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

Example 1 with Location

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

the class SBOLReader method parseSequenceAnnotationV1.

/**
 * @param SBOLDoc
 * @param sequenceAnnotation
 * @param precedePairs
 * @param parentURI
 * @param sa_num
 * @param instantiatedComponents
 * @return
 * @throws SBOLValidationException if either of the following conditions is satisfied:
 * <ul>
 * <li>if an SBOL validation rule violation occurred in any of the following constructors or methods:
 * 	<ul>
 * 		<li>{@link URIcompliance#createCompliantURI(String, String, String)}, </li>
 * 		<li>{@link #parseDnaComponentV1(SBOLDocument, IdentifiableDocument)}, </li>
 * 		<li>{@link Range#Range(URI, int, int)}, </li>
 * 		<li>{@link Range#setDisplayId(String)}, </li>
 * 		<li>{@link Range#setVersion(String)}, </li>
 * 		<li>{@link GenericLocation#GenericLocation(URI)}, </li>
 * 		<li>{@link SequenceAnnotation#SequenceAnnotation(URI, Set)}, </li>
 * 		<li>{@link SequenceAnnotation#setDisplayId(String)}, </li>
 * 		<li>{@link SequenceAnnotation#setVersion(String)}, </li>
 * 		<li>{@link SequenceAnnotation#setWasDerivedFrom(URI)}, </li>
 * 		<li>{@link SequenceAnnotation#setComponent(URI)}, or </li>
 * 		<li>{@link SequenceAnnotation#setAnnotations(List)}; or</li>
 * 	</ul>
 * </li>
 * <li>the following SBOL validation rule was violated: 11002.</li>
 * </ul>
 * @throws SBOLConversionException
 */
private static SequenceAnnotation parseSequenceAnnotationV1(SBOLDocument SBOLDoc, NestedDocument<QName> sequenceAnnotation, List<SBOLPair> precedePairs, String parentURI, int sa_num, Set<String> instantiatedComponents) throws SBOLValidationException, SBOLConversionException {
    Integer start = null;
    Integer end = null;
    String strand = null;
    URI componentURI = null;
    URI identity = sequenceAnnotation.getIdentity();
    String persIdentity = sequenceAnnotation.getIdentity().toString();
    List<Annotation> annotations = new ArrayList<>();
    if (URIPrefix != null) {
        persIdentity = createCompliantURI(parentURI, "annotation" + sa_num, "").toString();
        identity = createCompliantURI(parentURI, "annotation" + sa_num, version);
    }
    if (!sequenceAnnotation.getType().equals(Sbol1Terms.SequenceAnnotations.SequenceAnnotation)) {
        throw new SBOLConversionException("QName has to be" + Sbol1Terms.SequenceAnnotations.SequenceAnnotation.toString());
    }
    for (NamedProperty<QName> namedProperty : sequenceAnnotation.getProperties()) {
        if (namedProperty.getName().equals(Sbol1Terms.SequenceAnnotations.bioStart)) {
            if (!(namedProperty.getValue() instanceof Literal) || start != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-11102", sequenceAnnotation.getIdentity());
            }
            String temp = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
            start = Integer.parseInt(temp);
        } else if (namedProperty.getName().equals(Sbol1Terms.SequenceAnnotations.bioEnd)) {
            if (!(namedProperty.getValue() instanceof Literal) || end != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-11103", sequenceAnnotation.getIdentity());
            }
            String temp2 = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
            end = Integer.parseInt(temp2);
        } else if (namedProperty.getName().equals(Sbol1Terms.SequenceAnnotations.strand)) {
            if (!(namedProperty.getValue() instanceof Literal) || strand != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-11002", sequenceAnnotation.getIdentity());
            }
            strand = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol1Terms.SequenceAnnotations.subComponent)) {
            if (componentURI != null) {
                throw new SBOLValidationException("sbol-10904", sequenceAnnotation.getIdentity());
            }
            if (namedProperty.getValue() instanceof NestedDocument) {
                componentURI = parseDnaComponentV1(SBOLDoc, (NestedDocument<QName>) namedProperty.getValue()).getIdentity();
            } else {
                if (!(namedProperty.getValue() instanceof Literal) || (!(((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(Sbol1Terms.SequenceAnnotations.precedes)) {
            URI left = sequenceAnnotation.getIdentity();
            URI right = null;
            if (namedProperty.getValue() instanceof NestedDocument) {
                // TODO: need to check if ++sa_num here okay
                right = parseSequenceAnnotationV1(SBOLDoc, (NestedDocument<QName>) namedProperty.getValue(), precedePairs, parentURI, ++sa_num, instantiatedComponents).getIdentity();
            } else {
                if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                    throw new SBOLValidationException("sbol-11404", sequenceAnnotation.getIdentity());
                }
                right = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
            }
            SBOLPair pair = new SBOLPair(left, right);
            precedePairs.add(pair);
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    String componentDisplayId = URIcompliance.extractDisplayId(componentURI);
    String displayId = "annotation" + sa_num;
    if (compliant && componentDisplayId != null && !instantiatedComponents.contains(componentDisplayId)) {
        identity = createCompliantURI(parentURI, componentDisplayId + "_annotation", version);
        persIdentity = createCompliantURI(parentURI, componentDisplayId + "_annotation", "").toString();
        displayId = componentDisplayId + "_annotation";
    }
    // Note: Do not create a seqAnnotation if Location is empty
    Location location = null;
    if (// create SequenceAnnotation & Component
    start != null && end != null) {
        URI range_identity = createCompliantURI(persIdentity, "range", version);
        location = new Range(range_identity, start, end);
        if (!persIdentity.equals("")) {
            location.setPersistentIdentity(createCompliantURI(persIdentity, "range", ""));
            location.setDisplayId("range");
            location.setVersion(version);
        }
        if (strand != null) {
            if (strand.equals("+")) {
                location.setOrientation(OrientationType.INLINE);
            } else if (strand.equals("-")) {
                location.setOrientation(OrientationType.REVERSECOMPLEMENT);
            }
        }
    } else {
        URI dummyGenericLoc_id = createCompliantURI(persIdentity, "genericLocation", version);
        location = new GenericLocation(dummyGenericLoc_id);
        if (!persIdentity.equals("")) {
            location.setPersistentIdentity(createCompliantURI(persIdentity, "genericLocation", ""));
            location.setDisplayId("genericLocation");
            location.setVersion(version);
        }
        if (strand != null) {
            if (strand.equals("+")) {
                location.setOrientation(OrientationType.INLINE);
            } else if (strand.equals("-")) {
                location.setOrientation(OrientationType.REVERSECOMPLEMENT);
            }
        }
    }
    Set<Location> locations = new HashSet<>();
    locations.add(location);
    SequenceAnnotation s = new SequenceAnnotation(identity, locations);
    if (!persIdentity.equals("")) {
        s.setPersistentIdentity(URI.create(persIdentity));
        s.setDisplayId(displayId);
        s.setVersion(version);
    }
    if (identity != sequenceAnnotation.getIdentity())
        s.addWasDerivedFrom(sequenceAnnotation.getIdentity());
    if (componentURI != null)
        s.setComponent(componentURI);
    if (!annotations.isEmpty())
        s.setAnnotations(annotations);
    return s;
}

Example 2 with Location

use of org.sbolstandard.core2.Location 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;
}

Example 3 with Location

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

the class ComponentDefinition method createSequenceAnnotation.

/**
 * Creates a child sequence annotation for this component definition with the given arguments,
 * and then adds to this component definition's list of sequence annotations.
 *
 * @param displayId the display ID of the sequence annotation to be created
 * @param location the location of the sequence annotation to be created
 * @return the created sequence annotation
 * @throws SBOLValidationException if any of the following condition is satisfied:
 * <ul>
 * <li>an SBOL validation rule violation occurred in {@link URIcompliance#createCompliantURI(String, String, String)};</li>
 * <li>an SBOL validation rule violation occurred in {@link #createSequenceAnnotation(URI, Set)};</li>
 * <li>an SBOL validation rule violation occurred in {@link SequenceAnnotation#setDisplayId(String)}; or</li>
 * <li>an SBOL validation rule violation occurred in {@link SequenceAnnotation#setVersion(String)}.</li>
 * </ul>
 */
private SequenceAnnotation createSequenceAnnotation(String displayId, Location location) throws SBOLValidationException {
    String URIprefix = this.getPersistentIdentity().toString();
    String version = this.getVersion();
    URI newSequenceAnnotationURI = createCompliantURI(URIprefix, displayId, version);
    Set<Location> locations = new HashSet<>();
    locations.add(location);
    SequenceAnnotation sa = createSequenceAnnotation(newSequenceAnnotationURI, locations);
    sa.setPersistentIdentity(createCompliantURI(URIprefix, displayId, ""));
    sa.setDisplayId(displayId);
    sa.setVersion(version);
    return sa;
}

Example 4 with Location

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

the class SBOLDocument method updateReferences.

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

Example 5 with Location

use of org.sbolstandard.core2.Location 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()));
    }
}