequence

addSequence

getSequenceURIs

getSequenceIdentities

getSequences

getSequenceByEncoding

getImpliedNucleicAcidSequence

setSequences

removeSequence

clearSequences

containsSequence

createSequenceAnnotation

createSequenceAnnotation

createSequenceAnnotation

createSequenceAnnotation

createSequenceAnnotation

createSequenceAnnotation

removeSequenceAnnotation

getSequenceAnnotation

getSequenceAnnotation

getSequenceAnnotation

getSequenceAnnotations

getSortedComponents

getSortedSequenceAnnotations

clearSequenceAnnotations

createComponent

createComponent

createComponent

removeComponent

getComponent

getComponent

getComponents

clearComponents

createSequenceConstraint

createSequenceConstraint

removeSequenceConstraint

getSequenceConstraint

getSequenceConstraint

getSequenceConstraints

clearSequenceConstraints

hashCode

equals

toString