Examples with Path net.minecraft.server.v1_16_R3.Path used on opensource projects

Example 11 with Path

use of net.minecraft.server.v1_16_R3.Path in project jmulticard by ctt-gob-es.

the class CardOS method preloadCertificates.

private void preloadCertificates() throws FileNotFoundException, Iso7816FourCardException, IOException, Asn1Exception, TlvException {
    // Entramos en el directorio PKCS#15
    selectFileByName(PKCS15_NAME);
    // Seleccionamos el ODF, no nos devuelve FCI ni nada
    selectFileById(new byte[] { (byte) 0x50, (byte) 0x31 });
    // Leemos el ODF, que tiene esta estructura en cada uno de sus registros:
    // PKCS15Objects ::= CHOICE {
    // privateKeys         [0] PrivateKeys,
    // publicKeys          [1] PublicKeys,
    // trustedPublicKeys   [2] PublicKeys,
    // secretKeys          [3] SecretKeys,
    // certificates        [4] Certificates,
    // trustedCertificates [5] Certificates,
    // usefulCertificates  [6] Certificates,
    // dataObjects         [7] DataObjects,
    // authObjects         [8] AuthObjects,
    // ... -- For future extensions
    // }
    // A2
    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();
    // Seleccionamos el CDF
    selectFileById(cdfPath.getPathBytes());
    // Leemos el CDF mediante registros
    final List<byte[]> cdfRecords = readAllRecords();
    CertificateObject co;
    for (final byte[] b : cdfRecords) {
        try {
            co = new CertificateObject();
            co.setDerValue(HexUtils.subArray(b, 2, b.length - 2));
        } catch (final Exception e) {
            // $NON-NLS-1$
            LOGGER.warning("Omitido registro de certificado por no ser un CertificateObject de PKCS#15: " + e);
            continue;
        }
        final byte[] certPath = co.getPathBytes();
        if (certPath == null || certPath.length != 4) {
            // $NON-NLS-1$
            LOGGER.warning("Se omite una posicion de certificado porque su ruta no es de cuatro octetos: " + co.getAlias());
            continue;
        }
        final byte[] MASTER_FILE = { (byte) 0x50, (byte) 0x15 };
        sendArbitraryApdu(new CommandApdu(// CLA
        getCla(), // INS
        (byte) 0xA4, // P1
        (byte) 0x08, // P2
        (byte) 0x0C, new byte[] { MASTER_FILE[0], MASTER_FILE[1], certPath[0], certPath[1], certPath[2], certPath[3] }, null));
        final byte[] certBytes = readBinaryComplete(9999);
        final X509Certificate cert;
        try {
            cert = CertificateUtils.generateCertificate(certBytes);
        } catch (final CertificateException e) {
            LOGGER.severe(// $NON-NLS-1$ //$NON-NLS-2$
            "No ha sido posible generar el certificado para el alias " + co.getAlias() + ": " + e);
            continue;
        }
        certificatesByAlias.put(co.getAlias(), cert);
    }
}

Example 12 with Path

use of net.minecraft.server.v1_16_R3.Path in project dishevelled by heuermh.

the class ImportGfa2Task method run.

@Override
public void run(final TaskMonitor taskMonitor) throws Exception {
    taskMonitor.setTitle("Import a network in Graphical Fragment Assembly (GFA) 2.0 format");
    final Map<String, Segment> segmentsById = new HashMap<String, Segment>();
    taskMonitor.setStatusMessage("Reading segments from file ...");
    try (BufferedReader readable = new BufferedReader(new FileReader(inputFile))) {
        // stream segments, building cache
        stream(readable, new Gfa2Adapter() {

            @Override
            protected boolean segment(final Segment segment) {
                segmentsById.put(segment.getId(), segment);
                return true;
            }
        });
    }
    taskMonitor.setStatusMessage("Finding reverse orientation references ...");
    final Table<String, Orientation, Segment> segmentsByOrientation = HashBasedTable.create();
    final List<Edge> edges = new ArrayList<Edge>();
    final List<Gap> gaps = new ArrayList<Gap>();
    final List<Path> paths = new ArrayList<Path>();
    try (BufferedReader readable = new BufferedReader(new FileReader(inputFile))) {
        // stream edges, gaps, and paths, looking for reverse orientation references
        stream(readable, new Gfa2Adapter() {

            private void putIfAbsent(final Reference reference) {
                Segment segment = segmentsById.get(reference.getId());
                if (segment == null) {
                    throw new RuntimeException("could not find segment by id " + reference.getId());
                }
                if (!segmentsByOrientation.contains(reference.getId(), reference.getOrientation())) {
                    segmentsByOrientation.put(reference.getId(), reference.getOrientation(), segment);
                }
            }

            @Override
            public boolean edge(final Edge edge) {
                putIfAbsent(edge.getSource());
                putIfAbsent(edge.getTarget());
                edges.add(edge);
                return true;
            }

            @Override
            public boolean gap(final Gap gap) {
                putIfAbsent(gap.getSource());
                putIfAbsent(gap.getTarget());
                gaps.add(gap);
                return true;
            }

            @Override
            public boolean path(final Path path) {
                for (Reference reference : path.getReferences()) {
                    putIfAbsent(reference);
                }
                if (loadPaths) {
                    paths.add(path);
                }
                return true;
            }
        });
    }
    logger.info("read {} segments, {} edges, {} gaps, and {} paths from {}", new Object[] { segmentsById.size(), edges.size(), gaps.size(), paths.size(), inputFile });
    segmentsById.clear();
    taskMonitor.setStatusMessage("Building Cytoscape nodes from segments ...");
    final CyNetwork network = applicationManager.getCurrentNetwork();
    final Map<String, CyNode> nodes = new HashMap<String, CyNode>(segmentsByOrientation.size());
    for (Table.Cell<String, Orientation, Segment> c : segmentsByOrientation.cellSet()) {
        String id = c.getRowKey();
        Orientation orientation = c.getColumnKey();
        Segment segment = c.getValue();
        String name = id + (orientation.isForward() ? "+" : "-");
        if (!nodes.containsKey(name)) {
            CyNode node = network.addNode();
            CyTable nodeTable = network.getDefaultNodeTable();
            CyRow nodeRow = nodeTable.getRow(node.getSUID());
            Integer length = segment.getLength();
            Integer readCount = segment.getReadCountOpt().orElse(null);
            Integer fragmentCount = segment.getFragmentCountOpt().orElse(null);
            Integer kmerCount = segment.getKmerCountOpt().orElse(null);
            String sequenceChecksum = segment.containsSequenceChecksum() ? String.valueOf(segment.getSequenceChecksum()) : null;
            String sequenceUri = segment.getSequenceUriOpt().orElse(null);
            setValue(nodeTable, nodeRow, "name", String.class, name);
            setValue(nodeTable, nodeRow, "length", Integer.class, length);
            setValue(nodeTable, nodeRow, "readCount", Integer.class, readCount);
            setValue(nodeTable, nodeRow, "fragmentCount", Integer.class, fragmentCount);
            setValue(nodeTable, nodeRow, "kmerCount", Integer.class, kmerCount);
            setValue(nodeTable, nodeRow, "sequenceChecksum", String.class, sequenceChecksum);
            setValue(nodeTable, nodeRow, "sequenceUri", String.class, sequenceUri);
            // default display length to length
            Integer displayLength = length;
            String sequence = orientation.isForward() ? segment.getSequence() : reverseComplement(segment.getSequence());
            if (sequence != null) {
                Integer sequenceLength = sequence.length();
                String displaySequence = trimFromMiddle(sequence, displaySequenceLimit);
                Integer displaySequenceLength = displaySequence.length();
                if (loadSequences) {
                    setValue(nodeTable, nodeRow, "sequence", String.class, sequence);
                }
                setValue(nodeTable, nodeRow, "sequenceLength", Integer.class, sequenceLength);
                setValue(nodeTable, nodeRow, "displaySequence", String.class, displaySequence);
                setValue(nodeTable, nodeRow, "displaySequenceLength", Integer.class, displaySequenceLength);
                // override display length with sequence length if necessary
                if (length == null || length != sequenceLength) {
                    displayLength = sequenceLength;
                }
            }
            StringBuilder sb = new StringBuilder();
            sb.append(name);
            if (displayLength != null) {
                sb.append("  ");
                sb.append(displayLength);
                sb.append(" bp");
            }
            String displayName = sb.toString();
            if (readCount != null) {
                sb.append(" ");
                sb.append(readCount);
                sb.append(" reads");
            }
            if (fragmentCount != null) {
                sb.append(" ");
                sb.append(fragmentCount);
                sb.append(" fragments");
            }
            if (kmerCount != null) {
                sb.append(" ");
                sb.append(kmerCount);
                sb.append(" kmers");
            }
            String displayLabel = sb.toString();
            setValue(nodeTable, nodeRow, "displayName", String.class, displayName);
            setValue(nodeTable, nodeRow, "displayLength", Integer.class, displayLength);
            setValue(nodeTable, nodeRow, "displayLabel", String.class, displayLabel);
            nodes.put(name, node);
        }
    }
    logger.info("converted segments and orientation to " + nodes.size() + " nodes");
    segmentsByOrientation.clear();
    taskMonitor.setStatusMessage("Building Cytoscape edges from edges and gaps ...");
    for (Edge edge : edges) {
        String sourceId = edge.getSource().getId();
        String sourceOrientation = edge.getSource().isForwardOrientation() ? "+" : "-";
        String targetId = edge.getTarget().getId();
        String targetOrientation = edge.getTarget().isForwardOrientation() ? "+" : "-";
        CyNode sourceNode = nodes.get(sourceId + sourceOrientation);
        CyNode targetNode = nodes.get(targetId + targetOrientation);
        CyEdge cyEdge = network.addEdge(sourceNode, targetNode, true);
        CyTable edgeTable = network.getDefaultEdgeTable();
        CyRow edgeRow = edgeTable.getRow(cyEdge.getSUID());
        setValue(edgeTable, edgeRow, "id", String.class, edge.getIdOpt().orElse(null));
        setValue(edgeTable, edgeRow, "type", String.class, "edge");
        setValue(edgeTable, edgeRow, "sourceId", String.class, sourceId);
        setValue(edgeTable, edgeRow, "sourceOrientation", String.class, sourceOrientation);
        setValue(edgeTable, edgeRow, "targetId", String.class, targetId);
        setValue(edgeTable, edgeRow, "targetOrientation", String.class, targetOrientation);
        setValue(edgeTable, edgeRow, "sourceStart", String.class, edge.getSourceStart().toString());
        setValue(edgeTable, edgeRow, "sourceEnd", String.class, edge.getSourceEnd().toString());
        setValue(edgeTable, edgeRow, "targetStart", String.class, edge.getTargetStart().toString());
        setValue(edgeTable, edgeRow, "targetEnd", String.class, edge.getTargetEnd().toString());
        setValue(edgeTable, edgeRow, "alignment", String.class, edge.hasAlignment() ? edge.getAlignment().toString() : null);
        setValue(edgeTable, edgeRow, "readCount", Integer.class, edge.getReadCountOpt().orElse(null));
        setValue(edgeTable, edgeRow, "fragmentCount", Integer.class, edge.getFragmentCountOpt().orElse(null));
        setValue(edgeTable, edgeRow, "kmerCount", Integer.class, edge.getKmerCountOpt().orElse(null));
        setValue(edgeTable, edgeRow, "mappingQuality", Integer.class, edge.getMappingQualityOpt().orElse(null));
        setValue(edgeTable, edgeRow, "mismatchCount", Integer.class, edge.getMismatchCountOpt().orElse(null));
    }
    logger.info("converted edges to " + edges.size() + " edges");
    for (Gap gap : gaps) {
        String sourceId = gap.getSource().getId();
        String sourceOrientation = gap.getSource().isForwardOrientation() ? "+" : "-";
        String targetId = gap.getTarget().getId();
        String targetOrientation = gap.getTarget().isForwardOrientation() ? "+" : "-";
        CyNode sourceNode = nodes.get(sourceId + sourceOrientation);
        CyNode targetNode = nodes.get(targetId + targetOrientation);
        CyEdge edge = network.addEdge(sourceNode, targetNode, true);
        CyTable edgeTable = network.getDefaultEdgeTable();
        CyRow edgeRow = edgeTable.getRow(edge.getSUID());
        setValue(edgeTable, edgeRow, "id", String.class, gap.getIdOpt().orElse(null));
        setValue(edgeTable, edgeRow, "type", String.class, "gap");
        setValue(edgeTable, edgeRow, "sourceId", String.class, sourceId);
        setValue(edgeTable, edgeRow, "sourceOrientation", String.class, sourceOrientation);
        setValue(edgeTable, edgeRow, "targetId", String.class, targetId);
        setValue(edgeTable, edgeRow, "targetOrientation", String.class, targetOrientation);
        setValue(edgeTable, edgeRow, "distance", Integer.class, gap.getDistance());
        setValue(edgeTable, edgeRow, "variance", Integer.class, gap.getVarianceOpt().orElse(null));
    }
    logger.info("converted gaps to " + gaps.size() + " edges");
    nodes.clear();
    edges.clear();
    gaps.clear();
    // pass paths to AssemblyApp if requested
    if (loadPaths && !paths.isEmpty()) {
        taskMonitor.setStatusMessage("Loading paths in path view ...");
        assemblyModel.setInputFileName(inputFile.toString());
    // todo: convert to gfa1 paths?
    // note paths in gfa2 can have references to segments, edges, or other groups
    // assemblyModel.setPaths(paths, traversalsByPathName);
    }
}

Example 13 with Path

use of net.minecraft.server.v1_16_R3.Path in project dishevelled by heuermh.

the class AssemblyModel method setPath.

/**
 * Set the selected path for this assembly model to <code>path</code>.
 *
 * <p>This is a bound property.</p>
 *
 * @param path selected path for this assembly model, if any
 */
void setPath(final Path path) {
    Path oldPath = this.path;
    this.path = path;
    traversals.clear();
    if (this.path != null && traversalsByPath.containsKey(path)) {
        traversals.addAll(traversalsByPath.get(path));
    }
    propertyChangeSupport.firePropertyChange("path", oldPath, this.path);
}

Example 14 with Path

use of net.minecraft.server.v1_16_R3.Path in project Denizen by DenizenScript.

the class EntityHelperImpl method follow.

@Override
public void follow(final Entity target, final Entity follower, final double speed, final double lead, final double maxRange, final boolean allowWander, final boolean teleport) {
    if (target == null || follower == null) {
        return;
    }
    final net.minecraft.server.v1_16_R3.Entity nmsEntityFollower = ((CraftEntity) follower).getHandle();
    if (!(nmsEntityFollower instanceof EntityInsentient)) {
        return;
    }
    final EntityInsentient nmsFollower = (EntityInsentient) nmsEntityFollower;
    final NavigationAbstract followerNavigation = nmsFollower.getNavigation();
    UUID uuid = follower.getUniqueId();
    if (followTasks.containsKey(uuid)) {
        followTasks.get(uuid).cancel();
    }
    final int locationNearInt = (int) Math.floor(lead);
    final boolean hasMax = maxRange > lead;
    followTasks.put(follower.getUniqueId(), new BukkitRunnable() {

        private boolean inRadius = false;

        public void run() {
            if (!target.isValid() || !follower.isValid()) {
                this.cancel();
            }
            followerNavigation.a(2F);
            Location targetLocation = target.getLocation();
            PathEntity path;
            if (hasMax && !Utilities.checkLocation(targetLocation, follower.getLocation(), maxRange) && !target.isDead() && target.isOnGround()) {
                if (!inRadius) {
                    if (teleport) {
                        follower.teleport(Utilities.getWalkableLocationNear(targetLocation, locationNearInt));
                    } else {
                        cancel();
                    }
                } else {
                    inRadius = false;
                    path = followerNavigation.a(targetLocation.getX(), targetLocation.getY(), targetLocation.getZ(), 0);
                    if (path != null) {
                        followerNavigation.a(path, 1D);
                        followerNavigation.a(2D);
                    }
                }
            } else if (!inRadius && !Utilities.checkLocation(targetLocation, follower.getLocation(), lead)) {
                path = followerNavigation.a(targetLocation.getX(), targetLocation.getY(), targetLocation.getZ(), 0);
                if (path != null) {
                    followerNavigation.a(path, 1D);
                    followerNavigation.a(2D);
                }
            } else {
                inRadius = true;
            }
            if (inRadius && !allowWander) {
                followerNavigation.o();
            }
            nmsFollower.getAttributeInstance(GenericAttributes.MOVEMENT_SPEED).setValue(speed);
        }
    }.runTaskTimer(NMSHandler.getJavaPlugin(), 0, 10));
}

Example 15 with Path

use of net.minecraft.server.v1_16_R3.Path in project Denizen by DenizenScript.

the class EntityHelperImpl method walkTo.

@Override
public void walkTo(final LivingEntity entity, Location location, Double speed, final Runnable callback) {
    if (entity == null || location == null) {
        return;
    }
    net.minecraft.server.v1_16_R3.Entity nmsEntityEntity = ((CraftEntity) entity).getHandle();
    if (!(nmsEntityEntity instanceof EntityInsentient)) {
        return;
    }
    final EntityInsentient nmsEntity = (EntityInsentient) nmsEntityEntity;
    final NavigationAbstract entityNavigation = nmsEntity.getNavigation();
    final PathEntity path;
    final boolean aiDisabled = !entity.hasAI();
    if (aiDisabled) {
        entity.setAI(true);
        try {
            ENTITY_ONGROUND_SETTER.invoke(nmsEntity, true);
        } catch (Throwable ex) {
            Debug.echoError(ex);
        }
    }
    path = entityNavigation.a(location.getX(), location.getY(), location.getZ(), 0);
    if (path != null) {
        entityNavigation.a(path, 1D);
        entityNavigation.a(2D);
        final double oldSpeed = nmsEntity.getAttributeInstance(GenericAttributes.MOVEMENT_SPEED).getBaseValue();
        if (speed != null) {
            nmsEntity.getAttributeInstance(GenericAttributes.MOVEMENT_SPEED).setValue(speed);
        }
        new BukkitRunnable() {

            @Override
            public void run() {
                if (!entity.isValid()) {
                    if (callback != null) {
                        callback.run();
                    }
                    cancel();
                    return;
                }
                if (aiDisabled && entity instanceof Wolf) {
                    ((Wolf) entity).setAngry(false);
                }
                if (entityNavigation.m() || path.c()) {
                    if (callback != null) {
                        callback.run();
                    }
                    if (speed != null) {
                        nmsEntity.getAttributeInstance(GenericAttributes.MOVEMENT_SPEED).setValue(oldSpeed);
                    }
                    if (aiDisabled) {
                        entity.setAI(false);
                    }
                    cancel();
                }
            }
        }.runTaskTimer(NMSHandler.getJavaPlugin(), 1, 1);
    } else // if (!Utilities.checkLocation(location, entity.getLocation(), 20)) {
    // TODO: generate waypoints to the target location?
    {
        entity.teleport(location);
    }
}