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

Example 11 with Component

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

the class SBOLReader method parseComponent.

/**
 * @param component
 * @param nested
 * @return
 * @throws SBOLValidationException if either of the following conditions is satisfied:
 * <ul>
 * <li>any of the following SBOL validation rules was violated:
 * 10203, 10204, 10206, 10208, 10212, 10213, 10519, 10602, 10607; or
 *</li>
 * <li>an SBOL validation rule violation occurred in the following constructor or methods:
 * 	<ul>
 * 		<li>{@link #parseMapsTo(NestedDocument, boolean)},</li>
 * 		<li>{@link Component#Component(URI, AccessType, URI)},</li>
 * 		<li>{@link Component#setVersion(String)},</li>
 * 		<li>{@link Component#setDisplayId(String)},</li>
 * 		<li>{@link Component#setAccess(AccessType)},</li>
 * 		<li>{@link Component#setMapsTos(Set)},</li>
 * 		<li>{@link Component#setDefinition(URI)},</li>
 * 		<li>{@link Component#setWasDerivedFrom(URI)}, or</li>
 * 		<li>{@link Identified#setAnnotations(List)}.</li>
 * 	</ul>
 * </li>
 * </ul>
 */
@SuppressWarnings("unchecked")
private static Component parseComponent(SBOLDocument SBOLDoc, NestedDocument<QName> component, Map<URI, NestedDocument<QName>> nested) throws SBOLValidationException {
    // URIcompliance.extractDisplayId(component.getIdentity());
    String displayId = null;
    String name = null;
    String description = null;
    // URI.create(URIcompliance.extractPersistentId(component.getIdentity()));
    URI persistentIdentity = null;
    String version = null;
    URI subComponentURI = null;
    AccessType access = null;
    Set<URI> wasDerivedFroms = new HashSet<>();
    Set<URI> wasGeneratedBys = new HashSet<>();
    Set<URI> roles = new HashSet<>();
    URI roleIntegration = null;
    List<Annotation> annotations = new ArrayList<>();
    Set<MapsTo> mapsTo = new HashSet<>();
    for (NamedProperty<QName> namedProperty : component.getProperties()) {
        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", component.getIdentity());
            }
            persistentIdentity = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else 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", component.getIdentity());
            }
            version = ((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", component.getIdentity());
            }
            displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Component.roles)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10702", component.getIdentity());
            }
            roles.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.Component.roleIntegration)) {
            if (!(namedProperty.getValue() instanceof Literal) || roleIntegration != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10708", component.getIdentity());
            }
            roleIntegration = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.ComponentInstance.access)) {
            if (!(namedProperty.getValue() instanceof Literal) || access != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10607", component.getIdentity());
            }
            String accessTypeStr = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
            if (accessTypeStr.startsWith("http://www.sbolstandard.org/")) {
                System.err.println("Warning: namespace for access types should be http://sbols.org/v2#");
                accessTypeStr = accessTypeStr.replace("http://www.sbolstandard.org/", "http://sbols.org/v2#");
            }
            try {
                access = AccessType.convertToAccessType(URI.create(accessTypeStr));
            } catch (SBOLValidationException e) {
                throw new SBOLValidationException("sbol-10607", component.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.Module.hasMapsTo)) {
            if (namedProperty.getValue() instanceof NestedDocument) {
                NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
                if (nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.MapsTo.MapsTo)) {
                    throw new SBOLValidationException("sbol-10606", component.getIdentity());
                }
                mapsTo.add(parseMapsTo(((NestedDocument<QName>) namedProperty.getValue()), false));
            } 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.MapsTo.MapsTo)) {
                    throw new SBOLValidationException("sbol-10606", component.getIdentity());
                }
                mapsTo.add(parseMapsTo(nested.get(uri), false));
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.ComponentInstance.hasComponentDefinition)) {
            if (subComponentURI != null) {
                throw new SBOLValidationException("sbol-10602", component.getIdentity());
            }
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-10602", component.getIdentity());
                }
                subComponentURI = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
            } else if (namedProperty.getValue() instanceof IdentifiableDocument) {
                if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.ComponentDefinition.ComponentDefinition)) {
                    ComponentDefinition componentDefinition = parseComponentDefinition(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue(), nested);
                    subComponentURI = componentDefinition.getIdentity();
                } else {
                    throw new SBOLValidationException("sbol-10602", component.getIdentity());
                }
            } else {
                throw new SBOLValidationException("sbol-10602", component.getIdentity());
            }
        } 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", component.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", component.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", component.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", component.getIdentity());
            }
            wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    Component c = new Component(component.getIdentity(), access, subComponentURI);
    if (persistentIdentity != null)
        c.setPersistentIdentity(persistentIdentity);
    if (version != null)
        c.setVersion(version);
    if (displayId != null)
        c.setDisplayId(displayId);
    if (access != null)
        c.setAccess(access);
    if (roleIntegration != null)
        try {
            c.setRoleIntegration(RoleIntegrationType.convertToRoleIntegrationType(roleIntegration));
        } catch (SBOLValidationException e) {
            throw new SBOLValidationException("sbol-10708", c);
        }
    if (!roles.isEmpty())
        c.setRoles(roles);
    if (!mapsTo.isEmpty())
        c.setMapsTos(mapsTo);
    if (subComponentURI != null)
        c.setDefinition(subComponentURI);
    if (name != null)
        c.setName(name);
    if (description != null)
        c.setDescription(description);
    c.setWasDerivedFroms(wasDerivedFroms);
    c.setWasGeneratedBys(wasGeneratedBys);
    if (!annotations.isEmpty())
        c.setAnnotations(annotations);
    return c;
}

Example 12 with Component

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

the class Component method copy.

void copy(Component component) throws SBOLValidationException {
    ((ComponentInstance) this).copy((ComponentInstance) component);
    if (!component.getMapsTos().isEmpty()) {
        for (MapsTo mapsTo : component.getMapsTos()) {
            String displayId = URIcompliance.findDisplayId(mapsTo);
            String localDisplayId = URIcompliance.findDisplayId(mapsTo.getLocal());
            MapsTo newMapsTo = this.createMapsTo(displayId, mapsTo.getRefinement(), localDisplayId, mapsTo.getRemoteURI());
            newMapsTo.copy(mapsTo);
        }
    }
    for (URI role : component.getRoles()) {
        this.addRole(URI.create(role.toString()));
    }
}

Example 13 with Component

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

the class Component method createMapsTo.

/**
 * Creates a child mapsTo for this component 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 component's persistent identity URI, followed by
 * the given local component's display ID, followed by this component'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 components' URIs.
 * <p>
 * This method calls {@link ComponentDefinition#createComponent(String, AccessType, String, String)} to automatically
 * create a local component with the given display ID of referenced local component definition,
 * {@link AccessType#PUBLIC}, and an empty version string, if all of the following conditions are satisfied:
 * <ul>
 * <li>the associated SBOLDocument instance for this component is not {@code null};</li>
 * <li>if default 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 component's parent ComponentDefinition instance exists; and</li>
 * <li>if this component's parent ComponentDefinition instance does not already have a component
 * with the created compliant local URI.</li>
 * </ul>
 * This automatically created created 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 component
 * @param remoteId the display ID of the remote 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 ComponentDefinition#createComponent(String, AccessType, String, String)}; 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(componentDefinition.getPersistentIdentity().toString(), localId, componentDefinition.getVersion());
    if (this.getSBOLDocument() != null && this.getSBOLDocument().isCreateDefaults() && componentDefinition != null && componentDefinition.getComponent(localURI) == null) {
        componentDefinition.createComponent(localId, AccessType.PUBLIC, localId, "");
    }
    URI remoteURI = URIcompliance.createCompliantURI(getDefinition().getPersistentIdentity().toString(), remoteId, getDefinition().getVersion());
    return createMapsTo(displayId, refinement, localURI, remoteURI);
}

Example 14 with Component

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

the class ComponentDefinition method copy.

void copy(ComponentDefinition componentDefinition) throws SBOLValidationException {
    ((TopLevel) this).copy((TopLevel) componentDefinition);
    for (URI role : componentDefinition.getRoles()) {
        this.addRole(URI.create(role.toString()));
    }
    for (Component component : componentDefinition.getComponents()) {
        String displayId = URIcompliance.findDisplayId(component);
        Component newComponent = this.createComponent(displayId, component.getAccess(), component.getDefinitionURI());
        newComponent.copy(component);
    }
    for (SequenceConstraint sequenceConstraint : componentDefinition.getSequenceConstraints()) {
        String displayId = URIcompliance.findDisplayId(sequenceConstraint);
        String subjectDisplayId = URIcompliance.findDisplayId(sequenceConstraint.getSubject());
        String objectDisplayId = URIcompliance.findDisplayId(sequenceConstraint.getObject());
        SequenceConstraint newSequenceConstraint = this.createSequenceConstraint(displayId, sequenceConstraint.getRestriction(), subjectDisplayId, objectDisplayId);
        newSequenceConstraint.copy(sequenceConstraint);
    }
    for (SequenceAnnotation sequenceAnnotation : componentDefinition.getSequenceAnnotations()) {
        String displayId = URIcompliance.findDisplayId(sequenceAnnotation);
        SequenceAnnotation newSequenceAnnotation = this.createSequenceAnnotation(displayId, "DUMMY__LOCATION");
        newSequenceAnnotation.copy(sequenceAnnotation);
    }
    this.setSequences(componentDefinition.getSequenceURIs());
}

Example 15 with Component

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

the class ComponentDefinition method getImpliedNucleicAcidSequence.

/**
 *  Return the elements of a nucleic acid sequence implied by the hierarchically included components.
 *  <p>
 *  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 {@link 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.
 *
 *  @return the elements of a nucleic sequence implied by the hierarchically included components
 */
public String getImpliedNucleicAcidSequence() {
    URI type = null;
    if (this.getTypes().contains(ComponentDefinition.DNA)) {
        type = ComponentDefinition.DNA;
    } else if (this.getTypes().contains(ComponentDefinition.RNA)) {
        type = ComponentDefinition.RNA;
    } else {
        return null;
    }
    String elements = "";
    int length = 0;
    if (this.getSequenceByEncoding(Sequence.IUPAC_DNA) != null) {
        length = this.getSequenceByEncoding(Sequence.IUPAC_DNA).getElements().length();
    }
    for (SequenceAnnotation sequenceAnnotation : this.getSequenceAnnotations()) {
        for (Location location : sequenceAnnotation.getLocations()) {
            if (location instanceof Range) {
                Range range = (Range) location;
                if (range.getEnd() > length) {
                    length = range.getEnd();
                }
            }
        }
    }
    for (int i = 0; i < length; i++) {
        elements += "N";
    }
    char[] elementsArray = elements.toCharArray();
    for (SequenceAnnotation sequenceAnnotation : this.getSequenceAnnotations()) {
        String subElements = null;
        if (!sequenceAnnotation.isSetComponent())
            continue;
        if (sequenceAnnotation.getComponent().getDefinition() != null) {
            ComponentDefinition compDef = sequenceAnnotation.getComponent().getDefinition();
            if (compDef.getSequenceByEncoding(Sequence.IUPAC_DNA) != null) {
                subElements = compDef.getSequenceByEncoding(Sequence.IUPAC_DNA).getElements();
            } else {
                subElements = compDef.getImpliedNucleicAcidSequence();
            }
            for (Location location : sequenceAnnotation.getLocations()) {
                if (location instanceof Range) {
                    Range range = (Range) location;
                    if (range.isSetOrientation() && range.getOrientation().equals(OrientationType.REVERSECOMPLEMENT)) {
                        subElements = Sequence.reverseComplement(subElements, type);
                    }
                    for (int i = 0; i < subElements.length(); i++) {
                        // TODO: need to deal with when start index out of range
                        elementsArray[(range.getStart() + i) - 1] = subElements.charAt(i);
                    }
                }
            }
        }
    }
    elements = String.valueOf(elementsArray);
    return elements;
}