Example usage for java.util Set retainAll

List of usage examples for java.util Set retainAll

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Introduction

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

Prototype

boolean retainAll(Collection<?> c);

Source Link

Document

Retains only the elements in this set that are contained in the specified collection (optional operation).

Usage

From source file:no.sintef.ict.splcatool.CoveringArrayChvatal.java

public static Set<Pair2> intersect(Set<Pair2> set1, Set<Pair2> set2) {
    Set<Pair2> intersection = new HashSet<Pair2>(set1);
    intersection.retainAll(new HashSet<Pair2>(set2));
    return intersection;
}

From source file:org.callimachusproject.server.chain.TransactionHandler.java

private String closest(String origin, Set<String> origins) {
    Set<Character> base = toSet(origin.toCharArray());
    String closest = null;//from w  ww .j  a  v a  2 s  .c om
    Set<Character> common = null;
    for (String o : origins) {
        Set<Character> set = toSet(o.toCharArray());
        set.retainAll(base);
        if (common == null || set.size() > common.size()) {
            common = set;
            closest = o;
        }
    }
    return closest;
}

From source file:org.jasig.portlet.contacts.control.PortletViewController.java

@ModelAttribute("domains")
public Set<ContactDomain> getDomains(PortletPreferences prefs) {
    log.debug("finding Domains to return");
    final List<String> domainActive = Arrays.asList(prefs.getValues("domainsActive", new String[0]));

    String[] defaultOn = prefs.getValues("defaultOn", new String[0]);
    String[] userOn = prefs.getValues("domainOn", new String[0]);
    String[] userOff = prefs.getValues("domainOff", new String[0]);

    Set<String> domains = new HashSet<String>();
    domains.addAll(Arrays.asList(defaultOn));
    domains.addAll(Arrays.asList(userOn));
    domains.removeAll(Arrays.asList(userOff));
    domains.retainAll(domainActive);

    Set<ContactDomain> activeDomains = new TreeSet<ContactDomain>(new Comparator<ContactDomain>() {

        @Override// w w w  .  j  a v a 2  s.  c o  m
        public int compare(ContactDomain o1, ContactDomain o2) {
            int index1 = domainActive.indexOf(o1.getName());
            int index2 = domainActive.indexOf(o2.getName());
            return index1 - index2;
        }
    });
    for (ContactDomain domain : contactDomains) {
        if (domains.contains(domain.getName())) {
            activeDomains.add(domain);
        }
    }
    log.debug("returning " + activeDomains.size() + "domains");
    return activeDomains;
}

From source file:dk.netarkivet.harvester.harvesting.report.LegacyHarvestReport.java

/**
 * Post-processing happens on the scheduler side when ARC files
 * have been uploaded./*  w w  w.j a  v a 2 s  .  c o  m*/
 * @param job the actual job.
 */
@Override
public void postProcess(Job job) {

    if (LOG.isInfoEnabled()) {
        LOG.info("Starting post-processing of harvest report for job " + job.getJobID());
    }
    long startTime = System.currentTimeMillis();

    // Get the map from domain names to domain configurations
    Map<String, String> configurationMap = job.getDomainConfigurationMap();

    // For each domain harvested, check if it corresponds to a
    // domain configuration for this Job and if so add a new HarvestInfo
    // to the DomainHistory of the corresponding Domain object.
    // TODO  Information about the domains harvested by the crawler
    // without a domain configuration for this job is deleted!
    // Should this information be saved in some way (perhaps stored
    // in metadata.arc-files?)

    final Set<String> domainNames = new HashSet<String>();
    domainNames.addAll(getDomainNames());
    domainNames.retainAll(configurationMap.keySet());
    final DomainDAO dao = DomainDAO.getInstance();
    for (String domainName : domainNames) {
        Domain domain = dao.read(domainName);

        // Retrieve crawl data from log and add it to HarvestInfo
        StopReason stopReason = getStopReason(domainName);
        if (stopReason == null) {
            LOG.warn("No stopreason found for domain '" + domainName + "'");
        }
        Long countObjectRetrieved = getObjectCount(domainName);
        if (countObjectRetrieved == null) {
            LOG.warn("No count for objects retrieved found for domain '" + domainName + "'");
            countObjectRetrieved = -1L;
        }
        Long bytesReceived = getByteCount(domainName);
        if (bytesReceived == null) {
            LOG.warn("No count for bytes received found for domain '" + domainName + "'");
            bytesReceived = -1L;
        }
        //If StopReason is SIZE_LIMIT, we check if it's the harvests' size
        //limit, or rather a configuration size limit.

        //A harvest is considered to have hit the configuration limit if
        //1) The limit is lowest, or
        //2) The number of harvested bytes is greater than the limit

        // Note: Even though the per-config-byte-limit might have changed
        // between the time we calculated the job and now, it's okay we
        // compare with the new limit, since it gives us the most accurate
        // result for whether we want to harvest any more.
        if (stopReason == StopReason.SIZE_LIMIT) {
            long maxBytesPerDomain = job.getMaxBytesPerDomain();
            long configMaxBytes = domain.getConfiguration(configurationMap.get(domainName)).getMaxBytes();
            if (NumberUtils.compareInf(configMaxBytes, maxBytesPerDomain) <= 0
                    || NumberUtils.compareInf(configMaxBytes, bytesReceived) <= 0) {
                stopReason = StopReason.CONFIG_SIZE_LIMIT;
            }
        } else if (stopReason == StopReason.OBJECT_LIMIT) {
            long maxObjectsPerDomain = job.getMaxObjectsPerDomain();
            long configMaxObjects = domain.getConfiguration(configurationMap.get(domainName)).getMaxObjects();
            if (NumberUtils.compareInf(configMaxObjects, maxObjectsPerDomain) <= 0) {
                stopReason = StopReason.CONFIG_OBJECT_LIMIT;
            }
        }
        // Create the HarvestInfo object
        HarvestInfo hi = new HarvestInfo(job.getOrigHarvestDefinitionID(), job.getJobID(), domain.getName(),
                configurationMap.get(domain.getName()), new Date(), bytesReceived, countObjectRetrieved,
                stopReason);

        // Add HarvestInfo to Domain and make data persistent
        // by updating DAO
        domain.getHistory().addHarvestInfo(hi);
        dao.update(domain);
    }

    if (LOG.isInfoEnabled()) {
        long time = System.currentTimeMillis() - startTime;
        LOG.info("Finished post-processing of harvest report for job " + job.getJobID() + ", operation took "
                + StringUtils.formatDuration(time / TimeUtils.SECOND_IN_MILLIS));
    }

}

From source file:org.biopax.psidev.ontology_manager.impl.OntologyManagerImpl.java

public Set<OntologyTermI> searchTermByName(String name, Set<String> ontologies) {
    Set<OntologyTermI> found = new HashSet<OntologyTermI>();
    assert name != null : "searchTermByName: null arg.";

    Set<String> ontologyIDs = new HashSet<String>(getOntologyIDs());
    if (ontologies != null && !ontologies.isEmpty())
        ontologyIDs.retainAll(ontologies);

    for (String ontologyId : ontologyIDs) {
        OntologyAccess oa = getOntology(ontologyId);
        for (OntologyTermI term : oa.getOntologyTerms()) {
            String prefName = term.getPreferredName();
            if (prefName == null) {
                log.error("searchTermByName: NULL preffered name for term " + term.getTermAccession() + " in "
                        + ontologyId + "; report to authors.");
            } else if (name.equalsIgnoreCase(prefName)) {
                found.add(term);//from www.ja va  2  s.c o  m
            } else {
                for (String syn : term.getNameSynonyms()) {
                    if (syn.equalsIgnoreCase(name)) {
                        found.add(term);
                    }
                }
            }
        }
    }

    return found;
}

From source file:edu.wisc.my.portlets.dmp.web.ViewMenuController.java

/**
 * @see org.springframework.web.portlet.mvc.AbstractController#handleRenderRequestInternal(javax.portlet.RenderRequest, javax.portlet.RenderResponse)
 *///from w w  w  .j  av  a  2s  . c om
@Override
protected ModelAndView handleRenderRequestInternal(RenderRequest request, RenderResponse response)
        throws Exception {
    // find the username
    final String userName = request.getRemoteUser();
    if (this.logger.isDebugEnabled()) {
        this.logger.debug("remoteUser='" + userName + "'");
    }

    // get the menu name from the portlet properties
    final PortletPreferences pp = request.getPreferences();
    final String menuName = pp.getValue(MENU_NAME, null);

    //find all the groups this person is a member of
    final String[] userGroups = this.groupsDao.getContainingGroups(userName);

    if (this.logger.isInfoEnabled()) {
        this.logger.info("Rendering Dynamic Menu '" + menuName + "' with group list '"
                + Arrays.asList(userGroups) + "' for user '" + userName + "'");
    }

    final MenuItem menuRoot;
    if (userGroups != null) {
        //get the root MenuItem for the name and list of groups
        menuRoot = this.menuDao.getMenu(menuName, userGroups);
    } else {
        //Get the root MenuItem for the name
        menuRoot = this.menuDao.getMenu(menuName);
    }

    final Map<String, Object> model = new HashMap<String, Object>();
    model.put(MODEL_MENU_NAME, menuName);

    if (menuRoot != null) {
        //All the groups the menu supports
        final Set<String> menuGroups = this.getAllMenuGroups(menuRoot);
        //Reduce menu groups to just those that overlap with the user's group list
        menuGroups.retainAll(Arrays.asList(userGroups));

        final Serializable cacheKey = this.getCacheKey(menuName, menuGroups);
        model.put("contentCacheKey", cacheKey);
        model.put(MODEL_ROOT_ITEM, menuRoot);

        return new ModelAndView(VIEW_MENU, model);
    }

    return new ModelAndView(VIEW_NO_MENU, model);
}

From source file:io.minio.policy.Statement.java

/**
 * Returns whether given statement is valid to process for given bucket name.
 *//*from ww  w  .j  ava2 s  .c  o  m*/
public boolean isValid(String bucketName) {
    Set<String> intersection = new HashSet<String>(this.actions);
    intersection.retainAll(Constants.VALID_ACTIONS);
    if (intersection.isEmpty()) {
        return false;
    }

    if (!this.effect.equals("Allow")) {
        return false;
    }

    Set<String> aws = this.principal.aws();
    if (aws == null || !aws.contains("*")) {
        return false;
    }

    String bucketResource = Constants.AWS_RESOURCE_PREFIX + bucketName;

    if (this.resources.contains(bucketResource)) {
        return true;
    }

    if (this.resources.startsWith(bucketResource + "/").isEmpty()) {
        return false;
    }

    return true;
}

From source file:main.java.spelementex.Evaluator.java

/**
 * given result file, gets the true and false positive entity counts.
 * please note: this function is mainly intended for development purposes; 
 * it will not work if the result file does not have gold annotation labels 
 * in the second to the last column.//from  w w  w. j a  v a2s .  com
 * 
 * @param result
 * @return double[] of size 2 with true positive count at index 0 and
 * false positive count at index 1.
 */
public static double[] getTpFp(String[] result) {
    double[] tpFp = new double[2];

    Set<String> goldAnnotations = new HashSet<>();
    Set<Integer> visitedTokens = new HashSet<>();
    Set<String> predictedAnnotations = new HashSet<>();
    Set<Integer> predictedTokens = new HashSet<>();
    int tokenNum = 0;

    int length = result.length;
    for (int i = 0; i < length; i++) {
        String line = result[i].trim();
        if (line.equals(""))
            continue;

        String[] lineTokens = line.split("\\s+");

        if (lineTokens.length == 3) {
            tokenNum = 0;
            //# 0 0.076469
            if (lineTokens[1].equals("0") && !goldAnnotations.isEmpty()) {
                goldAnnotations.retainAll(predictedAnnotations);
                tpFp[0] += goldAnnotations.size();
                predictedAnnotations.removeAll(goldAnnotations);
                tpFp[1] += predictedAnnotations.size();

                goldAnnotations = new HashSet<>();
                visitedTokens = new HashSet<>();
                predictedAnnotations = new HashSet<>();
                predictedTokens = new HashSet<>();
            }
            continue;
        }

        String goldTag = lineTokens[lineTokens.length - 2];
        if (goldTag.matches("B\\-.*") && !visitedTokens.contains(tokenNum)) {
            int[] tokenOffsets = getTokenOffset(result, i, tokenNum);
            goldAnnotations.add(tokenOffsets[0] + "-" + tokenOffsets[1] + "-" + goldTag);
            visitedTokens.add(tokenNum);
        }

        String predictedTag = lineTokens[lineTokens.length - 1];
        if (predictedTag.matches("B\\-.*") && !predictedTokens.contains(tokenNum)) {
            if (lineTokens[0].matches("[^a-zA-Z0-9]+") || lineTokens[0].equals("-lrb-")
                    || lineTokens[0].equals("-rrb-")) {
                if (i + 1 == result.length) {
                    tokenNum++;
                    continue;
                }
                line = result[i + 1].trim();
                lineTokens = line.split("\\s+");
                if (line.equals("") || lineTokens.length == 3 || lineTokens[lineTokens.length - 1].equals("O")
                        || lineTokens[lineTokens.length - 1].matches("B\\-.*")) {
                    tokenNum++;
                    continue;
                }
            }
            int[] tokenOffsets = getTokenOffset(result, i, tokenNum);

            Set<Integer> tempPredictedTokens = new HashSet<>();
            for (int j = tokenOffsets[0]; j <= tokenOffsets[1]; j++)
                tempPredictedTokens.add(j);

            int before = tempPredictedTokens.size();
            tempPredictedTokens.removeAll(predictedTokens);
            int after = tempPredictedTokens.size();
            if (before == after) {
                predictedTokens.addAll(tempPredictedTokens);
                predictedAnnotations.add(tokenOffsets[0] + "-" + tokenOffsets[1] + "-" + predictedTag);
            }
        }

        tokenNum++;
    }

    goldAnnotations.retainAll(predictedAnnotations);
    tpFp[0] += goldAnnotations.size();
    predictedAnnotations.removeAll(goldAnnotations);
    tpFp[1] += predictedAnnotations.size();

    return tpFp;
}

From source file:main.java.spelementex.Evaluator.java

/**
 * given result file, gets the true and false positive entity counts.
 * please note: this function is mainly intended for development purposes; 
 * it will not work if the result file does not have gold annotation labels 
 * in the second to the last column.// w w w .  j  a v a  2  s. c  om
 * 
 * @param result
 * @param tagType
 * @return double[] of size 2 with true positive count at index 0 and
 * false positive count at index 1.
 */
public static double[] getTpFp(String[] result, String tagType) {
    double[] tpFp = new double[2];

    Set<String> goldAnnotations = new HashSet<>();
    Set<Integer> visitedTokens = new HashSet<>();
    Set<String> predictedAnnotations = new HashSet<>();
    Set<Integer> predictedTokens = new HashSet<>();
    int tokenNum = 0;

    int length = result.length;
    for (int i = 0; i < length; i++) {
        String line = result[i].trim();
        if (line.equals(""))
            continue;

        String[] lineTokens = line.split("\\s+");

        if (lineTokens.length == 3) {
            tokenNum = 0;
            //# 0 0.076469
            if (lineTokens[1].equals("0") && !goldAnnotations.isEmpty()) {
                goldAnnotations.retainAll(predictedAnnotations);
                tpFp[0] += goldAnnotations.size();
                predictedAnnotations.removeAll(goldAnnotations);
                tpFp[1] += predictedAnnotations.size();

                goldAnnotations = new HashSet<>();
                visitedTokens = new HashSet<>();
                predictedAnnotations = new HashSet<>();
                predictedTokens = new HashSet<>();
            }
            continue;
        }

        String goldTag = lineTokens[lineTokens.length - 2];
        if (goldTag.matches("B\\-" + tagType) && !visitedTokens.contains(tokenNum)) {
            int[] tokenOffsets = getTokenOffset(result, i, tokenNum);
            goldAnnotations.add(tokenOffsets[0] + "-" + tokenOffsets[1] + "-" + goldTag);
            visitedTokens.add(tokenNum);
        }

        String predictedTag = lineTokens[lineTokens.length - 1];
        if (predictedTag.matches("B\\-" + tagType) && !predictedTokens.contains(tokenNum)) {
            if (lineTokens[0].matches("[^a-zA-Z0-9]+") || lineTokens[0].equals("-lrb-")
                    || lineTokens[0].equals("-rrb-")) {
                if (i + 1 == result.length) {
                    tokenNum++;
                    continue;
                }
                line = result[i + 1].trim();
                lineTokens = line.split("\\s+");
                if (line.equals("") || lineTokens.length == 3 || lineTokens[lineTokens.length - 1].equals("O")
                        || lineTokens[lineTokens.length - 1].matches("B\\-.*")) {
                    tokenNum++;
                    continue;
                }
            }
            int[] tokenOffsets = getTokenOffset(result, i, tokenNum);

            Set<Integer> tempPredictedTokens = new HashSet<>();
            for (int j = tokenOffsets[0]; j <= tokenOffsets[1]; j++)
                tempPredictedTokens.add(j);

            int before = tempPredictedTokens.size();
            tempPredictedTokens.removeAll(predictedTokens);
            int after = tempPredictedTokens.size();
            if (before == after) {
                predictedTokens.addAll(tempPredictedTokens);
                predictedAnnotations.add(tokenOffsets[0] + "-" + tokenOffsets[1] + "-" + predictedTag);
            }
        }

        tokenNum++;
    }

    goldAnnotations.retainAll(predictedAnnotations);
    tpFp[0] += goldAnnotations.size();
    predictedAnnotations.removeAll(goldAnnotations);
    tpFp[1] += predictedAnnotations.size();

    return tpFp;
}

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

/**
 * The function removes similar chemicals from the substrates and products (conenzymes) and remove duplicates
 * within each category./* w  w  w.j  av  a2  s . c om*/
 * @param reaction The reaction being updated.
 */
private void findAndIsolateCoenzymesFromReaction(Reaction reaction) {
    // Build ordered sets of the substrates/products.
    LinkedHashSet<Long> substrates = new LinkedHashSet<>(Arrays.asList(reaction.getSubstrates()));
    LinkedHashSet<Long> products = new LinkedHashSet<>(Arrays.asList(reaction.getProducts()));

    // Compute the intersection between the sets.
    Set<Long> intersection = new HashSet<>(substrates);
    intersection.retainAll(products);

    // A - int(A, B) = A / B
    substrates.removeAll(intersection);
    products.removeAll(intersection);

    // Update the reaction with the new (ordered) substrates/products + coenzymes.
    reaction.setSubstrates(substrates.toArray(new Long[substrates.size()]));
    reaction.setProducts(products.toArray(new Long[products.size()]));

    // Keep any existing coenzymes, but don't use them when computing the difference--they might be there for a reason.
    intersection.addAll(Arrays.asList(reaction.getCoenzymes()));
    reaction.setCoenzymes(intersection.toArray(new Long[intersection.size()]));
}