Example usage for java.util Collection remove

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:uk.ac.ebi.intact.editor.services.curate.publication.PublicationEditorService.java

private void initialiseEvidences(Publication parent, Collection<Experiment> evidences) {
    Collection<Experiment> originalExperiments = new ArrayList<Experiment>(evidences);
    for (Experiment exp : originalExperiments) {
        if (!isExperimentInitialised(exp)) {
            Experiment reloaded = initialiseExperiment(exp);
            if (reloaded != exp) {
                evidences.remove(exp);
                parent.addExperiment(reloaded);
            }//from  w w  w.ja v  a  2 s.c  om
        }
    }
}

From source file:uk.ac.ebi.intact.editor.services.curate.interactor.InteractorEditorService.java

private void initialiseInteractorMembers(Collection<Interactor> interactors) {
    Collection<Interactor> originalMembers = new ArrayList<Interactor>(interactors);
    InteractorCloner cloner = new InteractorCloner();
    for (Interactor interactor : originalMembers) {
        if (!isInteractorInitialised(interactor)) {
            Interactor reloaded = initialiseInteractor(interactor, cloner);
            if (reloaded != null) {
                interactors.remove(interactor);
                interactors.add(reloaded);
            }/*from   w  w  w  . j  a  v  a  2s  .c o  m*/
        }
    }
}

From source file:edu.berkeley.compbio.ncbitaxonomy.NcbiTaxonomyServiceEngineImpl.java

public void writeSynonyms(final Writer out) {
    //DepthFirstTreeIterator<Integer, PhylogenyNode<Integer>> i = getTree().depthFirstIterator();
    Iterator<Integer> i = ncbiTaxonomyNodeDao.findAllIds().iterator(); //
    while (i.hasNext()) {
        //PhylogenyNode<Integer> n = i.next();
        //Integer id = n.getPayload();
        Integer id = i.next();/*from  ww w .j  a v a 2  s.  c o m*/
        try {
            out.append(id.toString()).append("\t");

            String scientificName = findScientificName(id);
            out.append(scientificName).append("\t");

            Collection<String> synonyms = synonymsOfIdNoCache(id);
            synonyms.remove(scientificName);
            out.append(DSStringUtils.join(synonyms, "\t")).append("\n");
        } catch (NoSuchNodeException e) {
            logger.error("Error", e);
        } catch (IOException e) {
            logger.error("Error", e);
        }
    }
}

From source file:ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceImpl.java

@Override
public Collection<Long> getHomologues(Long ncbiId) {

    Collection<Long> NcbiGeneIds = new HashSet<>();

    if (!this.ready.get()) {
        return NcbiGeneIds;
    }/*w w w .  j a v  a  2s .  c  om*/

    Long groupId = this.getHomologeneGroup(ncbiId);
    if (groupId == null)
        return NcbiGeneIds;
    NcbiGeneIds = this.getNCBIGeneIdsInGroup(groupId);
    NcbiGeneIds.remove(ncbiId); // remove the given gene from the list

    return NcbiGeneIds;

}

From source file:org.xwiki.filemanager.internal.job.MoveJob.java

/**
 * Deletes the given file from the specified parent folder. If the file has no other parent folders then it is moved
 * to the recycle bin. Otherwise it is only removed from the specified parent folder.
 * //from www  .ja  v a  2s .  co  m
 * @param file the file to be deleted
 * @param parentReference the folder from where to delete the file
 */
private void deleteFile(File file, DocumentReference parentReference) {
    Collection<DocumentReference> parentReferences = file.getParentReferences();
    parentReferences.remove(parentReference);
    if (parentReferences.isEmpty()) {
        fileSystem.delete(file.getReference());
    } else {
        fileSystem.save(file);
    }
}

From source file:at.ac.tuwien.qse.sepm.gui.controller.impl.GridViewImpl.java

private void handleUpdatePhotos(List<Photo> photos) {
    LOGGER.debug("updating {} photos in grid", photos.size());
    Platform.runLater(() -> {//  w  w w  .  ja v  a2s  .  co  m
        grid.updatePhotos(photos);

        // update the inspector selection
        Collection<Photo> entities = inspector.getEntities();

        boolean updated = false;
        for (Photo photo : photos) {
            Optional<Photo> entity = entities.stream().filter(p -> p.getId().equals(photo.getId())).findFirst();
            if (entity.isPresent()) {
                entities.remove(entity.get());
                entities.add(photo);
                updated = true;
            }
        }

        if (updated) {
            inspector.setEntities(entities);
        }
    });
}

From source file:de.dhke.projects.cutil.collections.aspect.AspectMultiMapTest.java

/**
 * Test of get method, of class AspectMultiMap.
 *//*  w  w w.j  ava2 s. c o  m*/
@Test
public void testGet_remove() {
    Collection<String> values = _aspectMap.get("1");
    TestHelper.assertSequenceEquals(Arrays.asList("a", "A"), values);
    values.remove("a");
    assertFalse(_aspectMap.containsValue("1", "a"));
    assertEquals(1, _listener.beforeRemoveEvents.size());
    assertEquals(new DefaultMapEntry<>("1", "a"), _listener.beforeRemoveEvents.get(0).getItem());
    assertEquals(1, _listener.afterRemoveEvents.size());
    assertEquals(new DefaultMapEntry<>("1", "a"), _listener.afterRemoveEvents.get(0).getItem());
}

From source file:uk.ac.ebi.intact.editor.services.curate.participant.ParticipantEditorService.java

private void initialiseCvs(Collection<CvTerm> detectionMethods) {
    Collection<CvTerm> dets = new ArrayList<CvTerm>(detectionMethods);
    for (CvTerm det : dets) {
        if (!isCvInitialised(det)) {
            CvTerm reloaded = initialiseCv(det);
            if (reloaded != det) {
                detectionMethods.remove(det);
                detectionMethods.add(reloaded);
            }/*from  w  w w .  jav a  2s  .c o m*/
        }
    }
}

From source file:org.apache.usergrid.tools.DupAdminRepair.java

/**
 * When our usernames are equal, we need to check if our emails are equal. If they're not, we need to change the one
 * that DOES NOT get returned on a lookup by username
 *//*from  w ww.j  a  v  a  2  s.com*/
private void resolveUsernameConflicts(String targetDir, String userName, Collection<UUID> ids)
        throws Exception {
    // lookup the admin id
    UserInfo existing = managementService.getAdminUserByUsername(userName);

    if (existing == null) {
        logger.warn("Could not determine an admin for colliding username '{}'.  Skipping", userName);
        return;
    }

    ids.remove(existing.getUuid());

    boolean collision = false;

    EntityManager em = emf.getEntityManager(MANAGEMENT_APPLICATION_ID);

    for (UUID id : ids) {
        UserInfo other = managementService.getAdminUserByUuid(id);

        // same username and email, these will be merged later in the process,
        // skip it
        if (other != null && other.getEmail() != null && other.getEmail().equals(existing.getEmail())) {
            logger.info(
                    "Users with the same username '{}' have the same email '{}'. This will be resolved later in "
                            + "the process, skipping",
                    userName, existing.getEmail());
            continue;
        }

        // if we get here, the emails do not match, but the usernames do. Force
        // both usernames to emails
        collision = true;

        setUserName(em, other, other.getEmail());
    }

    if (collision) {
        setUserName(em, existing, existing.getEmail());
    }
}

From source file:org.xwiki.filemanager.internal.job.MoveJob.java

/**
 * Move a file to a different parent folder.
 * /*  w  w  w .  j  a  v a2 s. c o m*/
 * @param file the file to be moved
 * @param oldParentReference the parent folder to replace
 * @param newParent the new parent folder
 */
private void moveFile(File file, DocumentReference oldParentReference, Folder newParent) {
    // Check if a file with the same name already exits under the new parent folder.
    if (!prepareOverwrite(file.getName(), newParent, file.getReference())) {
        return;
    }

    Collection<DocumentReference> parentReferences = file.getParentReferences();
    boolean save = parentReferences.remove(oldParentReference);
    save |= parentReferences.add(newParent.getReference());
    if (save) {
        fileSystem.save(file);
    }
}