Example usage for java.util Comparator Comparator

Introduction

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

Prototype

Comparator

Source Link

Usage

From source file:edu.msu.cme.rdp.alignment.pairwise.PairwiseKNN.java

public static List<Neighbor> getKNN(Sequence query, List<Sequence> dbSeqs, AlignmentMode mode, int k,
        int wordSize, int prefilter) throws IOException {
    List<Neighbor> ret = new ArrayList();
    Neighbor n;//from  w  ww. j av a2 s  .  co  m
    Comparator c = new Comparator<Neighbor>() {
        public int compare(Neighbor t, Neighbor t1) {
            return t.alignment.getScore() - t1.alignment.getScore();
        }
    };

    SequenceType seqType = SeqUtils.guessSequenceType(query);
    ScoringMatrix matrix;
    KmerMatchCore kerMatchCore;
    if (seqType == SequenceType.Nucleotide) {
        matrix = ScoringMatrix.getDefaultNuclMatrix();
        kerMatchCore = new NuclSeqMatch(dbSeqs, wordSize);
    } else {
        matrix = ScoringMatrix.getDefaultProteinMatrix();
        kerMatchCore = new ProteinSeqMatch(dbSeqs, wordSize);
    }

    List<Sequence> refList;

    if (prefilter == 0) { // do not pre-filter the reference seqs
        refList = dbSeqs;
    } else {
        refList = new ArrayList<Sequence>();
        ArrayList<ProteinSeqMatch.BestMatch> topKMatches = kerMatchCore.findTopKMatch(query, prefilter);
        for (KmerMatchCore.BestMatch bestTarget : topKMatches) {
            refList.add(bestTarget.getBestMatch());
        }
    }

    for (Sequence dbSeq : refList) {
        n = new Neighbor();
        n.dbSeq = dbSeq;
        PairwiseAlignment fwd = PairwiseAligner.align(n.dbSeq.getSeqString(), query.getSeqString(), matrix,
                mode);
        if (seqType == SequenceType.Nucleotide) {
            PairwiseAlignment rc = PairwiseAligner.align(n.dbSeq.getSeqString(),
                    IUBUtilities.reverseComplement(query.getSeqString()), matrix, mode);

            if (rc.getScore() > fwd.getScore()) {
                n.alignment = rc;
                n.reverse = true;
            } else {
                n.alignment = fwd;
                n.reverse = false;
            }
        } else {
            n.alignment = fwd;
            n.reverse = false;
        }

        insert(n, ret, c, k);
    }

    return ret;
}

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From source file:net.chrissearle.flickrvote.web.admin.TwitterOverviewAction.java

@Override
public String execute() throws Exception {
    List<PhotographerItem> photographerItemList = photographyService.getPhotographers();

    List<String> amFollowing = followService.amFollowing();

    List<String> followers = followService.followingMe();

    for (PhotographerItem item : photographerItemList) {
        final String twitterId = item.getTwitter();

        if (twitterId != null && !"".equals(twitterId)) {
            TwitterStatus status = new TwitterStatus(item.getName(), twitterId, amFollowing.contains(twitterId),
                    followers.contains(twitterId));

            statuses.add(status);/*from  w w w . j  a v a  2s.c om*/
        }
    }

    Collections.sort(statuses, new Comparator<TwitterStatus>() {
        public int compare(TwitterStatus o1, TwitterStatus o2) {
            return o1.getName().compareTo(o2.getName());
        }
    });

    return SUCCESS;
}

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From source file:com.taobao.ad.easyschedule.dao.datatrackinglog.impl.JPADataTrackingLogDAOImpl.java

@SuppressWarnings("unchecked")
public List<DatatrackingLogDO> getDataTrackingByGroupAndName(final DatatrackingLogDO datatrackingLog)
        throws DataAccessException {

    return (List<DatatrackingLogDO>) this.getJpaTemplate().execute(new JpaCallback() {
        @Override/* www . java  2s  .c o  m*/
        public Object doInJpa(EntityManager em) throws PersistenceException {
            Query query = em.createQuery(
                    "select t from es_datatracking_log t where t.jobName=?1 and t.jobGroup=?2  and t.createTime>=?3 and t.createTime<=?4 order by t.createTime desc")
                    .setParameter(1, datatrackingLog.getJobName())
                    .setParameter(2, datatrackingLog.getJobGroup())
                    .setParameter(3, datatrackingLog.getQueryStartTime())
                    .setParameter(4, datatrackingLog.getQueryEndTime());
            List<DatatrackingLogDO> dataList = query.getResultList();
            if (dataList != null && !dataList.isEmpty()) {
                Collections.sort(dataList, new Comparator<DatatrackingLogDO>() {
                    @Override
                    public int compare(DatatrackingLogDO o1, DatatrackingLogDO o2) {
                        return o1.getCreateTime().compareTo(o2.getCreateTime());
                    }
                });
            }
            return dataList;
        }
    });

}

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From source file:org.openmrs.web.controller.report.CohortListController.java

protected Object formBackingObject(HttpServletRequest request) throws ServletException {
    List<Cohort> cohorts = new ArrayList<Cohort>();
    if (Context.isAuthenticated()) {
        cohorts = Context.getCohortService().getAllCohorts();
        Collections.sort(cohorts, new Comparator<Cohort>() {

            public int compare(Cohort a, Cohort b) {
                int temp = a.isVoided().compareTo(b.isVoided());
                if (temp == 0)
                    temp = a.getCohortId().compareTo(b.getCohortId());
                return temp;
            }/*from w  w w  . j av  a2 s .c  om*/
        });
    }
    return cohorts;
}

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From source file:com.bigdata.dastor.service.RangeSliceResponseResolver.java

public List<Row> resolve(Collection<Message> responses) throws DigestMismatchException, IOException {
    CollatingIterator collator = new CollatingIterator(new Comparator<Pair<Row, InetAddress>>() {
        public int compare(Pair<Row, InetAddress> o1, Pair<Row, InetAddress> o2) {
            return partitioner.getToken(o1.left.key).compareTo(partitioner.getToken(o2.left.key));
        }//from w  w  w  . j  a v  a 2s  .com
    });

    int n = 0;
    for (Message response : responses) {
        RangeSliceReply reply = RangeSliceReply.read(response.getMessageBody());
        n = Math.max(n, reply.rows.size());
        collator.addIterator(new RowIterator(reply.rows.iterator(), response.getFrom()));
    }

    // for each row, compute the combination of all different versions seen, and repair incomplete versions
    ReducingIterator<Pair<Row, InetAddress>, Row> iter = new ReducingIterator<Pair<Row, InetAddress>, Row>(
            collator) {
        List<ColumnFamily> versions = new ArrayList<ColumnFamily>(sources.size());
        List<InetAddress> versionSources = new ArrayList<InetAddress>(sources.size());
        String key;

        @Override
        protected boolean isEqual(Pair<Row, InetAddress> o1, Pair<Row, InetAddress> o2) {
            return o1.left.key.equals(o2.left.key);
        }

        public void reduce(Pair<Row, InetAddress> current) {
            key = current.left.key;
            versions.add(current.left.cf);
            versionSources.add(current.right);
        }

        protected Row getReduced() {
            ColumnFamily resolved = ReadResponseResolver.resolveSuperset(versions);
            ReadResponseResolver.maybeScheduleRepairs(resolved, table, key, versions, versionSources);
            versions.clear();
            versionSources.clear();
            return new Row(key, resolved);
        }
    };

    List<Row> resolvedRows = new ArrayList<Row>(n);
    while (iter.hasNext())
        resolvedRows.add(iter.next());

    return resolvedRows;
}

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From source file:org.opencredo.couchdb.inbound.CouchDbChangesPollingMessageSource.java

/**
 * Creates an instance with a custom CouchDbChangesOperations.
 *///ww  w  . j ava  2s .c o m
public CouchDbChangesPollingMessageSource(CouchDbChangesOperations couchDbChangesOperations) {
    this.couchDbChangesOperations = couchDbChangesOperations;
    this.toBeReceived = new PriorityBlockingQueue<ChangedDocument>(DEFAULT_INTERNAL_QUEUE_CAPACITY,
            new Comparator<ChangedDocument>() {
                public int compare(ChangedDocument doc1, ChangedDocument doc2) {
                    long diff = doc1.getSequence() - doc2.getSequence();
                    if (diff == 0) {
                        return 0;
                    } else {
                        return diff > 0 ? 1 : -1;
                    }
                }
            });
}

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From source file:com.devnexus.ting.core.service.impl.DefaultTwitterService.java

/** {@inheritDoc} */
@Override//  w  w  w . j  a  v a2  s  .c o m
public Collection<TwitterMessage> getTwitterMessages() {
    SortedSet<TwitterMessage> twitterMessages = new TreeSet<TwitterMessage>(new Comparator<TwitterMessage>() {
        @Override
        public int compare(TwitterMessage twitterMessage1, TwitterMessage twitterMessage2) {
            return twitterMessage2.getCreatedAt().compareTo(twitterMessage1.getCreatedAt());
        }
    });

    twitterMessages.addAll(this.twitterMessages.asMap().values());
    return twitterMessages;
}

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From source file:edu.cornell.mannlib.vitro.webapp.controller.accounts.UserAccountsPage.java

/**
 * Create a list of all known non-public PermissionSets.
 *//*  w  w  w  . jav  a 2  s.c  o m*/
protected List<PermissionSet> buildListOfSelectableRoles() {
    List<PermissionSet> list = new ArrayList<PermissionSet>();
    for (PermissionSet ps : userAccountsDao.getAllPermissionSets()) {
        if (!ps.isForPublic()) {
            list.add(ps);
        }
    }

    Collections.sort(list, new Comparator<PermissionSet>() {
        @Override
        public int compare(PermissionSet ps1, PermissionSet ps2) {
            return ps1.getUri().compareTo(ps2.getUri());
        }
    });
    return list;
}

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From source file:eu.eubrazilcc.lvl.storage.security.PermissionHistory.java

public static @Nullable PermissionModification latestModification(final Set<PermissionModification> history,
        final String permission) {
    String permission2 = null;//from  w  w  w.ja v  a  2s .c om
    checkArgument(history != null, "Uninitialized or invalid history");
    checkArgument(isNotBlank(permission2 = trimToNull(permission)), "Uninitialized or invalid permission");
    final List<PermissionModification> sortedList = from(new Comparator<PermissionModification>() {
        @Override
        public int compare(final PermissionModification pm1, final PermissionModification pm2) {
            if (pm1 == pm2)
                return 0;
            return ComparisonChain.start().compare(pm1.getModificationDate(), pm2.getModificationDate())
                    .compare(pm1.getPermission(), pm2.getPermission())
                    .compare(pm1.getModificationType(), pm2.getModificationType()).result();
        }
    }).reverse().sortedCopy(history);
    PermissionModification latestModification = null;
    for (int i = 0; i < sortedList.size() && latestModification == null; i++) {
        final PermissionModification item = sortedList.get(i);
        if (permission2.equals(item.getPermission())) {
            latestModification = item;
        }
    }
    return latestModification;
}

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From source file:de.jgoldhammer.alfresco.jscript.jmx.JmxDumpUtil.java

/**
 * Dumps a local or remote MBeanServer's entire object tree for support
 * purposes. Nested arrays and CompositeData objects in MBean attribute
 * values are handled.//w  w w.ja  va  2  s  .c o  m
 * 
 * @param connection
 *            the server connection (or server itself)
 * @param out
 *            PrintWriter to write the output to
 * @throws IOException
 *             Signals that an I/O exception has occurred.
 */
public static void dumpConnection(MBeanServerConnection connection, PrintWriter out) throws IOException {
    JmxDumpUtil.showStartBanner(out);

    // Get all the object names
    Set<ObjectName> objectNames = connection.queryNames(null, null);

    // Sort the names (don't assume ObjectName implements Comparable in JDK
    // 1.5)
    Set<ObjectName> newObjectNames = new TreeSet<ObjectName>(new Comparator<ObjectName>() {
        public int compare(ObjectName o1, ObjectName o2) {
            return o1.toString().compareTo(o2.toString());
        }
    });
    newObjectNames.addAll(objectNames);
    objectNames = newObjectNames;

    // Dump each MBean
    for (ObjectName objectName : objectNames) {
        try {
            printMBeanInfo(connection, objectName, out, null);
        } catch (JMException e) {
            // Sometimes beans can disappear while we are examining them
        }
    }
}

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