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

Example 36 with ComponentDefinition

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

the class ModuleDefinitionOutput method getSequenceLength.

private static int getSequenceLength(SBOLDocument document, ComponentDefinition componentDef) throws Exception {
    if (componentDef.getSequences() != null && componentDef.getSequences().size() > 0) {
        Sequence sequence = componentDef.getSequences().iterator().next();
        return sequence.getElements().length();
    } else {
        int total = 0;
        for (SequenceAnnotation annotation : componentDef.getSequenceAnnotations()) {
            if (annotation.getComponent() != null) {
                Component component = annotation.getComponent();
                ComponentDefinition subComponentDef = component.getDefinition();
                total = total + getSequenceLength(document, subComponentDef);
            } else {
                throw new Exception("Can't get sequence length for an incomplete design");
            }
        }
        return total;
    }
}

Example 37 with ComponentDefinition

use of org.sbolstandard.core2.ComponentDefinition 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);
}

Example 38 with ComponentDefinition

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

the class SequenceConstraintOutput method main.

public static void main(String[] args) throws Exception {
    String prURI = "http://partsregistry.org/";
    SBOLDocument document = new SBOLDocument();
    document.setDefaultURIprefix(prURI);
    document.setTypesInURIs(true);
    ComponentDefinition promoter = document.createComponentDefinition("BBa_K174004", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
    promoter.addRole(SequenceOntology.PROMOTER);
    promoter.setName("pspac promoter");
    promoter.setDescription("LacI repressible promoter");
    ComponentDefinition constPromoter = document.createComponentDefinition("pspac", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
    constPromoter.addRole(SequenceOntology.PROMOTER);
    constPromoter.setName("constitutive promoter");
    constPromoter.setDescription("pspac core promoter region");
    ComponentDefinition operator = document.createComponentDefinition("LacI_operator", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
    operator.addRole(SequenceOntology.OPERATOR);
    operator.setName("LacI operator");
    operator.setDescription("LacI binding site");
    Component promoterComponent = promoter.createComponent("promoter", AccessType.PUBLIC, constPromoter.getIdentity());
    Component operatorComponent = promoter.createComponent("operator", AccessType.PUBLIC, operator.getIdentity());
    promoter.createSequenceConstraint("r1", RestrictionType.PRECEDES, promoterComponent.getIdentity(), operatorComponent.getIdentity());
    SBOLWriter.write(document, (System.out));
}

Example 39 with ComponentDefinition

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

the class AnnotationOutput method main.

public static void main(String[] args) throws Exception {
    String prURI = "http://partsregistry.org/";
    String prPrefix = "pr";
    SBOLDocument document = new SBOLDocument();
    document.setDefaultURIprefix(prURI);
    document.setTypesInURIs(true);
    document.addNamespace(URI.create(prURI), prPrefix);
    ComponentDefinition promoter = document.createComponentDefinition("BBa_J23119", "", new HashSet<URI>(Arrays.asList(URI.create("http://www.biopax.org/release/biopax-level3.owl#DnaRegion"))));
    promoter.addRole(SequenceOntology.PROMOTER);
    promoter.setName("J23119");
    promoter.setDescription("Constitutive promoter");
    promoter.createAnnotation(new QName(prURI, "group", prPrefix), "iGEM2006_Berkeley");
    promoter.createAnnotation(new QName(prURI, "experience", prPrefix), URI.create("http://parts.igem.org/cgi/partsdb/part_info.cgi?part_name=BBa_J23119"));
    Annotation sigmaFactor = new Annotation(QName(prURI, "sigmafactor", prPrefix), "//rnap/prokaryote/ecoli/sigma70");
    Annotation regulation = new Annotation(QName(prURI, "regulation", prPrefix), "//regulation/constitutive");
    promoter.createAnnotation(new QName(prURI, "information", prPrefix), new QName(prURI, "Information", prPrefix), URI.create("http://partsregistry.org/cd/BBa_J23119/information"), new ArrayList<Annotation>(Arrays.asList(sigmaFactor, regulation)));
    SBOLWriter.write(document, (System.out));
}

Example 40 with ComponentDefinition

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

the class GenericTopLevelOutput method main.

public static void main(String[] args) throws Exception {
    String myAppURI = "http://www.myapp.org/";
    String myAppPrefix = "myapp";
    String prURI = "http://www.partsregistry.org/";
    SBOLDocument document = new SBOLDocument();
    document.addNamespace(URI.create(myAppURI + "/"), myAppPrefix);
    document.setDefaultURIprefix(prURI);
    document.setTypesInURIs(true);
    GenericTopLevel topLevel = document.createGenericTopLevel("datasheet1", "", new QName("http://www.myapp.org", "Datasheet", myAppPrefix));
    topLevel.setName("Datasheet 1");
    topLevel.createAnnotation(new QName(myAppURI, "characterizationData", myAppPrefix), URI.create(myAppURI + "/measurement/1"));
    topLevel.createAnnotation(new QName(myAppURI, "transcriptionRate", myAppPrefix), "1");
    ComponentDefinition promoter = document.createComponentDefinition("BBa_J23119", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
    promoter.addRole(SequenceOntology.PROMOTER);
    promoter.setName("J23119");
    promoter.setDescription("Constitutive promoter");
    promoter.createAnnotation(new QName(myAppURI, "datasheet", myAppPrefix), topLevel.getIdentity());
    promoter.addWasDerivedFrom(URI.create("http://www.partsregistry.org/Part:BBa_J23119"));
    SBOLWriter.write(document, (System.out));
}