Example usage for java.util LinkedList addAll

List of usage examples for java.util LinkedList addAll

Introduction

In this page you can find the example usage for java.util LinkedList addAll.

Prototype

public boolean addAll(Collection<? extends E> c) 

Source Link

Document

Appends all of the elements in the specified collection to the end of this list, in the order that they are returned by the specified collection's iterator.

Usage

From source file:ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixColumnSort.java

/**
 * Sort biomaterials according to a list of ordered factors
 *
 * @param start   biomaterials to sort//from   w w  w . ja  v a  2  s. com
 * @param factors sorted list of factors to define sort order for biomaterials, cannot be null
 */
private static List<BioMaterial> orderBiomaterialsBySortedFactors(List<BioMaterial> start,
        List<ExperimentalFactor> factors) {

    if (start.size() == 1) {
        return start;
    }

    if (start.size() == 0) {
        throw new IllegalArgumentException("Must provide some biomaterials");
    }
    if (factors == null) {
        throw new IllegalArgumentException("Must provide sorted factors, or at least an empty list");
    }
    if (factors.isEmpty()) {
        // we're done.
        return start;
    }

    ExperimentalFactor simplest = factors.get(0);

    if (simplest == null) {
        // we're done.
        return start;
    }

    /*
     * Order this chunk by the selected factor
     */

    Map<FactorValue, List<BioMaterial>> fv2bms = ExpressionDataMatrixColumnSort.buildFv2BmMap(start);

    List<BioMaterial> ordered = ExpressionDataMatrixColumnSort.orderByFactor(simplest, fv2bms, start);

    // Abort ordering, so we are ordered only by the first continuous factor.
    if (ExperimentalDesignUtils.isContinuous(simplest)) {
        assert ordered != null;
        return ordered;
    }

    LinkedList<ExperimentalFactor> factorsStillToDo = new LinkedList<>();
    factorsStillToDo.addAll(factors);
    factorsStillToDo.remove(simplest);

    if (factorsStillToDo.size() == 0) {
        /*
         * No more ordering is necessary.
         */
        return ordered;
    }

    ExpressionDataMatrixColumnSort.log.debug("Factors: " + factors.size());

    /*
     * Recurse in and order each chunk. First split it up, but retaining the order we just made.
     */
    LinkedHashMap<FactorValue, List<BioMaterial>> chunks = ExpressionDataMatrixColumnSort
            .chunkOnFactor(simplest, ordered);

    if (chunks == null) {
        // this means we should bail, gracefully.
        return start;
    }

    /*
     * Process each chunk.
     */
    List<BioMaterial> result = new ArrayList<>();
    for (FactorValue fv : chunks.keySet()) {
        List<BioMaterial> chunk = chunks.get(fv);

        if (chunk.size() < 2) {
            result.addAll(chunk);
        } else {
            List<BioMaterial> orderedChunk = ExpressionDataMatrixColumnSort
                    .orderBiomaterialsBySortedFactors(chunk, factorsStillToDo);
            if (orderedChunk != null) {
                result.addAll(orderedChunk);
            }
        }
    }

    return result;

}

From source file:org.marketcetera.util.ws.types.TypeTest.java

private static <V> LinkedList<V> toLinkedList(List<V> in) {
    LinkedList<V> out = new LinkedList<V>();
    out.addAll(in);
    return out;//from ww  w. jav  a  2s .  com
}

From source file:org.apache.hadoop.hive.ql.exec.SerializationUtilities.java

/**
 * Clones using the powers of XML. Do not use unless necessary.
 * @param roots The roots.//from   www  .jav a  2 s . co  m
 * @return The clone.
 */
public static List<Operator<?>> cloneOperatorTree(List<Operator<?>> roots) {
    ByteArrayOutputStream baos = new ByteArrayOutputStream(4096);
    CompilationOpContext ctx = roots.isEmpty() ? null : roots.get(0).getCompilationOpContext();
    serializePlan(roots, baos, true);
    @SuppressWarnings("unchecked")
    List<Operator<?>> result = deserializePlan(new ByteArrayInputStream(baos.toByteArray()), roots.getClass(),
            true);
    // Restore the context.
    LinkedList<Operator<?>> newOps = new LinkedList<>(result);
    while (!newOps.isEmpty()) {
        Operator<?> newOp = newOps.poll();
        newOp.setCompilationOpContext(ctx);
        List<Operator<?>> children = newOp.getChildOperators();
        if (children != null) {
            newOps.addAll(children);
        }
    }
    return result;
}

From source file:org.knowrob.vis.model.util.algorithm.ACCUM.java

/**
 * Diffuses a vector field around one vertex, weighted by a Gaussian of width 
 * {@code 1/sqrt(invsigma2)}. Ported from trimesh2 (2.12) (Szymon Rusinkiewicz Princeton University)
 * //from  w w w. j  a  v a  2 s .  c o m
 * @see <a href="https://github.com/fcole/qrtsc/tree/master/trimesh2">trimesh2</a>
 * 
 * @param m
 *          CAD model analyzed
 * @param curvatures
 *          curvatures HashMap with model vertices as keys and their cuvatures as values
 * @param flags
 *          map of vertex to long value (default initialized with 0f and of the same length with the list of vertices of the model)
 * @param flag_curr
 *          atomic long value
 * @param accum
 *          accumulator
 * @param invsigma
 *          spread of the Gaussian used in weighting
 * @param flt
 *          3D vector field diffused based on the curvature
 */
@SuppressWarnings("javadoc")
private static void diffuse_vert_field(final Model m, HashMap<Vertex, Curvature> curvatures,
        Map<Vertex, Long> flags, AtomicLong flag_curr, final ACCUM accum, int v, float invsigma2, Vertex flt) {
    Vertex vert = m.getVertices().get(v);
    if (vert.getNeighbors().size() == 0) {
        // flt.set(0, 0, 0);
        accum.a(m, curvatures, vert, flt, .5f, vert);
        return;
    }

    // flt.set(0, 0, 0);
    accum.a(m, curvatures, vert, flt, vert.getPointarea(), vert);
    float sum_w = vert.getPointarea();
    final Vector3f nv = vert.getNormalVector();

    long flag_curr_val = flag_curr.incrementAndGet();
    flags.put(vert, flag_curr_val);
    LinkedList<Vertex> boundary = new LinkedList<Vertex>();
    boundary.addAll(vert.getNeighbors());
    while (boundary.size() > 0) {
        Vertex n = boundary.pop();
        if (flags.get(n) != null && flags.get(n) == flag_curr_val)
            continue;
        flags.put(n, flag_curr_val);
        if (nv.dot(n.getNormalVector()) <= 0.0f)
            continue;
        // Gaussian weight
        float w = wt(n, vert, invsigma2);
        if (w == 0.0f)
            continue;
        // Downweight things pointing in different directions
        w *= nv.dot(n.getNormalVector());
        // Surface area "belonging" to each point
        w *= n.getPointarea();
        // Accumulate weight times field at neighbor
        accum.a(m, curvatures, vert, flt, w, n);
        sum_w += w;
        for (Vertex nn : n.getNeighbors()) {
            if (flags.get(nn) != null && flags.get(nn) == flag_curr_val)
                continue;
            boundary.push(nn);
        }
    }
    flt.scale(1 / sum_w);
}

From source file:org.apache.hadoop.hive.ql.exec.SerializationUtilities.java

public static List<Operator<?>> cloneOperatorTree(List<Operator<?>> roots, int indexForTezUnion) {
    ByteArrayOutputStream baos = new ByteArrayOutputStream(4096);
    CompilationOpContext ctx = roots.isEmpty() ? null : roots.get(0).getCompilationOpContext();
    serializePlan(roots, baos, true);//w ww. ja v  a  2s.  c  om
    @SuppressWarnings("unchecked")
    List<Operator<?>> result = deserializePlan(new ByteArrayInputStream(baos.toByteArray()), roots.getClass(),
            true);
    // Restore the context.
    LinkedList<Operator<?>> newOps = new LinkedList<>(result);
    while (!newOps.isEmpty()) {
        Operator<?> newOp = newOps.poll();
        newOp.setIndexForTezUnion(indexForTezUnion);
        newOp.setCompilationOpContext(ctx);
        List<Operator<?>> children = newOp.getChildOperators();
        if (children != null) {
            newOps.addAll(children);
        }
    }
    return result;
}

From source file:com.newlandframework.avatarmq.core.MessageCache.java

private void commitMessage(ConcurrentLinkedQueue<T> messages) {

    LinkedList<T> list = new LinkedList<T>();

    list.addAll(messages);
    cache.clear();/*from  w ww  .  j  ava  2s  . c  om*/

    if (list != null && list.size() > 0) {
        parallelDispatch(list);
        list.clear();
    }
}

From source file:org.georchestra.console.ws.backoffice.users.UserRule.java

public List<String> getListUidProtected() {

    if (this.listOfprotectedUsers.isEmpty()) {
        UserRule.LOG.warn("There isn't any protected user configured");
    }//  w w w .j a v a  2 s .  co m
    LinkedList<String> res = new LinkedList<String>();
    res.addAll(this.listOfprotectedUsers);

    return res;
}

From source file:org.psidnell.omnifocus.integrationtest.IntegrationTest.java

private void runMainAndDiff(final String name, String[] extraArgs, boolean doDiff)
        throws Exception, IOException {
    File tmp = new File(tmpDataDir, name);
    String[] args = { "-import", PREVIOUSLY_EXPORTED_DATA_FILE.getPath(), "-o", tmp.getPath() };
    LinkedList<String> combinedArgs = new LinkedList<>();
    combinedArgs.addAll(Arrays.asList(args));
    combinedArgs.addAll(Arrays.asList(extraArgs));
    Main.main(combinedArgs.toArray(new String[combinedArgs.size()]));
    if (doDiff) {
        Diff.diff(new File("src/test/data/" + name), tmp);
    }/*from www .  j  a v  a2 s  . c om*/
}

From source file:net.sourceforge.fenixedu.domain.reports.FlunkedReportFile.java

@Override
public void renderReport(Spreadsheet spreadsheet) {
    spreadsheet.setHeader("nmero aluno");
    spreadsheet.setHeader("ciclo estudos");
    setDegreeHeaders(spreadsheet);/*from  w  w w .  ja  va2  s .c  o m*/

    for (final Degree degree : Degree.readNotEmptyDegrees()) {
        if (checkDegreeType(getDegreeType(), degree)) {
            for (final Registration registration : degree.getRegistrationsSet()) {
                LinkedList<RegistrationState> states = new LinkedList<RegistrationState>();
                states.addAll(registration.getRegistrationStatesSet());
                CollectionUtils.filter(states, new Predicate() {
                    @Override
                    public boolean evaluate(Object item) {
                        return ((RegistrationState) item).getExecutionYear() != null
                                && ((RegistrationState) item).getExecutionYear().equals(getExecutionYear());
                    }
                });
                Collections.sort(states, RegistrationState.DATE_COMPARATOR);
                if (!states.isEmpty()
                        && states.getLast().getStateType().equals(RegistrationStateType.FLUNKED)) {
                    final Row row = spreadsheet.addRow();
                    row.setCell(registration.getNumber());
                    CycleType cycleType = registration.getCycleType(states.getLast().getExecutionYear());
                    row.setCell(cycleType != null ? cycleType.toString() : "");
                    setDegreeCells(row, degree);
                }
            }
        }
    }
}

From source file:es.emergya.ui.gis.popups.ConsultaHistoricos.java

public static List<Object> getCurrentRecursos() {
    synchronized (recursosMostrados) {
        LinkedList<Object> res = new LinkedList<Object>();
        res.addAll(recursosMostrados);
        return res;
    }/*from w ww.  j  av  a  2s  . c o m*/
}