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

Example 31 with Component

use of org.sbolstandard.core2.Component 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 32 with Component

use of org.sbolstandard.core2.Component 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 33 with Component

use of org.sbolstandard.core2.Component 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 34 with Component

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

the class MapsToExample method main.

public static void main(String[] args) throws URISyntaxException, SBOLValidationException {
    SBOLDocument doc = new SBOLDocument();
    doc.setDefaultURIprefix("http://sbols.org/MapsToExample/");
    doc.setComplete(true);
    doc.setCreateDefaults(true);
    String version = "";
    ModuleDefinition md1 = doc.createModuleDefinition("md1", version);
    ComponentDefinition fc1_def = doc.createComponentDefinition("fc1_def", version, ComponentDefinition.DNA);
    ComponentDefinition fc2_def = doc.createComponentDefinition("fc2_def", version, ComponentDefinition.DNA);
    FunctionalComponent fc1 = md1.createFunctionalComponent("fc1", AccessType.PUBLIC, "fc1_def", version, DirectionType.NONE);
    FunctionalComponent fc2 = md1.createFunctionalComponent("fc2", AccessType.PUBLIC, "fc2_def", version, DirectionType.NONE);
    ComponentDefinition cd = doc.createComponentDefinition("cd", version, ComponentDefinition.DNA);
    fc1_def.createComponent("component", AccessType.PUBLIC, "cd");
    fc1.createMapsTo("mapsTo", RefinementType.USELOCAL, "fc2", "component");
    SBOLValidate.validateSBOL(doc, true, true, true);
    if (SBOLValidate.getNumErrors() > 0) {
        for (String error : SBOLValidate.getErrors()) {
            System.out.println(error);
        }
        return;
    }
}

Example 35 with Component

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

the class SequenceAnnotation method setComponent.

/**
 * Sets this sequence annotation's reference component (its identity URI) to the one matching
 * the given display ID.
 * <p>
 * This method first creates a compliant URI for the reference component. It starts with this sequence
 * annotation's parent component defintion's persistent identity URI, followed by the given display ID,
 * and ends with this sequence annotation's parent component defintion's version.
 *
 * @param displayId the given display ID for the reference component
 * @throws SBOLValidationException if either of the following conditions is satisfied:
 * <ul>
 * <li>either of the following SBOL validation rules was violated: 10204, 10206; or</li>
 * <li>if an SBOL validation rule violation occurred in any of the following constructors or methods:
 * 	<ul>
 * 		<li>{@link ComponentDefinition#createComponent(String, AccessType, String, String)}, or</li>
 * 		<li>{@link #setComponent(URI)}.</li>
 * 	</ul>
 * </li>
 * </ul>
 */
public void setComponent(String displayId) throws SBOLValidationException {
    URI componentURI = URIcompliance.createCompliantURI(componentDefinition.getPersistentIdentity().toString(), displayId, componentDefinition.getVersion());
    if (this.getSBOLDocument() != null && this.getSBOLDocument().isCreateDefaults() && componentDefinition != null && componentDefinition.getComponent(componentURI) == null) {
        componentDefinition.createComponent(displayId, AccessType.PUBLIC, displayId, "");
    }
    setComponent(componentURI);
}