Examples with Header org.dishevelled.bio.assembly.gfa1.Header used on opensource projects

Example 21 with Header

use of org.dishevelled.bio.assembly.gfa1.Header in project cas by apereo.

the class ECPSamlIdPProfileHandlerControllerTests method getEnvelope.

private Envelope getEnvelope(final String entityId) {
    var builder = (SOAPObjectBuilder) openSamlConfigBean.getBuilderFactory().getBuilder(Envelope.DEFAULT_ELEMENT_NAME);
    var envelope = (Envelope) builder.buildObject();
    builder = (SOAPObjectBuilder) openSamlConfigBean.getBuilderFactory().getBuilder(Header.DEFAULT_ELEMENT_NAME);
    val header = (Header) builder.buildObject();
    envelope.setHeader(header);
    builder = (SOAPObjectBuilder) openSamlConfigBean.getBuilderFactory().getBuilder(Body.DEFAULT_ELEMENT_NAME);
    val body = (Body) builder.buildObject();
    body.getUnknownXMLObjects().add(getAuthnRequest(entityId));
    envelope.setBody(body);
    return envelope;
}

Example 22 with Header

use of org.dishevelled.bio.assembly.gfa1.Header in project ddf by codice.

the class SamlProtocol method createSoapMessage.

public static Envelope createSoapMessage(SignableSAMLObject signableSAMLObject) {
    Body body = soapBodyBuilder.buildObject();
    body.getUnknownXMLObjects().add(signableSAMLObject);
    Envelope envelope = soapEnvelopeBuilder.buildObject();
    envelope.setBody(body);
    Header header = soapHeaderBuilder.buildObject();
    envelope.setHeader(header);
    return envelope;
}

Example 23 with Header

use of org.dishevelled.bio.assembly.gfa1.Header in project sdk-java by temporalio.

the class WorkflowContext method getPropagatedContexts.

/**
 * @return a map of propagated context objects, keyed by propagator name
 */
Map<String, Object> getPropagatedContexts() {
    if (contextPropagators == null || contextPropagators.isEmpty()) {
        return new HashMap<>();
    }
    Header headers = startedAttributes.getHeader();
    Map<String, Payload> headerData = new HashMap<>(headers.getFieldsMap());
    Map<String, Object> contextData = new HashMap<>();
    for (ContextPropagator propagator : contextPropagators) {
        contextData.put(propagator.getName(), propagator.deserializeContext(headerData));
    }
    return contextData;
}

Example 24 with Header

use of org.dishevelled.bio.assembly.gfa1.Header in project jradio by dernasherbrezon.

the class Painani1Beacon method readBeacon.

@Override
public void readBeacon(byte[] data) throws IOException, UncorrectableException {
    DataInputStream dis = new DataInputStream(new ByteArrayInputStream(data));
    header = new Header(dis);
    if (data.length == 30) {
        shortTelemetry = new ShortTelemetry(dis);
    } else if (data.length == 72) {
        int id = dis.readUnsignedShort();
        if (id != 0x3cc3) {
            throw new UncorrectableException("invalid id");
        }
        telemetry = new Telemetry(dis);
    } else {
        unknownPayload = new byte[dis.available()];
        dis.readFully(unknownPayload);
    }
}

Example 25 with Header

use of org.dishevelled.bio.assembly.gfa1.Header in project dishevelled-bio by heuermh.

the class SegmentsToPropertyGraph method call.

@Override
public Integer call() throws Exception {
    PrintWriter nodesWriter = null;
    try {
        nodesWriter = writer(outputNodesFile);
        nodesWriter.println(HEADER);
        final PrintWriter nw = nodesWriter;
        Gfa1Reader.stream(reader(inputGfa1File), new Gfa1Adapter() {

            @Override
            public boolean segment(final Segment segment) {
                StringBuilder sb = new StringBuilder();
                sb.append(segment.getName());
                sb.append(",");
                sb.append(segment.getSequenceOpt().orElse(""));
                sb.append(",");
                sb.append(segment.containsLength() ? segment.getLength() : "");
                sb.append(",");
                sb.append(segment.containsReadCount() ? segment.getReadCount() : "");
                sb.append(",");
                sb.append(segment.containsFragmentCount() ? segment.getFragmentCount() : "");
                sb.append(",");
                sb.append(segment.containsKmerCount() ? segment.getKmerCount() : "");
                sb.append(",");
                sb.append(segment.containsSequenceChecksum() ? String.valueOf(segment.getSequenceChecksum()) : "");
                sb.append(",");
                sb.append(segment.getSequenceUriOpt().orElse(""));
                nw.println(sb);
                return true;
            }
        });
        return 0;
    } finally {
        try {
            nodesWriter.close();
        } catch (Exception e) {
        // empty
        }
    }
}