Example usage for java.util HashSet iterator

Introduction

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

Prototype

public Iterator<E> iterator() 

Source Link

Document

Returns an iterator over the elements in this set.

Usage

From source file:org.mskcc.cbio.portal.servlet.GeneDataJSON.java

/**
 *
 * @param request//  w  w w .j a  v  a 2  s.  c om
 * @param response
 * @throws ServletException
 * @throws IOException
 */
@Override
public void doPost(HttpServletRequest request, HttpServletResponse response)
        throws ServletException, IOException {

    // OncoQuery Language string
    String oql = request.getParameter("oql");

    if (request instanceof XssRequestWrapper) {
        oql = ((XssRequestWrapper) request).getRawParameter("oql");
    }

    oql = oql.replaceAll("\n", " \n ");

    List<String> sampleIdList;
    try {
        sampleIdList = WebserviceParserUtils.getSampleIds(request);
    } catch (ProtocolException e) {
        throw new ServletException(e);
    } catch (DaoException e) {
        throw new ServletException(e);
    }

    String _geneticProfileIds = request.getParameter("geneticProfileIds");
    // list of geneticProfileIds separated by a space
    // e.g. gbm_mutations, gbm_cna_consensus

    HashSet<String> geneticProfileIdSet = new HashSet<String>(
            Arrays.asList(_geneticProfileIds.trim().split(" ")));

    // map geneticProfileIds -> geneticProfiles
    Iterator<String> gpSetIterator = geneticProfileIdSet.iterator();
    ArrayList<GeneticProfile> profileList = new ArrayList<GeneticProfile>();
    while (gpSetIterator.hasNext()) {
        String gp_str = gpSetIterator.next();

        GeneticProfile gp = DaoGeneticProfile.getGeneticProfileByStableId(gp_str);
        profileList.add(gp);
        // pointer to gp is local, but gets added to profileList which is outside
    }

    double zScoreThreshold = Double.valueOf(request.getParameter("z_score_threshold"));
    double rppaScoreThreshold = Double.valueOf(request.getParameter("rppa_score_threshold"));

    // todo: this is code duplication!
    // this is a duplication of work that is being done in QueryBuilder.
    // For now, we cannot remove it from QueryBuilder because other parts use it...for now
    // ...this is a temporary solution
    ParserOutput theOncoPrintSpecParserOutput = OncoPrintSpecificationDriver.callOncoPrintSpecParserDriver(oql,
            geneticProfileIdSet, profileList, zScoreThreshold, rppaScoreThreshold);

    ArrayList<String> listOfGenes = theOncoPrintSpecParserOutput.getTheOncoPrintSpecification().listOfGenes();

    String[] listOfGeneNames = new String[listOfGenes.size()];
    listOfGeneNames = listOfGenes.toArray(listOfGeneNames);

    ArrayList<ProfileData> profileDataList = new ArrayList<ProfileData>();
    Iterator<String> profileIterator = geneticProfileIdSet.iterator();

    XDebug xdebug = new XDebug(request);
    while (profileIterator.hasNext()) {
        String profileId = profileIterator.next();
        GeneticProfile profile = GeneticProfileUtil.getProfile(profileId, profileList);
        if (null == profile) {
            continue;
        }

        xdebug.logMsg(this, "Getting data for:  " + profile.getProfileName());

        GetProfileData remoteCall;
        List<Sample.Type> excludes = new ArrayList<Sample.Type>();
        excludes.add(Sample.Type.SOLID_NORMAL);
        excludes.add(Sample.Type.BLOOD_NORMAL);
        String sampleIds = StringUtils.join(sampleIdList, " ");

        try {
            remoteCall = new GetProfileData(profile, listOfGenes, sampleIds);
        } catch (DaoException e) {
            throw new ServletException(e);
        }
        ProfileData pData = remoteCall.getProfileData();
        if (pData == null) {
            System.err.println("pData == null");
        } else {
            if (pData.getGeneList() == null) {
                System.err.println("pData.getValidGeneList() == null");
            }
            if (pData.getCaseIdList().size() == 0) {
                System.err.println("pData.length == 0");
            }
        }
        if (pData != null) {
            xdebug.logMsg(this, "Got number of genes:  " + pData.getGeneList().size());
            xdebug.logMsg(this, "Got number of cases:  " + pData.getCaseIdList().size());
        }
        xdebug.logMsg(this, "Number of warnings received:  " + remoteCall.getWarnings().size());
        profileDataList.add(pData);
    }

    xdebug.logMsg(this, "Merging Profile Data");
    ProfileMerger merger = new ProfileMerger(profileDataList);
    ProfileData mergedProfile = merger.getMergedProfile();

    ProfileDataSummary dataSummary = new ProfileDataSummary(mergedProfile,
            theOncoPrintSpecParserOutput.getTheOncoPrintSpecification(), zScoreThreshold, rppaScoreThreshold);

    GeneticEvent geneticEvents[][] = ConvertProfileDataToGeneticEvents.convert(dataSummary, listOfGeneNames,
            theOncoPrintSpecParserOutput.getTheOncoPrintSpecification(), zScoreThreshold, rppaScoreThreshold);

    // out.write the matrix

    response.setContentType("application/json");
    PrintWriter out = response.getWriter();

    JSONArray jsonArray = mapGeneticEventMatrix(geneticEvents);
    JSONArray.writeJSONString(jsonArray, out);
}

---

From source file:com.sec.ose.osi.sdk.protexsdk.discovery.DCStringSearch.java

public ArrayList<String> resetFolder(String pFolderPath, String pStringSearch, String targetComponentName,
        String targetVersionName, UIResponseObserver mObserver, int compositeType) {
    ArrayList<String> resetTargetList = new ArrayList<String>();
    HashSet<String> hs = IdentificationDBManager.getStringSearchResetTargetFile(this.projectName, pFolderPath,
            pStringSearch);//from w  w  w . j a va  2  s . c o m
    String target = "";
    mObserver.setMessageHeader("Reset processing...\n");
    if (hs == null) {
        return resetTargetList;
    }
    Iterator<String> it = hs.iterator();
    while (it.hasNext()) {
        target = it.next();
        mObserver.pushMessageWithHeader(" > filePath : " + target);
        updateStringSearchResetForLocalDB(target);
        resetTargetList.add(target);
    }
    return resetTargetList;
}

---

From source file:org.apache.sysml.validation.ValidateLicAndNotice.java

/**
 * This will validate objects (class files) against license file.
 *
 * @param   licenseFile is the name of the license file.
 * @param    hashMapPackages is the list of package names to be validated for license.
 * @return  Success or Failure code/*from  w ww  .  jav a2s  . co  m*/
 */
public static int validatePackages(String licenseFile, HashMap<String, Boolean> hashMapPackages)
        throws Exception {
    int iRetCode = Constants.SUCCESS;
    BufferedReader reader = new BufferedReader(new FileReader(licenseFile));
    String line = null;
    HashSet<String> packageValidLic = new HashSet<String>();
    while ((line = reader.readLine()) != null) {
        line = line.trim();
        for (int i = 0; i < packageLicenses.length; ++i) {
            if (line.contains(packageLicenses[i][1])) {
                packageValidLic.add(packageLicenses[i][0]);
                Utility.debugPrint(Constants.DEBUG_INFO3,
                        "License for package " + packageLicenses[i][0] + " exists.");
            }
        }
    }

    Iterator<Map.Entry<String, Boolean>> itPackages = hashMapPackages.entrySet().iterator();
    while (itPackages.hasNext()) {
        Map.Entry<String, Boolean> pairPackage = (Map.Entry<String, Boolean>) itPackages.next();
        Iterator<String> itLicPackages = packageValidLic.iterator();
        while (itLicPackages.hasNext()) {
            if (((String) pairPackage.getKey()).startsWith((String) itLicPackages.next()))
                pairPackage.setValue(Boolean.TRUE);
        }
    }

    itPackages = hashMapPackages.entrySet().iterator();
    while (itPackages.hasNext()) {
        Map.Entry pairPackage = (Map.Entry) itPackages.next();
        if (!(Boolean) pairPackage.getValue()) {
            Utility.debugPrint(Constants.DEBUG_WARNING, "Could not validate license for package "
                    + pairPackage.getKey() + ", please validate manually.");
            iRetCode = Constants.LIC_NOT_EXIST;
        }
    }

    return iRetCode;
}

---

From source file:abs.backend.erlang.ClassGenerator.java

private void generateExports() {
    ecs.println("-export([get_val_internal/2,set_val_internal/3,init_internal/0,get_all_state/1]).");
    ecs.println("-compile(export_all).");
    ecs.println();// www  .j av  a 2s.c om

    HashSet<MethodSig> callable_sigs = new HashSet<MethodSig>();
    HashSet<InterfaceDecl> visited = new HashSet<InterfaceDecl>();
    for (InterfaceTypeUse i : classDecl.getImplementedInterfaceUseList()) {
        visited.add((InterfaceDecl) i.getDecl());
    }

    while (!visited.isEmpty()) {
        InterfaceDecl id = visited.iterator().next();
        visited.remove(id);
        for (MethodSig ms : id.getBodyList()) {
            if (ms.isHTTPCallable()) {
                callable_sigs.add(ms);
            }
        }
        for (InterfaceTypeUse i : id.getExtendedInterfaceUseList()) {
            visited.add((InterfaceDecl) i.getDecl());
        }
    }

    ecs.print("exported() -> #{ ");
    boolean first = true;
    for (MethodSig ms : callable_sigs) {
        if (ms.isHTTPCallable()) {
            if (!first)
                ecs.print(", ");
            first = false;
            ecs.print("<<\"" + ms.getName() + "\">> => { ");
            ecs.print("'m_" + ms.getName() + "'");
            ecs.print(", ");
            ecs.print("<<\"" + ms.getReturnType().getType().getQualifiedName() + "\">>");
            ecs.print(", ");
            ecs.print("[ ");
            boolean innerfirst = true;
            for (ParamDecl p : ms.getParamList()) {
                if (!innerfirst)
                    ecs.print(", ");
                innerfirst = false;
                ecs.print("{ ");
                ecs.print("<<\"" + p.getName() + "\">>");
                ecs.print(", ");
                ecs.print("<<\"" + p.getAccess().getType().getQualifiedName() + "\">>");
                ecs.print(" }");
            }
            ecs.print("] ");
            ecs.print("}");
        }
    }
    ecs.println(" }.");
    ecs.println();
}

---

From source file:org.paxle.crawler.impl.SubCrawlerManager.java

/**
 * @see ISubParserManager#disabledMimeType()
 *//*from   w w  w. j  a  v a2  s .  co m*/
public Set<String> disabledProtocols() {
    // get all available mime-types and remove enabled mime-types
    final HashSet<String> protocols = new HashSet<String>(this.subCrawlerList.keySet());

    final Iterator<String> protocolIter = protocols.iterator();
    while (protocolIter.hasNext()) {
        final String protocol = protocolIter.next();
        if (this.isSupported(protocol)) {
            protocolIter.remove();
        }
    }

    return protocols;
}

---

From source file:org.cloudgraph.hbase.mutation.Update.java

private void collectSingular(EdgeWriter edgeWriter, PlasmaDataObject dataObject,
        HashSet<PlasmaDataObject> oldValues, PlasmaProperty property, Object value) throws IOException {

    PlasmaNode dataNode = (PlasmaNode) dataObject;
    List<PlasmaEdge> edges = dataNode.getEdges(property);

    PlasmaDataObject oldDataObject = null;
    if (oldValues.size() > 0) {
        if (oldValues.size() == 1) {
            oldDataObject = (PlasmaDataObject) oldValues.iterator().next();
        } else//from ww  w  .java  2 s . c om
            throw new GraphServiceException(
                    "unexpected List as old value for property, " + property.toString());
    }
    // if has a new value
    PlasmaDataObject newDataObject = null;
    if (value != null) {
        PlasmaEdge edge = edges.get(0);

        newDataObject = edge.getOpposite(dataNode).getDataObject();
        if (oldDataObject != null)
            edgeWriter.replace(oldDataObject, newDataObject);
        else
            // add the new one
            edgeWriter.add(newDataObject);
    } else {
        if (oldDataObject != null)
            edgeWriter.remove(oldDataObject);
    }
}

---

From source file:org.paxle.core.impl.RuntimeSettings.java

public Dictionary<?, ?> getCurrentIniSettings() {
    final Dictionary<String, Object> props = new Hashtable<String, Object>();
    final List<String> iniSettings = readSettings();

    final StringBuilder sb = new StringBuilder();
    final HashSet<OptEntry> opts = new HashSet<OptEntry>(OPTIONS);
    outer: for (final String opt : iniSettings) {
        final Iterator<OptEntry> it = opts.iterator();
        while (it.hasNext()) {
            final OptEntry e = it.next();
            if (opt.startsWith(e.fixOpt)) {
                props.put(e.getPid(), e.getValue(opt, true));
                it.remove();/*from   w  ww . j  av  a  2  s.  co  m*/
                continue outer;
            }
        }
        if (sb.length() > 0)
            sb.append(OPT_OTHER_SPLIT);
        sb.append(opt);
    }
    for (final OptEntry e : opts)
        props.put(e.getPid(), e.getValue(null, true));
    if (sb.length() > 0)
        props.put(CM_OTHER_ENTRY.getPid(), sb.toString());

    return props;
}

---

From source file:org.plasma.provisioning.xsd.ConverterSupport.java

private void traverse(Class target, Class source, ClassVisitor visitor) {
    visitor.visit(target, source);// w w  w. ja  va2 s  .  c  o  m
    HashSet<Class> subclasses = this.subclassMap.get(target);
    if (subclasses != null) {
        Iterator<Class> iter = subclasses.iterator();
        while (iter.hasNext()) {
            traverse(iter.next(), target, visitor);
        }
    }
}

---

From source file:org.abs_models.backend.erlang.ClassGenerator.java

private void generateExports() {
    ecs.println(//from w  w w. j a v  a2s  .  c  om
            "-export([get_val_internal/2,set_val_internal/3,init_internal/0,get_state_for_modelapi/1,implemented_interfaces/0,exported/0]).");
    ecs.println("-compile(export_all).");
    ecs.println();

    HashSet<MethodSig> callable_sigs = new HashSet<>();
    HashSet<InterfaceDecl> visited = new HashSet<>();
    for (InterfaceTypeUse i : classDecl.getImplementedInterfaceUseList()) {
        visited.add((InterfaceDecl) i.getDecl());
    }

    while (!visited.isEmpty()) {
        InterfaceDecl id = visited.iterator().next();
        visited.remove(id);
        for (MethodSig ms : id.getBodyList()) {
            if (ms.isHTTPCallable()) {
                callable_sigs.add(ms);
            }
        }
        for (InterfaceTypeUse i : id.getExtendedInterfaceUseList()) {
            visited.add((InterfaceDecl) i.getDecl());
        }
    }

    ecs.print("implemented_interfaces() -> [ ");
    String separator = "";
    for (InterfaceDecl i : classDecl.getSuperTypes()) {
        ecs.format("%s<<\"%s\">>", separator, i.getName());
        separator = ", ";
    }
    ecs.println(" ].");
    ecs.println();

    ecs.print("exported() -> #{ ");
    boolean first = true;
    for (MethodSig ms : callable_sigs) {
        if (ms.isHTTPCallable()) {
            if (!first)
                ecs.print(", ");
            first = false;
            ecs.print("<<\"" + ms.getName() + "\">> => { ");
            ecs.print("'m_" + ms.getName() + "'");
            ecs.print(", ");
            ecs.print("<<\"" + ms.getReturnType().getType().toString() + "\">>");
            ecs.print(", ");
            ecs.print("[ ");
            boolean innerfirst = true;
            for (ParamDecl p : ms.getParamList()) {
                // For each parameter, we need name, human-readable type,
                // ABS type, and ABS type arguments (if present)
                if (!innerfirst)
                    ecs.print(", ");
                innerfirst = false;
                ecs.print("{ ");
                ecs.print("<<\"" + p.getName() + "\">>, ");
                ecs.print("<<\"" + p.getType().toString() + "\">>, ");
                generateParameterDescription(p.getType());
                ecs.print(" }");
            }
            ecs.print("] ");
            ecs.print("}");
        }
    }
    ecs.println(" }.");
    ecs.println();
}

---

From source file:crossbear.convergence.ConvergenceConnector.java

/**
 * Store a set of ConvergenceCertObservations in the local cache (i.e. the ConvergenceCertObservations-table). The local ConvergenceCertObservation-cache is used to reduce the network traffic generated by
 * Crossbear, to reduce the load on Convergence and to speed up the average response time of Certificate Verification Requests.
 * /*w  w  w. j a v  a2s.c  o m*/
 * @param ccos The set of ConvergenceCertObservations that is to store in the local cache
 * @throws SQLException
 */
private void storeCCOsInCache(HashSet<ConvergenceCertObservation> ccos) throws SQLException {

    // Iterate over the whole set ...
    Iterator<ConvergenceCertObservation> itr = (Iterator<ConvergenceCertObservation>) ccos.iterator();
    while (itr.hasNext()) {

        // ... and add each of its elements to the local cache
        storeCCOInCache(itr.next());
    }

}

---

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