Example usage for java.util HashSet addAll

List of usage examples for java.util HashSet addAll

  1. HOME
  2. Java
  3. java
  4. java.util.*
  5. HashSet
  6. addAll

Introduction

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

Prototype

boolean addAll(Collection<? extends E> c);

Source Link

Document

Adds all of the elements in the specified collection to this set if they're not already present (optional operation).

Usage

From source file:it.cnr.icar.eric.client.xml.registry.infomodel.RegistryObjectImpl.java

/**
 * RIM Composed objects are composed objects as defined by RIM.
 * Composed objects are composed objects as defined by JAXR.
 * JAXR defines more composed objects than RIM does.
 *///from   www.  ja  v a2 s  .co  m
@SuppressWarnings({ "rawtypes", "unchecked" })
public HashSet getRIMComposedObjects() throws JAXRException {
    HashSet composedObjects = super.getRIMComposedObjects();

    Collection classifications = getClassifications();
    composedObjects.addAll(classifications);

    Collection extIds = getExternalIdentifiers();
    composedObjects.addAll(extIds);

    Collection slotIds = getSlots();
    composedObjects.addAll(slotIds);

    return composedObjects;
}

From source file:it.cnr.icar.eric.client.xml.registry.infomodel.RegistryObjectImpl.java

@SuppressWarnings({ "rawtypes", "unchecked" })
public HashSet getComposedObjects() throws JAXRException {
    HashSet composedObjects = super.getComposedObjects();

    Collection classifications = getClassifications();
    composedObjects.addAll(classifications);

    Collection extIds = getExternalIdentifiers();
    composedObjects.addAll(extIds);/*from w  ww.  j  a  v  a 2 s. c  om*/

    Collection extLinks = getExternalLinks();
    composedObjects.addAll(extLinks);

    composedObjects.addAll(getAssociationsAndAssociatedObjects());

    Collection slotIds = getSlots();
    composedObjects.addAll(slotIds);

    return composedObjects;
}

From source file:com.twitter.pig.backend.hadoop.executionengine.tez.TezExecutionEngine.java

@SuppressWarnings("unchecked")
public PhysicalPlan compile(LogicalPlan plan, Properties properties) throws FrontendException {
    if (plan == null) {
        int errCode = 2041;
        String msg = "No Plan to compile";
        throw new FrontendException(msg, errCode, PigException.BUG);
    }//from  w  w  w . j ava2 s .  co  m

    newPreoptimizedPlan = new LogicalPlan(plan);

    if (pigContext.inIllustrator) {
        // disable all PO-specific optimizations
        POOptimizeDisabler pod = new POOptimizeDisabler(plan);
        pod.visit();
    }

    UidResetter uidResetter = new UidResetter(plan);
    uidResetter.visit();

    SchemaResetter schemaResetter = new SchemaResetter(plan, true /*skip duplicate uid check*/ );
    schemaResetter.visit();

    HashSet<String> disabledOptimizerRules;
    try {
        disabledOptimizerRules = (HashSet<String>) ObjectSerializer
                .deserialize(pigContext.getProperties().getProperty(PigImplConstants.PIG_OPTIMIZER_RULES_KEY));
    } catch (IOException ioe) {
        int errCode = 2110;
        String msg = "Unable to deserialize optimizer rules.";
        throw new FrontendException(msg, errCode, PigException.BUG, ioe);
    }
    if (disabledOptimizerRules == null) {
        disabledOptimizerRules = new HashSet<String>();
    }

    String pigOptimizerRulesDisabled = this.pigContext.getProperties()
            .getProperty(PigConstants.PIG_OPTIMIZER_RULES_DISABLED_KEY);
    if (pigOptimizerRulesDisabled != null) {
        disabledOptimizerRules.addAll(Lists.newArrayList((Splitter.on(",").split(pigOptimizerRulesDisabled))));
    }

    if (pigContext.inIllustrator) {
        disabledOptimizerRules.add("MergeForEach");
        disabledOptimizerRules.add("PartitionFilterOptimizer");
        disabledOptimizerRules.add("LimitOptimizer");
        disabledOptimizerRules.add("SplitFilter");
        disabledOptimizerRules.add("PushUpFilter");
        disabledOptimizerRules.add("MergeFilter");
        disabledOptimizerRules.add("PushDownForEachFlatten");
        disabledOptimizerRules.add("ColumnMapKeyPrune");
        disabledOptimizerRules.add("AddForEach");
        disabledOptimizerRules.add("GroupByConstParallelSetter");
    }

    StoreAliasSetter storeAliasSetter = new StoreAliasSetter(plan);
    storeAliasSetter.visit();

    // run optimizer
    LogicalPlanOptimizer optimizer = new LogicalPlanOptimizer(plan, 100, disabledOptimizerRules);
    optimizer.optimize();

    // compute whether output data is sorted or not
    SortInfoSetter sortInfoSetter = new SortInfoSetter(plan);
    sortInfoSetter.visit();

    if (!pigContext.inExplain) {
        // Validate input/output file. Currently no validation framework in
        // new logical plan, put this validator here first.
        // We might decide to move it out to a validator framework in future
        InputOutputFileValidator validator = new InputOutputFileValidator(plan, pigContext);
        validator.validate();
    }

    // translate new logical plan to physical plan
    LogToPhyTranslationVisitor translator = new LogToPhyTranslationVisitor(plan);

    translator.setPigContext(pigContext);
    translator.visit();
    newLogToPhyMap = translator.getLogToPhyMap();
    return translator.getPhysicalPlan();
}

From source file:org.egov.works.services.WorksService.java

/**
 * NOTE --- THIS API IS USED ONLY FOR WORK PROGRESS ABSTRACT REPORT BY DEPARTMENT IN WORKS MODULE
 *
 * @description -This method returns the approved CJV count and sum of CJVs amount for the approved CJVs made till date for a
 * list of Project codes for which there is a final bill created for it. Project code Ids present in the temporary table
 * WorkProgressProjectCode for a particular uuid are only considered NOTE --- ASSUMPTION IS THERE WILL BE ONLY 1 FINAL BILL
 * FOR AN ESTIMATE/*  w ww  .ja v a 2s  . c  o m*/
 * @param uuid - Only project codes ids associated with this uuid are considered
 * @return - List of Map of Maps. The outer map's key is the department name Inner map's keys "amount" and "count" represent
 * sum of CJVs amount and approved CJV count
 * @return - Null is returned in the case of no data
 * @throws ApplicationException - If anyone of the parameters is null or the ProjectCode list passed is empty.
 */
public List<Map<String, Map<String, BigDecimal>>> getTotalCJVCountAndAmounts(final String uuid)
        throws ApplicationException {

    Map<String, Map<String, BigDecimal>> resultMap = null;
    Map<String, BigDecimal> simpleMap = null;
    List<Object[]> payQueryResult;
    List<Object[]> countQueryResult;
    final List<Map<String, Map<String, BigDecimal>>> resultList = new ArrayList<Map<String, Map<String, BigDecimal>>>();

    final String payQuery = " select dept.dept_name , nvl(sum(bp.debitamount),0)  FROM "
            + " eg_billregister br,eg_billdetails bd, eg_billpayeedetails bp,voucherheader vh,eg_billregistermis ms , eg_department dept "
            + " WHERE br.id=bd.billid and bd.id=bp.BILLDETAILID and vh.id=ms.VOUCHERHEADERID and ms.BILLID=br.id and bp.pc_department=dept.id_dept  and vh.name='Contractor Journal'  "
            + " and br.STATUSID in(select id from egw_status where lower(code)='approved' and "
            + " moduletype in('CONTRACTORBILL')) " + " and bd.DEBITAMOUNT>0  and vh.STATUS="
            + FinancialConstants.CREATEDVOUCHERSTATUS
            + " and bp.ACCOUNTDETAILTYPEID= (SELECT id FROM accountdetailtype "
            + " WHERE name ='PROJECTCODE' AND description='PROJECTCODE' ) and (bp.ACCOUNTDETAILKEYID in(SELECT PC_ID FROM EGW_WORKPROGRESS_PROJECT_CODE WHERE UUID like '"
            + uuid + "'))"
            + " and bp.accountdetailkeyid in ( select bp1.ACCOUNTDETAILKEYID FROM eg_billregister br1, "
            + " eg_billdetails bd1, eg_billpayeedetails bp1 ,voucherheader vh1,eg_billregistermis ms1  WHERE br1.id =bd1.billid AND bd1.id =bp1.BILLDETAILID  "
            + "  and vh1.id=ms1.VOUCHERHEADERID and ms1.BILLID=br1.id and vh1.name='Contractor Journal' and vh1.STATUS="
            + FinancialConstants.CREATEDVOUCHERSTATUS
            + " AND br1.STATUSID IN (SELECT id FROM egw_status WHERE lower(code)='approved' AND moduletype  IN('CONTRACTORBILL')) "
            + " and br1.billtype in ('FinalBill', 'Final Bill') and bp1.ACCOUNTDETAILKEYID = bp.ACCOUNTDETAILKEYID "
            + " and bp1.ACCOUNTDETAILTYPEID=bp.ACCOUNTDETAILTYPEID ) group by dept.dept_name  order by dept.dept_name  ";

    final String countQuery = " select dept.dept_name , count(vh.id) FROM "
            + " eg_billregister br,eg_billdetails bd, eg_billpayeedetails bp,voucherheader vh,eg_billregistermis ms, eg_department dept  "
            + " WHERE br.id=bd.billid and bd.id=bp.BILLDETAILID and vh.id=ms.VOUCHERHEADERID and ms.BILLID=br.id and bp.pc_department=dept.id_dept  and vh.name='Contractor Journal' "
            + " and br.billtype in ('FinalBill', 'Final Bill') "
            + " and br.STATUSID in(select id from egw_status where lower(code)='approved' and "
            + " moduletype in('CONTRACTORBILL')) " + " and bd.DEBITAMOUNT>0  and vh.STATUS="
            + FinancialConstants.CREATEDVOUCHERSTATUS
            + " and bp.ACCOUNTDETAILTYPEID= (SELECT id FROM accountdetailtype "
            + " WHERE name ='PROJECTCODE' AND description='PROJECTCODE' ) and (bp.ACCOUNTDETAILKEYID in(SELECT PC_ID FROM EGW_WORKPROGRESS_PROJECT_CODE WHERE UUID like '"
            + uuid + "'))  group by dept.dept_name order by dept.dept_name ";

    payQueryResult = persistenceService.getSession().createSQLQuery(payQuery).list();
    countQueryResult = persistenceService.getSession().createSQLQuery(countQuery).list();
    final List<String> deptNameList = new ArrayList<String>();
    if (payQueryResult != null && payQueryResult.size() > 0)
        for (Integer i = 0; i < payQueryResult.size(); i++)
            deptNameList.add(payQueryResult.get(i)[0].toString());
    if (countQueryResult != null && countQueryResult.size() > 0)
        for (Integer i = 0; i < countQueryResult.size(); i++)
            deptNameList.add(countQueryResult.get(i)[0].toString());
    if (deptNameList == null || !(deptNameList.size() > 0))
        return null;
    // To remove duplicates
    final HashSet<String> tempSet = new HashSet<String>();
    tempSet.addAll(deptNameList);
    deptNameList.clear();
    deptNameList.addAll(tempSet);
    final BigDecimal[] payArray = new BigDecimal[deptNameList.size()];
    final BigDecimal[] countArray = new BigDecimal[deptNameList.size()];
    for (Integer i = 0; i < deptNameList.size(); i++) {
        payArray[i] = BigDecimal.ZERO;
        countArray[i] = BigDecimal.ZERO;
    }
    String deptName = null;
    Integer index = null;
    Integer i = null;
    for (i = 0; i < payQueryResult.size(); i++) {
        deptName = payQueryResult.get(i)[0].toString();
        index = deptNameList.indexOf(deptName);
        payArray[index] = new BigDecimal(payQueryResult.get(i)[1].toString());
    }
    for (i = 0; i < countQueryResult.size(); i++) {
        deptName = countQueryResult.get(i)[0].toString();
        index = deptNameList.indexOf(deptName);
        countArray[index] = new BigDecimal(countQueryResult.get(i)[1].toString());
    }
    for (i = 0; i < deptNameList.size(); i++) {
        deptName = deptNameList.get(i);
        simpleMap = new HashMap<String, BigDecimal>();
        simpleMap.put("amount", payArray[i]);
        simpleMap.put("count", countArray[i]);
        resultMap = new HashMap<String, Map<String, BigDecimal>>();
        resultMap.put(deptName, simpleMap);
        resultList.add(resultMap);
    }
    return resultList;
}

From source file:org.egov.works.services.WorksService.java

/**
 * NOTE --- THIS API IS USED ONLY FOR Works Report 2 dashboard BY DEPARTMENT IN WORKS MODULE
 *
 * @description -This method returns the approved CJV count and sum of CJVs amount for the approved CJVs made till date for a
 * list of Spill over Project codes for which there is a final bill created for it in current year. Project code Ids present
 * in the temporary table WorkProgProjCodeSpillOver for a particular uuid are only considered NOTE --- ASSUMPTION IS THERE
 * WILL BE ONLY 1 FINAL BILL FOR AN ESTIMATE
 * @param uuid - Only spill over project codes ids associated with this uuid are considered
 * @return - List of Map of Maps. The outer map's key is the department name Inner map's keys "amount" and "count" represent
 * sum of CJVs amount and approved Final CJV count
 * @return - Null is returned in the case of no data
 * @throws ApplicationException - If anyone of the parameters is null or the ProjectCode list passed is empty.
 *///from   w ww . ja  v  a2  s.co m
public List<Map<String, Map<String, BigDecimal>>> getCJVCountAndAmountsForSpillOver(final String uuid,
        final Date fromDate, final Date toDate) throws ApplicationException {

    Map<String, Map<String, BigDecimal>> resultMap = null;
    Map<String, BigDecimal> simpleMap = null;
    List<Object[]> payQueryResult;
    List<Object[]> countQueryResult;
    final List<Map<String, Map<String, BigDecimal>>> resultList = new ArrayList<Map<String, Map<String, BigDecimal>>>();

    final String payQuery = " select dept.dept_name , nvl(sum(bp.debitamount),0)  FROM "
            + " eg_billregister br,eg_billdetails bd, eg_billpayeedetails bp,voucherheader vh,eg_billregistermis ms , eg_department dept "
            + " WHERE br.id=bd.billid and bd.id=bp.BILLDETAILID and vh.id=ms.VOUCHERHEADERID and ms.BILLID=br.id and bp.pc_department=dept.id_dept  and vh.name='Contractor Journal'  "
            + " and br.STATUSID in(select id from egw_status where lower(code)='approved' and "
            + " moduletype in('CONTRACTORBILL')) " + " and br.billdate between '"
            + dateFormatter.format(fromDate) + "' and '" + dateFormatter.format(toDate) + "'"
            + " and bd.DEBITAMOUNT>0  and vh.STATUS=" + FinancialConstants.CREATEDVOUCHERSTATUS
            + " and bp.ACCOUNTDETAILTYPEID= (SELECT id FROM accountdetailtype "
            + " WHERE name ='PROJECTCODE' AND description='PROJECTCODE' ) and (bp.ACCOUNTDETAILKEYID in(SELECT PC_ID FROM EGW_WRKPROG_PROJCODE_SPILLOVER WHERE UUID like '"
            + uuid + "'))"
            + " and bp.accountdetailkeyid in ( select bp1.ACCOUNTDETAILKEYID FROM eg_billregister br1, "
            + " eg_billdetails bd1, eg_billpayeedetails bp1 ,voucherheader vh1,eg_billregistermis ms1  WHERE br1.id =bd1.billid AND bd1.id =bp1.BILLDETAILID  "
            + "  and vh1.id=ms1.VOUCHERHEADERID and ms1.BILLID=br1.id and vh1.name='Contractor Journal' and vh1.STATUS="
            + FinancialConstants.CREATEDVOUCHERSTATUS
            + " AND br1.STATUSID IN (SELECT id FROM egw_status WHERE lower(code)='approved' AND moduletype  IN('CONTRACTORBILL')) "
            + " and br1.billtype in ('FinalBill', 'Final Bill') and bp1.ACCOUNTDETAILKEYID = bp.ACCOUNTDETAILKEYID "
            + " and bp1.ACCOUNTDETAILTYPEID=bp.ACCOUNTDETAILTYPEID ) group by dept.dept_name  order by dept.dept_name  ";

    final String countQuery = " select dept.dept_name , count(vh.id) FROM "
            + " eg_billregister br,eg_billdetails bd, eg_billpayeedetails bp,voucherheader vh,eg_billregistermis ms, eg_department dept  "
            + " WHERE br.id=bd.billid and bd.id=bp.BILLDETAILID and vh.id=ms.VOUCHERHEADERID and ms.BILLID=br.id and bp.pc_department=dept.id_dept  and vh.name='Contractor Journal' "
            + " and br.billtype in ('FinalBill', 'Final Bill') "
            + " and br.STATUSID in(select id from egw_status where lower(code)='approved' and "
            + " moduletype in('CONTRACTORBILL')) " + " and br.billdate between '"
            + dateFormatter.format(fromDate) + "' and '" + dateFormatter.format(toDate) + "'"
            + " and bd.DEBITAMOUNT>0  and vh.STATUS=" + FinancialConstants.CREATEDVOUCHERSTATUS
            + " and bp.ACCOUNTDETAILTYPEID= (SELECT id FROM accountdetailtype "
            + " WHERE name ='PROJECTCODE' AND description='PROJECTCODE' ) and (bp.ACCOUNTDETAILKEYID in(SELECT PC_ID FROM EGW_WRKPROG_PROJCODE_SPILLOVER WHERE UUID like '"
            + uuid + "'))  group by dept.dept_name order by dept.dept_name ";

    payQueryResult = persistenceService.getSession().createSQLQuery(payQuery).list();
    countQueryResult = persistenceService.getSession().createSQLQuery(countQuery).list();
    final List<String> deptNameList = new ArrayList<String>();
    if (payQueryResult != null && payQueryResult.size() > 0)
        for (Integer i = 0; i < payQueryResult.size(); i++)
            deptNameList.add(payQueryResult.get(i)[0].toString());
    if (countQueryResult != null && countQueryResult.size() > 0)
        for (Integer i = 0; i < countQueryResult.size(); i++)
            deptNameList.add(countQueryResult.get(i)[0].toString());
    if (deptNameList == null || !(deptNameList.size() > 0))
        return null;
    // To remove duplicates
    final HashSet<String> tempSet = new HashSet<String>();
    tempSet.addAll(deptNameList);
    deptNameList.clear();
    deptNameList.addAll(tempSet);
    final BigDecimal[] payArray = new BigDecimal[deptNameList.size()];
    final BigDecimal[] countArray = new BigDecimal[deptNameList.size()];
    for (Integer i = 0; i < deptNameList.size(); i++) {
        payArray[i] = BigDecimal.ZERO;
        countArray[i] = BigDecimal.ZERO;
    }
    String deptName = null;
    Integer index = null;
    Integer i = null;
    for (i = 0; i < payQueryResult.size(); i++) {
        deptName = payQueryResult.get(i)[0].toString();
        index = deptNameList.indexOf(deptName);
        payArray[index] = new BigDecimal(payQueryResult.get(i)[1].toString());
    }
    for (i = 0; i < countQueryResult.size(); i++) {
        deptName = countQueryResult.get(i)[0].toString();
        index = deptNameList.indexOf(deptName);
        countArray[index] = new BigDecimal(countQueryResult.get(i)[1].toString());
    }
    for (i = 0; i < deptNameList.size(); i++) {
        deptName = deptNameList.get(i);
        simpleMap = new HashMap<String, BigDecimal>();
        simpleMap.put("amount", payArray[i]);
        simpleMap.put("count", countArray[i]);
        resultMap = new HashMap<String, Map<String, BigDecimal>>();
        resultMap.put(deptName, simpleMap);
        resultList.add(resultMap);
    }
    return resultList;
}

From source file:com.googlecode.fascinator.portal.process.RecordProcessor.java

/**
 * 'pre' - processing method.//  w w w. j ava 2s .co m
 * 
 * The Solr Query is executed and the resulting ID HashSet is stored on the
 * dataMap as the 'outputKey', along with any entries from 'includeList'
 * config entry. To manually process a certain record(s), add the id on the
 * 'includeList'. Processing will read the 'lastRun' config entry and pulls
 * records since then. <br/>
 * 
 * @param id
 * @param outputKey
 * @param configFilePath
 * @param dataMap
 * @return
 * @throws Exception
 */
private boolean getRecords(String id, String outputKey, String configFilePath, HashMap<String, Object> dataMap)
        throws Exception {
    Indexer indexer = (Indexer) dataMap.get("indexer");
    JsonSimple config = new JsonSimple(new File(configFilePath));
    String solrQuery = config.getString("", "query");
    String lastRun = config.getString(null, "lastrun");
    solrQuery += (lastRun != null ? " AND create_timestamp:[" + lastRun + " TO NOW]" : "");
    log.debug("Using solrQuery:" + solrQuery);
    SearchRequest searchRequest = new SearchRequest(solrQuery);
    int start = 0;
    int pageSize = 10;
    searchRequest.setParam("start", "" + start);
    searchRequest.setParam("rows", "" + pageSize);
    ByteArrayOutputStream result = new ByteArrayOutputStream();
    indexer.search(searchRequest, result);
    SolrResult resultObject = new SolrResult(result.toString());
    int numFound = resultObject.getNumFound();
    log.debug("Number found:" + numFound);
    HashSet<String> newRecords = new HashSet<String>();
    while (true) {
        List<SolrDoc> results = resultObject.getResults();
        for (SolrDoc docObject : results) {
            String oid = docObject.getString(null, "id");
            if (oid != null) {
                log.debug("Record found: " + oid);
                newRecords.add(oid);
            } else {
                log.debug("Record returned but has no id.");
                log.debug(docObject.toString());
            }
        }
        start += pageSize;
        if (start > numFound) {
            break;
        }
        searchRequest.setParam("start", "" + start);
        result = new ByteArrayOutputStream();
        indexer.search(searchRequest, result);
        resultObject = new SolrResult(result.toString());
    }
    // get the exception list..
    JSONArray includedArr = config.getArray("includeList");
    if (includedArr != null && includedArr.size() > 0) {
        newRecords.addAll(includedArr);
    }
    dataMap.put(outputKey, newRecords);
    return true;
}

From source file:com.onegravity.contactpicker.core.ContactPickerActivity.java

private void onDone() {

    HashSet<String> phoneHash = new HashSet<>();

    // return only checked contacts
    HashSet<Long> contactHash = new HashSet<>();
    if (mContacts != null) {
        for (Contact contact : mContacts) {
            if (contact.isChecked()) {
                phoneHash.addAll(contact.getPhones());
                contactHash.add(contact.getId());
            }/* ww  w  . j a  v  a 2  s.c o m*/
        }
    }

    // return only checked groups
    HashSet<Long> groupHash = new HashSet<>();
    if (mGroups != null) {
        for (Group group : mGroups) {
            if (group.isChecked()) {
                groupHash.add(group.getId());
            }
        }
    }

    ArrayList<Long> contactList = new ArrayList<>(contactHash);
    ArrayList<Long> groupList = new ArrayList<>(groupHash);
    ArrayList<String> phoneList = new ArrayList<>(phoneHash);

    Intent data = new Intent();
    data.putExtra(RESULT_CONTACT_DATA, contactList);
    data.putExtra(RESULT_GROUP_DATA, groupList);
    data.putExtra(RESULT_PHONE_DATA, phoneList);

    setResult(Activity.RESULT_OK, data);
    finish();
}

From source file:com.healthcit.cacure.businessdelegates.QuestionAnswerManager.java

@Transactional
public List<FormElement> buildNewQuestions(String[][] questionSet, int searchCriteria) {
    List<FormElement> newElements = new ArrayList<FormElement>();
    Map<String, DataElement> dataElements = new HashMap<String, DataElement>();
    int numElements = questionSet.length;
    String[] questionIdList = new String[numElements];
    String[] answerTypeList = new String[numElements];
    String[] deletedAnswerValuesList = new String[numElements];
    for (int i = 0; i < numElements; ++i) {
        questionIdList[i] = questionSet[i][0];
        answerTypeList[i] = questionSet[i][1];
        if (questionSet[i].length > 2)
            deletedAnswerValuesList[i] = questionSet[i][2];
    }//from w ww. j a v  a  2s  . c  o m

    for (int i = 0; i < numElements; ++i) {

        String uuid = questionIdList[i];

        // The following 2 variables are not used. I am leaving them in case the accessors are used 
        // to load lazy collections - LK
        String answerType = answerTypeList[i];
        HashSet<String> deletedAnswerValues = new HashSet<String>();
        if (StringUtils.isNotBlank(deletedAnswerValuesList[i])) {
            deletedAnswerValues.addAll(Arrays.asList(deletedAnswerValuesList[i].split("\\s*,\\s*")));
        }

        if (searchCriteria == FormElementSearchCriteria.SEARCH_BY_CADSR_TEXT // CADSR Text Search
                || searchCriteria == FormElementSearchCriteria.SEARCH_BY_CADSR_CART_USER) // CADSR Cart User Search
        {
            if (i == 0)
                dataElements = cadsrManager.findCADSRQuestionsById(StringUtils.join(questionIdList, SPLITTER));
            DataElement dataElement = dataElements.get(uuid);
            if (dataElement != null) {
                FormElement newElement;
                AnswerType answerTypeEnumEntry = AnswerType.valueOf(answerType);
                newElement = cadsrManager.transformCADSRQuestion(dataElement, answerTypeEnumEntry,
                        deletedAnswerValues);
                newElements.add(newElement);
            }
        } else // local
        {
            LinkElement linkElement = new LinkElement();
            FormElement source = linkDao.getLinkSource(uuid);
            linkElement.setLearnMore(source.getLearnMore());
            linkElement.setVisible(source.isVisible());
            linkElement.setRequired(source.isRequired());
            linkElement.setReadonly(source.isReadonly());
            linkElement.setDescription(source.getDescription());
            linkElement.setSource(source);
            newElements.add(linkElement);
        }
    }
    modifyShortNames(newElements);
    return newElements;
}

From source file:ch.unil.genescore.pathway.GeneSetLibrary.java

License:asdf

public void computeApproxPathwayCorrelation() {

    DenseMatrix corMat = new DenseMatrix(geneSets_.size(), geneSets_.size());
    for (int i = 0; i < geneSets_.size(); i++) {
        GeneSet leftSet = geneSets_.get(i);
        double leftSize = leftSet.genes_.size();
        for (int j = 0; j < geneSets_.size(); j++) {
            GeneSet rightSet = geneSets_.get(j);
            double rightSize = rightSet.genes_.size();
            HashSet<Gene> unpackedMetaGenes = new HashSet<Gene>();
            HashSet<Gene> allRightGenes = new HashSet<Gene>();
            if (null != rightSet.getMetaGenes())
                for (MetaGene mg : rightSet.getMetaGenes()) {
                    unpackedMetaGenes.addAll(mg.getGenes());
                }/*w  ww  .  ja  v a  2s  .  c  o m*/

            allRightGenes.addAll(unpackedMetaGenes);
            allRightGenes.addAll(rightSet.genes_);
            allRightGenes.removeAll(rightSet.getMetaGenes());

            HashSet<Gene> copiedLeftGenes = new HashSet<Gene>(leftSet.genes_);
            copiedLeftGenes.retainAll(allRightGenes);
            double count = copiedLeftGenes.size();
            if (null != leftSet.getMetaGenes())
                for (MetaGene mg : leftSet.getMetaGenes()) {
                    TreeSet<Gene> mgSetCopy = new TreeSet<Gene>(mg.getGenes());
                    mgSetCopy.retainAll(allRightGenes);
                    if (!mgSetCopy.isEmpty()) {
                        count++;
                    }
                }
            double corr = count / Math.sqrt(leftSize * rightSize);
            corMat.set(i, j, corr);
            //corMat.set(j, i, corr);
        }
    }
    pathwayCorMat_ = corMat;
}

From source file:com.lynnlyc.web.taintanalysis.JSTaintAnalysis.java

public Set<List<Integer>> getTaintPathsTo(Integer sinkId) {
    HashSet<List<Integer>> paths = new HashSet<>();

    HashSet<Integer> taintMarks = this.getTaintMarks(sinkId);

    if (taintMarks.isEmpty()) {
        List<Integer> path = new ArrayList<>();
        path.add(sinkId);// w  ww.  ja  v a  2 s .  c  o m
        paths.add(path);
    } else {
        for (int mark : taintMarks) {
            Set<List<Integer>> prevPaths = getTaintPathsTo(mark);
            for (List<Integer> path : prevPaths) {
                path.add(sinkId);
            }
            paths.addAll(prevPaths);
        }
    }

    return paths;
}