Example usage for java.util TreeSet addAll

Introduction

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

Prototype

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

Source Link

Document

Adds all of the elements in the specified collection to this set.

Usage

From source file:org.deegree.enterprise.WebUtils.java

private static void handleProxies(String protocol, HttpClient client, String host) {
    TreeSet<String> nops = new TreeSet<String>();

    String proxyHost = getProperty((protocol == null ? "" : protocol + ".") + "proxyHost");

    String proxyUser = getProperty((protocol == null ? "" : protocol + ".") + "proxyUser");
    String proxyPass = getProperty((protocol == null ? "" : protocol + ".") + "proxyPassword");

    if (proxyHost != null) {
        String nop = getProperty((protocol == null ? "" : protocol + ".") + "noProxyHosts");
        if (nop != null && !nop.equals("")) {
            nops.addAll(asList(nop.split("\\|")));
        }/*w ww.  ja  v a  2s  .  c om*/
        nop = getProperty((protocol == null ? "" : protocol + ".") + "nonProxyHosts");
        if (nop != null && !nop.equals("")) {
            nops.addAll(asList(nop.split("\\|")));
        }

        int proxyPort = parseInt(getProperty((protocol == null ? "" : protocol + ".") + "proxyPort"));

        HostConfiguration hc = client.getHostConfiguration();

        if (LOG.isDebug()) {
            LOG.logDebug("Found the following no- and nonProxyHosts", nops);
        }

        if (proxyUser != null) {
            Credentials creds = new UsernamePasswordCredentials(proxyUser, proxyPass);
            client.getState().setProxyCredentials(AuthScope.ANY, creds);
            client.getParams().setAuthenticationPreemptive(true);
        }

        if (!nops.contains(host)) {
            if (LOG.isDebug()) {
                LOG.logDebug("Using proxy " + proxyHost + ":" + proxyPort);
                if (protocol == null) {
                    LOG.logDebug("This overrides the protocol specific settings, if there were any.");
                }
            }
            hc.setProxy(proxyHost, proxyPort);
            client.setHostConfiguration(hc);
        } else {
            if (LOG.isDebug()) {
                LOG.logDebug("Proxy was set, but " + host + " was contained in the no-/nonProxyList!");
                if (protocol == null) {
                    LOG.logDebug("If a protocol specific proxy has been set, it will be used anyway!");
                }
            }
        }
    }

    if (protocol != null) {
        handleProxies(null, client, host);
    }
}

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From source file:uk.ac.ebi.intact.util.protein.utils.AliasUpdaterUtils.java

public static AliasUpdateReport updateAliases(UniprotProtein uniprotProtein, Protein protein, AliasDao aliasDao,
        TreeSet<InteractorAlias> sortedAliases) {

    sortedAliases.clear();//  w  w  w .  jav  a 2  s. c o m
    sortedAliases.addAll(protein.getAliases());
    Iterator<InteractorAlias> intactIterator = sortedAliases.iterator();

    AliasUpdateReport report = new AliasUpdateReport(protein);

    // process genes
    TreeSet<String> geneNames = new TreeSet<String>(uniprotProtein.getGenes());
    Iterator<String> geneIterator = geneNames.iterator();
    InteractorAlias currentIntact = null;

    if (geneIterator.hasNext()) {
        currentIntact = compareAndUpdateAliases(protein, null, intactIterator, geneIterator,
                CvAliasType.GENE_NAME_MI_REF, report, aliasDao);
    }

    // process synonyms
    TreeSet<String> geneSynonyms = new TreeSet<String>(uniprotProtein.getSynomyms());
    Iterator<String> geneSynonymsIterator = geneSynonyms.iterator();

    if (geneSynonymsIterator.hasNext()) {
        currentIntact = compareAndUpdateAliases(protein, currentIntact, intactIterator, geneSynonymsIterator,
                CvAliasType.GENE_NAME_SYNONYM_MI_REF, report, aliasDao);
    }

    // process orfs
    TreeSet<String> orfs = new TreeSet<String>(uniprotProtein.getOrfs());
    Iterator<String> orfsIterator = orfs.iterator();

    if (orfsIterator.hasNext()) {
        currentIntact = compareAndUpdateAliases(protein, currentIntact, intactIterator, orfsIterator,
                CvAliasType.ORF_NAME_MI_REF, report, aliasDao);
    }

    // process locus
    TreeSet<String> locuses = new TreeSet<String>(uniprotProtein.getLocuses());
    Iterator<String> locusesIterator = locuses.iterator();

    if (locusesIterator.hasNext()) {
        currentIntact = compareAndUpdateAliases(protein, currentIntact, intactIterator, locusesIterator,
                CvAliasType.LOCUS_NAME_MI_REF, report, aliasDao);
    }

    // delete remaining aliases
    if (currentIntact != null || intactIterator.hasNext()) {
        if (currentIntact == null) {
            currentIntact = intactIterator.next();
        }

        do {
            protein.removeAlias(currentIntact);
            report.getRemovedAliases().add(currentIntact);

            aliasDao.delete(currentIntact);

            if (intactIterator.hasNext()) {
                currentIntact = intactIterator.next();
            } else {
                currentIntact = null;
            }
        } while (currentIntact != null);
    }

    sortedAliases.clear();
    return report;
}

---

From source file:uk.ac.ebi.intact.util.protein.utils.AliasUpdaterUtils.java

public static AliasUpdateReport updateIsoformAliases(UniprotProtein master,
        UniprotProteinTranscript uniprotProteinTranscript, Protein protein, AliasDao aliasDao,
        TreeSet<InteractorAlias> sortedAliases) {

    sortedAliases.clear();/*from  w  w w  .  ja v a 2 s .  c  o  m*/
    sortedAliases.addAll(protein.getAliases());
    Iterator<InteractorAlias> intactIterator = sortedAliases.iterator();

    AliasUpdateReport report = new AliasUpdateReport(protein);

    // process genes
    TreeSet<String> geneNames = new TreeSet<String>(master.getGenes());
    Iterator<String> geneIterator = geneNames.iterator();

    InteractorAlias currentIntact = null;

    if (geneIterator.hasNext()) {
        currentIntact = compareAndUpdateAliases(protein, null, intactIterator, geneIterator,
                CvAliasType.GENE_NAME_MI_REF, report, aliasDao);
    }

    // process synonyms
    TreeSet<String> geneSynonyms = new TreeSet<String>(master.getSynomyms());
    Iterator<String> geneSynonymsIterator = geneSynonyms.iterator();

    if (geneSynonymsIterator.hasNext()) {
        currentIntact = compareAndUpdateAliases(protein, currentIntact, intactIterator, geneSynonymsIterator,
                CvAliasType.GENE_NAME_SYNONYM_MI_REF, report, aliasDao);
    }

    // process orfs
    TreeSet<String> orfs = new TreeSet<String>(master.getOrfs());
    Iterator<String> orfsIterator = orfs.iterator();

    if (orfsIterator.hasNext()) {
        currentIntact = compareAndUpdateAliases(protein, currentIntact, intactIterator, orfsIterator,
                CvAliasType.ORF_NAME_MI_REF, report, aliasDao);
    }

    // process locus
    TreeSet<String> locuses = new TreeSet<String>(master.getLocuses());
    Iterator<String> locusesIterator = locuses.iterator();

    if (locusesIterator.hasNext()) {
        currentIntact = compareAndUpdateAliases(protein, currentIntact, intactIterator, locusesIterator,
                CvAliasType.LOCUS_NAME_MI_REF, report, aliasDao);
    }

    // process isoform synonyms
    TreeSet<String> isoformSynonyms = new TreeSet<String>(uniprotProteinTranscript.getSynomyms());
    Iterator<String> isoformSynonymsIterator = isoformSynonyms.iterator();

    if (isoformSynonymsIterator.hasNext()) {
        currentIntact = compareAndUpdateAliases(protein, currentIntact, intactIterator, isoformSynonymsIterator,
                CvAliasType.ISOFORM_SYNONYM_MI_REF, report, aliasDao);
    }

    // delete remaining aliases
    if (currentIntact != null || intactIterator.hasNext()) {
        if (currentIntact == null) {
            currentIntact = intactIterator.next();
        }
        do {
            protein.removeAlias(currentIntact);
            report.getRemovedAliases().add(currentIntact);

            aliasDao.delete(currentIntact);

            if (intactIterator.hasNext()) {
                currentIntact = intactIterator.next();
            } else {
                currentIntact = null;
            }
        } while (currentIntact != null);
    }

    sortedAliases.clear();
    return report;
}

---

From source file:org.broadinstitute.gatk.utils.haplotype.EventMap.java

/**
 * Build event maps for each haplotype, returning the sorted set of all of the starting positions of all
 * events across all haplotypes/*from   w ww . j a va2s.  c  o  m*/
 *
 * @param haplotypes a list of haplotypes
 * @param ref the reference bases
 * @param refLoc the span of the reference bases
 * @param debug if true, we'll emit debugging information during this operation
 * @return a sorted set of start positions of all events among all haplotypes
 */
public static TreeSet<Integer> buildEventMapsForHaplotypes(final List<Haplotype> haplotypes, final byte[] ref,
        final GenomeLoc refLoc, final boolean debug) {
    // Using the cigar from each called haplotype figure out what events need to be written out in a VCF file
    final TreeSet<Integer> startPosKeySet = new TreeSet<Integer>();
    int hapNumber = 0;

    if (debug)
        logger.info("=== Best Haplotypes ===");
    for (final Haplotype h : haplotypes) {
        // Walk along the alignment and turn any difference from the reference into an event
        h.setEventMap(new EventMap(h, ref, refLoc, "HC" + hapNumber++));
        startPosKeySet.addAll(h.getEventMap().getStartPositions());

        if (debug) {
            logger.info(h.toString());
            logger.info("> Cigar = " + h.getCigar());
            logger.info(">> Events = " + h.getEventMap());
        }
    }

    return startPosKeySet;
}

---

From source file:base.Engine.java

static Set<TreeSet<PatternInstance>> resolveTree(Set<TreeSet<PatternInstance>> returnSet,
        Set<PatternInstance> colls) {
    TreeSet<PatternInstance> workingTree = new TreeSet<>(new InstanceComparator());
    for (PatternInstance p : colls) {
        TreeSet<PatternInstance> onThisTree = null;
        for (TreeSet<PatternInstance> it : returnSet) {
            if (it.contains(p)) {
                onThisTree = it;/*from w ww  .  j ava2 s.co m*/
                break;
            }
        }

        if (onThisTree == null) {
            workingTree.add(p);
        } else {
            workingTree.addAll(onThisTree);
            returnSet.remove(onThisTree);
        }
    }
    returnSet.add(workingTree);
    return returnSet;
}

---

From source file:com.linkedin.helix.TestHelper.java

public static void printCache(Map<String, ZNode> cache) {
    System.out.println("START:Print cache");
    TreeMap<String, ZNode> map = new TreeMap<String, ZNode>();
    map.putAll(cache);/*from w w w .  ja  va2s  .  com*/

    for (String key : map.keySet()) {
        ZNode node = map.get(key);
        TreeSet<String> childSet = new TreeSet<String>();
        childSet.addAll(node.getChildSet());
        System.out.print(key + "=" + node.getData() + ", " + childSet + ", "
                + (node.getStat() == null ? "null\n" : node.getStat()));
    }
    System.out.println("END:Print cache");
}

---

From source file:org.deegree.commons.utils.net.HttpUtils.java

private static void handleProxies(String protocol, HttpClient client, String host) {
    TreeSet<String> nops = new TreeSet<String>();

    String proxyHost = getProperty((protocol == null ? "" : protocol + ".") + "proxyHost");

    String proxyUser = getProperty((protocol == null ? "" : protocol + ".") + "proxyUser");
    String proxyPass = getProperty((protocol == null ? "" : protocol + ".") + "proxyPassword");

    if (proxyHost != null) {
        String nop = getProperty((protocol == null ? "" : protocol + ".") + "noProxyHosts");
        if (nop != null && !nop.equals("")) {
            nops.addAll(asList(nop.split("\\|")));
        }/*from  w  w  w  . j  a  v  a  2s . com*/
        nop = getProperty((protocol == null ? "" : protocol + ".") + "nonProxyHosts");
        if (nop != null && !nop.equals("")) {
            nops.addAll(asList(nop.split("\\|")));
        }

        int proxyPort = parseInt(getProperty((protocol == null ? "" : protocol + ".") + "proxyPort"));

        HostConfiguration hc = client.getHostConfiguration();

        if (LOG.isDebugEnabled()) {
            LOG.debug("Found the following no- and nonProxyHosts: {}", nops);
        }

        if (proxyUser != null) {
            Credentials creds = new UsernamePasswordCredentials(proxyUser, proxyPass);
            client.getState().setProxyCredentials(AuthScope.ANY, creds);
            client.getParams().setAuthenticationPreemptive(true);
        }

        if (!nops.contains(host)) {
            if (LOG.isDebugEnabled()) {
                LOG.debug("Using proxy {}:{}", proxyHost, proxyPort);
                if (protocol == null) {
                    LOG.debug("This overrides the protocol specific settings, if there were any.");
                }
            }
            hc.setProxy(proxyHost, proxyPort);
            client.setHostConfiguration(hc);
        } else {
            if (LOG.isDebugEnabled()) {
                LOG.debug("Proxy was set, but {} was contained in the no-/nonProxyList!", host);
                if (protocol == null) {
                    LOG.debug("If a protocol specific proxy has been set, it will be used anyway!");
                }
            }
        }
    }

    if (protocol != null) {
        handleProxies(null, client, host);
    }
}

---

From source file:org.apache.hadoop.hbase.backup.util.BackupUtils.java

public static boolean validate(HashMap<TableName, BackupManifest> backupManifestMap, Configuration conf)
        throws IOException {
    boolean isValid = true;

    for (Entry<TableName, BackupManifest> manifestEntry : backupManifestMap.entrySet()) {
        TableName table = manifestEntry.getKey();
        TreeSet<BackupImage> imageSet = new TreeSet<BackupImage>();

        ArrayList<BackupImage> depList = manifestEntry.getValue().getDependentListByTable(table);
        if (depList != null && !depList.isEmpty()) {
            imageSet.addAll(depList);
        }//www.  j  av  a2 s  .  c o m

        LOG.info("Dependent image(s) from old to new:");
        for (BackupImage image : imageSet) {
            String imageDir = HBackupFileSystem.getTableBackupDir(image.getRootDir(), image.getBackupId(),
                    table);
            if (!BackupUtils.checkPathExist(imageDir, conf)) {
                LOG.error("ERROR: backup image does not exist: " + imageDir);
                isValid = false;
                break;
            }
            LOG.info("Backup image: " + image.getBackupId() + " for '" + table + "' is available");
        }
    }
    return isValid;
}

---

From source file:com.genentech.application.calcProps.SDFCalcProps.java

/**
 * Get the list of SD tags that a property produces
 * also gets the tags that are produced by calculators this property depends on aka "required tags"
 * "required tags" are defined in the keepRequiredCalculators field on the XML files
*//*w w w .  ja  v  a2s .c o  m*/
private static TreeSet<String> getOutputFields(String prop, Set<Calculator> calculators, boolean verbose) {
    TreeSet<String> tags = new TreeSet<String>(String.CASE_INSENSITIVE_ORDER);
    for (Calculator calc : calculators) {
        if (calc.getName().equals(prop)) {
            //add tags for calculator
            tags.addAll(calc.getOutputFields());
            if (verbose) {
                tags.addAll(calc.getVerboseFields());
            }
            //get tags for keepRequiredCalculators, recursively
            Set<String> requiredCalcs = calc.getKeepRequiredCalculators();
            for (String c : requiredCalcs) {
                tags.addAll(getOutputFields(c, calculators, verbose));
            }
        }
    }
    return tags;
}

---

From source file:org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.java

/**
 * Gets the header fields from all VCF rods input by the user
 *
 * @param toolkit    GATK engine/*from  w ww .  jav  a  2  s.  c o  m*/
 * @param rodNames   names of rods to use, or null if we should use all possible ones
 *
 * @return a set of all fields
 */
public static Set<VCFHeaderLine> getHeaderFields(GenomeAnalysisEngine toolkit, Collection<String> rodNames) {

    // keep a map of sample name to occurrences encountered
    TreeSet<VCFHeaderLine> fields = new TreeSet<VCFHeaderLine>();

    // iterate to get all of the sample names
    List<ReferenceOrderedDataSource> dataSources = toolkit.getRodDataSources();
    for (ReferenceOrderedDataSource source : dataSources) {
        // ignore the rod if it's not in our list
        if (rodNames != null && !rodNames.contains(source.getName()))
            continue;

        if (source.getRecordType().equals(VariantContext.class)) {
            VCFHeader header = (VCFHeader) source.getHeader();
            if (header != null)
                fields.addAll(header.getMetaDataInSortedOrder());
        }
    }

    return fields;
}

---

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