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

Example 21 with Module

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

the class SimpleModuleDefinition method main.

public static void main(String[] args) throws Exception {
    SBOLDocument document = new SBOLDocument();
    setDefaultNameSpace(document, example.getNamespaceURI());
    document.setTypesInURIs(true);
    ModuleDefinition module = document.createModuleDefinition("GFP_expression");
    FunctionalComponent cds = module.createFunctionalComponent("Constitutive_GFP", AccessType.PUBLIC, URI.create("http://sbolstandard.org/example/GFP_generator"), DirectionType.IN);
    FunctionalComponent protein = module.createFunctionalComponent("GFP_protein", AccessType.PUBLIC, URI.create("http://sbolstandard.org/example/GFP"), DirectionType.OUT);
    Interaction interaction = module.createInteraction("express_GFP", new HashSet<URI>(Arrays.asList(URI.create("Transcription"))));
    interaction.createParticipation("CDS", cds.getIdentity(), SystemsBiologyOntology.PROMOTER);
    interaction.createParticipation("Protein", protein.getIdentity(), SystemsBiologyOntology.PRODUCT);
    SBOLWriter.write(document, (System.out));
}

Example 22 with Module

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

the class TestCircularModules method main.

// Check if an SBOLValidationException is thrown in every run, and check if it throws the right exception.
/**
 * Tests circular reference between ModuleDefinition and Module (validation rules 11704 and 11705).
 * @param args
 * @throws Exception
 */
public static void main(String[] args) throws Exception {
    ModuleDefModuleTree tree = new ModuleDefModuleTree(maxDepth, numOfModules);
    tree.setRandomSeed(12);
    for (int i = 0; i < numOfRuns; i++) {
        boolean exceptionCaught = false;
        // String expectedError = null;
        try {
            tree.generateModel();
        } catch (SBOLValidationException e) {
            exceptionCaught = true;
            if (!e.getMessage().contains(tree.getExpectedError())) {
                throw new Exception("Unexpected exception!");
            }
        }
        if (!exceptionCaught) {
            throw new Exception("Exception NOT caught!");
        }
    }
}

Example 23 with Module

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

the class ModuleDefModuleTree method createModuleMDGraph.

public void createModuleMDGraph(SBOLDocument doc, int depth, ArrayList<String> mdNames, ArrayList<Integer> address, ModuleDefinition parentMd) throws SBOLValidationException {
    // System.out.println("depth = " + depth);
    if (depth > 0) {
        for (int i = 1; i <= numOfModules; i++) {
            address.add(i);
            System.out.println("address = " + intArrayListToString(address));
            System.out.println("addrSelfRef = " + intArrayListToString(addrCirfRef));
            String mdId = "md_" + intArrayListToString(address);
            String mId = "m_" + intArrayListToString(address);
            System.out.println("mdId = " + mdId);
            // System.out.println("mId = " + mId);
            if (intArrayListToString(address).equals(intArrayListToString(addrCirfRef))) {
                int circularRefIndex = randInt(0, mdNames.size() - 1);
                // int circleRefIndex = mdNames.size()-1; // Force 10704 to occur.
                System.out.println("circleRefIndex = " + circularRefIndex);
                System.out.println("address = " + intArrayListToString(address));
                System.out.println("addrCirRef = " + intArrayListToString(addrCirfRef));
                System.out.println("mdNames = " + mdNames);
                if (circularRefIndex == mdNames.size() - 1) {
                    System.out.println("Expect 11704");
                    expectedError = "11704";
                } else {
                    System.out.println("Expect 11705");
                    expectedError = "11705";
                }
                System.out.println("Last module displayId (mId) = " + mId);
                System.out.println("parentMd displayId = " + parentMd.getDisplayId());
                System.out.println("mdName = " + mdNames.get(circularRefIndex));
                // create the circular reference from module with mId to module definition selected by mdNames.get(circularRefIndex).
                parentMd.createModule(mId, mdNames.get(circularRefIndex));
            } else {
                ModuleDefinition childMd = doc.createModuleDefinition(mdId);
                parentMd.createModule(mId, mdId);
                mdNames.add(mdId);
                // System.out.println(mdId);
                // System.out.println("Interm. Module displayId = " + m.getDisplayId());
                System.out.println("mdNames = " + mdNames);
                createModuleMDGraph(doc, depth - 1, mdNames, address, childMd);
                mdNames.remove(mdId);
            }
            address.remove(address.size() - 1);
        }
    }
}