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

Example 26 with Component

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

the class Module method createMapsTo.

/**
 * Creates a child mapsTo for this module with the given arguments, and then adds it to its list of mapsTos.
 * <p>
 * This method creates compliant local and remote URIs first.
 * The compliant local URI is created with this module's persistent identity URI, followed by
 * the given local module's display ID, followed by this module's version.
 * The compliant remote URI is created following the same pattern.
 * It then calls {@link #createMapsTo(String, RefinementType, URI, URI)} with the given mapsTo's display ID, its refinement type,
 * and the created compliant local and remote functional components' URIs.
 * <p>
 * This method calls {@link ModuleDefinition#createFunctionalComponent(String, AccessType, String, String, DirectionType)}
 * to automatically create a local functional component with the given display ID of referenced local component definition,
 * {@link AccessType#PUBLIC}, an empty version string, and {@link DirectionType#INOUT}, if all of the following conditions are satisfied:
 * <ul>
 * <li>the associated SBOLDocument instance for this module is not {@code null};</li>
 * <li>if default functional components should be automatically created when not present in the associated SBOLDocument instance,
 * i.e., {@link SBOLDocument#isCreateDefaults} returns {@code true};</li>
 * <li>if this module's parent ModuleDefinition instance exists; and</li>
 * <li>if this module's parent ModuleDefinition instance does not already have a functional component
 * with the created compliant local URI.</li>
 * </ul>
 * This automatically created created functional component has the same display ID as its referenced component definition.
 *
 * @param displayId the display ID of the mapsTo to be created
 * @param refinement the relationship between the local and remote components
 * @param localId the display ID of the local functional component
 * @param remoteId the display ID of the remote functional component
 * @return the created mapsTo
 * @throws SBOLValidationException if any of the following condition is satisfied:
 * <ul>
 * <li>if either of the following SBOL validation rules was violated: 10204, 10206;</li>
 * <li>an SBOL validation exception occurred in {@link ModuleDefinition#createFunctionalComponent(String, AccessType, String, String, DirectionType)}; or</li>
 * <li>an SBOL validation exception occurred in {@link #createMapsTo(String, RefinementType, URI, URI)}.</li>
 * </ul>
 */
public MapsTo createMapsTo(String displayId, RefinementType refinement, String localId, String remoteId) throws SBOLValidationException {
    URI localURI = URIcompliance.createCompliantURI(moduleDefinition.getPersistentIdentity().toString(), localId, moduleDefinition.getVersion());
    if (this.getSBOLDocument() != null && this.getSBOLDocument().isCreateDefaults() && moduleDefinition != null && moduleDefinition.getFunctionalComponent(localURI) == null) {
        moduleDefinition.createFunctionalComponent(localId, AccessType.PUBLIC, localId, "", DirectionType.INOUT);
    }
    URI remoteURI = URIcompliance.createCompliantURI(getDefinition().getPersistentIdentity().toString(), remoteId, getDefinition().getVersion());
    return createMapsTo(displayId, refinement, localURI, remoteURI);
}

Example 27 with Component

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

the class ModuleDefinition method copy.

/*
	 * (non-Javadoc)
	 *
	 * @see
	 * org.sbolstandard.core2.abstract_classes.TopLevel#copy(java.lang.String,
	 * java.lang.String, java.lang.String)
	 */
/**
 * @throws SBOLValidationException if an SBOL validation rule violation occurred in
 * any one of the following methods:
 * <ul>
 * <li>{@link #deepCopy()},</li>
 * <li>{@link URIcompliance#createCompliantURI(String, String, String)},</li>
 * <li>{@link #setDisplayId(String)},</li>
 * <li>{@link #setVersion(String)},</li>
 * <li>{@link #setWasDerivedFrom(URI)},</li>
 * <li>{@link #setIdentity(URI)},</li>
 * <li>{@link FunctionalComponent#setDisplayId(String)}</li>
 * <li>{@link FunctionalComponent#updateCompliantURI(String, String, String)},</li>
 * <li>{@link #addFunctionalComponent(FunctionalComponent)},</li>
 * <li>{@link Module#setDisplayId(String)}</li>
 * <li>{@link Module#updateCompliantURI(String, String, String)},</li>
 * <li>{@link #addModule(Module)},</li>
 * <li>{@link Interaction#setDisplayId(String)},</li>
 * <li>{@link Interaction#updateCompliantURI(String, String, String)}, or</li>
 * <li>{@link #addInteraction(Interaction)}.</li>
 * </ul>
 */
@Override
ModuleDefinition copy(String URIprefix, String displayId, String version) throws SBOLValidationException {
    ModuleDefinition cloned = this.deepCopy();
    cloned.setPersistentIdentity(createCompliantURI(URIprefix, displayId, ""));
    cloned.setDisplayId(displayId);
    cloned.setVersion(version);
    URI newIdentity = createCompliantURI(URIprefix, displayId, version);
    if (!this.getIdentity().equals(newIdentity)) {
        cloned.addWasDerivedFrom(this.getIdentity());
    } else {
        cloned.setWasDerivedFroms(this.getWasDerivedFroms());
    }
    cloned.setIdentity(newIdentity);
    int count = 0;
    for (FunctionalComponent component : cloned.getFunctionalComponents()) {
        if (!component.isSetDisplayId())
            component.setDisplayId("functionalComponent" + ++count);
        component.updateCompliantURI(cloned.getPersistentIdentity().toString(), component.getDisplayId(), version);
        cloned.removeChildSafely(component, cloned.functionalComponents);
        cloned.addFunctionalComponent(component);
    }
    count = 0;
    for (Module module : cloned.getModules()) {
        if (!module.isSetDisplayId())
            module.setDisplayId("module" + ++count);
        module.updateCompliantURI(cloned.getPersistentIdentity().toString(), module.getDisplayId(), version);
        cloned.removeChildSafely(module, cloned.modules);
        cloned.addModule(module);
    }
    count = 0;
    for (Interaction interaction : cloned.getInteractions()) {
        if (!interaction.isSetDisplayId())
            interaction.setDisplayId("interaction" + ++count);
        interaction.updateCompliantURI(cloned.getPersistentIdentity().toString(), interaction.getDisplayId(), version);
        cloned.removeChildSafely(interaction, cloned.interactions);
        cloned.addInteraction(interaction);
    }
    return cloned;
}

Example 28 with Component

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

the class ModuleDefinition method copy.

void copy(ModuleDefinition moduleDefinition) throws SBOLValidationException {
    ((TopLevel) this).copy((TopLevel) moduleDefinition);
    for (URI role : moduleDefinition.getRoles()) {
        this.addRole(role);
    }
    for (FunctionalComponent component : moduleDefinition.getFunctionalComponents()) {
        String displayId = URIcompliance.findDisplayId(component);
        FunctionalComponent newComponent = this.createFunctionalComponent(displayId, component.getAccess(), component.getDefinitionURI(), component.getDirection());
        newComponent.copy(component);
    }
    for (Module subModule : moduleDefinition.getModules()) {
        String displayId = URIcompliance.findDisplayId(subModule);
        Module newModule = this.createModule(displayId, subModule.getDefinitionURI());
        newModule.copy(subModule);
    }
    for (Interaction interaction : moduleDefinition.getInteractions()) {
        String displayId = URIcompliance.findDisplayId(interaction);
        Interaction newInteraction = this.createInteraction(displayId, interaction.getTypes());
        newInteraction.copy(interaction);
    }
    this.setModels(moduleDefinition.getModelURIs());
}

Example 29 with Component

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

the class CombinatorialDerivation method addVariableComponent.

/**
 * Adds the given variable component to the list of variable components.
 *
 * @param variableComponent
 */
private void addVariableComponent(VariableComponent variableComponent) throws SBOLValidationException {
    variableComponent.setSBOLDocument(this.getSBOLDocument());
    variableComponent.setCombinatorialDerivation(this);
    ComponentDefinition template = this.getTemplate();
    if (template != null) {
        if (template.getComponent(variableComponent.getVariableURI()) == null) {
            throw new SBOLValidationException("sbol-13005", this);
        }
    }
    for (URI cdURI : variableComponent.getVariantDerivationURIs()) {
        if (this.getSBOLDocument() != null && this.getSBOLDocument().isComplete()) {
            CombinatorialDerivation cd = this.getSBOLDocument().getCombinatorialDerivation(cdURI);
            if (cd != null && this.getIdentity().equals(cd.getIdentity())) {
                throw new SBOLValidationException("sbol-13015", variableComponent);
            }
            Set<URI> visited = new HashSet<>();
            visited.add(this.getIdentity());
            try {
                SBOLValidate.checkCombinatorialDerivationCycle(this.getSBOLDocument(), cd, visited);
            } catch (SBOLValidationException e) {
                throw new SBOLValidationException("sbol-13015", variableComponent);
            }
        }
    }
    addChildSafely(variableComponent, variableComponents, "variableComponent");
}

Example 30 with Component

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

the class FunctionalComponent method createMapsTo.

/**
 * Creates a child MapsTo instance for this module with the given arguments, and then adds to this module's list of mapsTos.
 * <p>
 * This method creates compliant local and remote URIs first.
 * The compliant local URI is created with this module's persistent identity URI, followed by
 * the given local component's display ID, followed by this module's version.
 * The compliant remote URI is created following the same pattern.
 * It then calls {@link #createMapsTo(String, RefinementType, URI, URI)} to create
 * a MapsTo instance.
 * <p>
 * This method automatically creates a local functional component if all of the following conditions are satisfied:
 * <ul>
 * <li>the associated SBOLDocument instance for this module is not {@code null};</li>
 * <li>if default functional components should be automatically created when not present for the associated SBOLDocument instance,
 * i.e., {@link SBOLDocument#isCreateDefaults} returns {@code true};</li>
 * <li>if this module's parent module definition exists; and</li>
 * <li>if this module's parent module definition does not already have a functional component
 * with the created compliant local functional component URI.</li>
 * </ul>
 * @param displayId the display ID of the mapsTo to be created
 * @param refinement the relationship between the local and remote functional components
 * @param localId the display ID of the local functional component
 * @param remoteId the display ID of the remote functional component
 * @return the created mapsTo
 * @throws SBOLValidationException if any of the following conditions is satisfied:
 * <ul>
 * <li>if either of the following SBOL validation rules was violated: 10204, 10206;</li>
 * <li>an SBOL validation rule violation occurred in {@link ModuleDefinition#createFunctionalComponent(String, AccessType, String, String, DirectionType)}; or</li>
 * <li>an SBOL validation rule violation occurred in {@link #createMapsTo(String, RefinementType, URI, URI)}.</li>
 * </ul>
 */
public MapsTo createMapsTo(String displayId, RefinementType refinement, String localId, String remoteId) throws SBOLValidationException {
    URI localURI = URIcompliance.createCompliantURI(moduleDefinition.getPersistentIdentity().toString(), localId, moduleDefinition.getVersion());
    if (this.getSBOLDocument() != null && this.getSBOLDocument().isCreateDefaults() && moduleDefinition != null && moduleDefinition.getFunctionalComponent(localURI) == null) {
        moduleDefinition.createFunctionalComponent(localId, AccessType.PUBLIC, localId, "", DirectionType.INOUT);
    }
    URI remoteURI = URIcompliance.createCompliantURI(getDefinition().getPersistentIdentity().toString(), remoteId, getDefinition().getVersion());
    return createMapsTo(displayId, refinement, localURI, remoteURI);
}