Example usage for java.util LinkedHashSet retainAll

Introduction

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

Prototype

boolean retainAll(Collection<?> c);

Source Link

Document

Retains only the elements in this set that are contained in the specified collection (optional operation).

Usage

From source file:jenkins.plugins.ivyreport.IvyAccess.java

String[] expandConfs(String[] requested) {
    if (moduleDescriptor == null) {
        recomputeModuleDescriptor();//from  w  w w. j  a  va 2  s.c  om
        if (moduleDescriptor == null) {
            return requested;
        }
    }
    String[] expanded = ConfigurationUtils.replaceWildcards(requested, moduleDescriptor);
    LinkedHashSet<String> result = new LinkedHashSet<String>();
    Collections.addAll(result, expanded);
    result.retainAll(Arrays.asList(moduleDescriptor.getConfigurationsNames()));
    return result.toArray(new String[result.size()]);
}

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From source file:org.mskcc.cbio.importer.converter.internal.ConverterImpl.java

/**
 * Generates case lists for the given portal.
 *
  * @param portal String/*from w  w w.  j  a v a  2 s  .  c  om*/
 * @throws Exception
 */
@Override
public void generateCaseLists(String portal) throws Exception {

    if (LOG.isInfoEnabled()) {
        LOG.info("generateCaseLists()");
    }

    // check args
    if (portal == null) {
        throw new IllegalArgumentException("portal must not be null");
    }

    // get portal metadata
    PortalMetadata portalMetadata = config.getPortalMetadata(portal).iterator().next();
    if (portalMetadata == null) {
        if (LOG.isInfoEnabled()) {
            LOG.info("convertData(), cannot find PortalMetadata, returning");
        }
        return;
    }

    // get CaseListMetadata
    Collection<CaseListMetadata> caseListMetadatas = config.getCaseListMetadata(Config.ALL);

    // iterate over all cancer studies
    for (CancerStudyMetadata cancerStudyMetadata : config.getCancerStudyMetadata(portalMetadata.getName())) {
        // iterate over case lists
        for (CaseListMetadata caseListMetadata : caseListMetadatas) {
            if (LOG.isInfoEnabled()) {
                LOG.info("generateCaseLists(), processing cancer study: " + cancerStudyMetadata
                        + ", case list: " + caseListMetadata.getCaseListFilename());
            }
            // how many staging files are we working with?
            String[] stagingFilenames = null;
            // setup union/intersection bools
            boolean unionCaseList = caseListMetadata.getStagingFilenames()
                    .contains(CaseListMetadata.CASE_LIST_UNION_DELIMITER);
            boolean intersectionCaseList = caseListMetadata.getStagingFilenames()
                    .contains(CaseListMetadata.CASE_LIST_INTERSECTION_DELIMITER);
            // union (like all cases)
            if (unionCaseList) {
                stagingFilenames = caseListMetadata.getStagingFilenames()
                        .split("\\" + CaseListMetadata.CASE_LIST_UNION_DELIMITER);
            }
            // intersection (like complete or cna-seq)
            else if (intersectionCaseList) {
                stagingFilenames = caseListMetadata.getStagingFilenames()
                        .split("\\" + CaseListMetadata.CASE_LIST_INTERSECTION_DELIMITER);
            }
            // just a single staging file
            else {
                stagingFilenames = new String[] { caseListMetadata.getStagingFilenames() };
            }
            if (LOG.isInfoEnabled()) {
                LOG.info("generateCaseLists(), stagingFilenames: "
                        + java.util.Arrays.toString(stagingFilenames));
            }
            // this is the set we will pass to writeCaseListFile
            LinkedHashSet<String> caseSet = new LinkedHashSet<String>();
            // this indicates the number of staging files processed -
            // used to verify that an intersection should be written
            int numStagingFilesProcessed = 0;
            for (String stagingFilename : stagingFilenames) {
                if (LOG.isInfoEnabled()) {
                    LOG.info("generateCaseLists(), processing stagingFile: " + stagingFilename);
                }
                // compute the case set
                List<String> caseList = fileUtils.getCaseListFromStagingFile(caseIDs, portalMetadata,
                        cancerStudyMetadata, stagingFilename);
                // we may not have this datatype in study
                if (caseList.size() == 0) {
                    if (LOG.isInfoEnabled()) {
                        LOG.info("generateCaseLists(), stagingFileHeader is empty: " + stagingFilename
                                + ", skipping...");
                    }
                    continue;
                }
                // intersection 
                if (intersectionCaseList) {
                    if (caseSet.isEmpty()) {
                        caseSet.addAll(caseList);
                    } else {
                        caseSet.retainAll(caseList);
                    }
                }
                // otherwise union or single staging (treat the same)
                else {
                    caseSet.addAll(caseList);
                }
                ++numStagingFilesProcessed;
            }
            // write the case list file (don't make empty case lists)
            if (caseSet.size() > 0) {
                if (LOG.isInfoEnabled()) {
                    LOG.info("generateCaseLists(), calling writeCaseListFile()...");
                }
                // do not write out complete cases file unless we've processed all the files required
                if (intersectionCaseList && (numStagingFilesProcessed != stagingFilenames.length)) {
                    if (LOG.isInfoEnabled()) {
                        LOG.info(
                                "generateCaseLists(), number of staging files processed != number staging files required for cases_complete.txt, skipping call to writeCaseListFile()...");
                    }
                    continue;
                }
                fileUtils.writeCaseListFile(portalMetadata, cancerStudyMetadata, caseListMetadata,
                        caseSet.toArray(new String[0]));
            } else if (LOG.isInfoEnabled()) {
                LOG.info("generateCaseLists(), caseSet.size() <= 0, skipping call to writeCaseListFile()...");
            }
            // if union, write out the cancer study metadata file
            if (caseSet.size() > 0 && caseListMetadata.getCaseListFilename().equals(ALL_CASES_FILENAME)) {
                if (LOG.isInfoEnabled()) {
                    LOG.info(
                            "generateCaseLists(), processed all cases list, we can now update cancerStudyMetadata file()...");
                }
                fileUtils.writeCancerStudyMetadataFile(portalMetadata, cancerStudyMetadata, caseSet.size());
            }
        }
    }

}

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