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

Example 11 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(URI originalIdentity, URI newIdentity) throws SBOLValidationException {
    for (TopLevel topLevel : getTopLevels()) {
        for (URI wasDerivedFrom : topLevel.getWasDerivedFroms()) {
            if (wasDerivedFrom.equals(originalIdentity)) {
                topLevel.removeWasDerivedFrom(originalIdentity);
                topLevel.addWasDerivedFrom(newIdentity);
            }
        }
        for (URI wasGeneratedBy : topLevel.getWasGeneratedBys()) {
            if (wasGeneratedBy.equals(originalIdentity)) {
                topLevel.removeWasGeneratedBy(originalIdentity);
                topLevel.addWasGeneratedBy(newIdentity);
            }
        }
        for (URI attachmentURI : topLevel.getAttachmentURIs()) {
            if (attachmentURI.equals(originalIdentity)) {
                topLevel.removeAttachment(originalIdentity);
                topLevel.addAttachment(newIdentity);
            }
        }
    }
    for (Collection collection : getCollections()) {
        for (URI memberURI : collection.getMemberURIs()) {
            if (memberURI.equals(originalIdentity)) {
                collection.removeMember(originalIdentity);
                collection.addMember(newIdentity);
            }
        }
        updateReferences(collection, originalIdentity, newIdentity);
    }
    for (ComponentDefinition componentDefinition : getComponentDefinitions()) {
        updateReferences(componentDefinition, originalIdentity, newIdentity);
        for (Component component : componentDefinition.getComponents()) {
            if (component.getDefinitionURI().equals(originalIdentity)) {
                component.setDefinition(newIdentity);
                for (MapsTo mapsTo : component.getMapsTos()) {
                    ComponentDefinition cd = getComponentDefinition(newIdentity);
                    if (cd != null) {
                        String displayId = URIcompliance.extractDisplayId(mapsTo.getRemoteURI());
                        URI newURI = URIcompliance.createCompliantURI(cd.getPersistentIdentity().toString(), displayId, cd.getVersion());
                        mapsTo.setRemote(newURI);
                    }
                }
            }
            updateReferences(component, originalIdentity, newIdentity);
            for (MapsTo mapsTo : component.getMapsTos()) {
                updateReferences(mapsTo, originalIdentity, newIdentity);
            }
        }
        for (SequenceAnnotation sa : componentDefinition.getSequenceAnnotations()) {
            for (Location loc : sa.getLocations()) {
                updateReferences(loc, originalIdentity, newIdentity);
            }
            updateReferences(sa, originalIdentity, newIdentity);
        }
        for (SequenceConstraint sc : componentDefinition.getSequenceConstraints()) {
            updateReferences(sc, originalIdentity, newIdentity);
        }
        for (URI sequenceURI : componentDefinition.getSequenceURIs()) {
            if (sequenceURI.equals(originalIdentity)) {
                componentDefinition.removeSequence(originalIdentity);
                componentDefinition.addSequence(newIdentity);
            }
        }
    }
    for (ModuleDefinition moduleDefinition : getModuleDefinitions()) {
        updateReferences(moduleDefinition, originalIdentity, newIdentity);
        for (FunctionalComponent functionalComponent : moduleDefinition.getFunctionalComponents()) {
            if (functionalComponent.getDefinitionURI().equals(originalIdentity)) {
                functionalComponent.setDefinition(newIdentity);
                for (MapsTo mapsTo : functionalComponent.getMapsTos()) {
                    ComponentDefinition cd = getComponentDefinition(newIdentity);
                    if (cd != null) {
                        String displayId = URIcompliance.extractDisplayId(mapsTo.getRemoteURI());
                        URI newURI = URIcompliance.createCompliantURI(cd.getPersistentIdentity().toString(), displayId, cd.getVersion());
                        mapsTo.setRemote(newURI);
                    }
                }
            }
            updateReferences(functionalComponent, originalIdentity, newIdentity);
            for (MapsTo mapsTo : functionalComponent.getMapsTos()) {
                updateReferences(mapsTo, originalIdentity, newIdentity);
            }
        }
        for (Module module : moduleDefinition.getModules()) {
            if (module.getDefinitionURI().equals(originalIdentity)) {
                module.setDefinition(newIdentity);
                for (MapsTo mapsTo : module.getMapsTos()) {
                    ModuleDefinition md = getModuleDefinition(newIdentity);
                    if (md != null) {
                        String displayId = URIcompliance.extractDisplayId(mapsTo.getRemoteURI());
                        URI newURI = URIcompliance.createCompliantURI(md.getPersistentIdentity().toString(), displayId, md.getVersion());
                        mapsTo.setRemote(newURI);
                    }
                }
            }
            updateReferences(module, originalIdentity, newIdentity);
            for (MapsTo mapsTo : module.getMapsTos()) {
                updateReferences(mapsTo, originalIdentity, newIdentity);
            }
        }
        for (Interaction interaction : moduleDefinition.getInteractions()) {
            updateReferences(interaction, originalIdentity, newIdentity);
            for (Participation participation : interaction.getParticipations()) {
                updateReferences(participation, originalIdentity, newIdentity);
            }
        }
        for (URI modelURI : moduleDefinition.getModelURIs()) {
            if (modelURI.equals(originalIdentity)) {
                moduleDefinition.removeModel(originalIdentity);
                moduleDefinition.addModel(newIdentity);
            }
        }
    }
    for (Model model : getModels()) {
        updateReferences(model, originalIdentity, newIdentity);
    }
    for (Attachment attachment : getAttachments()) {
        updateReferences(attachment, originalIdentity, newIdentity);
    }
    for (Implementation implementation : getImplementations()) {
        if (implementation.isSetBuilt() && implementation.getBuiltURI().equals(originalIdentity)) {
            implementation.setBuilt(newIdentity);
        }
        updateReferences(implementation, originalIdentity, newIdentity);
    }
    for (Sequence sequence : getSequences()) {
        updateReferences(sequence, originalIdentity, newIdentity);
    }
    for (GenericTopLevel genericTopLevel : getGenericTopLevels()) {
        updateReferences(genericTopLevel, originalIdentity, newIdentity);
    }
    for (CombinatorialDerivation combinatorialDerivation : getCombinatorialDerivations()) {
        updateReferences(combinatorialDerivation, originalIdentity, newIdentity);
        if (combinatorialDerivation.getTemplateURI().equals(originalIdentity)) {
            combinatorialDerivation.setTemplate(newIdentity);
            ComponentDefinition cd = getComponentDefinition(newIdentity);
            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, originalIdentity, newIdentity);
        }
    }
    for (Activity activity : getActivities()) {
        updateReferences(activity, originalIdentity, newIdentity);
        for (Association association : activity.getAssociations()) {
            if (association.getAgentURI().equals(originalIdentity)) {
                association.setAgent(newIdentity);
            }
            if (association.isSetPlan() && association.getPlanURI().equals(originalIdentity)) {
                association.setPlan(newIdentity);
            }
            updateReferences(association, originalIdentity, newIdentity);
        }
        for (Usage usage : activity.getUsages()) {
            if (usage.getEntityURI().equals(originalIdentity)) {
                usage.setEntity(newIdentity);
            }
            updateReferences(usage, originalIdentity, newIdentity);
        }
    }
    for (Agent agent : getAgents()) {
        updateReferences(agent, originalIdentity, newIdentity);
    }
    for (Plan plan : getPlans()) {
        updateReferences(plan, originalIdentity, newIdentity);
    }
}

Example 12 with Location

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

the class ModuleDefinitionOutput method addSubComponents.

private static void addSubComponents(SBOLDocument document, ComponentDefinition componentDef, List<ComponentDefinition> subComponents) throws Exception {
    int i = 1;
    int start = 0;
    int end = 0;
    for (ComponentDefinition subComponent : subComponents) {
        Component component = componentDef.createComponent(subComponent.getDisplayId(), AccessType.PUBLIC, subComponent.getIdentity());
        start = end + 1;
        end = start + getSequenceLength(document, subComponent);
        SequenceAnnotation annotation = componentDef.createSequenceAnnotation("anno" + i, "location" + i, start, end, OrientationType.INLINE);
        annotation.setComponent(component.getIdentity());
        i++;
    }
}

Example 13 with Location

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

the class SequenceAnnotationTest method test_locationMethods.

@Test
public void test_locationMethods() throws SBOLValidationException {
    Cut promoter_cut = promoter_SA.addCut("promoter_cut", 1);
    assertTrue(gRNA_b_gene.getSequenceAnnotation("promoter_SA").getLocation("promoter_cut").equals(promoter_cut));
    promoter_cut.unsetOrientation();
    assertNull(promoter_cut.getOrientation());
    Location test = promoter_cut;
    assertNotNull(test.toString());
    Cut terminator_cut = terminator_SA.addCut("terminator_cut", 100);
    assertTrue(gRNA_b_gene.getSequenceAnnotation("terminator_SA").getLocation("terminator_cut").equals(terminator_cut));
    Cut gene_cut = gene_SA.addCut("gene_cut", 50, OrientationType.INLINE);
    assertTrue(gRNA_b_gene.getSequenceAnnotation("gene_SA").getLocation("gene_cut").equals(gene_cut));
    gene_SA.removeLocation(gene_cut);
    assertNull(gene_SA.getLocation("gene_cut"));
    Range gene_range = gene_SA.addRange("gene_range", 50, 99);
    assertTrue(gRNA_b_gene.getSequenceAnnotation("gene_SA").getLocation("gene_range").equals(gene_range));
    gene_range.unsetOrientation();
    assertNull(gene_range.getOrientation());
    promoter_SA.removeLocation(promoter_cut);
    assertNull(promoter_SA.getLocation(promoter_cut.getIdentity()));
    GenericLocation promoter_glocation = promoter_SA.addGenericLocation("promoter_glocation");
    assertTrue(gRNA_b_gene.getSequenceAnnotation("promoter_SA").getLocation("promoter_glocation").equals(promoter_glocation));
    terminator_SA.removeLocation(terminator_cut);
    assertNull(terminator_SA.getLocation("terminator_cut"));
    GenericLocation terminator_glocation = terminator_SA.addGenericLocation("terminator_glocation", OrientationType.INLINE);
    assertTrue(gRNA_b_gene.getSequenceAnnotation("terminator_SA").getLocation("terminator_glocation").equals(terminator_glocation));
}

Example 14 with Location

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

the class SequenceAnnotationTest method test_LocToString.

/*
	 * 
	 * move to Location Test class
	 */
@Test
public void test_LocToString() throws SBOLValidationException {
    Location test = promoter_SA.addGenericLocation("promoter_cut");
    assertTrue(test.toString().length() != 0);
    assertNotNull(test.toString());
    assertTrue(test.toString().contains("identity="));
    assertTrue(test.toString().contains("displayId="));
    assertTrue(!test.toString().contains("description="));
    assertTrue(!test.toString().contains("orientation="));
    assertTrue(!test.toString().contains("name="));
}

Example 15 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
 * @param orientation the orientation type
 * @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, OrientationType orientation) 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());
    genericLocation.setOrientation(orientation);
    addLocation(genericLocation);
    return genericLocation;
}