Examples with SequenceConstraint org.sbolstandard.core2.SequenceConstraint used on opensource projects

Example 6 with SequenceConstraint

use of org.sbolstandard.core2.SequenceConstraint in project libSBOLj by SynBioDex.

the class SBOLReader method parseComponentDefinition.

/**
 * @param SBOLDoc
 * @param topLevel
 * @param nested
 * @return
 * @throws SBOLValidationException if either of the following conditions is satisfied:
 * <ul>
 * <li>any of the following SBOL validation rules was violated:
 * 10202, 10203, 10204, 10206, 10208, 10212, 10213, 10502, 10507, 10512, or</li>
 * <li>an SBOL validation rule violation occurred in the following constructor or methods:
 * 	<ul>
 * 		<li>{@link #parseComponent(NestedDocument, Map)},</li>
 * 		<li>{@link #parseSequenceAnnotation(NestedDocument, Map)},</li>
 * 		<li>{@link ComponentDefinition#ComponentDefinition(URI, Set)}, </li>
 * 		<li>{@link ComponentDefinition#setDisplayId(String)}, </li>
 * 		<li>{@link ComponentDefinition#setVersion(String)}, </li>
 * 		<li>{@link ComponentDefinition#setWasDerivedFrom(URI)}, </li>
 * 		<li>{@link Identified#setAnnotations(List)},</li>
 * 		<li>{@link ComponentDefinition#setComponents(Set)},</li>
 * 		<li>{@link ComponentDefinition#setSequenceAnnotations(Set)},</li>
 * 		<li>{@link ComponentDefinition#setSequenceConstraints(Set)}, or</li>
 * 		<li>{@link SBOLDocument#addComponentDefinition(ComponentDefinition)}.</li>
 * 	</ul>
 * </li>
 * </ul>
 */
@SuppressWarnings("unchecked")
private static ComponentDefinition parseComponentDefinition(SBOLDocument SBOLDoc, IdentifiableDocument<QName> topLevel, Map<URI, NestedDocument<QName>> nested) throws SBOLValidationException {
    // URIcompliance.extractDisplayId(topLevel.getIdentity());
    String displayId = null;
    String name = null;
    String description = null;
    // URI.create(URIcompliance.extractPersistentId(topLevel.getIdentity()));
    URI persistentIdentity = null;
    String version = null;
    Set<URI> wasDerivedFroms = new HashSet<>();
    Set<URI> wasGeneratedBys = new HashSet<>();
    Set<URI> attachments = new HashSet<>();
    Set<URI> type = new HashSet<>();
    Set<URI> roles = new HashSet<>();
    Set<URI> sequences = new HashSet<>();
    Set<Component> components = new HashSet<>();
    List<Annotation> annotations = new ArrayList<>();
    Set<SequenceAnnotation> sequenceAnnotations = new HashSet<>();
    Set<SequenceConstraint> sequenceConstraints = new HashSet<>();
    for (NamedProperty<QName> namedProperty : topLevel.getProperties()) {
        if (namedProperty.getName().equals(Sbol2Terms.Identified.version)) {
            if (!(namedProperty.getValue() instanceof Literal) || version != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10206", topLevel.getIdentity());
            }
            version = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.persistentIdentity)) {
            if (!(namedProperty.getValue() instanceof Literal) || persistentIdentity != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10203", topLevel.getIdentity());
            }
            persistentIdentity = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.displayId)) {
            if (!(namedProperty.getValue() instanceof Literal) || displayId != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10204", topLevel.getIdentity());
            }
            displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.type)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10502", topLevel.getIdentity());
            }
            type.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.roles)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10507", topLevel.getIdentity());
            }
            roles.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.hasComponent) || namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.hasSubComponent)) {
            if (namedProperty.getValue() instanceof NestedDocument) {
                NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
                if (nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.Component.Component)) {
                    throw new SBOLValidationException("sbol-10519", topLevel.getIdentity());
                }
                components.add(parseComponent(SBOLDoc, ((NestedDocument<QName>) namedProperty.getValue()), nested));
            } else {
                URI uri = (URI) ((Literal<QName>) namedProperty.getValue()).getValue();
                NestedDocument<QName> nestedDocument = nested.get(uri);
                if (nestedDocument == null || nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.Component.Component)) {
                    throw new SBOLValidationException("sbol-10519", topLevel.getIdentity());
                }
                components.add(parseComponent(SBOLDoc, nested.get(uri), nested));
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.hasSequence)) {
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-10512", topLevel.getIdentity());
                }
                sequences.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
            } else if (namedProperty.getValue() instanceof IdentifiableDocument) {
                if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.Sequence.Sequence)) {
                    Sequence sequence = parseSequence(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue());
                    sequences.add(sequence.getIdentity());
                } else {
                    throw new SBOLValidationException("sbol-10512", topLevel.getIdentity());
                }
            } else {
                throw new SBOLValidationException("sbol-10512", topLevel.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.hasSequenceAnnotations)) {
            if (namedProperty.getValue() instanceof NestedDocument) {
                NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
                if (nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.SequenceAnnotation.SequenceAnnotation)) {
                    throw new SBOLValidationException("sbol-10521", topLevel.getIdentity());
                }
                sequenceAnnotations.add(parseSequenceAnnotation(((NestedDocument<QName>) namedProperty.getValue()), nested));
            } else {
                URI uri = (URI) ((Literal<QName>) namedProperty.getValue()).getValue();
                NestedDocument<QName> nestedDocument = nested.get(uri);
                if (nestedDocument == null || nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.SequenceAnnotation.SequenceAnnotation)) {
                    throw new SBOLValidationException("sbol-10521", topLevel.getIdentity());
                }
                sequenceAnnotations.add(parseSequenceAnnotation(nested.get(uri), nested));
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.hasSequenceConstraints)) {
            if (namedProperty.getValue() instanceof NestedDocument) {
                NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
                if (nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.SequenceConstraint.SequenceConstraint)) {
                    throw new SBOLValidationException("sbol-10524", topLevel.getIdentity());
                }
                sequenceConstraints.add(parseSequenceConstraint(((NestedDocument<QName>) namedProperty.getValue())));
            } else {
                URI uri = (URI) ((Literal<QName>) namedProperty.getValue()).getValue();
                NestedDocument<QName> nestedDocument = nested.get(uri);
                if (nestedDocument == null || nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.SequenceConstraint.SequenceConstraint)) {
                    throw new SBOLValidationException("sbol-10524", topLevel.getIdentity());
                }
                sequenceConstraints.add(parseSequenceConstraint(nested.get(uri)));
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.title)) {
            if (!(namedProperty.getValue() instanceof Literal) || name != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10212", topLevel.getIdentity());
            }
            name = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.description)) {
            if (!(namedProperty.getValue() instanceof Literal) || description != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10213", topLevel.getIdentity());
            }
            description = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.wasDerivedFrom)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10208", topLevel.getIdentity());
            }
            wasDerivedFroms.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.wasGeneratedBy)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10221", topLevel.getIdentity());
            }
            wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.TopLevel.hasAttachment)) {
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-XXXXX", topLevel.getIdentity());
                }
                attachments.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
            } else if (namedProperty.getValue() instanceof IdentifiableDocument) {
                if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.Attachment.Attachment)) {
                    Attachment attachment = parseAttachment(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue());
                    attachments.add(attachment.getIdentity());
                } else {
                    throw new SBOLValidationException("sbol-XXXXX", topLevel.getIdentity());
                }
            } else {
                throw new SBOLValidationException("sbol-XXXXX", topLevel.getIdentity());
            }
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    // ComponentDefinition c = SBOLDoc.createComponentDefinition(topLevel.getIdentity(), type, roles);
    // c.setPersistentIdentity(topLevel.getOptionalUriPropertyValue(Sbol2Terms.Identified.persistentIdentity));
    // ComponentDefinition c = SBOLDoc.createComponentDefinition(topLevel.getIdentity(), type);
    ComponentDefinition c = new ComponentDefinition(topLevel.getIdentity(), type);
    if (roles != null)
        c.setRoles(roles);
    if (displayId != null)
        c.setDisplayId(displayId);
    if (persistentIdentity != null)
        c.setPersistentIdentity(persistentIdentity);
    if (!sequences.isEmpty())
        c.setSequences(sequences);
    if (!components.isEmpty())
        c.setComponents(components);
    if (!sequenceAnnotations.isEmpty())
        c.setSequenceAnnotations(sequenceAnnotations);
    if (!sequenceConstraints.isEmpty())
        c.setSequenceConstraints(sequenceConstraints);
    if (name != null)
        c.setName(name);
    if (description != null)
        c.setDescription(description);
    if (!annotations.isEmpty())
        c.setAnnotations(annotations);
    if (version != null)
        c.setVersion(version);
    c.setWasDerivedFroms(wasDerivedFroms);
    c.setWasGeneratedBys(wasGeneratedBys);
    c.setAttachments(attachments);
    ComponentDefinition oldC = SBOLDoc.getComponentDefinition(topLevel.getIdentity());
    if (oldC == null) {
        SBOLDoc.addComponentDefinition(c);
    } else {
        if (!c.equals(oldC)) {
            throw new SBOLValidationException("sbol-10202", c);
        }
    }
    return c;
}

Example 7 with SequenceConstraint

use of org.sbolstandard.core2.SequenceConstraint in project libSBOLj by SynBioDex.

the class SBOLDocument method updateReferences.

// TODO: need to update persistentIdentities too
private void updateReferences(URI originalIdentity, URI newIdentity) throws SBOLValidationException {
    for (TopLevel topLevel : getTopLevels()) {
        for (URI wasDerivedFrom : topLevel.getWasDerivedFroms()) {
            if (wasDerivedFrom.equals(originalIdentity)) {
                topLevel.removeWasDerivedFrom(originalIdentity);
                topLevel.addWasDerivedFrom(newIdentity);
            }
        }
        for (URI wasGeneratedBy : topLevel.getWasGeneratedBys()) {
            if (wasGeneratedBy.equals(originalIdentity)) {
                topLevel.removeWasGeneratedBy(originalIdentity);
                topLevel.addWasGeneratedBy(newIdentity);
            }
        }
        for (URI attachmentURI : topLevel.getAttachmentURIs()) {
            if (attachmentURI.equals(originalIdentity)) {
                topLevel.removeAttachment(originalIdentity);
                topLevel.addAttachment(newIdentity);
            }
        }
    }
    for (Collection collection : getCollections()) {
        for (URI memberURI : collection.getMemberURIs()) {
            if (memberURI.equals(originalIdentity)) {
                collection.removeMember(originalIdentity);
                collection.addMember(newIdentity);
            }
        }
        updateReferences(collection, originalIdentity, newIdentity);
    }
    for (ComponentDefinition componentDefinition : getComponentDefinitions()) {
        updateReferences(componentDefinition, originalIdentity, newIdentity);
        for (Component component : componentDefinition.getComponents()) {
            if (component.getDefinitionURI().equals(originalIdentity)) {
                component.setDefinition(newIdentity);
                for (MapsTo mapsTo : component.getMapsTos()) {
                    ComponentDefinition cd = getComponentDefinition(newIdentity);
                    if (cd != null) {
                        String displayId = URIcompliance.extractDisplayId(mapsTo.getRemoteURI());
                        URI newURI = URIcompliance.createCompliantURI(cd.getPersistentIdentity().toString(), displayId, cd.getVersion());
                        mapsTo.setRemote(newURI);
                    }
                }
            }
            updateReferences(component, originalIdentity, newIdentity);
            for (MapsTo mapsTo : component.getMapsTos()) {
                updateReferences(mapsTo, originalIdentity, newIdentity);
            }
        }
        for (SequenceAnnotation sa : componentDefinition.getSequenceAnnotations()) {
            for (Location loc : sa.getLocations()) {
                updateReferences(loc, originalIdentity, newIdentity);
            }
            updateReferences(sa, originalIdentity, newIdentity);
        }
        for (SequenceConstraint sc : componentDefinition.getSequenceConstraints()) {
            updateReferences(sc, originalIdentity, newIdentity);
        }
        for (URI sequenceURI : componentDefinition.getSequenceURIs()) {
            if (sequenceURI.equals(originalIdentity)) {
                componentDefinition.removeSequence(originalIdentity);
                componentDefinition.addSequence(newIdentity);
            }
        }
    }
    for (ModuleDefinition moduleDefinition : getModuleDefinitions()) {
        updateReferences(moduleDefinition, originalIdentity, newIdentity);
        for (FunctionalComponent functionalComponent : moduleDefinition.getFunctionalComponents()) {
            if (functionalComponent.getDefinitionURI().equals(originalIdentity)) {
                functionalComponent.setDefinition(newIdentity);
                for (MapsTo mapsTo : functionalComponent.getMapsTos()) {
                    ComponentDefinition cd = getComponentDefinition(newIdentity);
                    if (cd != null) {
                        String displayId = URIcompliance.extractDisplayId(mapsTo.getRemoteURI());
                        URI newURI = URIcompliance.createCompliantURI(cd.getPersistentIdentity().toString(), displayId, cd.getVersion());
                        mapsTo.setRemote(newURI);
                    }
                }
            }
            updateReferences(functionalComponent, originalIdentity, newIdentity);
            for (MapsTo mapsTo : functionalComponent.getMapsTos()) {
                updateReferences(mapsTo, originalIdentity, newIdentity);
            }
        }
        for (Module module : moduleDefinition.getModules()) {
            if (module.getDefinitionURI().equals(originalIdentity)) {
                module.setDefinition(newIdentity);
                for (MapsTo mapsTo : module.getMapsTos()) {
                    ModuleDefinition md = getModuleDefinition(newIdentity);
                    if (md != null) {
                        String displayId = URIcompliance.extractDisplayId(mapsTo.getRemoteURI());
                        URI newURI = URIcompliance.createCompliantURI(md.getPersistentIdentity().toString(), displayId, md.getVersion());
                        mapsTo.setRemote(newURI);
                    }
                }
            }
            updateReferences(module, originalIdentity, newIdentity);
            for (MapsTo mapsTo : module.getMapsTos()) {
                updateReferences(mapsTo, originalIdentity, newIdentity);
            }
        }
        for (Interaction interaction : moduleDefinition.getInteractions()) {
            updateReferences(interaction, originalIdentity, newIdentity);
            for (Participation participation : interaction.getParticipations()) {
                updateReferences(participation, originalIdentity, newIdentity);
            }
        }
        for (URI modelURI : moduleDefinition.getModelURIs()) {
            if (modelURI.equals(originalIdentity)) {
                moduleDefinition.removeModel(originalIdentity);
                moduleDefinition.addModel(newIdentity);
            }
        }
    }
    for (Model model : getModels()) {
        updateReferences(model, originalIdentity, newIdentity);
    }
    for (Attachment attachment : getAttachments()) {
        updateReferences(attachment, originalIdentity, newIdentity);
    }
    for (Implementation implementation : getImplementations()) {
        if (implementation.isSetBuilt() && implementation.getBuiltURI().equals(originalIdentity)) {
            implementation.setBuilt(newIdentity);
        }
        updateReferences(implementation, originalIdentity, newIdentity);
    }
    for (Sequence sequence : getSequences()) {
        updateReferences(sequence, originalIdentity, newIdentity);
    }
    for (GenericTopLevel genericTopLevel : getGenericTopLevels()) {
        updateReferences(genericTopLevel, originalIdentity, newIdentity);
    }
    for (CombinatorialDerivation combinatorialDerivation : getCombinatorialDerivations()) {
        updateReferences(combinatorialDerivation, originalIdentity, newIdentity);
        if (combinatorialDerivation.getTemplateURI().equals(originalIdentity)) {
            combinatorialDerivation.setTemplate(newIdentity);
            ComponentDefinition cd = getComponentDefinition(newIdentity);
            if (cd != null) {
                for (VariableComponent variableComponent : combinatorialDerivation.getVariableComponents()) {
                    String displayId = URIcompliance.extractDisplayId(variableComponent.getVariableURI());
                    URI newURI = URIcompliance.createCompliantURI(cd.getPersistentIdentity().toString(), displayId, cd.getVersion());
                    variableComponent.setVariable(newURI);
                }
            }
        }
        for (VariableComponent variableComponent : combinatorialDerivation.getVariableComponents()) {
            updateReferences(variableComponent, originalIdentity, newIdentity);
        }
    }
    for (Activity activity : getActivities()) {
        updateReferences(activity, originalIdentity, newIdentity);
        for (Association association : activity.getAssociations()) {
            if (association.getAgentURI().equals(originalIdentity)) {
                association.setAgent(newIdentity);
            }
            if (association.isSetPlan() && association.getPlanURI().equals(originalIdentity)) {
                association.setPlan(newIdentity);
            }
            updateReferences(association, originalIdentity, newIdentity);
        }
        for (Usage usage : activity.getUsages()) {
            if (usage.getEntityURI().equals(originalIdentity)) {
                usage.setEntity(newIdentity);
            }
            updateReferences(usage, originalIdentity, newIdentity);
        }
    }
    for (Agent agent : getAgents()) {
        updateReferences(agent, originalIdentity, newIdentity);
    }
    for (Plan plan : getPlans()) {
        updateReferences(plan, originalIdentity, newIdentity);
    }
}

Example 8 with SequenceConstraint

use of org.sbolstandard.core2.SequenceConstraint in project libSBOLj by SynBioDex.

the class ComponentDefinition method createSequenceConstraint.

/**
 * 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.
 * <p>
 * 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 {@link #createSequenceConstraint(String, RestrictionType, URI, URI)} to create
 * the sequence constraint.
 * <p>
 * This method automatically creates a subject component if all of the following conditions are satisfied:
 * <ul>
 * <li>the associated SBOLDocument, i.e., the SBOLDocument instance hosting this component definition, is not {@code null};</li>
 * <li>if default components should be automatically created when not present for the associated SBOLDocument instance,
 * i.e., {@link SBOLDocument#isCreateDefaults} returns {@code true}; and</li>
 * <li>if this component definition does not already have a component with the created compliant subject component URI.</li>
 * </ul>
 * An object component is automatically created if the similar set of conditions hold.
 *
 * @param displayId the display ID of the sequence constraint to be created
 * @param restriction the structural restriction of the subject and object components
 * @param subjectId the display ID of the subject component
 * @param objectId the display ID of the object component
 * @return the created sequence constraint
 * @throws SBOLValidationException if any of the following condition is satisfied:
 * <ul>
 * <li>if any of the following SBOL validation rules was violated:
 * 10201, 10202, 10204, 10206, 10602, 10604, 10605, 10607, 10803; or</li>
 * <li>an SBOL validation rule violation occurred in {@link #createSequenceConstraint(String, RestrictionType, URI, URI)}.</li>
 * </ul>
 */
public SequenceConstraint createSequenceConstraint(String displayId, RestrictionType restriction, String subjectId, String objectId) throws SBOLValidationException {
    URI subjectURI = URIcompliance.createCompliantURI(this.getPersistentIdentity().toString(), subjectId, this.getVersion());
    if (this.getSBOLDocument() != null && this.getSBOLDocument().isCreateDefaults() && this.getComponent(subjectURI) == null) {
        this.createComponent(subjectId, AccessType.PUBLIC, subjectId, "");
    }
    URI objectURI = URIcompliance.createCompliantURI(this.getPersistentIdentity().toString(), objectId, this.getVersion());
    if (this.getSBOLDocument() != null && this.getSBOLDocument().isCreateDefaults() && this.getComponent(objectURI) == null) {
        this.createComponent(objectId, AccessType.PUBLIC, objectId, "");
    }
    return createSequenceConstraint(displayId, restriction, subjectURI, objectURI);
}

Example 9 with SequenceConstraint

use of org.sbolstandard.core2.SequenceConstraint in project libSBOLj by SynBioDex.

the class SequenceConstraintTest method test_toString.

@Test
public void test_toString() throws URISyntaxException {
    assertNotNull(repression_doc);
    URI gRNA_gene = new URI("http://sbols.org/CRISPR_Example/gRNA_b_gene/1.0");
    ComponentDefinition gRNA_b_gene = repression_doc.getComponentDefinition(gRNA_gene);
    assertNotNull(gRNA_b_gene);
    assertTrue(gRNA_b_gene.getSequenceConstraints().size() == 2);
    SequenceConstraint gRNA_b_gene_constraint1 = gRNA_b_gene.getSequenceConstraint("gRNA_b_gene_constraint1");
    assertTrue(gRNA_b_gene_constraint1.toString().length() != 0);
    assertNotNull(gRNA_b_gene_constraint1.toString());
    assertTrue(gRNA_b_gene_constraint1.toString().contains("identity="));
    assertTrue(gRNA_b_gene_constraint1.toString().contains("displayId="));
    assertFalse(gRNA_b_gene_constraint1.toString().contains("name="));
    assertFalse(gRNA_b_gene_constraint1.toString().contains("description="));
    assertTrue(gRNA_b_gene_constraint1.toString().contains("restriction="));
    assertTrue(gRNA_b_gene_constraint1.toString().contains("subject="));
    assertTrue(gRNA_b_gene_constraint1.toString().contains("object="));
}