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

Example 11 with Sequence

use of org.sbolstandard.core2.Sequence 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 12 with Sequence

use of org.sbolstandard.core2.Sequence 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 13 with Sequence

use of org.sbolstandard.core2.Sequence 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 14 with Sequence

use of org.sbolstandard.core2.Sequence 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 15 with Sequence

use of org.sbolstandard.core2.Sequence 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;
}