Examples with Activity org.orcid.jaxb.model.record_rc2.Activity used on opensource projects

Example 21 with Activity

use of org.orcid.jaxb.model.record_rc2.Activity 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);
}