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

Example 6 with Path

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

the class AssemblyModel method setPaths.

/**
 * Set the paths for this assembly model to the specified GFA 1.0 paths.
 *
 * @param paths zero or more GFA 1.0 paths, must not be null
 * @param traversalsByPathName traversals keyed by path name, must not be null
 */
void setPaths(final Iterable<Path> paths, final ListMultimap<String, Traversal> traversalsByPathName) {
    checkNotNull(paths);
    checkNotNull(traversalsByPathName);
    // reset if necessary
    if (!this.paths.isEmpty()) {
        setPath(null);
        this.paths.clear();
        traversals.clear();
        traversalsByPath.clear();
    }
    // create traversals from paths if necessary
    for (Path path : paths) {
        List<Traversal> traversals = traversalsByPathName.get(path.getName());
        traversalsByPath.putAll(path, traversals.isEmpty() ? traversalsFor(path) : traversals);
    }
    if (!traversalsByPath.isEmpty()) {
        Set<Path> keys = traversalsByPath.keySet();
        paths().addAll(keys);
        setPath(keys.iterator().next());
    }
}

Example 7 with Path

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

the class AssemblyModel method traversalsFor.

/**
 * Create and return a list of path traversals for the specified path.
 *
 * @param path path, must not be null
 * @return a list of path traversals for the specified path
 */
static List<Traversal> traversalsFor(final Path path) {
    checkNotNull(path);
    int size = path.getSegments().size();
    List<Traversal> traversals = new ArrayList<Traversal>(size);
    Reference source = null;
    Reference target = null;
    String overlap = null;
    Map<String, Annotation> emptyAnnotations = Collections.emptyMap();
    for (int i = 0; i < size; i++) {
        target = path.getSegments().get(i);
        if (i > 0) {
            overlap = (path.getOverlaps() != null && path.getOverlaps().size() > i) ? path.getOverlaps().get(i - 1) : null;
        }
        if (source != null) {
            Traversal traversal = new Traversal(path.getName(), i - 1, source, target, overlap, emptyAnnotations);
            traversals.add(traversal);
        }
        source = target;
    }
    return traversals;
}

Example 8 with Path

use of org.dishevelled.bio.assembly.gfa1.Path in project jmulticard by ctt-gob-es.

the class SmartCafePkcs15Applet method preloadCertificates.

private void preloadCertificates() throws FileNotFoundException, Iso7816FourCardException, IOException, Asn1Exception, TlvException {
    selectMasterFile();
    // Seleccionamos el ODF, no nos devuelve FCI ni nada
    selectFileById(ODF_PATH);
    // Leemos el ODF
    final byte[] odfBytes = readBinaryComplete(162);
    final Odf odf = new Odf();
    odf.setDerValue(odfBytes);
    // Sacamos del ODF la ruta del CDF
    final Path cdfPath = odf.getCdfPath();
    // Leemos el CDF
    final Cdf cdf = new Cdf();
    try {
        selectMasterFile();
        final byte[] cdfBytes = selectFileByIdAndRead(cdfPath.getPathBytes());
        cdf.setDerValue(cdfBytes);
    } catch (final Exception e) {
        throw new ApduConnectionException(// $NON-NLS-1$
        "No se ha podido cargar el CDF de la tarjeta", // $NON-NLS-1$
        e);
    }
    if (cdf.getCertificateCount() < 1) {
        // $NON-NLS-1$
        LOGGER.warning("La tarjeta no contiene ningun certificado");
    }
    for (int i = 0; i < cdf.getCertificateCount(); i++) {
        try {
            int fileLength = -1;
            Location certLocation = new Location(cdf.getCertificatePath(i));
            while (certLocation != null) {
                final byte[] id = certLocation.getFile();
                try {
                    fileLength = selectFileById(id);
                } catch (final FileNotFoundException e) {
                    LOGGER.warning(// $NON-NLS-1$//$NON-NLS-2$
                    "El CDF indicaba un certificado en la ruta '" + certLocation + "', pero un elemento de esta no existe, se ignorara: " + e);
                }
                certLocation = certLocation.getChild();
            }
            final byte[] certBytes;
            if (fileLength <= 0) {
                // A veces hay punteros que apuntan a localizaciones vacias
                LOGGER.warning(// $NON-NLS-1$ //$NON-NLS-2$
                "El certificado " + i + " del dispositivo esta vacio");
                continue;
            }
            certBytes = readBinaryComplete(fileLength);
            CERTS_BY_ALIAS.put(cdf.getCertificateAlias(i), CertificateUtils.generateCertificate(certBytes));
        } catch (final Exception e) {
            // Puede darse el caso de que el puntero apunte a algo que no es un certificado
            LOGGER.severe(// $NON-NLS-1$ //$NON-NLS-2$
            "Error en la lectura del certificado " + i + " del dispositivo: " + e);
            continue;
        }
    }
}

Example 9 with Path

use of org.dishevelled.bio.assembly.gfa1.Path in project ets-ogcapi-edr10 by opengeospatial.

the class CollectionsTime method zParameterDefinition.

/**
 * Abstract Test 40 (/conf/edr/rc-z-definition): Validate that the vertical level query parameters are constructed correctly. (position)
 * Abstract Test 56 (/conf/edr/rc-z-definition): Validate that the vertical level query parameters are constructed correctly. (area)
 *
 * @param testPoint the testPoint under test, never <code>null</code>
 * @param model api definition, never <code>null</code>
 */
public void zParameterDefinition(TestPoint testPoint, OpenApi3 model) {
    Parameter z = null;
    String paramName = "z";
    for (Path path : model.getPaths().values()) {
        if (testPoint.getPath().equals(path.getPathString())) {
            for (Operation op : path.getOperations().values()) {
                for (Parameter param : op.getParameters()) {
                    if (hasName(param)) {
                        if (param.getName().equals(paramName)) {
                            z = param;
                        }
                    }
                }
            }
        }
    }
    if (z != null) {
        String msg = "Expected property '%s' with value '%s' but was '%s'";
        assertEquals(z.getName(), paramName, String.format(msg, "name", paramName, z.getName()));
        assertEquals(z.getIn(), "query", String.format(msg, "in", "query", z.getIn()));
        assertTrue(isRequired(z), String.format(msg, "required", "true", z.getRequired()));
        assertEquals(z.getStyle(), "form", String.format(msg, "style", "form", z.getStyle()));
        assertFalse(isExplode(z), String.format(msg, "explode", "false", z.getExplode()));
    }
}

Example 10 with Path

use of org.dishevelled.bio.assembly.gfa1.Path in project ets-ogcapi-edr10 by opengeospatial.

the class CollectionsTime method resolutionxParameterDefinition.

/**
 * <pre>
 * Requirement A.25: /req/edr/resolution-x-definition Parameter resolution-x
 * definition
 * </pre>
 * NOTE: Not referenced by ATS
 *
 * @param testPoint the testPoint under test, never <code>null</code>
 * @param model api definition, never <code>null</code>
 */
public void resolutionxParameterDefinition(TestPoint testPoint, OpenApi3 model) {
    Parameter resolutionx = null;
    String paramName = "resolution-x";
    for (Path path : model.getPaths().values()) {
        if (testPoint.getPath().equals(path.getPathString())) {
            for (Operation op : path.getOperations().values()) {
                for (Parameter param : op.getParameters()) {
                    if (hasName(param)) {
                        if (param.getName().equals(paramName)) {
                            resolutionx = param;
                        }
                    }
                }
            }
        }
    }
    if (resolutionx != null) {
        String msg = "Expected property '%s' with value '%s' but was '%s'";
        assertEquals(resolutionx.getName(), paramName, String.format(msg, "name", paramName, resolutionx.getName()));
        assertEquals(resolutionx.getIn(), "query", String.format(msg, "in", "query", resolutionx.getIn()));
        assertFalse(isRequired(resolutionx), String.format(msg, "required", "false", resolutionx.getRequired()));
        assertEquals(resolutionx.getStyle(), "form", String.format(msg, "style", "form", resolutionx.getStyle()));
        assertFalse(isExplode(resolutionx), String.format(msg, "explode", "false", resolutionx.getExplode()));
    }
}