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

Example 11 with ModuleDefinition

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

the class ModuleDefinition method copy.

/*
	 * (non-Javadoc)
	 *
	 * @see
	 * org.sbolstandard.core2.abstract_classes.TopLevel#copy(java.lang.String,
	 * java.lang.String, java.lang.String)
	 */
/**
 * @throws SBOLValidationException if an SBOL validation rule violation occurred in
 * any one of the following methods:
 * <ul>
 * <li>{@link #deepCopy()},</li>
 * <li>{@link URIcompliance#createCompliantURI(String, String, String)},</li>
 * <li>{@link #setDisplayId(String)},</li>
 * <li>{@link #setVersion(String)},</li>
 * <li>{@link #setWasDerivedFrom(URI)},</li>
 * <li>{@link #setIdentity(URI)},</li>
 * <li>{@link FunctionalComponent#setDisplayId(String)}</li>
 * <li>{@link FunctionalComponent#updateCompliantURI(String, String, String)},</li>
 * <li>{@link #addFunctionalComponent(FunctionalComponent)},</li>
 * <li>{@link Module#setDisplayId(String)}</li>
 * <li>{@link Module#updateCompliantURI(String, String, String)},</li>
 * <li>{@link #addModule(Module)},</li>
 * <li>{@link Interaction#setDisplayId(String)},</li>
 * <li>{@link Interaction#updateCompliantURI(String, String, String)}, or</li>
 * <li>{@link #addInteraction(Interaction)}.</li>
 * </ul>
 */
@Override
ModuleDefinition copy(String URIprefix, String displayId, String version) throws SBOLValidationException {
    ModuleDefinition cloned = this.deepCopy();
    cloned.setPersistentIdentity(createCompliantURI(URIprefix, displayId, ""));
    cloned.setDisplayId(displayId);
    cloned.setVersion(version);
    URI newIdentity = createCompliantURI(URIprefix, displayId, version);
    if (!this.getIdentity().equals(newIdentity)) {
        cloned.addWasDerivedFrom(this.getIdentity());
    } else {
        cloned.setWasDerivedFroms(this.getWasDerivedFroms());
    }
    cloned.setIdentity(newIdentity);
    int count = 0;
    for (FunctionalComponent component : cloned.getFunctionalComponents()) {
        if (!component.isSetDisplayId())
            component.setDisplayId("functionalComponent" + ++count);
        component.updateCompliantURI(cloned.getPersistentIdentity().toString(), component.getDisplayId(), version);
        cloned.removeChildSafely(component, cloned.functionalComponents);
        cloned.addFunctionalComponent(component);
    }
    count = 0;
    for (Module module : cloned.getModules()) {
        if (!module.isSetDisplayId())
            module.setDisplayId("module" + ++count);
        module.updateCompliantURI(cloned.getPersistentIdentity().toString(), module.getDisplayId(), version);
        cloned.removeChildSafely(module, cloned.modules);
        cloned.addModule(module);
    }
    count = 0;
    for (Interaction interaction : cloned.getInteractions()) {
        if (!interaction.isSetDisplayId())
            interaction.setDisplayId("interaction" + ++count);
        interaction.updateCompliantURI(cloned.getPersistentIdentity().toString(), interaction.getDisplayId(), version);
        cloned.removeChildSafely(interaction, cloned.interactions);
        cloned.addInteraction(interaction);
    }
    return cloned;
}

Example 12 with ModuleDefinition

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

the class ModuleDefinition method copy.

void copy(ModuleDefinition moduleDefinition) throws SBOLValidationException {
    ((TopLevel) this).copy((TopLevel) moduleDefinition);
    for (URI role : moduleDefinition.getRoles()) {
        this.addRole(role);
    }
    for (FunctionalComponent component : moduleDefinition.getFunctionalComponents()) {
        String displayId = URIcompliance.findDisplayId(component);
        FunctionalComponent newComponent = this.createFunctionalComponent(displayId, component.getAccess(), component.getDefinitionURI(), component.getDirection());
        newComponent.copy(component);
    }
    for (Module subModule : moduleDefinition.getModules()) {
        String displayId = URIcompliance.findDisplayId(subModule);
        Module newModule = this.createModule(displayId, subModule.getDefinitionURI());
        newModule.copy(subModule);
    }
    for (Interaction interaction : moduleDefinition.getInteractions()) {
        String displayId = URIcompliance.findDisplayId(interaction);
        Interaction newInteraction = this.createInteraction(displayId, interaction.getTypes());
        newInteraction.copy(interaction);
    }
    this.setModels(moduleDefinition.getModelURIs());
}

Example 13 with ModuleDefinition

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

the class FunctionalComponent method createMapsTo.

/**
 * Creates a child MapsTo instance for this module with the given arguments, and then adds to this module's list of mapsTos.
 * <p>
 * This method creates compliant local and remote URIs first.
 * The compliant local URI is created with this module's persistent identity URI, followed by
 * the given local component's display ID, followed by this module's version.
 * The compliant remote URI is created following the same pattern.
 * It then calls {@link #createMapsTo(String, RefinementType, URI, URI)} to create
 * a MapsTo instance.
 * <p>
 * This method automatically creates a local functional component if all of the following conditions are satisfied:
 * <ul>
 * <li>the associated SBOLDocument instance for this module is not {@code null};</li>
 * <li>if default functional components should be automatically created when not present for the associated SBOLDocument instance,
 * i.e., {@link SBOLDocument#isCreateDefaults} returns {@code true};</li>
 * <li>if this module's parent module definition exists; and</li>
 * <li>if this module's parent module definition does not already have a functional component
 * with the created compliant local functional component URI.</li>
 * </ul>
 * @param displayId the display ID of the mapsTo to be created
 * @param refinement the relationship between the local and remote functional components
 * @param localId the display ID of the local functional component
 * @param remoteId the display ID of the remote functional component
 * @return the created mapsTo
 * @throws SBOLValidationException if any of the following conditions is satisfied:
 * <ul>
 * <li>if either of the following SBOL validation rules was violated: 10204, 10206;</li>
 * <li>an SBOL validation rule violation occurred in {@link ModuleDefinition#createFunctionalComponent(String, AccessType, String, String, DirectionType)}; or</li>
 * <li>an SBOL validation rule violation occurred in {@link #createMapsTo(String, RefinementType, URI, URI)}.</li>
 * </ul>
 */
public MapsTo createMapsTo(String displayId, RefinementType refinement, String localId, String remoteId) throws SBOLValidationException {
    URI localURI = URIcompliance.createCompliantURI(moduleDefinition.getPersistentIdentity().toString(), localId, moduleDefinition.getVersion());
    if (this.getSBOLDocument() != null && this.getSBOLDocument().isCreateDefaults() && moduleDefinition != null && moduleDefinition.getFunctionalComponent(localURI) == null) {
        moduleDefinition.createFunctionalComponent(localId, AccessType.PUBLIC, localId, "", DirectionType.INOUT);
    }
    URI remoteURI = URIcompliance.createCompliantURI(getDefinition().getPersistentIdentity().toString(), remoteId, getDefinition().getVersion());
    return createMapsTo(displayId, refinement, localURI, remoteURI);
}

Example 14 with ModuleDefinition

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

the class CombinatorialDesignTest method setupDocument.

@Before
public void setupDocument() throws SBOLValidationException {
    doc.setDefaultURIprefix("http://sbols.org/CRISPR_Example/");
    doc.setComplete(true);
    doc.setCreateDefaults(true);
    String version = "1.0.0";
    // Create ComponentDefinition for cas9_generic protein
    doc.createComponentDefinition("cas9_generic", version, ComponentDefinition.PROTEIN);
    // Create ComponentDefinition for gRNA_generic RNA
    doc.createComponentDefinition("gRNA_generic", version, ComponentDefinition.RNA).addRole(SequenceOntology.SGRNA);
    // Create ComponentDefinition for cas9_gRNA_complex
    doc.createComponentDefinition("cas9_gRNA_complex", version, ComponentDefinition.COMPLEX);
    // Create ComponentDefinition for target gene
    doc.createComponentDefinition("target_gene", version, ComponentDefinition.DNA).addRole(SequenceOntology.PROMOTER);
    // Create ComponentDefinition for target protein
    doc.createComponentDefinition("target", version, ComponentDefinition.PROTEIN);
    // Create ModuleDefinition for CRISPR_Repression_Template
    ModuleDefinition CRISPR_Template = doc.createModuleDefinition("CRISPR_Template", version);
    // Complex Formation Interaction for Cas9m_BFP and gRNA
    Interaction Cas9Complex_Formation = CRISPR_Template.createInteraction("cas9_complex_formation", SystemsBiologyOntology.NON_COVALENT_BINDING);
    Cas9Complex_Formation.createParticipation("cas9_generic", "cas9_generic", SystemsBiologyOntology.REACTANT);
    Cas9Complex_Formation.createParticipation("gRNA_generic", "gRNA_generic", SystemsBiologyOntology.REACTANT);
    Cas9Complex_Formation.createParticipation("cas9_gRNA_complex", "cas9_gRNA_complex", SystemsBiologyOntology.PRODUCT);
    // Production of target from target gene
    Interaction EYFP_production = CRISPR_Template.createInteraction("target_production", SystemsBiologyOntology.GENETIC_PRODUCTION);
    EYFP_production.createParticipation("target_gene", "target_gene", SystemsBiologyOntology.PROMOTER);
    EYFP_production.createParticipation("target", "target", SystemsBiologyOntology.PRODUCT);
    // Inhibition of target by cas9m_BFP_gRNA
    Interaction target_generic_gene_inhibition = CRISPR_Template.createInteraction("target_gene_inhibition", SystemsBiologyOntology.INHIBITION);
    target_generic_gene_inhibition.createParticipation("cas9_gRNA_complex", "cas9_gRNA_complex", SystemsBiologyOntology.INHIBITOR);
    target_generic_gene_inhibition.createParticipation("target_gene", "target_gene", SystemsBiologyOntology.PROMOTER);
    // Create Sequence for CRa_U6 promoter
    String CRa_U6_seq_elements = "GGTTTACCGAGCTCTTATTGGTTTTCAAACTTCATTGACTGTGCC" + "AAGGTCGGGCAGGAAGAGGGCCTATTTCCCATGATTCCTTCATAT" + "TTGCATATACGATACAAGGCTGTTAGAGAGATAATTAGAATTAAT" + "TTGACTGTAAACACAAAGATATTAGTACAAAATACGTGACGTAGA" + "AAGTAATAATTTCTTGGGTAGTTTGCAGTTTTAAAATTATGTTTT" + "AAAATGGACTATCATATGCTTACCGTAACTTGAAATATAGAACCG" + "ATCCTCCCATTGGTATATATTATAGAACCGATCCTCCCATTGGCT" + "TGTGGAAAGGACGAAACACCGTACCTCATCAGGAACATGTGTTTA" + "AGAGCTATGCTGGAAACAGCAGAAATAGCAAGTTTAAATAAGGCT" + "AGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTT" + "TTGGTGCGTTTTTATGCTTGTAGTATTGTATAATGTTTTT";
    doc.createSequence("CRa_U6_seq", version, CRa_U6_seq_elements, Sequence.IUPAC_DNA);
    // Create Sequence for gRNA_b coding sequence
    String gRNA_b_elements = "AAGGTCGGGCAGGAAGAGGGCCTATTTCCCATGATTCCTTCATAT" + "TTGCATATACGATACAAGGCTGTTAGAGAGATAATTAGAATTAAT" + "TTGACTGTAAACACAAAGATATTAGTACAAAATACGTGACGTAGA" + "AAGTAATAATTTCTTGGGTAGTTTGCAGTTTTAAAATTATGTTTT" + "AAAATGGACTATCATATGCTTACCGTAACTTGAAAGTATTTCGAT" + "TTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGTACCT" + "CATCAGGAACATGTGTTTAAGAGCTATGCTGGAAACAGCAGAAAT" + "AGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGG" + "CACCGAGTCGGTGCTTTTTTT";
    doc.createSequence("gRNA_b_seq", version, gRNA_b_elements, Sequence.IUPAC_DNA);
    // Create Sequence for mKate
    String mKate_seq_elements = "TCTAAGGGCGAAGAGCTGATTAAGGAGAACATGCACATGAAGCTG" + "TACATGGAGGGCACCGTGAACAACCACCACTTCAAGTGCACATCC" + "GAGGGCGAAGGCAAGCCCTACGAGGGCACCCAGACCATGAGAATC" + "AAGGTGGTCGAGGGCGGCCCTCTCCCCTTCGCCTTCGACATCCTG" + "GCTACCAGCTTCATGTACGGCAGCAAAACCTTCATCAACCACACC" + "CAGGGCATCCCCGACTTCTTTAAGCAGTCCTTCCCTGAGGTAAGT" + "GGTCCTACCTCATCAGGAACATGTGTTTTAGAGCTAGAAATAGCA" + "AGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACC" + "GAGTCGGTGCTACTAACTCTCGAGTCTTCTTTTTTTTTTTCACAG" + "GGCTTCACATGGGAGAGAGTCACCACATACGAAGACGGGGGCGTG" + "CTGACCGCTACCCAGGACACCAGCCTCCAGGACGGCTGCCTCATC" + "TACAACGTCAAGATCAGAGGGGTGAACTTCCCATCCAACGGCCCT" + "GTGATGCAGAAGAAAACACTCGGCTGGGAGGCCTCCACCGAGATG" + "CTGTACCCCGCTGACGGCGGCCTGGAAGGCAGAAGCGACATGGCC" + "CTGAAGCTCGTGGGCGGGGGCCACCTGATCTGCAACTTGAAGACC" + "ACATACAGATCCAAGAAACCCGCTAAGAACCTCAAGATGCCCGGC" + "GTCTACTATGTGGACAGAAGACTGGAAAGAATCAAGGAGGCCGAC" + "AAAGAGACCTACGTCGAGCAGCACGAGGTGGCTGTGGCCAGATAC" + "TGCG";
    doc.createSequence("mKate_seq", version, mKate_seq_elements, Sequence.IUPAC_DNA);
    // Create Sequence for CRP_b promoter
    String CRP_b_seq_elements = "GCTCCGAATTTCTCGACAGATCTCATGTGATTACGCCAAGCTACG" + "GGCGGAGTACTGTCCTCCGAGCGGAGTACTGTCCTCCGAGCGGAG" + "TACTGTCCTCCGAGCGGAGTACTGTCCTCCGAGCGGAGTTCTGTC" + "CTCCGAGCGGAGACTCTAGATACCTCATCAGGAACATGTTGGAAT" + "TCTAGGCGTGTACGGTGGGAGGCCTATATAAGCAGAGCTCGTTTA" + "GTGAACCGTCAGATCGCCTCGAGTACCTCATCAGGAACATGTTGG" + "ATCCAATTCGACC";
    doc.createSequence("CRP_b_seq", version, CRP_b_seq_elements, Sequence.IUPAC_DNA);
    // Create ComponentDefinition for a Constitutive Promoter
    doc.createComponentDefinition("pConst", version, ComponentDefinition.DNA).addRole(SequenceOntology.PROMOTER);
    // Create ComponentDefinition for cas9m_BFP coding sequence
    doc.createComponentDefinition("cas9m_BFP_cds", version, ComponentDefinition.DNA).addRole(SequenceOntology.CDS);
    // Create ComponentDefinition for cas9m_BFP gene
    ComponentDefinition cas9m_BFP_gene = doc.createComponentDefinition("cas9m_BFP_gene", version, ComponentDefinition.DNA);
    cas9m_BFP_gene.addRole(SequenceOntology.PROMOTER);
    cas9m_BFP_gene.createSequenceConstraint("cas9m_BFP_gene_constraint", RestrictionType.PRECEDES, "pConst", "cas9m_BFP_cds");
    // Create ComponentDefintion for cas9m_BFP protein
    doc.createComponentDefinition("cas9m_BFP", version, ComponentDefinition.PROTEIN);
    // Create ComponentDefintion for CRa_U6 promoter
    ComponentDefinition CRa_U6 = doc.createComponentDefinition("CRa_U6", version, ComponentDefinition.DNA);
    CRa_U6.addRole(SequenceOntology.PROMOTER);
    CRa_U6.addSequence("CRa_U6_seq");
    // Create ComponentDefintion for gRNA_b coding sequence
    ComponentDefinition gRNA_b_nc = doc.createComponentDefinition("gRNA_b_nc", version, ComponentDefinition.DNA);
    gRNA_b_nc.addRole(SequenceOntology.CDS);
    gRNA_b_nc.addSequence("gRNA_b_seq");
    // Create ComponentDefinition for gRNA_b terminator
    doc.createComponentDefinition("gRNA_b_terminator", version, ComponentDefinition.DNA).addRole(SequenceOntology.TERMINATOR);
    // Create ComponentDefinition for gRNA_b gene
    ComponentDefinition gRNA_b_gene = doc.createComponentDefinition("gRNA_b_gene", version, ComponentDefinition.DNA);
    gRNA_b_gene.addRole(SequenceOntology.PROMOTER);
    gRNA_b_gene.createSequenceConstraint("gRNA_b_gene_constraint1", RestrictionType.PRECEDES, "CRa_U6", "gRNA_b_nc");
    gRNA_b_gene.createSequenceConstraint("gRNA_b_gene_constraint2", RestrictionType.PRECEDES, "gRNA_b_nc", "gRNA_b_terminator");
    // Create ComponentDefinition for gRNA_b RNA
    doc.createComponentDefinition("gRNA_b", version, ComponentDefinition.RNA).addRole(SequenceOntology.SGRNA);
    SequenceOntology so = new SequenceOntology();
    URI sgrna = so.getURIbyName("sgRNA");
    // Create ComponentDefinition for cas9m_BFP gRNA_b complex
    doc.createComponentDefinition("cas9m_BFP_gRNA_b", version, ComponentDefinition.COMPLEX);
    // Create ComponentDefinition for mKate coding sequence
    ComponentDefinition mKate_cds = doc.createComponentDefinition("mKate_cds", version, ComponentDefinition.DNA);
    mKate_cds.addRole(SequenceOntology.CDS);
    mKate_cds.addSequence("mKate_seq");
    // Create ComponentDefinition for mKate gene
    ComponentDefinition mKate_gene = doc.createComponentDefinition("mKate_gene", version, ComponentDefinition.DNA);
    mKate_gene.addRole(SequenceOntology.PROMOTER);
    mKate_gene.createSequenceConstraint("mKate_gene_constraint", RestrictionType.PRECEDES, "pConst", "mKate_cds");
    // Create ComponentDefinition for mKate protein
    doc.createComponentDefinition("mKate", version, ComponentDefinition.PROTEIN);
    // Create ComponentDefinition for Gal4VP16 coding sequence
    ComponentDefinition Gal4VP16_cds = doc.createComponentDefinition("Gal4VP16_cds", version, ComponentDefinition.DNA);
    Gal4VP16_cds.addRole(SequenceOntology.CDS);
    // Create ComponentDefintion for Gal4VP16 gene
    ComponentDefinition Gal4VP16_gene = doc.createComponentDefinition("Gal4VP16_gene", version, ComponentDefinition.DNA);
    Gal4VP16_gene.addRole(SequenceOntology.PROMOTER);
    Gal4VP16_gene.createSequenceConstraint("GAL4VP16_gene_constraint", RestrictionType.PRECEDES, "pConst", "Gal4VP16_cds");
    // Create ComponentDefintion for Gal4VP16 protein
    doc.createComponentDefinition("Gal4VP16", version, ComponentDefinition.PROTEIN);
    // Create ComponentDefinition for CRP_b promoter
    ComponentDefinition CRP_b = doc.createComponentDefinition("CRP_b", version, ComponentDefinition.DNA);
    CRP_b.addRole(SequenceOntology.PROMOTER);
    CRP_b.addSequence("CRP_b_seq");
    // Create ComponentDefintiion for EYFP coding sequence
    ComponentDefinition EYFP_cds = doc.createComponentDefinition("EYFP_cds", version, ComponentDefinition.DNA);
    EYFP_cds.addRole(SequenceOntology.CDS);
    // Create ComponentDefinition for EYFP gene
    ComponentDefinition EYFP_gene = doc.createComponentDefinition("EYFP_gene", version, ComponentDefinition.DNA);
    EYFP_gene.addRole(SequenceOntology.PROMOTER);
    EYFP_gene.createSequenceConstraint("EYFP_gene_constraint", RestrictionType.PRECEDES, "CRP_b", "EYFP_cds");
    // Create ComponentDefintiion for EYFP protein
    doc.createComponentDefinition("EYFP", version, ComponentDefinition.PROTEIN);
    // Create ModuleDefintion for CRISPR Repression
    ModuleDefinition CRPb_circuit = doc.createModuleDefinition("CRPb_characterization_circuit", version);
    // Create the FunctionalComponents for the ModuleDefinition CRISPR_Repression
    CRPb_circuit.createFunctionalComponent("cas9m_BFP", AccessType.PRIVATE, "cas9m_BFP", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("cas9m_BFP_gene", AccessType.PRIVATE, "cas9m_BFP_gene", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("gRNA_b", AccessType.PRIVATE, "gRNA_b", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("gRNA_b_gene", AccessType.PRIVATE, "gRNA_b_gene", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("mKate", AccessType.PRIVATE, "mKate", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("mKate_gene", AccessType.PRIVATE, "mKate_gene", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("Gal4VP16", AccessType.PRIVATE, "Gal4VP16", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("Gal4VP16_gene", AccessType.PRIVATE, "Gal4VP16_gene", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("EYFP", AccessType.PRIVATE, "EYFP", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("EYFP_gene", AccessType.PRIVATE, "EYFP_gene", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("cas9m_BFP_gRNA_b", AccessType.PRIVATE, "cas9m_BFP_gRNA_b", version, DirectionType.NONE);
    /* Production of mKate from the mKate gene */
    Interaction mKate_production = CRPb_circuit.createInteraction("mKate_production", SystemsBiologyOntology.GENETIC_PRODUCTION);
    mKate_production.createParticipation("mKate", "mKate", SystemsBiologyOntology.PRODUCT);
    mKate_production.createParticipation("mKate_gene", "mKate_gene", SystemsBiologyOntology.PROMOTER);
    // Production of GAL4VP16 from the GAL4VP16 gene
    Interaction GAL4VP16_production = CRPb_circuit.createInteraction("Gal4VP16_production", SystemsBiologyOntology.GENETIC_PRODUCTION);
    GAL4VP16_production.createParticipation("Gal4VP16_gene", "Gal4VP16_gene", SystemsBiologyOntology.PROMOTER);
    GAL4VP16_production.createParticipation("Gal4VP16", "Gal4VP16", SystemsBiologyOntology.PRODUCT);
    // Production of cas9m_BFP from the cas9m_BFP gene
    Interaction cas9m_BFP_production = CRPb_circuit.createInteraction("cas9m_BFP_production", SystemsBiologyOntology.GENETIC_PRODUCTION);
    cas9m_BFP_production.createParticipation("cas9m_BFP_gene", "cas9m_BFP_gene", SystemsBiologyOntology.PROMOTER);
    cas9m_BFP_production.createParticipation("cas9m_BFP", "cas9m_BFP", SystemsBiologyOntology.PRODUCT);
    // Production of gRNA_b from the gRNA_b gene
    Interaction gRNA_b_production = CRPb_circuit.createInteraction("gRNA_b_production", SystemsBiologyOntology.GENETIC_PRODUCTION);
    gRNA_b_production.createParticipation("gRNA_b_gene", "gRNA_b_gene", SystemsBiologyOntology.PROMOTER);
    gRNA_b_production.createParticipation("gRNA_b", "gRNA_b", SystemsBiologyOntology.PRODUCT);
    // Activation of EYFP production by GAL4VP16
    Interaction EYFP_Activation = CRPb_circuit.createInteraction("EYFP_Activation", SystemsBiologyOntology.STIMULATION);
    EYFP_Activation.createParticipation("Gal4VP16", "Gal4VP16", SystemsBiologyOntology.STIMULATOR);
    EYFP_Activation.createParticipation("EYFP_gene", "EYFP_gene", SystemsBiologyOntology.PROMOTER);
    // Degradation of mKate
    Interaction mKate_deg = CRPb_circuit.createInteraction("mKate_deg", SystemsBiologyOntology.DEGRADATION);
    mKate_deg.createParticipation("mKate", "mKate", SystemsBiologyOntology.REACTANT);
    // Degradation of GAL4VP16
    Interaction GAL4VP16_deg = CRPb_circuit.createInteraction("Gal4VP16_deg", SystemsBiologyOntology.DEGRADATION);
    GAL4VP16_deg.createParticipation("Gal4VP16", "Gal4VP16", SystemsBiologyOntology.REACTANT);
    // Degradation of cas9m_BFP
    Interaction cas9m_BFP_deg = CRPb_circuit.createInteraction("cas9m_BFP_deg", SystemsBiologyOntology.DEGRADATION);
    cas9m_BFP_deg.createParticipation("cas9m_BFP", "cas9m_BFP", SystemsBiologyOntology.REACTANT);
    // Degradation of gRNA_b
    Interaction gRNA_b_deg = CRPb_circuit.createInteraction("gRNA_b_deg", SystemsBiologyOntology.DEGRADATION);
    gRNA_b_deg.createParticipation("gRNA_b", "gRNA_b", SystemsBiologyOntology.REACTANT);
    // Degradation of EYFP
    Interaction EYFP_deg = CRPb_circuit.createInteraction("EYFP_deg", SystemsBiologyOntology.DEGRADATION);
    EYFP_deg.createParticipation("EYFP", "EYFP", SystemsBiologyOntology.REACTANT);
    // Degradation of cas9m_BFP_gRNA_b
    Interaction cas9m_BFP_gRNA_b_deg = CRPb_circuit.createInteraction("cas9m_BFP_gRNA_b_deg", SystemsBiologyOntology.DEGRADATION);
    cas9m_BFP_gRNA_b_deg.createParticipation("cas9m_BFP_gRNA_b", "cas9m_BFP_gRNA_b", SystemsBiologyOntology.REACTANT);
    // Create Template Module
    Module Template_Module = CRPb_circuit.createModule("CRISPR_Template", "CRISPR_Template", version);
    // Add MapsTos to Template Module
    Template_Module.createMapsTo("cas9m_BFP_map", RefinementType.USELOCAL, "cas9m_BFP", "cas9_generic");
    Template_Module.createMapsTo("gRNA_b_map", RefinementType.USELOCAL, "gRNA_b", "gRNA_generic");
    Template_Module.createMapsTo("cas9m_BFP_gRNA_map", RefinementType.USELOCAL, "cas9m_BFP_gRNA_b", "cas9_gRNA_complex");
    Template_Module.createMapsTo("EYFP_map", RefinementType.USELOCAL, "EYFP", "target");
    Template_Module.createMapsTo("EYFP_gene_map", RefinementType.USELOCAL, "EYFP_gene", "target_gene");
    // Create CombinatorialDerivations
    CombinatorialDerivation Combinatorial_Derivation = doc.createCombinatorialDerivation("combDev", version, "Gal4VP16", version);
    Combinatorial_Derivation.setStrategy(StrategyType.SAMPLE);
    SBOLValidate.validateSBOL(doc, true, true, true);
    if (SBOLValidate.getNumErrors() > 0) {
        for (String error : SBOLValidate.getErrors()) {
            System.out.println(error);
        }
        fail();
    }
}

Example 15 with ModuleDefinition

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

the class ModuleDefinitionTest method setUp.

@Before
public void setUp() throws Exception {
    doc = new SBOLDocument();
    doc.setDefaultURIprefix("http://sbols.org/CRISPR_Example/");
    doc.setComplete(true);
    doc.setCreateDefaults(true);
    doc.setComplete(true);
    /*add the main ModuleDefinition to the document*/
    geneticToggleSwitch = doc.createModuleDefinition("geneticToggleSwitch");
    /*create MD's for each of the Modules*/
    TetRInverter_MD = doc.createModuleDefinition("TetRInverter_MD");
    LacIInverter_MD = doc.createModuleDefinition("LacIInverter_MD");
    TetRInverter = geneticToggleSwitch.createModule("TetRInverter", "TetRInverter_MD");
    LacIInverter = geneticToggleSwitch.createModule("LacIInverter", "LacIInverter_MD");
    /*create CDs*/
    TetR_CD = doc.createComponentDefinition("TetR_CD", ComponentDefinition.DNA);
    LacI_CD = doc.createComponentDefinition("LacI_CD", ComponentDefinition.DNA);
    doc.createComponentDefinition("TetR_Promoter_CD", ComponentDefinition.DNA);
    doc.createComponentDefinition("TetR_Terminator_CD", ComponentDefinition.DNA);
    doc.createComponentDefinition("TetR_Gene_CD", ComponentDefinition.DNA);
    doc.createComponentDefinition("LacI_Promoter_CD", ComponentDefinition.DNA);
    doc.createComponentDefinition("LacI_Terminator_CD", ComponentDefinition.DNA);
    doc.createComponentDefinition("LacI_Gene_CD", ComponentDefinition.DNA);
    doc.createComponentDefinition("target_gene", ComponentDefinition.DNA);
    TetR_CD.createComponent("gene", AccessType.PUBLIC, "target_gene");
    /*add the corresponding components to the appropriate CD*/
    TetR_CD.createComponent("TetR_promoter", AccessType.PUBLIC, "TetR_Promoter_CD", "");
    TetR_CD.createComponent("TetR_terminator", AccessType.PUBLIC, "TetR_Terminator_CD", "");
    TetR_CD.createComponent("TetR_gene", AccessType.PUBLIC, "TetR_Gene_CD", "");
    LacI_CD.createComponent("LacI_promoter", AccessType.PUBLIC, "LacI_Promoter_CD", "");
    LacI_CD.createComponent("LacI_terminator", AccessType.PUBLIC, "LacI_Terminator_CD", "");
    LacI_CD.createComponent("LacI_gene", AccessType.PUBLIC, "LacI_Gene_CD", "");
    TetR_FC = TetRInverter_MD.createFunctionalComponent("TetR_FC", AccessType.PUBLIC, "TetR_CD", DirectionType.NONE);
    LacI_FC = LacIInverter_MD.createFunctionalComponent("LacI_FC", AccessType.PUBLIC, "LacI_CD", DirectionType.NONE);
    TetRInverter_MD.createFunctionalComponent("TetR_Promoter_FC", AccessType.PUBLIC, "TetR_Promoter_CD", DirectionType.NONE);
    TetRInverter_MD.createFunctionalComponent("TetR_Terminator_FC", AccessType.PUBLIC, "TetR_Terminator_CD", DirectionType.NONE);
    TetRInverter_MD.createFunctionalComponent("TetR_Gene_FC", AccessType.PUBLIC, "TetR_Gene_CD", DirectionType.NONE);
    /*create some Interactions*/
    TetR_promotes_LacI = geneticToggleSwitch.createInteraction("TetR_promotes_LacI", new URI("http://identifiers.org/biomodels.sbo/SBO:0000169"));
    TetR_promotes_LacI.createParticipation("TetR_simulator", "TetR_CD", new URI("http://identifiers.org/biomodels.sbo/SBO:0000459"));
    TetR_promotes_LacI.createParticipation("LacI_product", "LacI_CD", new URI("http://identifiers.org/biomodels.sbo/SBO:0000011"));
}