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

Example 71 with SBOLDocument

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

Example 72 with SBOLDocument

use of org.sbolstandard.core2.SBOLDocument 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 73 with SBOLDocument

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

the class ModuleTest 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);
    geneticToggleSwitch = doc.createModuleDefinition("toggle_switch");
    LacIInverter_MD = doc.createModuleDefinition("LacIInverter_MD");
    TetRInverter_MD = doc.createModuleDefinition("TetRInverter_MD");
    TetR = doc.createComponentDefinition("TetR", ComponentDefinition.PROTEIN);
    LacI = doc.createComponentDefinition("LacI", ComponentDefinition.PROTEIN);
    TF_TetR = doc.createComponentDefinition("TF_TetR", ComponentDefinition.PROTEIN);
    TF_LacI = doc.createComponentDefinition("TF_LacI", ComponentDefinition.PROTEIN);
    TetRInverter_fc = geneticToggleSwitch.createFunctionalComponent("TetRInverter_fc", AccessType.PUBLIC, TetR.getIdentity(), DirectionType.INOUT);
    LacIInverter_fc = geneticToggleSwitch.createFunctionalComponent("LacIInverter_fc", AccessType.PUBLIC, LacI.getIdentity(), DirectionType.INOUT);
    TF_TetR_fc = TetRInverter_MD.createFunctionalComponent("TF_TetR_fc", AccessType.PUBLIC, TF_TetR.getIdentity(), DirectionType.NONE);
    TF_LacI_fc = LacIInverter_MD.createFunctionalComponent("TF_LacI_fc", AccessType.PUBLIC, TF_LacI.getIdentity(), DirectionType.NONE);
    TetRInverter = geneticToggleSwitch.createModule("TetRInverter", TetRInverter_MD.getIdentity());
    LacIInverter = geneticToggleSwitch.createModule("LacIInverter", LacIInverter_MD.getIdentity());
}

Example 74 with SBOLDocument

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

the class ModuleDefModuleTree method generateModel.

public String generateModel() throws SBOLValidationException, IOException, SBOLConversionException {
    SBOLDocument doc = new SBOLDocument();
    String version = "1.0";
    doc.setDefaultURIprefix("http://sbols.org/CRISPR_Example/");
    doc.setComplete(true);
    doc.setCreateDefaults(true);
    ModuleDefinition md1 = doc.createModuleDefinition("md_top", version);
    ArrayList<String> mdNames = new ArrayList<String>();
    mdNames.add("md_top");
    int depth = maxDepth;
    ArrayList<Integer> address = new ArrayList<Integer>();
    int selectedDepth = randInt(1, maxDepth);
    for (int i = 0; i < selectedDepth; i++) {
        addrCirfRef.add(randInt(1, numOfModules));
    }
    System.out.println("depth = " + depth);
    System.out.println("mdNames = " + mdNames);
    System.out.println("address = " + address);
    System.out.println("addrSelfRef = " + addrCirfRef);
    createModuleMDGraph(doc, depth, mdNames, address, md1);
    SBOLWriter.write(doc, "TestCircularModules.rdf");
    System.out.println("Finished writing.");
    // SBOLReader.read("/Users/zhangz/libSBOLproject/libSBOLj/examples/TestCircularModules.rdf");
    // SBOLReader.read("/Users/zhangz/libSBOLproject/libSBOLj/core2/src/test/resources/test/data/Validation/sbol-11705.rdf");
    SBOLValidate.validateSBOL(doc, true, true, true);
    if (SBOLValidate.getNumErrors() > 0) {
        for (String error : SBOLValidate.getErrors()) {
            System.out.println("TEST: error = " + error);
        }
    }
    return expectedError;
}

Example 75 with SBOLDocument

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