Example usage for java.util LinkedList removeFirst

List of usage examples for java.util LinkedList removeFirst

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Introduction

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

Prototype

public E removeFirst()

Source Link

Document

Removes and returns the first element from this list.

Usage

From source file:gate.creole.tokeniser.SimpleTokeniser.java

/**
 * Converts the finite state machine to a deterministic one.
 *
 * @param s/*  w w  w.  j  av  a2  s .  co m*/
 */
private AbstractSet<FSMState> lambdaClosure(Set<FSMState> s) {

    //the stack/queue used by the algorithm
    LinkedList<FSMState> list = new LinkedList<FSMState>(s);

    //the set to be returned
    AbstractSet<FSMState> lambdaClosure = new HashSet<FSMState>(s);

    FSMState top;
    FSMState currentState;
    Set<FSMState> nextStates;
    Iterator<FSMState> statesIter;

    while (!list.isEmpty()) {
        top = list.removeFirst();
        nextStates = top.nextSet(null);

        if (null != nextStates) {
            statesIter = nextStates.iterator();

            while (statesIter.hasNext()) {
                currentState = statesIter.next();
                if (!lambdaClosure.contains(currentState)) {
                    lambdaClosure.add(currentState);
                    list.addFirst(currentState);
                } //if(!lambdaClosure.contains(currentState))
            } //while(statesIter.hasNext())

        } //if(null != nextStates)
    }
    return lambdaClosure;
}

From source file:ORG.oclc.os.SRW.SRWDatabase.java

public static SRWDatabase getDB(String dbname, Properties properties, String servletContext,
        HttpServletRequest request) {/* w  w w .j a v  a2s. com*/
    log.debug("enter SRWDatabase.getDB");
    if (badDbs.get(dbname) != null) // we've seen this one before
        return null;

    LinkedList<SRWDatabase> queue = dbs.get(dbname);
    SRWDatabase db = null;
    try {
        if (queue == null)
            log.info("No databases created yet for database " + dbname);
        else {
            log.debug("about to synchronize #1 on queue");
            synchronized (queue) {
                if (queue.isEmpty())
                    log.info("No databases available for database " + dbname);
                else {
                    db = queue.removeFirst();
                    if (db == null)
                        log.debug("popped a null database off the queue for database " + dbname);
                }
            }
            log.debug("done synchronize #1 on queue");
        }
        if (db == null) {
            log.info("creating a database for " + dbname);
            try {
                while (db == null) {
                    createDB(dbname, properties, servletContext, request);
                    queue = dbs.get(dbname);
                    log.debug("about to synchronize #2 on queue");
                    synchronized (queue) {
                        if (!queue.isEmpty()) // crap, someone got to it before us
                            db = queue.removeFirst();
                    }
                }
                log.debug("done synchronize #2 on queue");
            } catch (Exception e) { // database not available
                badDbs.put(dbname, dbname);
                log.error(e, e);
                return null;
            }
        }
    } catch (Exception e) {
        log.error(e, e);
        log.error("shoot!");
    }
    if (log.isDebugEnabled())
        log.debug("getDB: db=" + db);
    log.debug("exit SRWDatabase.getDB");
    return db;
}

From source file:appeng.items.tools.powered.ToolColorApplicator.java

private ItemStack findNextColor(final ItemStack is, final ItemStack anchor, final int scrollOffset) {
    ItemStack newColor = null;//from  w w w .j  ava2  s . c  om

    final IMEInventory<IAEItemStack> inv = AEApi.instance().registries().cell().getCellInventory(is, null,
            StorageChannel.ITEMS);
    if (inv != null) {
        final IItemList<IAEItemStack> itemList = inv
                .getAvailableItems(AEApi.instance().storage().createItemList());
        if (anchor == null) {
            final IAEItemStack firstItem = itemList.getFirstItem();
            if (firstItem != null) {
                newColor = firstItem.getItemStack();
            }
        } else {
            final LinkedList<IAEItemStack> list = new LinkedList<IAEItemStack>();

            for (final IAEItemStack i : itemList) {
                list.add(i);
            }

            Collections.sort(list, new Comparator<IAEItemStack>() {

                @Override
                public int compare(final IAEItemStack a, final IAEItemStack b) {
                    return ItemSorters.compareInt(a.getItemDamage(), b.getItemDamage());
                }
            });

            if (list.size() <= 0) {
                return null;
            }

            IAEItemStack where = list.getFirst();
            int cycles = 1 + list.size();

            while (cycles > 0 && !where.equals(anchor)) {
                list.addLast(list.removeFirst());
                cycles--;
                where = list.getFirst();
            }

            if (scrollOffset > 0) {
                list.addLast(list.removeFirst());
            }

            if (scrollOffset < 0) {
                list.addFirst(list.removeLast());
            }

            return list.get(0).getItemStack();
        }
    }

    if (newColor != null) {
        this.setColor(is, newColor);
    }

    return newColor;
}

From source file:org.vaadin.addons.sitekit.module.content.ContentModule.java

@Override
public void injectDynamicContent(final SiteDescriptor dynamicSiteDescriptor) {
    final Company company = Site.getCurrent().getSiteContext().getObject(Company.class);
    final EntityManager entityManager = Site.getCurrent().getSiteContext().getObject(EntityManager.class);
    final User user = ((SecurityProviderSessionImpl) Site.getCurrent().getSecurityProvider())
            .getUserFromSession();/* ww  w . ja v a 2  s.  c  o m*/
    final List<Group> groups;
    if (user == null) {
        groups = new ArrayList<Group>();
        groups.add(UserDao.getGroup(entityManager, company, "anonymous"));
    } else {
        groups = UserDao.getUserGroups(entityManager, company, user);
    }

    final List<Content> contents = ContentDao.getContens(entityManager, company);
    final LinkedList<Content> queue = new LinkedList<Content>();
    final Map<String, List<Content>> dependencies = new HashMap<String, List<Content>>();
    for (final Content content : contents) {
        final String dependency;
        if (!StringUtils.isEmpty(content.getAfterPage())) {
            dependency = content.getAfterPage();
        } else if (!StringUtils.isEmpty(content.getParentPage())) {
            dependency = content.getParentPage();
        } else {
            dependency = null;
        }
        if (dependency != null) {
            if (!dependencies.containsKey(dependency)) {
                dependencies.put(dependency, new ArrayList<Content>());
            }
            dependencies.get(dependency).add(content);
        } else {
            queue.add(content);
        }
    }

    final List<Content> ordered = new ArrayList<Content>();
    while (queue.size() > 0) {
        final Content content = queue.removeFirst();
        ordered.add(content);
        if (dependencies.containsKey(content.getPage())) {
            queue.addAll(dependencies.get(content.getPage()));
        }
    }

    final NavigationVersion navigationVersion = dynamicSiteDescriptor.getNavigation().getProductionVersion();

    for (final Content content : ordered) {
        boolean viewPrivilege = PrivilegeCache.hasPrivilege(company, user, "view", content.getContentId());
        if (!viewPrivilege) {
            for (final Group group : groups) {
                if (PrivilegeCache.hasPrivilege(company, group, "view", content.getContentId())) {
                    viewPrivilege = true;
                    break;
                }
            }
        }

        if (!viewPrivilege) {
            continue;
        }

        boolean editPrivilege = UserDao.hasUserPrivilege(entityManager, user, "edit", content.getContentId());
        if (!editPrivilege) {
            for (final Group group : groups) {
                if (UserDao.hasGroupPrivilege(entityManager, group, "edit", content.getContentId())) {
                    editPrivilege = true;
                    break;
                }
            }
        }

        final String page = content.getPage();
        if (page == null) {
            continue;
        }
        final String parentPage = content.getParentPage();
        final String afterPage = content.getAfterPage();
        final String title = content.getTitle();
        final MarkupType markupType = content.getMarkupType();
        final String markup = content.getMarkup();

        if (StringUtils.isEmpty(parentPage)) {
            if (StringUtils.isEmpty(afterPage)) {
                navigationVersion.addRootPage(0, page);
                navigationVersion.setDefaultPageName(page);
            } else {
                navigationVersion.addRootPage(afterPage, page);
            }
        } else {
            if (StringUtils.isEmpty(afterPage)) {
                navigationVersion.addChildPage(parentPage, page);
            } else {
                navigationVersion.addChildPage(parentPage, afterPage, page);
            }
        }

        // Describe content view.
        final ViewDescriptor viewDescriptor = new ViewDescriptor(page, title, DefaultView.class);
        viewDescriptor.getProductionVersion().setDynamic(true);
        if (editPrivilege) {
            viewDescriptor.setViewletClass("content", RenderFlow.class, content);
        } else {
            viewDescriptor.setViewletClass("content", RenderViewlet.class, markup);
        }
        dynamicSiteDescriptor.getViewDescriptors().add(viewDescriptor);
    }

}

From source file:org.bubblecloud.ilves.module.content.ContentModule.java

@Override
public void injectDynamicContent(final SiteDescriptor dynamicSiteDescriptor) {
    final Company company = Site.getCurrent().getSiteContext().getObject(Company.class);
    final EntityManager entityManager = Site.getCurrent().getSiteContext().getObject(EntityManager.class);
    final User user = ((SecurityProviderSessionImpl) Site.getCurrent().getSecurityProvider())
            .getUserFromSession();//from w w w . j av a  2  s. c  o m
    final List<Group> groups;
    if (user == null) {
        groups = new ArrayList<Group>();
        groups.add(UserDao.getGroup(entityManager, company, "anonymous"));
    } else {
        groups = UserDao.getUserGroups(entityManager, company, user);
    }

    final List<Content> contents = ContentDao.getContens(entityManager, company);
    final LinkedList<Content> queue = new LinkedList<Content>();
    final Map<String, List<Content>> dependencies = new HashMap<String, List<Content>>();
    for (final Content content : contents) {
        final String dependency;
        if (!StringUtils.isEmpty(content.getAfterPage())) {
            dependency = content.getAfterPage();
        } else if (!StringUtils.isEmpty(content.getParentPage())) {
            dependency = content.getParentPage();
        } else {
            dependency = null;
        }
        if (dependency != null) {
            if (!dependencies.containsKey(dependency)) {
                dependencies.put(dependency, new ArrayList<Content>());
            }
            dependencies.get(dependency).add(content);
        } else {
            queue.add(content);
        }
    }

    final List<Content> ordered = new ArrayList<Content>();
    while (queue.size() > 0) {
        final Content content = queue.removeFirst();
        ordered.add(content);
        if (dependencies.containsKey(content.getPage())) {
            queue.addAll(dependencies.get(content.getPage()));
        }
    }

    final NavigationVersion navigationVersion = dynamicSiteDescriptor.getNavigation().getProductionVersion();

    for (final Content content : ordered) {
        boolean viewPrivilege = PrivilegeCache.hasPrivilege(entityManager, company, user, "view",
                content.getContentId());
        if (!viewPrivilege) {
            for (final Group group : groups) {
                if (PrivilegeCache.hasPrivilege(entityManager, company, group, "view",
                        content.getContentId())) {
                    viewPrivilege = true;
                    break;
                }
            }
        }

        if (!viewPrivilege) {
            continue;
        }

        boolean editPrivilege = UserDao.hasUserPrivilege(entityManager, user, "edit", content.getContentId());
        if (!editPrivilege) {
            for (final Group group : groups) {
                if (UserDao.hasGroupPrivilege(entityManager, group, "edit", content.getContentId())) {
                    editPrivilege = true;
                    break;
                }
            }
        }

        final String page = content.getPage();
        if (page == null) {
            continue;
        }
        final String parentPage = content.getParentPage();
        final String afterPage = content.getAfterPage();
        final String title = content.getTitle();
        final MarkupType markupType = content.getMarkupType();
        final String markup = content.getMarkup();

        if (StringUtils.isEmpty(parentPage)) {
            if (StringUtils.isEmpty(afterPage)) {
                navigationVersion.addRootPage(0, page);
                navigationVersion.setDefaultPageName(page);
            } else {
                navigationVersion.addRootPage(afterPage, page);
            }
        } else {
            if (StringUtils.isEmpty(afterPage)) {
                navigationVersion.addChildPage(parentPage, page);
            } else {
                navigationVersion.addChildPage(parentPage, afterPage, page);
            }
        }

        // Describe content view.
        final ViewDescriptor viewDescriptor = new ViewDescriptor(page, title, DefaultValoView.class);
        viewDescriptor.getProductionVersion().setDynamic(true);
        if (editPrivilege) {
            viewDescriptor.setViewletClass("content", RenderFlow.class, content);
        } else {
            viewDescriptor.setViewletClass("content", RenderViewlet.class, markup);
        }
        dynamicSiteDescriptor.getViewDescriptors().add(viewDescriptor);
    }

}

From source file:org.deeplearning4j.nn.conf.ComputationGraphConfiguration.java

/**
 * Add preprocessors automatically, given the specified types of inputs for the network. Inputs are specified using the
 * {@link InputType} class, in the same order in which the inputs were defined in the original configuration.<br>
 * For example, in a network with two inputs: a convolutional input (28x28x1 images) and feed forward inputs, use
 * {@code .addPreProcessors(InputType.convolutional(1,28,28),InputType.feedForward())}.<br>
 * For the CNN->Dense and CNN->RNN transitions, the nIns on the Dense/RNN layers will also be added automatically.
 * <b>NOTE</b>: This method will be called automatically when using the
 * {@link org.deeplearning4j.nn.conf.ComputationGraphConfiguration.GraphBuilder#setInputTypes(InputType...)} functionality.
 * See that method for details.//  w ww. j av a  2 s .  co m
 */
public void addPreProcessors(InputType... inputTypes) {

    if (inputTypes == null || inputTypes.length != networkInputs.size()) {
        throw new IllegalArgumentException(
                "Invalid number of InputTypes: cannot add preprocessors if number of InputType "
                        + "objects differs from number of network inputs");
    }

    //Now: need to do essentially a forward pass through the network, to work out what type of preprocessors to add
    //To do this: need to know what the output types are for each GraphVertex.

    //First step: build network in reverse order (i.e., define map of a -> list(b) instead of list(a) -> b)
    Map<String, List<String>> verticesOutputTo = new HashMap<>(); //Key: vertex. Values: vertices that this node is an input for
    for (Map.Entry<String, GraphVertex> entry : vertices.entrySet()) {
        String vertexName = entry.getKey();
        List<String> vertexInputNames;
        vertexInputNames = vertexInputs.get(vertexName);

        if (vertexInputNames == null)
            continue;

        //Build reverse network structure:
        for (String s : vertexInputNames) {
            List<String> list = verticesOutputTo.get(s);
            if (list == null) {
                list = new ArrayList<>();
                verticesOutputTo.put(s, list);
            }
            list.add(vertexName); //Edge: s -> vertexName
        }
    }

    //Now: do topological sort
    LinkedList<String> noIncomingEdges = new LinkedList<>(networkInputs); //Set of all nodes with no incoming edges
    List<String> topologicalOrdering = new ArrayList<>();

    Map<String, Set<String>> inputEdges = new HashMap<>();
    for (Map.Entry<String, List<String>> entry : vertexInputs.entrySet()) {
        inputEdges.put(entry.getKey(), new HashSet<>(entry.getValue()));
    }

    while (noIncomingEdges.size() > 0) {
        String next = noIncomingEdges.removeFirst();
        topologicalOrdering.add(next);

        //Remove edges next -> vertexOuputsTo[...] from graph;
        List<String> nextEdges = verticesOutputTo.get(next);

        if (nextEdges != null && nextEdges.size() > 0) {
            for (String s : nextEdges) {
                Set<String> set = inputEdges.get(s);
                set.remove(next);
                if (set.size() == 0) {
                    noIncomingEdges.add(s); //No remaining edges for vertex i -> add to list for processing
                }
            }
        }
    }

    //If any edges remain in the graph: graph has cycles:
    for (Map.Entry<String, Set<String>> entry : inputEdges.entrySet()) {
        Set<String> set = entry.getValue();
        if (set == null)
            continue;
        if (set.size() > 0)
            throw new IllegalStateException(
                    "Invalid configuration: cycle detected in graph. Cannot calculate topological ordering with graph cycle ("
                            + "cycle includes vertex \"" + entry.getKey() + "\")");
    }

    //Now, given the topological sort: do equivalent of forward pass
    Map<String, InputType> vertexOutputs = new HashMap<>();
    for (String s : topologicalOrdering) {
        int inputIdx = networkInputs.indexOf(s);
        if (inputIdx != -1) {
            vertexOutputs.put(s, inputTypes[inputIdx]);
            continue;
        }
        GraphVertex gv = vertices.get(s);

        List<InputType> inputTypeList = new ArrayList<>();

        if (gv instanceof LayerVertex) {
            //Add preprocessor, if necessary:
            String in = vertexInputs.get(s).get(0);
            InputType layerInput = vertexOutputs.get(in);

            LayerVertex lv = (LayerVertex) gv;
            if (lv.getPreProcessor() != null)
                continue; //skip: preprocessor is manually defined

            Layer l = lv.getLayerConf().getLayer();
            if (l instanceof ConvolutionLayer || l instanceof SubsamplingLayer) {
                //To add x-to-CNN preprocessor: need to know image depth/width/height
                //But this can't be inferred from the FF/RNN activations directly (could be anything)

                switch (layerInput.getType()) {
                case FF:
                    //FF -> CNN
                    log.warn("Automatic addition of FF -> CNN preprocessors: not yet implemented (layer: " + s
                            + ")");
                    break;
                case RNN:
                    //RNN -> CNN
                    log.warn("Automatic addition of RNN -> CNN preprocessors: not yet implemented (layer: " + s
                            + ")");
                    break;
                case CNN:
                    //CNN -> CNN: no preprocessor required
                    //UNLESS: network input -> CNN layer. Input is in 2d format, not 4d format...
                    if (networkInputs.contains(vertexInputs.get(s).get(0))) {
                        InputType.InputTypeConvolutional conv = (InputType.InputTypeConvolutional) layerInput;
                        lv.setPreProcessor(new FeedForwardToCnnPreProcessor(conv.getHeight(), conv.getWidth(),
                                conv.getDepth()));
                    }
                    break;
                }
            } else if (l instanceof BaseRecurrentLayer || l instanceof RnnOutputLayer) {
                switch (layerInput.getType()) {
                case FF:
                    //FF -> RNN
                    lv.setPreProcessor(new FeedForwardToRnnPreProcessor());
                    //Also set nIn if possible:
                    setNInIfNecessary(lv, layerInput);
                    break;
                case RNN:
                    //RNN -> RNN: no preprocessor required. But set nIn if possible/required
                    setNInIfNecessary(lv, layerInput);
                    break;
                case CNN:
                    //CNN -> RNN
                    InputType.InputTypeConvolutional conv = (InputType.InputTypeConvolutional) layerInput;
                    lv.setPreProcessor(
                            new CnnToRnnPreProcessor(conv.getHeight(), conv.getWidth(), conv.getDepth()));
                    int nIn = conv.getHeight() * conv.getWidth() * conv.getDepth();
                    ((FeedForwardLayer) lv.getLayerConf().getLayer()).setNIn(nIn);
                    break;
                }

            } else {
                //Feed forward layer
                switch (layerInput.getType()) {
                case FF:
                    //FF -> FF: no preprocessor required. But set nIn if possible/required
                    setNInIfNecessary(lv, layerInput);
                    break;
                case RNN:
                    //RNN -> FF
                    lv.setPreProcessor(new RnnToFeedForwardPreProcessor());
                    //Set nIn if possible/required
                    setNInIfNecessary(lv, layerInput);
                    break;
                case CNN:
                    //CNN -> FF
                    InputType.InputTypeConvolutional conv = (InputType.InputTypeConvolutional) layerInput;
                    lv.setPreProcessor(new CnnToFeedForwardPreProcessor(conv.getHeight(), conv.getWidth(),
                            conv.getDepth()));
                    int nIn = conv.getHeight() * conv.getWidth() * conv.getDepth();
                    ((FeedForwardLayer) lv.getLayerConf().getLayer()).setNIn(nIn);
                    break;
                }
            }
            inputTypeList.add(layerInput);
        } else {
            List<String> inputs = vertexInputs.get(s);
            if (inputs != null) {
                for (String inputVertexName : inputs) {
                    inputTypeList.add(vertexOutputs.get(inputVertexName));
                }
            }
        }

        InputType outputFromVertex = gv
                .getOutputType(inputTypeList.toArray(new InputType[inputTypeList.size()]));
        vertexOutputs.put(s, outputFromVertex);
    }
}

From source file:com.streamsets.pipeline.lib.jdbc.JdbcMultiRowRecordWriter.java

@SuppressWarnings("unchecked")
private void processPartition(Connection connection, Multimap<Long, Record> partitions, Long partitionKey,
        List<OnRecordErrorException> errorRecords) throws SQLException, OnRecordErrorException {
    Collection<Record> partition = partitions.get(partitionKey);
    // Fetch the base insert query for this partition.
    SortedMap<String, String> columnsToParameters = getFilteredColumnsToParameters(getColumnsToParameters(),
            partition.iterator().next());

    // put all the records in a queue for consumption
    LinkedList<Record> queue = new LinkedList<>(partition);

    // compute number of rows per batch
    if (columnsToParameters.isEmpty()) {
        throw new OnRecordErrorException(Errors.JDBCDEST_22);
    }// w ww. j ava 2s.  com
    int maxRowsPerBatch = maxPrepStmtParameters / columnsToParameters.size();

    PreparedStatement statement = null;

    // parameters are indexed starting with 1
    int paramIdx = 1;
    int rowCount = 0;
    while (!queue.isEmpty()) {
        // we're at the start of a batch.
        if (statement == null) {
            // instantiate the new statement
            statement = generatePreparedStatement(columnsToParameters,
                    // the next batch will have either the max number of records, or however many are left.
                    Math.min(maxRowsPerBatch, queue.size()), getTableName(), connection);
        }

        // process the next record into the current statement
        Record record = queue.removeFirst();
        for (String column : columnsToParameters.keySet()) {
            Field field = record.get(getColumnsToFields().get(column));
            Field.Type fieldType = field.getType();
            Object value = field.getValue();

            try {
                switch (fieldType) {
                case LIST:
                    List<Object> unpackedList = unpackList((List<Field>) value);
                    Array array = connection.createArrayOf(getSQLTypeName(fieldType), unpackedList.toArray());
                    statement.setArray(paramIdx, array);
                    break;
                case DATE:
                case DATETIME:
                    // Java Date types are not accepted by JDBC drivers, so we need to convert to java.sql.Date
                    java.util.Date date = field.getValueAsDatetime();
                    statement.setObject(paramIdx, new java.sql.Date(date.getTime()));
                    break;
                default:
                    statement.setObject(paramIdx, value, getColumnType(column));
                    break;
                }
            } catch (SQLException e) {
                LOG.error(Errors.JDBCDEST_23.getMessage(), column, fieldType.toString(), e);
                throw new OnRecordErrorException(record, Errors.JDBCDEST_23, column, fieldType.toString());
            }
            ++paramIdx;
        }

        rowCount++;

        // check if we've filled up the current batch
        if (rowCount == maxRowsPerBatch) {
            // time to execute the current batch
            statement.addBatch();
            statement.executeBatch();
            statement.close();
            statement = null;

            // reset our counters
            rowCount = 0;
            paramIdx = 1;
        }
    }

    // check if there are any records left. this should occur whenever there isn't *exactly* maxRowsPerBatch records in
    // this partition.
    if (statement != null) {
        statement.addBatch();
        statement.executeBatch();
        statement.close();
    }
}

From source file:Graph.java

/**
 * Perform a breadth first search of this graph, starting at v. The vist may
 * be cut short if visitor throws an exception during a vist callback.
 * /*from  w w w. j a v a  2  s .  c  o m*/
 * @param <E>
 * 
 * @param v -
 *          the search starting point
 * @param visitor -
 *          the vistor whose vist method is called prior to visting a vertex.
 * @throws E
 *           if vistor.visit throws an exception
 */
public <E extends Exception> void breadthFirstSearch(Vertex<T> v, VisitorEX<T, E> visitor) throws E {
    LinkedList<Vertex<T>> q = new LinkedList<Vertex<T>>();

    q.add(v);
    if (visitor != null)
        visitor.visit(this, v);
    v.visit();
    while (q.isEmpty() == false) {
        v = q.removeFirst();
        for (int i = 0; i < v.getOutgoingEdgeCount(); i++) {
            Edge<T> e = v.getOutgoingEdge(i);
            Vertex<T> to = e.getTo();
            if (!to.visited()) {
                q.add(to);
                if (visitor != null)
                    visitor.visit(this, to);
                to.visit();
            }
        }
    }
}

From source file:edu.ucla.cs.scai.canali.core.index.utils.BiomedicalOntologyUtils.java

private void computeSameAsGroups() throws IOException {
    //load all entities and assign an id to them
    //dbpedia entites are loaded first
    String regex = "(\\s|\\t)*<([^<>]*)>(\\s|\\t)*<([^<>]*)>(\\s|\\t)*(<|\")(.*)(>|\")";
    Pattern p = Pattern.compile(regex);
    for (String fileName : fileNames) {
        try (BufferedReader in = new BufferedReader(new FileReader(downloadedFilesPath + fileName))) {
            String l = in.readLine();
            while (l != null) {
                Matcher m = p.matcher(l);
                if (m.find()) {
                    String s = m.group(2);
                    if ((s.startsWith("http://www.dbpedia.org/resource")
                            || s.startsWith("http://dbpedia.org/resource")) && !entityIds.containsKey(s)
                            && !classIds.containsKey(s) && !propertyIds.containsKey(s)) {
                        entityIds.put(s, entityIds.size() + 1);
                    }//from   ww w .  jav  a2 s .co  m
                    String v = m.group(7);
                    if ((v.startsWith("http://www.dbpedia.org/resource")
                            || v.startsWith("http://dbpedia.org/resource")) && !entityIds.containsKey(v)
                            && !classIds.containsKey(s) && !propertyIds.containsKey(s)) {
                        entityIds.put(v, entityIds.size() + 1);
                    }
                }
                l = in.readLine();
            }
        }
    }

    //now non-dpedia entities are loaded: http://www4.wiwiss.fu-berlin.de, http://data.linkedct.org, http://purl.org, http://bio2rdf.org, http://www.ncbi.nlm.nih.gov        
    for (String fileName : fileNames) {
        try (BufferedReader in = new BufferedReader(new FileReader(downloadedFilesPath + fileName))) {
            String l;
            while ((l = in.readLine()) != null) {
                Matcher m = p.matcher(l);
                if (m.find()) {
                    String s = m.group(2);
                    if (s.startsWith("http://www4.wiwiss.fu-berlin.de") && !entityIds.containsKey(s)
                            && !classIds.containsKey(s) && !propertyIds.containsKey(s)) {
                        entityIds.put(s, entityIds.size() + 1);
                    }
                    String v = m.group(7);
                    if ((v.startsWith("http://www4.wiwiss.fu-berlin.de")
                            //|| v.startsWith("http://data.linkedct.org")
                            || v.startsWith("http://129.128.185.122")) && !entityIds.containsKey(v)
                            && !classIds.containsKey(s) && !propertyIds.containsKey(s)) {
                        entityIds.put(v, entityIds.size() + 1);
                    }
                }
                if (entityIds.size() == 12413) {
                    System.out.println();
                }
            }
        }
    }

    //create the sameAsEdges sets        
    sameAsEdges = new HashSet[entityIds.size() + 1];
    entityById = new String[entityIds.size() + 1];
    for (Map.Entry<String, Integer> e : entityIds.entrySet()) {
        entityById[e.getValue()] = e.getKey();
    }

    for (String fileName : fileNames) {
        try (BufferedReader in = new BufferedReader(new FileReader(downloadedFilesPath + fileName))) {
            String l;
            while ((l = in.readLine()) != null) {
                Matcher m = p.matcher(l);
                if (m.find()) {
                    String a = m.group(4);
                    if (a.equals("http://www.w3.org/2002/07/owl#sameAs")) {
                        String s = m.group(2);
                        int idS = entityIds.get(s);
                        String v = m.group(7);
                        Integer idV = entityIds.get(v);
                        if (idV == null) {
                            continue;
                        }
                        if (sameAsEdges[idS] == null) {
                            sameAsEdges[idS] = new HashSet<>();
                        }
                        sameAsEdges[idS].add(idV);
                        if (sameAsEdges[idV] == null) {
                            sameAsEdges[idV] = new HashSet<>();
                        }
                        sameAsEdges[idV].add(idS);
                    } /* else if (a.equals("http://www.w3.org/1999/02/22-rdf-syntax-ns#type")) {
                      String s = m.group(2);
                      String v = m.group(7);
                      if (v.equals("http://www.w3.org/1999/02/22-rdf-syntax-ns#Property")) {
                      properties.add(s);
                      } else if (v.equals("http://www.w3.org/2000/01/rdf-schema#Class")) {
                      classes.add(s);
                      }
                      }*/

                }
                l = in.readLine();
            }
        }
    }
    sameAs = new int[entityIds.size() + 1];

    int i = 1;
    while (i < sameAs.length) {

        LinkedList<Integer> q = new LinkedList<>();
        q.addLast(i);
        while (!q.isEmpty()) {
            int j = q.removeFirst();
            if (sameAs[j] != 0) {
                if (sameAs[j] != i) {
                    System.out.println("Error");
                    System.exit(0);
                }
            } else {
                sameAs[j] = i;
                if (sameAsEdges[j] != null) {
                    for (int k : sameAsEdges[j]) {
                        q.addLast(k);
                    }
                }
            }
        }

        i++;
        while (i < sameAs.length && sameAs[i] != 0) {
            i++;
        }
    }
}

From source file:edu.ucla.cs.scai.canali.core.index.utils.BiomedicalOntologyUtils.java

private void computeEquivalentPropertyGroups() throws IOException {
    //load all classes and assign an id to them
    //dbpedia properties are loaded first
    String regex = "(\\s|\\t)*<([^<>]*)>(\\s|\\t)*<([^<>]*)>(\\s|\\t)*(<|\")(.*)(>|\")";
    Pattern p = Pattern.compile(regex);
    for (String fileName : fileNames) {
        try (BufferedReader in = new BufferedReader(new FileReader(downloadedFilesPath + fileName))) {
            String l = in.readLine();
            while (l != null) {
                Matcher m = p.matcher(l);
                if (m.find()) {
                    String s = m.group(2);
                    String a = m.group(4);
                    String v = m.group(7);
                    if (a.equals("http://www.w3.org/1999/02/22-rdf-syntax-ns#type")
                            && v.equals("http://www.w3.org/1999/02/22-rdf-syntax-ns#Property")
                            && (s.startsWith("http://www.dbpedia.org") || s.startsWith("http://dbpedia.org"))
                            && !propertyIds.containsKey(s)) {
                        propertyIds.put(s, propertyIds.size() + 1);
                    } else if (a.equals("http://www.w3.org/2002/07/owl#equivalentProperty")) {
                        if ((s.startsWith("http://www.dbpedia.org") || s.startsWith("http://dbpedia.org"))
                                && !propertyIds.containsKey(s)) {
                            propertyIds.put(s, propertyIds.size() + 1);
                        }/*from  w w w  .ja  v a 2  s .  c  o  m*/
                        if ((v.startsWith("http://www.dbpedia.org") || v.startsWith("http://dbpedia.org"))
                                && !propertyIds.containsKey(v)) {
                            propertyIds.put(v, propertyIds.size() + 1);
                        }
                    }
                }
                l = in.readLine();
            }
        }
    }

    //now non-dpedia properties are loaded
    for (String fileName : fileNames) {
        try (BufferedReader in = new BufferedReader(new FileReader(downloadedFilesPath + fileName))) {
            String l = in.readLine();
            while (l != null) {
                Matcher m = p.matcher(l);
                if (m.find()) {
                    String s = m.group(2);
                    String a = m.group(4);
                    String v = m.group(7);
                    if (a.equals("http://www.w3.org/1999/02/22-rdf-syntax-ns#type")
                            && v.equals("http://www.w3.org/1999/02/22-rdf-syntax-ns#Property")
                            && !(s.equals("http://www.w3.org/2000/01/rdf-schema#label")
                                    || s.equals("http://www.w3.org/2002/07/owl#sameAs")
                                    || s.startsWith("http://www.dbpedia.org")
                                    || s.startsWith("http://dbpedia.org"))
                            && !propertyIds.containsKey(s)) {
                        propertyIds.put(s, propertyIds.size() + 1);
                    } else if (a.equals("http://www.w3.org/2002/07/owl#equivalentProperty")) {
                        if (!(s.startsWith("http://www.dbpedia.org") || s.startsWith("http://dbpedia.org"))
                                && !propertyIds.containsKey(s)) {
                            propertyIds.put(s, propertyIds.size() + 1);
                        }
                        if (!(v.startsWith("http://www.dbpedia.org") || v.startsWith("http://dbpedia.org"))
                                && !propertyIds.containsKey(v)) {
                            propertyIds.put(v, propertyIds.size() + 1);
                        }
                    }
                }
                l = in.readLine();
            }
        }
    }

    //create the equivalentPropertyEdges sets        
    equivalentPropertyEdges = new HashSet[propertyIds.size() + 1];
    propertyById = new String[propertyIds.size() + 1];
    for (Map.Entry<String, Integer> e : propertyIds.entrySet()) {
        propertyById[e.getValue()] = e.getKey();
    }

    for (String fileName : fileNames) {
        try (BufferedReader in = new BufferedReader(new FileReader(downloadedFilesPath + fileName))) {
            String l = in.readLine();
            while (l != null) {
                Matcher m = p.matcher(l);
                if (m.find()) {
                    String a = m.group(4);
                    if (a.equals("http://www.w3.org/2002/07/owl#equivalentProperty")) {
                        String s = m.group(2);
                        int idS = propertyIds.get(s);
                        String v = m.group(7);
                        int idV = propertyIds.get(v);
                        if (equivalentPropertyEdges[idS] == null) {
                            equivalentPropertyEdges[idS] = new HashSet<>();
                        }
                        equivalentPropertyEdges[idS].add(idV);
                        if (equivalentPropertyEdges[idV] == null) {
                            equivalentPropertyEdges[idV] = new HashSet<>();
                        }
                        equivalentPropertyEdges[idV].add(idS);
                    } /* else if (a.equals("http://www.w3.org/1999/02/22-rdf-syntax-ns#type")) {
                      String s = m.group(2);
                      String v = m.group(7);
                      if (v.equals("http://www.w3.org/1999/02/22-rdf-syntax-ns#Property")) {
                      properties.add(s);
                      } else if (v.equals("http://www.w3.org/2000/01/rdf-schema#Class")) {
                      classes.add(s);
                      }
                      }*/

                }
                l = in.readLine();
            }
        }
    }
    equivalentProperty = new int[propertyIds.size() + 1];

    int i = 1;
    while (i < equivalentProperty.length) {

        LinkedList<Integer> q = new LinkedList<>();
        q.addLast(i);
        while (!q.isEmpty()) {
            int j = q.removeFirst();
            if (equivalentProperty[j] != 0) {
                if (equivalentProperty[j] != i) {
                    System.out.println("Error");
                    System.exit(0);
                }
            } else {
                equivalentProperty[j] = i;
                if (equivalentPropertyEdges[j] != null) {
                    for (int k : equivalentPropertyEdges[j]) {
                        q.addLast(k);
                    }
                }
            }
        }

        i++;
        while (i < equivalentProperty.length && equivalentProperty[i] != 0) {
            i++;
        }
    }
}