Example usage for java.util LinkedHashSet addAll

Introduction

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

Prototype

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

Source Link

Document

Adds all of the elements in the specified collection to this set if they're not already present (optional operation).

Usage

From source file:com.act.biointerpretation.cofactorremoval.CofactorRemover.java

/**
 * This function is the meat of the cofactor removal process.  It extracts all cofactors based on their ids and
 * places them in the appropriate collection within the reaciton.  Note that because this is executed by
 * BiointerpretationProcessor's `runSpecializedReactionProcessing` hook, the chemical ids have already been updated
 * to reference the chemical entries in the WriteDB.
 * @param reaction The reaction to update.
 * @param component Update substrates or products.
 *///from   w ww  .j  a va2s.c  om
private void updateReactionProductOrSubstrate(Reaction reaction, ReactionComponent component) {
    Long[] chemIds, originalCofactorIds;
    if (component == SUBSTRATE) {
        chemIds = reaction.getSubstrates();
        originalCofactorIds = reaction.getSubstrateCofactors();
    } else {
        chemIds = reaction.getProducts();
        originalCofactorIds = reaction.getProductCofactors();
    }

    Map<Boolean, List<Long>> partitionedIds = Arrays.asList(chemIds).stream()
            .collect(Collectors.partitioningBy(knownCofactorWriteDBIds::contains));

    List<Long> cofactorIds = partitionedIds.containsKey(true) ? partitionedIds.get(true)
            : Collections.EMPTY_LIST;
    List<Long> nonCofactorIds = partitionedIds.containsKey(false) ? partitionedIds.get(false)
            : Collections.EMPTY_LIST;

    // Retain previously partitioned cofactors if any exist.
    if (originalCofactorIds != null && originalCofactorIds.length > 0) {
        // Use an ordered set to unique the partitioned and previously specified cofactors.  Original cofactors go first.
        LinkedHashSet<Long> uniqueCofactorIds = new LinkedHashSet<>(Arrays.asList(originalCofactorIds));
        uniqueCofactorIds.addAll(cofactorIds);
        /* We do this potentially expensive de-duplication step only in the presumably rare case that we find a reaction
         * that already has cofactors set.  A reaction that has not already undergone cofactor removal is very unlikely to
         * have cofactors partitioned from substrates/products. */
        cofactorIds = new ArrayList<>(uniqueCofactorIds);
    }

    // Coefficients for cofactors should automatically fall out when we update the substrate/product list.
    if (component == SUBSTRATE) {
        reaction.setSubstrateCofactors(cofactorIds.toArray(new Long[cofactorIds.size()]));
        reaction.setSubstrates(nonCofactorIds.toArray(new Long[nonCofactorIds.size()]));
        /* Coefficients should already have been set when the reaction was migrated to the new DB, so no need to update.
         * Note that this assumption depends strongly on the current coefficient implementation in the Reaction model. */
    } else {
        reaction.setProductCofactors(cofactorIds.toArray(new Long[cofactorIds.size()]));
        reaction.setProducts(nonCofactorIds.toArray(new Long[nonCofactorIds.size()]));
    }
}

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From source file:org.osaf.cosmo.atom.provider.DetachedItemCollectionAdapter.java

private NoteItem detachOccurrence(NoteItem master, NoteItem copy, NoteItem occurrence) {

    ThisAndFutureHelper tafHelper = new ThisAndFutureHelper();
    LinkedHashSet<ContentItem> updates = new LinkedHashSet<ContentItem>();

    // need to update master, create new master
    updates.add(master);//from ww w  .  j  a v  a 2 s .  c o  m
    updates.add(copy);

    // get all modifications to remove/add
    updates.addAll(tafHelper.breakRecurringEvent(master, copy, occurrence));

    // This service call will update/remove/create items in one transaction
    // Any new items will be added to all specified parents.
    getContentService().updateContentItems(master.getParents(), updates);

    return copy;
}

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From source file:com.geewhiz.pacify.managers.FilterManager.java

private LinkedHashSet<Defect> filterPFile(PFile pFile) {
    logger.info("      Customize File [{}]", pFile.getRelativePath());
    logger.debug("          Filtering [{}] using encoding [{}] and filter [{}]",
            pMarker.getAbsoluteFileFor(pFile).getAbsolutePath(), pFile.getEncoding(), pFile.getFilterClass());

    File fileToFilter = pMarker.getAbsoluteFileFor(pFile);
    PacifyFilter pacifyFilter = getFilterForPFile(pFile);

    Map<String, String> propertyValues = new HashMap<String, String>();
    LinkedHashSet<Defect> defects = fillPropertyValuesFor(propertyValues, pFile);

    String beginToken = pMarker.getBeginTokenFor(pFile);
    String endToken = pMarker.getEndTokenFor(pFile);
    String encoding = pFile.getEncoding();

    defects.addAll(pacifyFilter.filter(propertyValues, beginToken, endToken, fileToFilter, encoding));
    logger.info("          [{}] placeholders replaced.", pFile.getPProperties().size());

    return defects;
}

---

From source file:org.loklak.api.server.SuggestServlet.java

@Override
protected void doGet(HttpServletRequest request, HttpServletResponse response)
        throws ServletException, IOException {
    RemoteAccess.Post post = RemoteAccess.evaluate(request);

    // manage DoS
    if (post.isDoS_blackout()) {
        response.sendError(503, "your request frequency is too high");
        return;//from w w  w.jav a  2s. co  m
    }

    String callback = post.get("callback", "");
    boolean jsonp = callback != null && callback.length() > 0;
    boolean minified = post.get("minified", false);

    int requestkey = post.hashCode();
    Map<String, Object> m = post.isDoS_servicereduction() ? cache.get(requestkey) : null;
    if (m == null) {
        boolean local = post.isLocalhostAccess();
        boolean delete = post.get("delete", false);
        int count = post.get("count", 10); // number of queries
        String query = post.get("q", ""); // to get a list of queries which match; to get all latest: leave q empty
        String source = post.get("source", "all"); // values: all,query,geo
        String orders = post.get("order", query.length() == 0 ? "desc" : "asc").toUpperCase();
        SortOrder order = SortOrder.valueOf(orders);
        String orderby = post.get("orderby", query.length() == 0 ? "retrieval_next" : "query_count");
        int timezoneOffset = post.get("timezoneOffset", 0);
        Date since = post.get("since", "").equals("now") ? new Date()
                : post.get("since", (Date) null, timezoneOffset);
        Date until = post.get("until", "").equals("now") ? new Date()
                : post.get("until", (Date) null, timezoneOffset);
        String selectby = post.get("selectby", "retrieval_next");
        ResultList<QueryEntry> queryList = new ResultList<>();

        if ((source.equals("all") || source.equals("query")) && query.length() >= 0) {
            long start = System.currentTimeMillis();
            queryList = DAO.SearchLocalQueries(query, count, orderby, "long", order, since, until, selectby);
            post.recordEvent("localqueries_time", System.currentTimeMillis() - start);
        }

        if (delete && local && queryList.size() > 0) {
            long start = System.currentTimeMillis();
            for (QueryEntry qe : queryList)
                DAO.deleteQuery(qe.getQuery(), qe.getSourceType());
            queryList.clear();
            queryList = DAO.SearchLocalQueries(query, count, orderby, "long", order, since, until, selectby);
            post.recordEvent("localquerydelete_time", System.currentTimeMillis() - start);
        }

        if (source.equals("all") || source.equals("geo")) {
            long start = System.currentTimeMillis();
            LinkedHashSet<String> suggestions = DAO.geoNames.suggest(query, count, 0);
            if (suggestions.size() < count && query.length() > 2)
                suggestions.addAll(DAO.geoNames.suggest(query, count, 1));
            if (suggestions.size() < count && query.length() > 5)
                suggestions.addAll(DAO.geoNames.suggest(query, count, 2));
            for (String s : suggestions) {
                QueryEntry qe = new QueryEntry(s, 0, Long.MAX_VALUE, SourceType.IMPORT, false);
                queryList.add(qe);
            }
            post.recordEvent("suggestionsquery_time", System.currentTimeMillis() - start);
        }

        long start = System.currentTimeMillis();
        post.setResponse(response, "application/javascript");

        List<Object> queries = new ArrayList<>();
        if (queryList != null)
            for (QueryEntry t : queryList)
                queries.add(t.toMap());

        int random = post.get("random", -1);
        if (random > 0 && random < queries.size()) {
            // take the given number from the result list and use random to choose
            List<Object> random_queries = new ArrayList<>();
            Random r = new Random(System.currentTimeMillis());
            while (random-- > 0) {
                random_queries.add(queries.remove(r.nextInt(queries.size())));
                int shrink = Math.max(queries.size() / 2, random * 10);
                while (queries.size() > shrink)
                    queries.remove(queries.size() - 1); // prefer from top
            }
            queries = random_queries;
        }

        // generate json
        m = new LinkedHashMap<String, Object>();
        Map<String, Object> metadata = new LinkedHashMap<String, Object>();
        metadata.put("count", queryList == null ? "0" : Integer.toString(queries.size()));
        metadata.put("hits", queryList.getHits());
        metadata.put("query", query);
        metadata.put("order", orders);
        metadata.put("orderby", orderby);
        if (since != null)
            metadata.put("since", AbstractIndexEntry.utcFormatter.print(since.getTime()));
        if (until != null)
            metadata.put("until", AbstractIndexEntry.utcFormatter.print(until.getTime()));
        if (since != null || until != null)
            metadata.put("selectby", selectby);
        metadata.put("client", post.getClientHost());
        m.put("search_metadata", metadata);

        m.put("queries", queries);
        post.recordEvent("postprocessing_time", System.currentTimeMillis() - start);
    }

    // write json
    response.setCharacterEncoding("UTF-8");
    PrintWriter sos = response.getWriter();
    if (jsonp)
        sos.print(callback + "(");
    sos.print(minified ? new ObjectMapper().writer().writeValueAsString(m)
            : new ObjectMapper().writerWithDefaultPrettyPrinter().writeValueAsString(m));
    if (jsonp)
        sos.println(");");
    sos.println();
    post.finalize();
}

---

From source file:org.loklak.api.search.SuggestServlet.java

@Override
protected void doGet(HttpServletRequest request, HttpServletResponse response)
        throws ServletException, IOException {
    Query post = RemoteAccess.evaluate(request);

    // manage DoS
    if (post.isDoS_blackout()) {
        response.sendError(503, "your request frequency is too high");
        return;//from w  w w  . j a  v  a 2 s  .  c o m
    }

    String callback = post.get("callback", "");
    boolean jsonp = callback != null && callback.length() > 0;
    boolean minified = post.get("minified", false);

    int requestkey = post.hashCode();
    JSONObject m = post.isDoS_servicereduction() ? cache.get(requestkey) : null;
    if (m == null) {
        boolean local = post.isLocalhostAccess();
        boolean delete = post.get("delete", false);
        int count = post.get("count", 10); // number of queries
        String query = post.get("q", ""); // to get a list of queries which match; to get all latest: leave q empty
        String source = post.get("source", "all"); // values: all,query,geo
        String orders = post.get("order", query.length() == 0 ? "desc" : "asc").toUpperCase();
        SortOrder order = SortOrder.valueOf(orders);
        String orderby = post.get("orderby", query.length() == 0 ? "retrieval_next" : "query_count");
        int timezoneOffset = post.get("timezoneOffset", 0);
        Date since = post.get("since", "").equals("now") ? new Date()
                : post.get("since", (Date) null, timezoneOffset);
        Date until = post.get("until", "").equals("now") ? new Date()
                : post.get("until", (Date) null, timezoneOffset);
        String selectby = post.get("selectby", "retrieval_next");
        ResultList<QueryEntry> queryList = new ResultList<>();

        if ((source.equals("all") || source.equals("query")) && query.length() >= 0) {
            long start = System.currentTimeMillis();
            queryList = DAO.SearchLocalQueries(query, count, orderby, "long", order, since, until, selectby);
            post.recordEvent("localqueries_time", System.currentTimeMillis() - start);
        }

        if (delete && local && queryList.size() > 0) {
            long start = System.currentTimeMillis();
            for (QueryEntry qe : queryList)
                DAO.deleteQuery(qe.getQuery(), qe.getSourceType());
            queryList.clear();
            queryList = DAO.SearchLocalQueries(query, count, orderby, "long", order, since, until, selectby);
            post.recordEvent("localquerydelete_time", System.currentTimeMillis() - start);
        }

        if (source.equals("all") || source.equals("geo")) {
            long start = System.currentTimeMillis();
            LinkedHashSet<String> suggestions = DAO.geoNames.suggest(query, count, 0);
            if (suggestions.size() < count && query.length() > 2)
                suggestions.addAll(DAO.geoNames.suggest(query, count, 1));
            if (suggestions.size() < count && query.length() > 5)
                suggestions.addAll(DAO.geoNames.suggest(query, count, 2));
            for (String s : suggestions) {
                QueryEntry qe = new QueryEntry(s, 0, Long.MAX_VALUE, SourceType.TWITTER, false);
                queryList.add(qe);
            }
            post.recordEvent("suggestionsquery_time", System.currentTimeMillis() - start);
        }

        long start = System.currentTimeMillis();
        post.setResponse(response, "application/javascript");

        List<Object> queries = new ArrayList<>();
        if (queryList != null)
            for (QueryEntry t : queryList)
                queries.add(t.toJSON().toMap());

        int random = post.get("random", -1);
        if (random > 0 && random < queries.size()) {
            // take the given number from the result list and use random to choose
            List<Object> random_queries = new ArrayList<>();
            Random r = new Random(System.currentTimeMillis());
            while (random-- > 0) {
                random_queries.add(queries.remove(r.nextInt(queries.size())));
                int shrink = Math.max(queries.size() / 2, random * 10);
                while (queries.size() > shrink)
                    queries.remove(queries.size() - 1); // prefer from top
            }
            queries = random_queries;
        }

        // generate json
        m = new JSONObject(true);
        JSONObject metadata = new JSONObject(true);
        metadata.put("count", queryList == null ? "0" : Integer.toString(queries.size()));
        metadata.put("hits", queryList.getHits());
        metadata.put("query", query);
        metadata.put("order", orders);
        metadata.put("orderby", orderby);
        if (since != null)
            metadata.put("since", AbstractObjectEntry.utcFormatter.print(since.getTime()));
        if (until != null)
            metadata.put("until", AbstractObjectEntry.utcFormatter.print(until.getTime()));
        if (since != null || until != null)
            metadata.put("selectby", selectby);
        metadata.put("client", post.getClientHost());
        m.put("search_metadata", metadata);

        m.put("queries", queries);
        post.recordEvent("postprocessing_time", System.currentTimeMillis() - start);
    }

    // write json
    response.setCharacterEncoding("UTF-8");
    PrintWriter sos = response.getWriter();
    if (jsonp)
        sos.print(callback + "(");
    sos.print(m.toString(minified ? 0 : 2));
    if (jsonp)
        sos.println(");");
    sos.println();
    post.finalize();
}

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From source file:org.rapidcontext.core.type.WebService.java

/**
 * Returns the HTTP methods supported for the specified request.
 * The OPTIONS method is always supported and the HEAD method is
 * automatically added if GET is supported.
 *
 * @param request        the request to check
 *
 * @return the array of HTTP method names supported
 *///from w w w .  j av a  2s.  c om
public String[] methods(Request request) {
    LinkedHashSet set = new LinkedHashSet();
    set.add(METHOD.OPTIONS);
    set.addAll(Arrays.asList(methodsImpl(request)));
    for (int i = 0; i < matchers.size(); i++) {
        WebMatcher m = (WebMatcher) matchers.get(i);
        if (m.method() != null && m.match(request) > 0) {
            set.add(m.method());
        }
    }
    if (set.contains(METHOD.GET)) {
        set.add(METHOD.HEAD);
    }
    return (String[]) set.toArray(new String[set.size()]);
}

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From source file:com.geewhiz.pacify.Replacer.java

public LinkedHashSet<Defect> doReplacement(EntityManager entityManager) {
    LinkedHashSet<Defect> defects = new LinkedHashSet<Defect>();
    for (PMarker pMarker : entityManager.getPMarkers()) {
        logger.info("   Processing Marker File [{}],", pMarker.getFile().getAbsolutePath());
        FilterManager filterManager = new FilterManager(propertyResolveManager, pMarker);
        defects.addAll(filterManager.doFilter());
    }// w ww  .  ja  v  a2 s . c  o m
    return defects;
}

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From source file:org.search.niem.uml.qvt.NiemQvtLibrary.java

@Operation(contextual = true, kind = Operation.Kind.QUERY)
public static LinkedHashSet<Package> getPimConstraintModels(final Package self) {
    final LinkedHashSet<Package> pimConstraintModels = new LinkedHashSet<>();
    for (final Dependency d : self.getClientDependencies()) {
        if (UMLPackage.Literals.REALIZATION.isInstance(d) && getAppliedReferencesStereotype(d) != null) {
            pimConstraintModels
                    .addAll(EcoreUtil.<Package>getObjectsByType(d.getClients(), UMLPackage.Literals.PACKAGE));
        }/*from  w  w  w.j  a v a 2s.c o m*/
    }
    return pimConstraintModels;
}

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From source file:de.hybris.platform.classification.impl.DefaultClassificationClassesResolverStrategy.java

@Override
public List<ClassAttributeAssignmentModel> getAllClassAttributeAssignments(
        final Set<ClassificationClassModel> classificationClasses) {
    if (classificationClasses != null && !classificationClasses.isEmpty()) {
        final LinkedHashSet<ClassAttributeAssignmentModel> list = new LinkedHashSet<ClassAttributeAssignmentModel>();
        for (final ClassificationClassModel ccl : classificationClasses) {
            list.addAll(ccl.getAllClassificationAttributeAssignments());
        }/* ww w.  java  2  s.c  o  m*/
        return new ArrayList(list);
    } else {
        return Collections.EMPTY_LIST;
    }
}

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From source file:org.openflexo.foundation.sg.implmodel.TechnologyModuleDefinition.java

/**
 * Recursively retrieve all modules required by this module, including itself.
 * //w ww  .j  a  va 2  s .  com
 * @return the retrieved required modules.
 */
public Set<TechnologyModuleDefinition> getAllRequiredModules() {

    Map<Integer, LinkedHashSet<TechnologyModuleDefinition>> requiredModules = getAllRequiredModulesByLevel();

    LinkedHashSet<TechnologyModuleDefinition> result = new LinkedHashSet<TechnologyModuleDefinition>();
    for (LinkedHashSet<TechnologyModuleDefinition> set : requiredModules.values()) {
        result.addAll(set);
    }

    return result;
}

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