Example usage for java.util Collection remove

List of usage examples for java.util Collection remove

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Introduction

In this page you can find the example usage for java.util Collection remove.

Prototype

boolean remove(Object o);

Source Link

Document

Removes a single instance of the specified element from this collection, if it is present (optional operation).

Usage

From source file:ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl.java

@Override
@Transactional//from  w  ww.  jav  a  2  s.  c  om
public ExpressionExperiment replaceRawVectors(ExpressionExperiment ee,
        Collection<RawExpressionDataVector> newVectors) {

    if (newVectors == null || newVectors.isEmpty()) {
        throw new UnsupportedOperationException("Only use this method for replacing vectors, not erasing them");
    }

    // to attach to session correctly.
    ExpressionExperiment eeToUpdate = this.load(ee.getId());

    Collection<QuantitationType> qtsToRemove = new HashSet<>();
    for (RawExpressionDataVector oldV : eeToUpdate.getRawExpressionDataVectors()) {
        qtsToRemove.add(oldV.getQuantitationType());
    }
    rawExpressionDataVectorDao.remove(eeToUpdate.getRawExpressionDataVectors()); // should not be necessary
    processedVectorService.remove(eeToUpdate.getProcessedExpressionDataVectors()); // should not be necessary
    eeToUpdate.getProcessedExpressionDataVectors().clear(); // this should be sufficient
    eeToUpdate.getRawExpressionDataVectors().clear(); // should be sufficient

    // These QTs might still be getting used by the replaced vectors.
    for (RawExpressionDataVector newVec : newVectors) {
        qtsToRemove.remove(newVec.getQuantitationType());
    }

    for (QuantitationType oldQt : qtsToRemove) {
        quantitationTypeDao.remove(oldQt);
    }

    // Split the vectors up by bioassay dimension, if need be. This could be modified to handle multiple quantitation types if need be.
    Map<BioAssayDimension, Collection<RawExpressionDataVector>> BADs = new HashMap<>();
    for (RawExpressionDataVector vec : newVectors) {
        BioAssayDimension b = vec.getBioAssayDimension();
        if (!BADs.containsKey(b)) {
            BADs.put(b, new HashSet<RawExpressionDataVector>());
        }
        BADs.get(b).add(vec);
    }

    for (Collection<RawExpressionDataVector> vectors : BADs.values()) {
        ee = this.addRawVectors(eeToUpdate, vectors);
    }
    return ee;
}

From source file:com.adito.activedirectory.ActiveDirectoryUserDatabase.java

private void loadRoles(String filter, InitialLdapContext context, boolean removeMissingEntries)
        throws Exception {
    final Collection<String> groupNames = groupContainer.retrievePrincipalNames();
    PagedResultMapper mapper = new AbstractPagedResultMapper() {
        public void mapSearchResult(SearchResult searchResult) throws NamingException {
            String dn = searchResult.getNameInNamespace();
            Attributes attributes = searchResult.getAttributes();
            String commonName = getAttributeValue(attributes, COMMON_NAME_ATTRIBUTE);
            if (commonName.length() != 0) {
                Long rid = ActiveDirectoryGroup
                        .getRIDFromSID((byte[]) attributes.get(OBJECT_SID_ATTRIBUTE).get());
                ActiveDirectoryGroup group = new ActiveDirectoryGroup(commonName, dn, getEscapedDn(dn), rid,
                        getRealm());//from   ww  w  . j  av  a  2s  .  c  o m
                String[] parents = getParents(attributes);
                String key = groupContainer.storeGroup(group, parents);
                groupNames.remove(key);
            }
        }
    };

    try {
        String replacedFilter = buildGroupFilter(filter);
        PagedResultTemplate pagedResultTemplate = configuration.getPagedResultTemplate();
        pagedResultTemplate.search(context, replacedFilter, GROUP_ATTRS, mapper);
    } finally {
        if (removeMissingEntries) {
            groupContainer.updateRemovedGroups(groupNames);
        }
    }
}

From source file:com.haulmont.cuba.gui.data.impl.CollectionPropertyDatasourceImpl.java

@SuppressWarnings("unchecked")
public void replaceItem(T item) {
    checkNotNullArgument(item, "item is null");
    Collection<T> collection = getCollection();
    if (collection != null) {
        for (T t : collection) {
            if (t.equals(item)) {
                detachListener(t);/*w  w w .  ja va 2  s. c o  m*/
                if (collection instanceof List) {
                    List list = (List) collection;
                    int itemIdx = list.indexOf(t);
                    list.set(itemIdx, item);
                } else if (collection instanceof LinkedHashSet) {
                    LinkedHashSet set = (LinkedHashSet) collection;

                    List list = new ArrayList(set);
                    int itemIdx = list.indexOf(t);
                    list.set(itemIdx, item);

                    set.clear();
                    set.addAll(list);
                } else {
                    collection.remove(t);
                    collection.add(item);
                }
                attachListener(item);

                if (item.equals(this.item)) {
                    this.item = item;
                }
                break;
            }
        }
        if (sortInfos != null)
            doSort();

        fireCollectionChanged(Operation.UPDATE, Collections.singletonList(item));
    }
}

From source file:ubic.gemma.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl.java

/**
 * Copy sequences into the original versions, or create new sequences in the DB, as needed.
 * /*  w  w w .  j a  v  a2  s.co m*/
 * @param accessionsToFetch
 * @param retrievedSequences
 * @param force If true, if an existing BioSequence that matches if found in the system, any existing sequence
 *        information in the BioSequence will be overwritten.
 * @return Items that were found.
 */
private Map<String, BioSequence> findOrUpdateSequences(Collection<String> accessionsToFetch,
        Collection<BioSequence> retrievedSequences, Taxon taxon, boolean force) {

    Map<String, BioSequence> found = new HashMap<String, BioSequence>();
    for (BioSequence sequence : retrievedSequences) {
        if (log.isDebugEnabled())
            log.debug("Processing retrieved sequence: " + sequence);
        sequence.setTaxon(taxon);
        sequence = createOrUpdateGenbankSequence(sequence, force);
        String accession = sequence.getSequenceDatabaseEntry().getAccession();
        found.put(accession, sequence);
        accessionsToFetch.remove(accession);
    }
    return found;
}

From source file:de.escidoc.core.test.aa.UserAttributeTestBase.java

/**
 * Check if xml is valid and contains all attributes that are in given attributeList and only these attributes.
 *
 * @param attributesXml xml with user-attributes
 * @param userId        userId/*from   w  w w.jav  a2s .c o m*/
 * @param attributeList list of expected user-attributes
 * @throws Exception If anything fails.
 */
//CHECKSTYLE:OFF
protected void assertValidUserAttributes(final String attributesXml, final String userId,
        Collection<String> attributeList) throws Exception {
    //CHECKSTYLE:ON

    assertXmlValidAttributes(attributesXml);

    String href = "/aa/user-account/" + userId + "/resources/attributes";
    Document attributesXmlDocument = getDocument(attributesXml);
    selectSingleNodeAsserted(attributesXmlDocument, "/attributes/@base");
    selectSingleNodeAsserted(attributesXmlDocument, "/attributes[@href = '" + href + "']");
    int count = attributeList.size();
    if (count > 0) {
        selectSingleNodeAsserted(attributesXmlDocument, "/attributes/attribute[" + count + "]");
    }

    // check if every entry from given collection is in the document
    NodeList attributeElements = selectNodeList(attributesXmlDocument, "/attributes/attribute");
    int elementCount = attributeElements.getLength();
    // iterate elements of the xml document
    for (int i = 0; i < elementCount; i++) {
        // check if key value pair is in given map
        String attributeName = attributeElements.item(i).getAttributes().getNamedItem("name").getNodeValue();
        String attributeValue = attributeElements.item(i).getTextContent();
        String isInternal = attributeElements.item(i).getAttributes().getNamedItem("internal").getNodeValue();
        if (!attributeList.contains(attributeName + attributeValue + isInternal)) {
            fail("Unexpected attribute found. [" + attributeName + attributeValue + isInternal + "]");
        }
        attributeList.remove(attributeName + attributeValue + isInternal);
    }
    // all entries should be removed from hashes(-out-of-map), now
    if (!attributeList.isEmpty()) {
        fail("Expected attributes not found. [" + attributeList.toString() + "]");
    }
}

From source file:eu.medsea.mimeutil.MimeUtil2.java

public final Collection getMimeTypes(final URL url, final MimeType unknownMimeType) throws MimeException {
    Collection mimeTypes = new MimeTypeHashSet();

    if (url == null) {
        log.error("URL reference cannot be null.");
    } else {//from ww  w .j a  v  a  2  s . c  o m
        if (log.isDebugEnabled()) {
            log.debug("Getting MIME types for URL [" + url + "].");
        }

        // Test if this is a directory
        File file = new File(url.getPath());
        if (file.isDirectory()) {
            mimeTypes.add(MimeUtil2.DIRECTORY_MIME_TYPE);
        } else {
            // defer these calls to the file name and stream methods
            mimeTypes.addAll(mimeDetectorRegistry.getMimeTypes(url));

            // We don't want the unknownMimeType added to the collection by MimeDetector(s)
            mimeTypes.remove(unknownMimeType);
        }
    }
    // If the collection is empty we want to add the unknownMimetype
    if (mimeTypes.isEmpty()) {
        mimeTypes.add(unknownMimeType);
    }
    if (log.isDebugEnabled()) {
        log.debug("Retrieved MIME types [" + mimeTypes.toString() + "]");
    }
    return mimeTypes;
}

From source file:org.fao.geonet.services.user.Update.java

private void setUserGroups(final User user, List<GroupElem> userGroups) throws Exception {
    UserGroupRepository userGroupRepository = ApplicationContextHolder.get().getBean(UserGroupRepository.class);
    GroupRepository groupRepository = ApplicationContextHolder.get().getBean(GroupRepository.class);

    Collection<UserGroup> all = userGroupRepository.findAll(UserGroupSpecs.hasUserId(user.getId()));

    // Have a quick reference of existing groups and profiles for this user
    Set<String> listOfAddedProfiles = new HashSet<String>();
    for (UserGroup ug : all) {
        String key = ug.getProfile().name() + ug.getGroup().getId();
        if (!listOfAddedProfiles.contains(key)) {
            listOfAddedProfiles.add(key);
        }//from  w w  w. ja v a 2  s  .  c o m
    }

    // We start removing all old usergroup objects. We will remove the
    // explicitly defined for this call
    Collection<UserGroup> toRemove = new ArrayList<UserGroup>();
    toRemove.addAll(all);

    // New pairs of group-profile we need to add
    Collection<UserGroup> toAdd = new ArrayList<UserGroup>();

    // For each of the parameters on the request, make sure the group is
    // updated.
    for (GroupElem element : userGroups) {
        Integer groupId = element.getId();
        Group group = groupRepository.findOne(groupId);
        String profile = element.getProfile();
        // The user has a new group and profile

        // Combine all groups editor and reviewer groups
        if (profile.equals(Profile.Reviewer.name())) {
            final UserGroup userGroup = new UserGroup().setGroup(group).setProfile(Profile.Editor)
                    .setUser(user);
            String key = Profile.Editor.toString() + group.getId();
            if (!listOfAddedProfiles.contains(key)) {
                toAdd.add(userGroup);
                listOfAddedProfiles.add(key);
            }

            // If the user is already part of this group with this profile,
            // leave it alone:
            for (UserGroup g : all) {
                if (g.getGroup().getId() == groupId && g.getProfile().equals(Profile.Editor)) {
                    toRemove.remove(g);
                }
            }
        }

        final UserGroup userGroup = new UserGroup().setGroup(group)
                .setProfile(Profile.findProfileIgnoreCase(profile)).setUser(user);
        String key = profile + group.getId();
        if (!listOfAddedProfiles.contains(key)) {
            toAdd.add(userGroup);
            listOfAddedProfiles.add(key);

        }

        // If the user is already part of this group with this profile,
        // leave it alone:
        for (UserGroup g : all) {
            if (g.getGroup().getId() == groupId && g.getProfile().name().equalsIgnoreCase(profile)) {
                toRemove.remove(g);
            }
        }
    }

    // Remove deprecated usergroups (if any)
    userGroupRepository.delete(toRemove);

    // Add only new usergroups (if any)
    userGroupRepository.save(toAdd);

}

From source file:uk.nhs.cfh.dsp.snomed.normaliser.impl.NormalFormGeneratorImpl.java

/**
 * Gets the non redundant merged relationships.
 *
 * @param relationships the relationships
 * @return the non redundant merged relationships
 *//*from w  w  w  . j a  v  a 2  s. c o  m*/
private Collection<SnomedRelationshipPropertyExpression> getNonRedundantMergedRelationships(
        Collection<SnomedRelationshipPropertyExpression> relationships) {

    List<SnomedRelationshipPropertyExpression> relationshipList = new ArrayList<SnomedRelationshipPropertyExpression>(
            relationships);
    for (int i = 0; i < relationshipList.size(); i++) {
        for (int j = i + 1; j < relationshipList.size(); j++) {
            SnomedRelationshipPropertyExpression r1 = relationshipList.get(i);
            SnomedRelationshipPropertyExpression r2 = relationshipList.get(j);
            ExpressionComparator.Subsumption_Relation relation = expressionComparator.getSubsumptionRelation(r1,
                    getExpressionWithShortNormalFormAsValue(r2));
            if (ExpressionComparator.Subsumption_Relation.SUBSUMED_BY == relation) {
                relationships.remove(r2);
            } else if (ExpressionComparator.Subsumption_Relation.SUBSUMES == relation) {
                relationships.remove(r1);
            } else if (ExpressionComparator.Subsumption_Relation.SAME == relation) {
                // remove one relationship
                relationships.remove(r2);
            }
        }
    }

    return relationships;
}

From source file:com.nextep.designer.sqlgen.postgre.impl.PostgreSqlCapturer.java

@Override
public Collection<IIndex> getIndexes(ICaptureContext context, IProgressMonitor monitor) {
    final Map<String, IIndex> indexMap = new HashMap<String, IIndex>();
    final Collection<IIndex> indexes = getPostgresIndexes(context, monitor);

    // Processing indexes to remove PK or UK indexes (DES-694)
    /*/*w w w.ja v  a2  s. co  m*/
     * FIXME [BGA] Now that indexes are captured by a PostgreSQL specific implementation, PK or
     * UK indexes can be filtered out upstream, so this block of code should not be necessary
     * anymore.
     */
    for (IIndex index : new ArrayList<IIndex>(indexes)) {
        final Object obj = context.getCapturedObject(IElementType.getInstance(UniqueKeyConstraint.TYPE_ID),
                CaptureHelper.getUniqueIndexName(index));
        if (obj != null) {
            indexes.remove(index);
        } else {
            indexMap.put(index.getIndexName(), index);
        }
    }
    // Fetching index tablespaces
    fillTablespaces("i", context, indexMap, IIndexPhysicalProperties.class); //$NON-NLS-1$
    return indexes;
}

From source file:org.nabucco.alfresco.enhScriptEnv.common.script.registry.VersionRegisterableScriptClasspathScanner.java

/**
 * Matches and processes a folder level defining a range of versions a script is applicable to.
 *
 * @param resourcePattern//from  w  ww.  ja v  a  2  s.co m
 *            the resource pattern for the current level
 * @param patternStack
 *            the stack of patterns evaluated thus far
 * @param versionDataContainer
 *            the container for collection version information
 * @param subRegistry
 *            the sub-registry to register the script in or {@code null} if no sub-registry is to be used
 * @param fileName
 *            the name of the file currently evaluated
 * @throws IOException
 *             if any exception occurs handling the resource
 */
protected void matchVersionRange(final String resourcePattern, final Collection<String> patternStack,
        final VersionRegisterableScriptAdapter<Script> versionDataContainer, final String subRegistry,
        final String fileName) throws IOException {
    LOGGER.debug("Matched version range {} fragment", fileName);

    final Matcher matcher = Pattern.compile(VERSION_RANGE_PATTERN).matcher(fileName);
    matcher.find();

    final String lowerBoundExclusivity = matcher.group(2);
    final String lowerVersion = matcher.group(3);
    final String upperVersion = matcher.group(6);
    final String upperBoundExclusivity = matcher.group(8);

    versionDataContainer.setAppliesFromExclusive("[".equals(lowerBoundExclusivity));
    versionDataContainer.setAppliesToExclusive("]".equals(upperBoundExclusivity));
    if (lowerVersion != null && lowerVersion.length() != 0) {
        versionDataContainer.setAppliesFrom(lowerVersion);
    }
    if (upperVersion != null && upperVersion.length() != 0) {
        versionDataContainer.setAppliesTo(upperVersion);
    }

    patternStack.add(VERSION_RANGE_PATTERN);
    try {
        this.scanNextLevel(resourcePattern + "/" + fileName, patternStack, versionDataContainer, subRegistry);
    } finally {
        versionDataContainer.setAppliesFromExclusive(false);
        versionDataContainer.setAppliesToExclusive(false);
        versionDataContainer.setAppliesFrom((VersionNumber) null);
        versionDataContainer.setAppliesTo((VersionNumber) null);
        patternStack.remove(VERSION_RANGE_PATTERN);
    }
}