Example usage for java.util LinkedHashSet add

List of usage examples for java.util LinkedHashSet add

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Introduction

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

Prototype

boolean add(E e);

Source Link

Document

Adds the specified element to this set if it is not already present (optional operation).

Usage

From source file:net.sf.taverna.t2.activities.beanshell.BeanshellActivityHealthChecker.java

public VisitReport visit(BeanshellActivity activity, List<Object> ancestors) {
    Object subject = (Processor) VisitReport.findAncestor(ancestors, Processor.class);
    if (subject == null) {
        // Fall back to using the activity itself as the subject of the reports
        subject = activity;/*from   ww  w  .j  a  va  2s  .c  o  m*/
    }
    List<VisitReport> reports = new ArrayList<VisitReport>();

    String script = activity.getConfiguration().get("script").textValue();
    if (!script.trim().endsWith(";")) {
        /** Missing ; on last line is not allowed by Parser,
         * but is allowed by Interpreter.eval() used at runtime
         */
        script = script + ";";
    }
    Parser parser = new Parser(new StringReader(script));
    try {
        while (!parser.Line())
            ;
        reports.add(new VisitReport(HealthCheck.getInstance(), subject, "Script OK", HealthCheck.NO_PROBLEM,
                Status.OK));
    } catch (ParseException e) {
        VisitReport report = new VisitReport(HealthCheck.getInstance(), subject, e.getMessage(),
                HealthCheck.INVALID_SCRIPT, Status.SEVERE);
        report.setProperty("exception", e);
        reports.add(report);
    }

    // Check if we can find all the Beanshell's dependencies
    if (activity.getConfiguration().has("localDependency")) {
        LinkedHashSet<String> localDependencies = new LinkedHashSet<>();
        for (JsonNode localDependency : activity.getConfiguration().get("localDependency")) {
            localDependencies.add(localDependency.textValue());
        }

        String[] jarArray = activity.libDir.list(new FileExtFilter(".jar"));
        if (jarArray != null) {
            List<String> jarFiles = Arrays.asList(jarArray); // URLs of all jars found in the lib directory
            for (String jar : localDependencies) {
                if (jarFiles.contains(jar)) {
                    localDependencies.remove(jar);
                }
            }
        }
        if (localDependencies.isEmpty()) { // all dependencies found
            reports.add(new VisitReport(HealthCheck.getInstance(), subject, "Beanshell dependencies found",
                    HealthCheck.NO_PROBLEM, Status.OK));
        } else {
            VisitReport vr = new VisitReport(HealthCheck.getInstance(), subject,
                    "Beanshell dependencies missing", HealthCheck.MISSING_DEPENDENCY, Status.SEVERE);
            vr.setProperty("dependencies", localDependencies);
            vr.setProperty("directory", activity.libDir);
            reports.add(vr);
        }

    }
    Status status = VisitReport.getWorstStatus(reports);
    VisitReport report = new VisitReport(HealthCheck.getInstance(), subject, "Beanshell report",
            HealthCheck.NO_PROBLEM, status, reports);

    return report;

}

From source file:azkaban.utils.PropsUtils.java

private static String resolveVariableReplacement(String value, Props props,
        LinkedHashSet<String> visitedVariables) {
    StringBuffer buffer = new StringBuffer();
    int startIndex = 0;

    Matcher matcher = VARIABLE_REPLACEMENT_PATTERN.matcher(value);
    while (matcher.find(startIndex)) {
        if (startIndex < matcher.start()) {
            // Copy everything up front to the buffer
            buffer.append(value.substring(startIndex, matcher.start()));
        }/*w w w.java2  s .c o  m*/

        String subVariable = matcher.group(1);
        // Detected a cycle
        if (visitedVariables.contains(subVariable)) {
            throw new IllegalArgumentException(
                    String.format("Circular variable substitution found: [%s] -> [%s]",
                            StringUtils.join(visitedVariables, "->"), subVariable));
        } else {
            // Add substitute variable and recurse.
            String replacement = props.get(subVariable);
            visitedVariables.add(subVariable);

            if (replacement == null) {
                throw new UndefinedPropertyException(
                        String.format("Could not find variable substitution for variable(s) [%s]",
                                StringUtils.join(visitedVariables, "->")));
            }

            buffer.append(resolveVariableReplacement(replacement, props, visitedVariables));
            visitedVariables.remove(subVariable);
        }

        startIndex = matcher.end();
    }

    if (startIndex < value.length()) {
        buffer.append(value.substring(startIndex));
    }

    return buffer.toString();
}

From source file:com.qwazr.library.realm.table.TableRealmConnector.java

@Override
public Account verify(final String id, final Credential credential) {

    // This realm only support one type of credential
    if (!(credential instanceof PasswordCredential))
        throw new RuntimeException("Unsupported credential type: " + credential.getClass().getName());

    PasswordCredential passwordCredential = (PasswordCredential) credential;

    // We request the database
    final Map<String, ?> row;
    try {/*from   w w w.ja v  a  2s . c o m*/
        row = tableService.getRow(table_name, id, columns);
        if (row == null)
            return null;
    } catch (WebApplicationException e) {
        if (e.getResponse().getStatusInfo().getFamily() == Response.Status.Family.CLIENT_ERROR)
            return authenticationFailure("Unknown user: " + id);
        throw e;
    }

    Object password = row.get(password_column);
    if (password == null)
        return null;
    if (password instanceof String[]) {
        String[] passwordArray = (String[]) password;
        if (passwordArray.length == 0)
            return null;
        password = passwordArray[0];
    }

    // The password is stored hashed
    final String passwd = new String(passwordCredential.getPassword());
    String digest = DigestUtils.sha256Hex(passwd);
    if (!digest.equals(password))
        return authenticationFailure("Wrong password: " + id + " " + digest + '/' + passwd + '/' + password);

    //We retrieve the roles
    final Object object = row.get(roles_column);
    final LinkedHashSet<String> roles = new LinkedHashSet<>();
    if (object instanceof String[]) {
        for (Object o : (String[]) object)
            roles.add(o.toString());
    } else
        roles.add(object.toString());

    return new Account() {
        @Override
        public Principal getPrincipal() {
            return () -> id;
        }

        @Override
        public Set<String> getRoles() {
            return roles;
        }
    };
}

From source file:com.qwazr.connectors.TableRealmConnector.java

@Override
public Account verify(String id, Credential credential) {

    // This realm only support one type of credential
    if (!(credential instanceof PasswordCredential))
        throw new RuntimeException("Unsupported credential type: " + credential.getClass().getName());

    PasswordCredential passwordCredential = (PasswordCredential) credential;

    // We request the database
    final LinkedHashMap<String, Object> row;
    try {/*  w  w w  .j ava 2s . c  o m*/
        row = tableService.getRow(table_name, id, columns);
        if (row == null)
            return null;
    } catch (WebApplicationException e) {
        if (e.getResponse().getStatusInfo().getFamily() == Response.Status.Family.CLIENT_ERROR)
            return authenticationFailure("Unknown user: " + id);
        throw e;
    }

    Object password = row.get(password_column);
    if (password == null)
        return null;
    if (password instanceof String[]) {
        String[] passwordArray = (String[]) password;
        if (passwordArray.length == 0)
            return null;
        password = passwordArray[0];
    }

    // The password is stored hashed
    final String passwd = new String(passwordCredential.getPassword());
    String digest = DigestUtils.sha256Hex(passwd);
    if (!digest.equals(password))
        return authenticationFailure("Wrong password: " + id + " " + digest + '/' + passwd + '/' + password);

    //We retrieve the roles
    Object object = row.get(roles_column);
    LinkedHashSet<String> roles = new LinkedHashSet<String>();
    if (object instanceof String[]) {
        for (Object o : (String[]) object)
            roles.add(o.toString());
    } else
        roles.add(object.toString());

    return new Account() {
        @Override
        public Principal getPrincipal() {
            return new Principal() {
                @Override
                public String getName() {
                    return id;
                }
            };
        }

        @Override
        public Set<String> getRoles() {
            return roles;
        }
    };
}

From source file:ca.on.oicr.pde.workflows.GATKGenotypeGVCFsWorkflow.java

private <T, S> Set<T> getLeftCollection(Collection<Pair<T, S>> pairs) {
    LinkedHashSet<T> ts = new LinkedHashSet<>();
    for (Pair<T, S> p : pairs) {
        ts.add(p.getLeft());
    }//from  w  ww.ja v  a2 s. c o  m
    return ts;
}

From source file:ca.on.oicr.pde.workflows.GATKGenotypeGVCFsWorkflow.java

private <S, T> Set<T> getRightCollection(Collection<Pair<S, T>> pairs) {
    LinkedHashSet<T> ts = new LinkedHashSet<>();
    for (Pair<S, T> p : pairs) {
        ts.add(p.getRight());
    }/* www.  ja  v a 2s  .  c o  m*/
    return ts;
}

From source file:biomine.bmvis2.pipeline.RepresentiveHighlightOperation.java

public ArrayList<VisualNode> initList(VisualGraph g) {
    SimpleVisualGraph sg = new SimpleVisualGraph(g.getRootNode().getDescendants());
    ArrayList<ProbDijkstra> positive = new ArrayList<ProbDijkstra>();
    ArrayList<ProbDijkstra> negative = new ArrayList<ProbDijkstra>();
    int poicount = 0;

    LinkedHashSet<Integer> remaining = new LinkedHashSet<Integer>();
    for (int i = 0; i < sg.n; i++)
        remaining.add(i);

    for (Map.Entry<VisualNode, Double> ent : g.getNodesOfInterest().entrySet()) {
        VisualNode vn = ent.getKey();/*w  w  w.j a v  a2s .c om*/
        double val = ent.getValue();
        int ivn = sg.getInt(vn);
        remaining.remove(ivn);
        ProbDijkstra pd = new ProbDijkstra(sg, ivn);
        if (val > 0)
            positive.add(pd);
        else
            negative.add(pd);
        poicount++;
    }

    ArrayList<VisualNode> rlist = new ArrayList<VisualNode>();
    ArrayList<Double> posProb = new ArrayList<Double>();
    ArrayList<Double> posSquareSum = new ArrayList<Double>();
    for (int i = 0; i < sg.n; i++) {
        double p = 1;
        double ss = 0;
        for (ProbDijkstra pd : positive) {
            p *= pd.getProbTo(i);
            ss += Math.pow(pd.getProbTo(i), 2);
        }
        posProb.add(p);
        posSquareSum.add(ss);
    }

    ArrayList<Double> negProb = new ArrayList<Double>();
    for (int i = 0; i < sg.n; i++) {
        double p = 1;
        for (ProbDijkstra pd : negative) {
            p *= (1 - pd.getProbTo(i));
        }
        negProb.add(p);
    }

    int it = 0;
    while (negative.size() + positive.size() < sg.n) {
        it++;
        //add 
        //select n with highest posProb[n]*(1-negProb[n])
        //in case of a tie, select n with lowest square sum distance from 
        //positive nodes

        int best = -1;
        double bestSS = 100000;
        double bestProb = 0;
        for (int n : remaining) {
            double prob = posProb.get(n) * (negProb.get(n));
            double ss = posSquareSum.get(n);
            if (prob == bestProb) {
                if (ss < bestSS) {
                    bestSS = ss;
                    best = n;
                }
            }
            if (prob > bestProb) {
                bestProb = prob;
                bestSS = ss;
                best = n;
            }
        }
        if (best < 0)
            break;

        System.out.println("it " + it + " best = " + best + " prob = " + bestProb);

        rlist.add(sg.getVisualNode(best));
        ProbDijkstra newPD = new ProbDijkstra(sg, best);
        negative.add(newPD);

        remaining.remove(best);
        for (int i : remaining) {
            double ol = negProb.get(i);
            ol *= 1 - newPD.getProbTo(i);
            negProb.set(i, ol);
        }
    }
    return rlist;
}

From source file:opennlp.tools.fca.ConceptLattice.java

public void createLatticeFromBinaryContext() {
    LinkedHashSet<Integer> obj;
    ArrayList<Integer> intent;
    // attributes list
    ArrayList<Integer> attributes = new ArrayList<Integer>();
    for (int i = 0; i < attributeCount; i++) {
        attributes.add(i);//from w w w .j  a v  a 2 s . c  o  m
    }
    // objects set
    LinkedHashSet<Integer> objects = new LinkedHashSet<Integer>();
    for (int i = 0; i < objectCount; i++) {
        objects.add(i);
    }

    this.conceptList.get(0).setIntent(attributes);
    for (int i = 0; i < objectCount; i++) {
        intent = new ArrayList<Integer>();
        obj = new LinkedHashSet<Integer>();
        obj.add(i);
        for (int j = 0; j < attributeCount; j++) {
            if (binaryContext[i][j] == 1) {
                intent.add(j);
            }
        }
        this.AddIntent(intent, obj, 0);
    }
}

From source file:de.ovgu.featureide.featurehouse.FeatureHouseComposer.java

private static LinkedHashSet<String> createExtensions() {
    LinkedHashSet<String> extensions = new LinkedHashSet<String>();
    extensions.add("java");
    extensions.add("cs");
    extensions.add("c");
    extensions.add("h");
    extensions.add("hs");
    extensions.add("jj");
    extensions.add("als");
    extensions.add("xmi");
    return extensions;
}

From source file:com.cenrise.test.azkaban.PropsUtils.java

private static String resolveVariableReplacement(final String value, final Props props,
        final LinkedHashSet<String> visitedVariables) {
    final StringBuffer buffer = new StringBuffer();
    int startIndex = 0;

    final Matcher matcher = VARIABLE_REPLACEMENT_PATTERN.matcher(value);
    while (matcher.find(startIndex)) {
        if (startIndex < matcher.start()) {
            // Copy everything up front to the buffer
            buffer.append(value.substring(startIndex, matcher.start()));
        }/*from   w w w  .  ja  v  a2 s .  co  m*/

        final String subVariable = matcher.group(1);
        // Detected a cycle
        if (visitedVariables.contains(subVariable)) {
            throw new IllegalArgumentException(
                    String.format("Circular variable substitution found: [%s] -> [%s]",
                            StringUtils.join(visitedVariables, "->"), subVariable));
        } else {
            // Add substitute variable and recurse.
            final String replacement = props.get(subVariable);
            visitedVariables.add(subVariable);

            if (replacement == null) {
                throw new UndefinedPropertyException(
                        String.format("Could not find variable substitution for variable(s) [%s]",
                                StringUtils.join(visitedVariables, "->")));
            }

            buffer.append(resolveVariableReplacement(replacement, props, visitedVariables));
            visitedVariables.remove(subVariable);
        }

        startIndex = matcher.end();
    }

    if (startIndex < value.length()) {
        buffer.append(value.substring(startIndex));
    }

    return buffer.toString();
}