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

Example 31 with Sequence

use of org.sbolstandard.core2.Sequence in project jasn1 by openmuc.

the class ModulesTest method encodingDecoding.

@Test
public void encodingDecoding() throws IOException {
    ReverseByteArrayOutputStream berOS = new ReverseByteArrayOutputStream(1000);
    MyDate1 dateOfHire = new MyDate1();
    // MyDate1 dateOfHire = new MyDate1("19710917");
    dateOfHire.value = new String("19710917").getBytes();
    dateOfHire.encode(berOS, true);
    MyInt2 myInt2Encode = new MyInt2(2);
    berOS.reset();
    myInt2Encode.encode(berOS, true);
    MyInt2 myInt2Decode = new MyInt2();
    byte[] code = HexConverter.fromShortHexString("a303020102");
    InputStream is = new ByteArrayInputStream(code);
    myInt2Decode.decode(is, true);
    Assert.assertEquals(myInt2Decode.value.intValue(), 2);
    PersonnelRecord pr = new PersonnelRecord();
    Name name = new Name();
    name.setGivenName(new BerVisibleString("givenName".getBytes()));
    name.setFamilyName(new BerVisibleString("familyName".getBytes()));
    name.setInitial(new BerVisibleString("initial".getBytes()));
    pr.setName(name);
    pr.setTitle(new BerVisibleString("title".getBytes()));
    pr.setNumber(new EmployeeNumberZ(1));
    pr.setDateOfHire(new Date("23121981".getBytes()));
    pr.setNameOfSpouse(name);
    ChildInformation child = new ChildInformation();
    child.setName(new Name("child name".getBytes()));
    child.setDateOfBirth(new Date("12121912".getBytes()));
    PersonnelRecord.Children children = new PersonnelRecord.Children();
    List<ChildInformation> childInformation = children.getChildInformation();
    childInformation.add(child);
    childInformation.add(child);
    pr.setTestBitString(new MyBitString(new byte[] { (byte) 0x80, (byte) 0xff }, 10));
    pr.setTest(new MyInt(3));
    TestChoice testChoice = new TestChoice();
    testChoice.setChoiceElement1(child);
    pr.setTest2(testChoice);
    pr.setTest3(testChoice);
    pr.setTest4(testChoice);
    pr.setTest5(testChoice);
    pr.setTest6(testChoice);
    TestSequenceOf testSequenceOf = new TestSequenceOf();
    List<BerInteger> berIntegers = testSequenceOf.getBerInteger();
    for (int i = 0; i < 10; i++) {
        berIntegers.add(new BerInteger(i));
    }
    pr.setTestSequenceOf(testSequenceOf);
    TestSequenceOf2 testSequenceOf2 = new TestSequenceOf2();
    List<SEQUENCE> sequences = testSequenceOf2.getSEQUENCE();
    for (int i = 0; i < 10; i++) {
        SEQUENCE sequence = new SEQUENCE();
        sequence.setTest1(new BerInteger(i++));
        sequence.setTest2(new BerInteger(i));
        sequences.add(sequence);
    }
    pr.setTestSequenceOf2(testSequenceOf2);
    BerEmbeddedPdv berEmbeddedPdv = new BerEmbeddedPdv();
    pr.setEmbeddedPdv(berEmbeddedPdv);
    System.out.println("PersonnelRecord.toString():\n" + pr);
}

Example 32 with Sequence

use of org.sbolstandard.core2.Sequence in project ice by JBEI.

the class SBOL2Formatter method format.

@Override
public void format(Sequence sequence, OutputStream outputStream) throws IOException {
    SBOLDocument doc = new SBOLDocument();
    try {
        SBOL2Visitor visitor = new SBOL2Visitor(doc);
        visitor.visit(sequence);
        doc.write(outputStream);
    } catch (SBOLValidationException | SBOLConversionException | URISyntaxException e) {
        throw new IOException(e);
    }
}

Example 33 with Sequence

use of org.sbolstandard.core2.Sequence in project ice by JBEI.

the class SBOL2Visitor method visit.

public void visit(Sequence sequence) throws SBOLValidationException {
    // ice data model conflates the sequence and component
    Entry entry = sequence.getEntry();
    // Set required properties
    String partId = entry.getPartNumber();
    componentDefinition = doc.createComponentDefinition(uriString, partId, "1", ComponentDefinition.DNA);
    componentDefinition.setName(entry.getName());
    componentDefinition.setDescription(entry.getShortDescription());
    String dsUri = "sequence_" + sequence.getFwdHash().replaceAll("[\\s\\-()]", "");
    org.sbolstandard.core2.Sequence dnaSequence = doc.createSequence(uriString, dsUri, "1", sequence.getSequence(), org.sbolstandard.core2.Sequence.IUPAC_DNA);
    dnaSequence.setElements(sequence.getSequence());
    componentDefinition.addSequence(dnaSequence);
    List<SequenceFeature> features = new ArrayList<>(sequence.getSequenceFeatures());
    Collections.sort(features, new SequenceFeatureComparator());
    for (SequenceFeature feature : features) {
        visit(feature);
    }
    componentDefinition.createAnnotation(new QName(ICE_NS, "id", ICE_PREFIX), entry.getId());
    if (entry.getRecordId() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "recordId", ICE_PREFIX), entry.getRecordId());
    if (entry.getVersionId() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "versionId", ICE_PREFIX), entry.getVersionId());
    if (entry.getRecordType() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "recordType", ICE_PREFIX), entry.getRecordType());
    if (entry.getOwner() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "owner", ICE_PREFIX), entry.getOwner());
    if (entry.getOwnerEmail() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "ownerEmail", ICE_PREFIX), entry.getOwnerEmail());
    if (entry.getCreator() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "creator", ICE_PREFIX), entry.getCreator());
    if (entry.getCreatorEmail() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "creatorEmail", ICE_PREFIX), entry.getCreatorEmail());
    if (entry.getStatus() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "status", ICE_PREFIX), entry.getStatus());
    if (entry.getAlias() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "alias", ICE_PREFIX), entry.getAlias());
    for (SelectionMarker selectionMarker : entry.getSelectionMarkers()) {
        componentDefinition.createAnnotation(new QName(ICE_NS, "selectionMarker", ICE_PREFIX), selectionMarker.getName());
    }
    if (entry.getLinks() != null) {
        for (Link link : entry.getLinks()) {
            if (StringUtils.isNotEmpty(link.getLink()) && StringUtils.isNotEmpty(link.getUrl()))
                componentDefinition.createAnnotation(new QName(ICE_NS, link.getLink(), ICE_PREFIX), link.getUrl());
        }
    }
    if (entry.getKeywords() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "keywords", ICE_PREFIX), entry.getKeywords());
    if (entry.getShortDescription() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "shortDescription", ICE_PREFIX), entry.getShortDescription());
    if (entry.getLongDescription() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "longDescription", ICE_PREFIX), entry.getLongDescription());
    if (entry.getLongDescriptionType() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "longDescriptionType", ICE_PREFIX), entry.getLongDescriptionType());
    if (entry.getReferences() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "references", ICE_PREFIX), entry.getReferences());
    if (entry.getCreationTime() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "creationTime", ICE_PREFIX), entry.getCreationTime().toString());
    if (entry.getModificationTime() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "modificationTime", ICE_PREFIX), entry.getModificationTime().toString());
    if (entry.getBioSafetyLevel() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "bioSafetyLevel", ICE_PREFIX), entry.getBioSafetyLevel());
    if (entry.getIntellectualProperty() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "intellectualProperty", ICE_PREFIX), entry.getIntellectualProperty());
    if (entry.getVisibility() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "visibility", ICE_PREFIX), entry.getVisibility());
    if (entry.getParameters() != null) {
        for (Parameter parameter : entry.getParameters()) {
            if (StringUtils.isNotEmpty(parameter.getKey()) && StringUtils.isNotEmpty(parameter.getValue()))
                componentDefinition.createAnnotation(new QName(ICE_NS, parameter.getKey(), ICE_PREFIX), parameter.getValue());
        }
    }
    if (entry.getFundingSource() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "fundingSource", ICE_PREFIX), entry.getFundingSource());
    if (entry.getPrincipalInvestigator() != null)
        componentDefinition.createAnnotation(new QName(ICE_NS, "principalInvestigator", ICE_PREFIX), entry.getPrincipalInvestigator());
// TODO: samples
// TODO: attachments
}