Example usage for java.util Set removeAll

List of usage examples for java.util Set removeAll

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Introduction

In this page you can find the example usage for java.util Set removeAll.

Prototype

boolean removeAll(Collection<?> c);

Source Link

Document

Removes from this set all of its elements that are contained in the specified collection (optional operation).

Usage

From source file:ch.unil.genescore.pathway.GeneSetLibrary.java

License:asdf

/** Compute enrichment for the given set using rank-sum-Test */
private void computeRankSumPvalue(GeneSet set) {

    Set<Gene> complementSet = new HashSet<Gene>(genesForSimulation_);
    complementSet.removeAll(set.genes_);
    double[] complementVals = new double[complementSet.size()];
    double[] setVals = new double[set.genes_.size()];
    int count = 0;
    for (Gene g : set.genes_) {
        setVals[count] = g.getChi2Stat();
        count++;//from  w ww . j  a  va  2  s .c om
    }
    count = 0;
    for (Gene g : complementSet) {
        complementVals[count] = g.getChi2Stat();
        count++;
    }
    //   TODO cleanup
    double pval = 1;
    double pval6 = 1;

    MannWhitneyUTest test = new MannWhitneyUTest();
    try {
        pval = test.mannWhitneyUTest(setVals, complementVals);
        RankSumTest test2 = new RankSumTest();
        double pval2 = test2.pValue("greater", setVals, complementVals);
        double pval3 = test2.pValue("equal", setVals, complementVals);
        MannWhitneyTest test3 = new MannWhitneyTest(setVals, complementVals);
        double pval5 = test3.approxSP();
        MannWhitneyTest test4 = new MannWhitneyTest(setVals, complementVals, H1.GREATER_THAN);
        pval6 = test4.approxSP();
    } catch (Exception e) {

        System.out.println("Couldn't compute ManWhitneyU:" + e.getMessage());
    }

    set.setRankSumPvalue(pval6);
}

From source file:eu.trentorise.smartcampus.permissionprovider.manager.ResourceManager.java

/**
 * Try to remove the resource parameter and its children. Operation is recursive.
 * If one of the derived resources is already in use, an exception is thrown.
 * @param rpId/* www. j a  v a 2  s  . c  o  m*/
 */
public void removeResourceParameter(Long rpId) {
    // main parameter
    ResourceParameter rpdb = resourceParameterRepository.findOne(rpId);
    if (rpdb != null) {
        String clientId = rpdb.getClientId();
        Set<String> ids = new HashSet<String>();
        Set<String> scopes = new HashSet<String>();
        // aggregate all derived resource uris
        Collection<String> uris = findResourceURIs(rpdb).keySet();
        for (String uri : uris) {
            Resource r = resourceRepository.findByResourceUri(uri);
            if (r != null) {
                ids.add(r.getResourceId().toString());
                scopes.add(r.getResourceUri());
            }
        }
        ClientDetailsEntity owner = null;
        // check the resource uri usages
        for (ClientDetailsEntity cd : clientDetailsRepository.findAll()) {
            if (cd.getClientId().equals(clientId)) {
                owner = cd;
                continue;
            }
            if (!Collections.disjoint(cd.getResourceIds(), ids)) {
                throw new IllegalArgumentException("Resource is in use by other client app.");
            }
        }
        // delete main and its children
        for (String id : ids) {
            resourceRepository.delete(Long.parseLong(id));
        }
        if (owner != null) {
            Set<String> oldScopes = new HashSet<String>(owner.getScope());
            oldScopes.removeAll(scopes);
            owner.setScope(StringUtils.collectionToCommaDelimitedString(oldScopes));
            Set<String> oldIds = new HashSet<String>(owner.getResourceIds());
            oldIds.removeAll(ids);
            owner.setResourceIds(StringUtils.collectionToCommaDelimitedString(oldIds));
            clientDetailsRepository.save(owner);

        }
        resourceParameterRepository.delete(rpdb);
    }
}

From source file:edu.zipcloud.cloudstreetmarket.core.services.StockProductServiceOfflineImpl.java

private void updateStocksAndQuotesFromYahoo(Set<StockProduct> askedContent) {
    if (askedContent.isEmpty()) {
        return;/*from  w  w  w.  j a v  a2  s  .c o m*/
    }

    Set<StockProduct> recentlyUpdated = askedContent.stream()
            .filter(t -> t.getLastUpdate() != null && DateUtil.isRecent(t.getLastUpdate(), 1))
            .collect(Collectors.toSet());

    if (askedContent.size() != recentlyUpdated.size()) {

        String guid = AuthenticationUtil.getPrincipal().getUsername();

        String token = usersConnectionRepository.getRegisteredSocialUser(guid).getAccessToken();
        ConnectionRepository connectionRepository = usersConnectionRepository.createConnectionRepository(guid);
        Connection<Yahoo2> connection = connectionRepository.getPrimaryConnection(Yahoo2.class);

        if (connection != null) {
            askedContent.removeAll(recentlyUpdated);

            Map<String, StockProduct> updatableTickers = askedContent.stream()
                    .collect(Collectors.toMap(StockProduct::getId, Function.identity()));

            List<YahooQuote> yahooQuotes = connection.getApi().financialOperations()
                    .getYahooQuotes(new ArrayList<String>(updatableTickers.keySet()), token);

            Set<StockProduct> updatableProducts = yahooQuotes.stream()
                    .filter(yq -> StringUtils.isNotBlank(yq.getExchange()))
                    .filter(yq -> updatableTickers.get(yq.getId()) != null).map(yq -> {
                        StockQuote sq = new StockQuote(yq, updatableTickers.get((yq.getId())));
                        return syncProduct(updatableTickers.get((yq.getId())), sq);
                    }).collect(Collectors.toSet());

            if (!updatableProducts.isEmpty()) {
                stockProductRepository.save(updatableProducts);
            }

            //This job below should decrease with the time
            Set<StockProduct> removableProducts = yahooQuotes.stream()
                    .filter(yq -> StringUtils.isBlank(yq.getExchange())).map(yq -> {
                        StockQuote sq = new StockQuote(yq, updatableTickers.get((yq.getId())));
                        return syncProduct(updatableTickers.get((yq.getId())), sq);
                    }).collect(Collectors.toSet());

            if (!removableProducts.isEmpty()) {
                stockProductRepository.delete(removableProducts);
            }
        }
    }
}

From source file:cz.cuni.amis.planning4j.external.impl.itsimple.ItSimplePlanningProcess.java

/**
 * Spawns a new planner process and sets {@link #processPid} to it's PID. To work correctly,
 * the code relies on the fact that no other method in this JVM runs processes with names
 * that would be correspond to our planners and
 * that no method kills a process unless it acquires lock on spawnProcessMutex.
 * @param procBuilder//from  w  ww.j a  v  a2  s. co  m
 * @param identifying process name / command line fragment
 * @return 
 */
private Process spawnPlanner(ProcessBuilder procBuilder, String processCommandFragment) throws IOException {
    synchronized (spawnProcessMutex) {
        JavaSysMon monitor = new JavaSysMon();
        DirectPlannerChildVisitor beforeVisitor = new DirectPlannerChildVisitor(processCommandFragment);
        monitor.visitProcessTree(monitor.currentPid(), beforeVisitor);
        Set<Integer> alreadySpawnedProcesses = beforeVisitor.getPids();

        Process proc = procBuilder.start();

        DirectPlannerChildVisitor afterVisitor = new DirectPlannerChildVisitor(processCommandFragment);

        Set<Integer> newProcesses = afterVisitor.getPids();
        long startTime = System.currentTimeMillis();
        while (newProcesses.isEmpty() && System.currentTimeMillis() - startTime < PROCESS_SPAWN_TIMEOUT) {
            monitor.visitProcessTree(monitor.currentPid(), afterVisitor);
            newProcesses = afterVisitor.getPids();

            newProcesses.removeAll(alreadySpawnedProcesses);
        }

        if (newProcesses.isEmpty()) {
            logger.warn("There is no new planner PID.");
        } else if (newProcesses.size() > 1) {
            logger.warn("Multiple new candidate planner PIDs");
        } else {
            processPid = newProcesses.iterator().next();
        }
        logger.info("Spawned planning process. Pid:" + processPid);
        return proc;
    }
}

From source file:org.waarp.common.filemonitor.FileMonitor.java

/**
 * /*from ww  w  . j  av a2 s .c o m*/
 * @return the status (updated only) in JSON format
 */
public String getStatus() {
    Set<String> removedFileItems = null;
    ConcurrentHashMap<String, FileItem> newFileItems = new ConcurrentHashMap<String, FileMonitor.FileItem>();
    if (!lastFileItems.isEmpty()) {
        removedFileItems = lastFileItems.keySet();
        removedFileItems.removeAll(fileItems.keySet());
        for (Entry<String, FileItem> key : fileItems.entrySet()) {
            if (!key.getValue().isStrictlySame(lastFileItems.get(key.getKey()))) {
                newFileItems.put(key.getKey(), key.getValue());
            }
        }
    } else {
        for (Entry<String, FileItem> key : fileItems.entrySet()) {
            newFileItems.put(key.getKey(), key.getValue());
        }
    }
    FileMonitorInformation fileMonitorInformation = new FileMonitorInformation(name, newFileItems,
            removedFileItems, directories, stopFile, statusFile, elapseTime, scanSubDir, globalok, globalerror,
            todayok, todayerror);
    for (Entry<String, FileItem> key : fileItems.entrySet()) {
        FileItem clone = key.getValue().clone();
        lastFileItems.put(key.getKey(), clone);
    }
    createChkFile();
    String status = JsonHandler.writeAsString(fileMonitorInformation);
    if (removedFileItems != null) {
        removedFileItems.clear();
    }
    newFileItems.clear();
    return status;
}

From source file:edu.zipcloud.cloudstreetmarket.api.services.StockProductServiceOnlineImpl.java

private void updateStocksAndQuotesFromYahoo(Set<StockProduct> askedContent) {
    if (askedContent.isEmpty()) {
        return;//from  w w  w .  j  a v  a 2  s . com
    }

    Set<StockProduct> recentlyUpdated = askedContent.stream()
            .filter(t -> t.getLastUpdate() != null && DateUtil.isRecent(t.getLastUpdate(), 1))
            .collect(Collectors.toSet());

    if (askedContent.size() != recentlyUpdated.size()) {

        String guid = AuthenticationUtil.getPrincipal().getUsername();
        SocialUser socialUser = usersConnectionRepository.getRegisteredSocialUser(guid);
        if (socialUser == null) {
            return;
        }
        String token = socialUser.getAccessToken();
        Connection<Yahoo2> connection = connectionRepository.getPrimaryConnection(Yahoo2.class);

        if (connection != null) {
            askedContent.removeAll(recentlyUpdated);

            Map<String, StockProduct> updatableTickers = askedContent.stream()
                    .collect(Collectors.toMap(StockProduct::getId, Function.identity()));

            List<YahooQuote> yahooQuotes = connection.getApi().financialOperations()
                    .getYahooQuotes(new ArrayList<String>(updatableTickers.keySet()), token);

            Set<StockProduct> updatableProducts = yahooQuotes.stream()
                    .filter(yq -> StringUtils.isNotBlank(yq.getExchange()))
                    .filter(yq -> updatableTickers.get(yq.getId()) != null).map(yq -> {
                        StockQuote sq = new StockQuote(yq, updatableTickers.get((yq.getId())));
                        return syncProduct(updatableTickers.get((yq.getId())), sq);
                    }).collect(Collectors.toSet());

            if (!updatableProducts.isEmpty()) {
                stockProductRepository.save(updatableProducts);
            }

            //This job below should decrease with the time
            Set<StockProduct> removableProducts = yahooQuotes.stream()
                    .filter(yq -> StringUtils.isBlank(yq.getExchange())).map(yq -> {
                        StockQuote sq = new StockQuote(yq, updatableTickers.get((yq.getId())));
                        return syncProduct(updatableTickers.get((yq.getId())), sq);
                    }).collect(Collectors.toSet());

            if (!removableProducts.isEmpty()) {
                stockProductRepository.delete(removableProducts);
            }
        }
    }
}

From source file:webim.controller.WebimController.java

@RequestMapping(value = "/online", method = RequestMethod.POST)
@ResponseBody/*from   w  w  w  . j  a  va 2s  .  co  m*/
public Map<String, Object> online(HttpServletRequest request, HttpServletResponse response) throws Exception {
    System.out.println("online.....");
    WebimEndpoint endpoint = currentEndpoint(request, response);
    String uid = endpoint.getId();
    String show = request.getParameter("show");
    if (show != null) {
        endpoint.setShow(show);
    }
    Map<String, Object> data = new HashMap<String, Object>();
    List<WebimEndpoint> buddies = this.plugin.buddies(uid);

    //pending buddies ids that need to read buddy
    Set<String> pendingIds = new HashSet<String>();
    String chatlinkIds = request.getParameter("chatlink_ids");
    if (chatlinkIds != null) {
        for (String id : chatlinkIds.split(",")) {
            pendingIds.add(id);
        }
        ;
    }
    List<WebimHistory> offlineHistories = this.model.offlineHistories(uid, 100);
    for (WebimHistory h : offlineHistories) {
        pendingIds.add(h.getFrom());
    }
    pendingIds.removeAll(buddyIds(buddies));

    if (pendingIds.size() > 0) {
        buddies.addAll(this.plugin.buddiesByIds(uid, pendingIds.toArray(new String[pendingIds.size()])));
    }

    List<WebimRoom> rooms = this.plugin.rooms(uid);
    rooms.addAll(this.model.rooms(uid));
    // Forward Online to IM Server
    WebimClient client = this.client(endpoint, request, "");
    Set<String> buddyIds = buddyIds(buddies);
    Set<String> roomIds = roomIds(rooms);
    try {
        data = client.online(buddyIds, roomIds);
        System.out.println(data.toString());

        // Online Buddies
        Map<String, WebimEndpoint> buddyMap = new HashMap<String, WebimEndpoint>();
        for (WebimEndpoint e : buddies) {
            buddyMap.put(e.getId(), e);
        }

        @SuppressWarnings("unchecked")
        Map<String, String> presences = (Map<String, String>) data.get("presences");
        Iterator<String> it = presences.keySet().iterator();
        while (it.hasNext()) {
            String key = it.next();
            WebimEndpoint buddy = buddyMap.get(key);
            show = presences.get(key);
            if (!show.equals("invisible")) {
                buddy.setPresence("online");
                buddy.setShow(show);
            }
        }

        Collection<WebimEndpoint> rtBuddies;
        if (this.config.getBoolean("show_unavailable")) {
            rtBuddies = buddyMap.values();
        } else {
            rtBuddies = new ArrayList<WebimEndpoint>();
            for (WebimEndpoint e : buddyMap.values()) {
                if (e.getPresence() == "online")
                    rtBuddies.add(e);
            }
        }
        // need test
        this.model.offlineHistoriesReaded(uid);
        //data.remove("presences");
        data.put("buddies", rtBuddies.toArray());
        data.put("rooms", rooms.toArray());
        data.put("new_messages", offlineHistories.toArray());
        data.put("server_time", System.currentTimeMillis()); // TODO: /
        data.put("user", endpoint);
    } catch (Exception e) {
        e.printStackTrace();
        data.put("success", false);
        data.put("error_msg", "IM Server is not found");
    }
    return data;
}

From source file:com.aurel.track.item.ItemBL.java

/**
 * Get all descendants which are not included in the original query result
 * @param baseWorkItemIDsArr//from   ww  w  . j a  v a2 s  .c o  m
 * @return
 */
public static List<TWorkItemBean> getAncestorItems(int[] baseWorkItemIDsArr) {
    List<TWorkItemBean> ancestorWorkItemBeans = new LinkedList<TWorkItemBean>();
    Set<Integer> allDescendentIDsSet = new HashSet<Integer>();
    Set<Integer> directChildrenIDsSet;
    int[] directChildrenArr = baseWorkItemIDsArr;
    Set<Integer> toRemoveSet = GeneralUtils.createSetFromIntArr(baseWorkItemIDsArr);
    do {
        //get the next level of children workItems
        List<TWorkItemBean> childWorkItemBeans = getChildren(directChildrenArr, false, null, null, null);
        ancestorWorkItemBeans.addAll(childWorkItemBeans);
        //get the ID set of children
        directChildrenIDsSet = GeneralUtils.createIntegerSetFromBeanList(childWorkItemBeans);
        //remove the children which are already present in the gathered list (theoretically remove might occur only first time)
        directChildrenIDsSet.removeAll(toRemoveSet);

        //gather the not yet present children to the list
        allDescendentIDsSet.addAll(directChildrenIDsSet);
        toRemoveSet = allDescendentIDsSet;
        directChildrenArr = GeneralUtils.createIntArrFromSet(directChildrenIDsSet);
    } while (directChildrenIDsSet != null && !directChildrenIDsSet.isEmpty());
    return ancestorWorkItemBeans;
}

From source file:org.itracker.services.implementations.UserServiceImpl.java

/**
 * @param userId         - id of update-user
 * @param newPermissions - set of new permissions for this user
 *//*from w  w w.  jav a2 s . c om*/
@Override
public boolean setUserPermissions(final Integer userId, final List<Permission> newPermissions) {

    boolean hasChanges = false;
    // rewriting this method

    TreeSet<Permission> pSet = new TreeSet<Permission>(Permission.PERMISSION_PROPERTIES_COMPARATOR);
    pSet.addAll(newPermissions);

    User usermodel = this.getUser(userId);

    Set<Permission> current = new TreeSet<Permission>(Permission.PERMISSION_PROPERTIES_COMPARATOR);

    current.addAll(usermodel.getPermissions());

    // setup permissions to be removed
    Set<Permission> remove = new TreeSet<Permission>(Permission.PERMISSION_PROPERTIES_COMPARATOR);
    remove.addAll(current);
    remove.removeAll(pSet);
    // setup permissions to be added
    Set<Permission> add = new TreeSet<Permission>(Permission.PERMISSION_PROPERTIES_COMPARATOR);
    add.addAll(pSet);
    add.removeAll(current);

    // look permission
    Permission p;
    Iterator<Permission> pIt = remove.iterator();
    while (pIt.hasNext()) {
        p = find(usermodel.getPermissions(), (Permission) pIt.next());
        if (null == p) {
            continue;
        }
        if (usermodel.getPermissions().contains(p)) {
            usermodel.getPermissions().remove(p);
            permissionDAO.delete(p);
            hasChanges = true;
        }
    }

    pIt = add.iterator();
    while (pIt.hasNext()) {
        p = pIt.next();
        if (null == find(usermodel.getPermissions(), p) && !usermodel.getPermissions().contains(p)) {
            p.setUser(usermodel);
            usermodel.getPermissions().add(p);
            permissionDAO.save(p);
            hasChanges = true;
        }
    }

    if (hasChanges) {
        userDAO.saveOrUpdate(usermodel);
    }

    return hasChanges;
}