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

Example 6 with Location

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

the class SequenceAnnotation method addGenericLocation.

/**
 * Creates a generic location with the given arguments and then adds it to this sequence annotation's
 * list of locations.
 * <p>
 * This method first creates a compliant URI for the generic location to be created.
 * It starts with this sequence annotation's persistent identity URI,
 * followed by the given display ID, and ends an empty string for version.
 *
 * @param displayId the display ID for the generic location to be created
 * @return the created generic location instance
 * @throws SBOLValidationException if any of the following SBOL validation rules was violated:
 * 10201, 10202, 10204, 10206.
 */
public GenericLocation addGenericLocation(String displayId) throws SBOLValidationException {
    URI identity = createCompliantURI(this.getPersistentIdentity().toString(), displayId, this.getVersion());
    GenericLocation genericLocation = new GenericLocation(identity);
    genericLocation.setPersistentIdentity(createCompliantURI(this.getPersistentIdentity().toString(), displayId, ""));
    genericLocation.setDisplayId(displayId);
    genericLocation.setVersion(this.getVersion());
    addLocation(genericLocation);
    return genericLocation;
}

Example 7 with Location

use of org.sbolstandard.core2.Location in project java-client by appium.

the class IOSDriverTest method geolocationTest.

@Test
public void geolocationTest() {
    Location location = new Location(45, 45, 100);
    driver.setLocation(location);
}

Example 8 with Location

use of org.sbolstandard.core2.Location in project java-client by appium.

the class AndroidDriverTest method geolocationTest.

@Test
public void geolocationTest() {
    Location location = new Location(45, 45, 100);
    driver.setLocation(location);
}

Example 9 with Location

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

the class SBOLReader method parseSequenceAnnotation.

/**
 * @param sequenceAnnotation
 * @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,
 * 10512,
 * 10904; or
 *</li>
 * <li>an SBOL validation rule violation occurred in the following constructor or methods:
 * 	<ul>
 * 		<li>{@link #parseLocation(NestedDocument)},</li>
 * 		<li>{@link SequenceAnnotation#SequenceAnnotation(URI, Set)},</li>
 * 		<li>{@link SequenceAnnotation#setDisplayId(String)},</li>
 * 		<li>{@link SequenceAnnotation#setVersion(String)},</li>
 * 		<li>{@link SequenceAnnotation#setComponent(URI)},</li>
 * 		<li>{@link SequenceAnnotation#setWasDerivedFrom(URI)}, or</li>
 * 		<li>{@link Identified#setAnnotations(List)}.</li>
 * 	</ul>
 * </li>
 * </ul>
 */
private static SequenceAnnotation parseSequenceAnnotation(NestedDocument<QName> sequenceAnnotation, Map<URI, NestedDocument<QName>> nested) throws SBOLValidationException {
    // URIcompliance.extractDisplayId(sequenceAnnotation.getIdentity());
    String displayId = null;
    String name = null;
    String description = null;
    // URI.create(URIcompliance.extractPersistentId(sequenceAnnotation.getIdentity()));
    URI persistentIdentity = null;
    Location location = null;
    URI componentURI = null;
    String version = null;
    Set<URI> wasDerivedFroms = new HashSet<>();
    Set<URI> wasGeneratedBys = new HashSet<>();
    Set<URI> roles = new HashSet<>();
    Set<Location> locations = new HashSet<>();
    List<Annotation> annotations = new ArrayList<>();
    for (NamedProperty<QName> namedProperty : sequenceAnnotation.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", sequenceAnnotation.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", sequenceAnnotation.getIdentity());
            }
            displayId = ((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", sequenceAnnotation.getIdentity());
            }
            version = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.SequenceAnnotation.roles)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10906", sequenceAnnotation.getIdentity());
            }
            roles.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.Location.Location)) {
            if (namedProperty.getValue() instanceof NestedDocument) {
                NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
                if (nestedDocument.getType() == null || !(nestedDocument.getType().equals(Sbol2Terms.Range.Range) || nestedDocument.getType().equals(Sbol2Terms.Cut.Cut) || nestedDocument.getType().equals(Sbol2Terms.GenericLocation.GenericLocation))) {
                    throw new SBOLValidationException("sbol-10902", sequenceAnnotation.getIdentity());
                }
                location = parseLocation((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.Range.Range) || nestedDocument.getType().equals(Sbol2Terms.Cut.Cut) || nestedDocument.getType().equals(Sbol2Terms.GenericLocation.GenericLocation))) {
                    throw new SBOLValidationException("sbol-10902", sequenceAnnotation.getIdentity());
                }
                location = parseLocation(nested.get(uri));
            }
            locations.add(location);
        } else if (namedProperty.getName().equals(Sbol2Terms.SequenceAnnotation.hasComponent)) {
            if (!(namedProperty.getValue() instanceof Literal) || componentURI != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10904", sequenceAnnotation.getIdentity());
            }
            componentURI = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } 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", sequenceAnnotation.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", sequenceAnnotation.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", sequenceAnnotation.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", sequenceAnnotation.getIdentity());
            }
            wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    SequenceAnnotation s = new SequenceAnnotation(sequenceAnnotation.getIdentity(), locations);
    if (persistentIdentity != null)
        s.setPersistentIdentity(persistentIdentity);
    if (version != null)
        s.setVersion(version);
    if (displayId != null)
        s.setDisplayId(displayId);
    if (componentURI != null)
        s.setComponent(componentURI);
    if (name != null)
        s.setName(name);
    if (description != null)
        s.setDescription(description);
    s.setWasDerivedFroms(wasDerivedFroms);
    s.setWasGeneratedBys(wasGeneratedBys);
    if (!annotations.isEmpty())
        s.setAnnotations(annotations);
    if (!roles.isEmpty())
        s.setRoles(roles);
    // }
    return s;
}

Example 10 with Location

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

the class SBOLReader method parseRange.

/**
 * @param typeRange
 * @return
 * @throws SBOLValidationException if either of the following conditions is satisfied:
 * <ul>
 * <li>any of the following SBOL validation rules was violated:
 * 10201, 10203, 10204, 10206, 10208, 10212, 10213, 11002, 11102, 11103; or
 *</li>
 * <li>an SBOL validation rule violation occurred in the following constructor or methods:
 * 	<ul>
 * 		<li>{@link Range#Range(URI, int, int)},</li>
 * 		<li>{@link Range#setDisplayId(String)},</li>
 * 		<li>{@link Range#setVersion(String)},</li>
 * 		<li>{@link Range#setWasDerivedFrom(URI)}, or</li>
 * 		<li>{@link Identified#setAnnotations(List)}.</li>
 * 	</ul>
 * </li>
 * </ul>
 */
private static Location parseRange(NestedDocument<QName> typeRange) throws SBOLValidationException {
    // URIcompliance.extractDisplayId(typeRange.getIdentity());
    String displayId = null;
    String name = null;
    String description = null;
    // URI.create(URIcompliance.extractPersistentId(typeRange.getIdentity()));
    URI persistentIdentity = null;
    Integer start = null;
    Integer end = null;
    URI orientation = null;
    String version = null;
    Set<URI> wasDerivedFroms = new HashSet<>();
    Set<URI> wasGeneratedBys = new HashSet<>();
    List<Annotation> annotations = new ArrayList<>();
    for (NamedProperty<QName> namedProperty : typeRange.getProperties()) {
        String temp;
        if (namedProperty.getName().equals(Sbol2Terms.Range.start)) {
            if (!(namedProperty.getValue() instanceof Literal) || start != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-11102", typeRange.getIdentity());
            }
            temp = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
            // start = Integer.parseInt(temp);
            try {
                start = Integer.parseInt(temp);
            } catch (NumberFormatException e) {
                throw new SBOLValidationException("sbol-11102", typeRange.getIdentity());
            }
        } 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", typeRange.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", typeRange.getIdentity());
            }
            displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } 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", typeRange.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", typeRange.getIdentity());
            }
            description = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Range.end)) {
            if (!(namedProperty.getValue() instanceof Literal) || end != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-11103", typeRange.getIdentity());
            }
            temp = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
            // end  = Integer.parseInt(temp);
            try {
                end = Integer.parseInt(temp);
            } catch (NumberFormatException e) {
                throw new SBOLValidationException("sbol-11103", typeRange.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.Range.orientation)) {
            if (!(namedProperty.getValue() instanceof Literal) || orientation != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-11002", typeRange.getIdentity());
            }
            orientation = 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", typeRange.getIdentity());
            }
            version = ((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", typeRange.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", typeRange.getIdentity());
            }
            wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    Location r = new Range(typeRange.getIdentity(), start, end);
    if (displayId != null)
        r.setDisplayId(displayId);
    if (name != null)
        r.setName(name);
    if (description != null)
        r.setDescription(description);
    if (persistentIdentity != null)
        r.setPersistentIdentity(persistentIdentity);
    if (orientation != null)
        try {
            r.setOrientation(OrientationType.convertToOrientationType(orientation));
        } catch (SBOLValidationException e) {
            throw new SBOLValidationException("sbol-11002", r);
        }
    if (version != null)
        r.setVersion(version);
    r.setWasDerivedFroms(wasDerivedFroms);
    r.setWasGeneratedBys(wasGeneratedBys);
    if (!annotations.isEmpty())
        r.setAnnotations(annotations);
    return r;
}