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

Example 1 with Cut

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

the class SequenceAnnotation method addCut.

/**
 * Creates a cut 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 cut 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 cut to be created
 * @param at the at property for the cut to be created
 * @param orientation the orientation type
 * @return the created cut
 * @throws SBOLValidationException if any of the following SBOL validation rules was violated:
 * 10201, 10202, 10204, 10206, 11202.
 */
public Cut addCut(String displayId, int at, OrientationType orientation) throws SBOLValidationException {
    URI identity = createCompliantURI(this.getPersistentIdentity().toString(), displayId, this.getVersion());
    Cut cut = new Cut(identity, at);
    cut.setPersistentIdentity(createCompliantURI(this.getPersistentIdentity().toString(), displayId, ""));
    cut.setDisplayId(displayId);
    cut.setVersion(this.getVersion());
    cut.setOrientation(orientation);
    addLocation(cut);
    return cut;
}

Example 2 with Cut

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

the class SequenceAnnotation method copy.

void copy(SequenceAnnotation sequenceAnnotation) throws SBOLValidationException {
    ((Identified) this).copy((Identified) sequenceAnnotation);
    for (Location location : sequenceAnnotation.getLocations()) {
        String displayId = URIcompliance.findDisplayId(location);
        if (location instanceof Range) {
            Range range = (Range) location;
            Range newRange;
            if (range.isSetOrientation()) {
                newRange = this.addRange(displayId, range.getStart(), range.getEnd(), range.getOrientation());
            } else {
                newRange = this.addRange(displayId, range.getStart(), range.getEnd());
            }
            newRange.copy(range);
        } else if (location instanceof Cut) {
            Cut cut = (Cut) location;
            Cut newCut;
            if (cut.isSetOrientation()) {
                newCut = this.addCut(displayId, cut.getAt(), cut.getOrientation());
            } else {
                newCut = this.addCut(displayId, cut.getAt());
            }
            newCut.copy(cut);
        } else if (location instanceof GenericLocation) {
            GenericLocation genericLocation = (GenericLocation) location;
            GenericLocation newGenericLocation;
            if (genericLocation.isSetOrientation()) {
                newGenericLocation = this.addGenericLocation(displayId, genericLocation.getOrientation());
            } else {
                newGenericLocation = this.addGenericLocation(displayId);
            }
            newGenericLocation.copy(genericLocation);
        }
    }
    Location location = this.getLocation("DUMMY__LOCATION");
    if (location != null) {
        this.removeLocation(location);
    }
    if (sequenceAnnotation.isSetComponent()) {
        String componentDisplayId = URIcompliance.findDisplayId(sequenceAnnotation.getComponent());
        this.setComponent(componentDisplayId);
    }
    this.roles = new HashSet<>();
    for (URI role : sequenceAnnotation.getRoles()) {
        this.addRole(URI.create(role.toString()));
    }
}

Example 3 with Cut

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

the class SequenceAnnotation method addCut.

/**
 * Creates a cut 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 cut 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 cut to be created
 * @param at the at property for the cut to be created
 * @return the created cut
 * @throws SBOLValidationException if any of the following SBOL validation rules was violated:
 * 10201, 10202, 10204, 10206, 11202.
 */
public Cut addCut(String displayId, int at) throws SBOLValidationException {
    URI identity = createCompliantURI(this.getPersistentIdentity().toString(), displayId, this.getVersion());
    Cut cut = new Cut(identity, at);
    cut.setPersistentIdentity(createCompliantURI(this.getPersistentIdentity().toString(), displayId, ""));
    cut.setDisplayId(displayId);
    cut.setVersion(this.getVersion());
    addLocation(cut);
    return cut;
}

Example 4 with Cut

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

the class SBOLReader method parseCut.

/**
 * @param typeCut
 * @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,
 * 11002, 11202; or
 *</li>
 * <li>an SBOL validation rule violation occurred in the following constructor or methods:
 * 	<ul>
 * 		<li>{@link Cut#Cut(URI, int)},</li>
 * 		<li>{@link Cut#setDisplayId(String)},</li>
 * 		<li>{@link Cut#setVersion(String)},</li>
 * 		<li>{@link Cut#setWasDerivedFrom(URI)}, or</li>
 * 		<li>{@link Identified#setAnnotations(List)}.</li>
 * 	</ul>
 * </li>
 * </ul>
 */
private static Cut parseCut(NestedDocument<QName> typeCut) throws SBOLValidationException {
    // URIcompliance.extractDisplayId(typeCut.getIdentity());
    String displayId = null;
    String name = null;
    String description = null;
    // URI.create(URIcompliance.extractPersistentId(typeCut.getIdentity()));
    URI persistentIdentity = null;
    Integer at = 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 : typeCut.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", typeCut.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", typeCut.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", typeCut.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", typeCut.getIdentity());
            }
            description = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Cut.at)) {
            if (!(namedProperty.getValue() instanceof Literal) || at != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-11202", typeCut.getIdentity());
            }
            String temp = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
            // at 			= Integer.parseInt(temp);
            try {
                at = Integer.parseInt(temp);
            } catch (NumberFormatException e) {
                throw new SBOLValidationException("sbol-11202", typeCut.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.Cut.orientation)) {
            if (!(namedProperty.getValue() instanceof Literal) || orientation != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-11002", typeCut.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", typeCut.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", typeCut.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", typeCut.getIdentity());
            }
            wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    if (at == null) {
        throw new SBOLValidationException("Cut requires at property.");
    }
    Cut c = new Cut(typeCut.getIdentity(), at);
    if (persistentIdentity != null)
        c.setPersistentIdentity(persistentIdentity);
    if (displayId != null)
        c.setDisplayId(displayId);
    if (name != null)
        c.setName(name);
    if (description != null)
        c.setDescription(description);
    if (orientation != null)
        try {
            c.setOrientation(OrientationType.convertToOrientationType(orientation));
        } catch (SBOLValidationException e) {
            throw new SBOLValidationException("sbol-11002", c);
        }
    if (version != null)
        c.setVersion(version);
    c.setWasDerivedFroms(wasDerivedFroms);
    c.setWasGeneratedBys(wasGeneratedBys);
    if (!annotations.isEmpty())
        c.setAnnotations(annotations);
    return c;
}

Example 5 with Cut

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

the class Provenance_SpecifyBuildOperations method specifyCutOperation.

/**
 * specifies to perform a cut operation in order to linearize a vector using a restriction enzyme
 *
 * @throws Exception
 */
public static void specifyCutOperation() throws Exception {
    // instantiate a document
    SBOLDocument document = new SBOLDocument();
    document.setDefaultURIprefix(BUILD_PREFIX);
    ComponentDefinition vector = document.createComponentDefinition("vector", VECTOR_PLASMID);
    vector.setName("vector");
    ComponentDefinition enzyme = document.createComponentDefinition("restriction_enzyme", RESTRICTION_ENZYME);
    enzyme.setName("restriction_enzyme");
    // Create the generic top level entity for the cut operation
    Activity activity = document.createActivity("cut_" + vector.getName() + "_with_" + enzyme.getName());
    activity.setName("cut(" + vector.getName() + ", " + enzyme.getName() + ")");
    // Create the qualifiedUsage annotation to describe the inputs of the cut operation
    activity.createUsage("vector", vector.getIdentity()).addRole(VECTOR_PLASMID);
    activity.createUsage("enzyme", enzyme.getIdentity()).addRole(RESTRICTION_ENZYME);
    // the result of the cut operation
    ComponentDefinition linearized_vector = document.createComponentDefinition("linearized_vector", LINEAR_DOUBLE_STRANDED_DNA);
    linearized_vector.setName("linearized_vector");
    linearized_vector.addWasGeneratedBy(activity.getIdentity());
    // serialize the document to a file
    SBOLWriter.write(document, System.out);
}