Example usage for java.util SortedSet addAll

Introduction

In this page you can find the example usage for java.util SortedSet 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:org.broadinstitute.gatk.engine.recalibration.BQSRGatherer.java

/**
 * Gathers the input recalibration reports into a single report.
 *
 * @param inputs Input recalibration GATK reports
 * @return gathered recalibration GATK report
 *///w  w  w .  j a va 2  s  . c o  m
public static GATKReport gatherReport(final List<File> inputs) {
    final SortedSet<String> allReadGroups = new TreeSet<String>();
    final LinkedHashMap<File, Set<String>> inputReadGroups = new LinkedHashMap<File, Set<String>>();

    // Get the read groups from each input report
    for (final File input : inputs) {
        final Set<String> readGroups = RecalibrationReport.getReadGroups(input);
        inputReadGroups.put(input, readGroups);
        allReadGroups.addAll(readGroups);
    }

    // Log the read groups that are missing from specific inputs
    for (Map.Entry<File, Set<String>> entry : inputReadGroups.entrySet()) {
        final File input = entry.getKey();
        final Set<String> readGroups = entry.getValue();
        if (allReadGroups.size() != readGroups.size()) {
            // Since this is not completely unexpected, more than debug, but less than a proper warning.
            logger.info(MISSING_READ_GROUPS + ": " + input.getAbsolutePath());
            for (final Object readGroup : CollectionUtils.subtract(allReadGroups, readGroups)) {
                logger.info("  " + readGroup);
            }
        }
    }

    RecalibrationReport generalReport = null;
    for (File input : inputs) {
        final RecalibrationReport inputReport = new RecalibrationReport(input, allReadGroups);
        if (inputReport.isEmpty()) {
            continue;
        }

        if (generalReport == null)
            generalReport = inputReport;
        else
            generalReport.combine(inputReport);
    }
    if (generalReport == null)
        throw new ReviewedGATKException(EMPTY_INPUT_LIST);

    generalReport.calculateQuantizedQualities();

    return generalReport.createGATKReport();
}

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From source file:net.dontdrinkandroot.utils.collections.CollectionUtils.java

public static <K, V extends Comparable<? super V>> SortedSet<Map.Entry<K, V>> entriesSortedByValuesInverse(
        Map<K, V> map) {//from ww  w.  j a  v a 2  s . c om

    SortedSet<Map.Entry<K, V>> sortedEntries = new TreeSet<Map.Entry<K, V>>(new Comparator<Map.Entry<K, V>>() {

        @Override
        public int compare(Map.Entry<K, V> e1, Map.Entry<K, V> e2) {

            int res = e2.getValue().compareTo(e1.getValue());
            /* Preserve items with equal values */
            return res != 0 ? res : -1;
        }
    });
    sortedEntries.addAll(map.entrySet());

    return sortedEntries;
}

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From source file:com.tussle.main.Utility.java

public static Collection<ProjectionVector> prunedProjections(Collection<ProjectionVector> vectors) {
    SortedSet<ProjectionVector> sortedVectors = new ConcurrentSkipListSet<>(
            Comparator.comparingDouble((ProjectionVector p) -> -p.magnitude()));
    sortedVectors.addAll(vectors);
    if (isPruned(sortedVectors))
        return sortedVectors;
    double reduceMagnitude = 0;
    Iterator<ProjectionVector> i = sortedVectors.iterator();
    ProjectionVector p0 = i.next();//from w ww.j  a va  2 s  .c o  m
    ProjectionVector p1 = i.next();
    double cos0 = p0.xNorm();
    double sin0 = p0.yNorm();
    double cos1 = p1.xNorm();
    double sin1 = p1.yNorm();
    //zeroth on the right, first on the left
    if (cos0 * sin1 < cos1 * sin0) {
        double tmpcos = cos1;
        double tmpsin = sin1;
        cos1 = cos0;
        sin1 = sin0;
        cos0 = tmpcos;
        sin0 = tmpsin;
    }
    while (i.hasNext()) {
        ProjectionVector next = i.next();
        double nextcos = next.xNorm();
        double nextsin = next.yNorm();
        if (nextcos * sin0 >= cos0 * nextsin && cos1 * nextsin >= nextcos * sin1) {
            //Case 0: Within cross product bounds
        } else if (nextcos * sin0 >= cos0 * nextsin) {
            //Case 1: Over the left, extend those bounds
            cos1 = nextcos;
            sin1 = nextsin;
        } else if (cos1 * nextsin >= nextcos * sin1) {
            //Case 2: Over the right, extend those bounds
            cos0 = nextcos;
            sin0 = nextsin;
        } else {
            //Case 3: Opposite side, immediately return false
            reduceMagnitude = next.magnitude();
            break;
        }
    }
    //Now given reduceMagnitude, remove elements with lesser magnitude and
    //reduce the magnitude of remaining elements
    if (Double.isFinite(reduceMagnitude)) {
        for (Iterator<ProjectionVector> j = sortedVectors.iterator(); j.hasNext();) {
            ProjectionVector vec = j.next();
            if (vec.magnitude() <= reduceMagnitude)
                j.remove();
            else
                vec = new ProjectionVector(vec.xNorm(), vec.yNorm(), vec.magnitude() - reduceMagnitude);
        }
    }
    return sortedVectors;
}

---

From source file:org.jenkins.ci.plugins.jobimport.RemoteJobUtils.java

protected static SortedSet<RemoteJob> fromHudsonXml(final String xml)
        throws SAXException, IOException, ParserConfigurationException, XPathExpressionException {
    final SortedSet<RemoteJob> remoteJobs = new TreeSet<RemoteJob>();

    if (StringUtils.isEmpty(xml)) {
        return remoteJobs;
    }// ww w  . j a  va  2 s. c om

    if (!xml.startsWith("<hudson>")) {
        return remoteJobs;
    }

    final Document document = XPathUtils.parse(xml);

    for (final String jobUrl : XPathUtils.evaluateNodeListTextXPath(document,
            XPATH_EXPRESSION_HUDSON_JOB_URL)) {
        remoteJobs.addAll(fromXml(URLUtils.fetchUrl(jobUrl + "/api/xml")));
    }

    return remoteJobs;
}

---

From source file:org.jbosson.plugins.amq.ArtemisMBeanDiscoveryComponent.java

protected static String formatMessage(String messageTemplate, Map<String, String> variableValues) {

    StringBuffer result = new StringBuffer();

    // collect keys and values to determine value size limit if needed
    final Map<String, String> replaceMap = new HashMap<String, String>();

    final Matcher matcher = PROPERTY_NAME_PATTERN.matcher(messageTemplate);
    int count = 0;
    while (matcher.find()) {
        final String key = matcher.group(1);
        final String value = variableValues.get(key);

        if (value != null) {
            replaceMap.put(key, value);//w  w  w.j a v a2  s.  c  om
            matcher.appendReplacement(result, Matcher.quoteReplacement(value));
        } else {
            matcher.appendReplacement(result, Matcher.quoteReplacement(matcher.group()));
        }

        count++;
    }
    matcher.appendTail(result);

    // check if the result exceeds MAX_LENGTH for formatted properties
    if (!replaceMap.isEmpty() && result.length() > MAX_LENGTH) {
        // sort values according to size
        final SortedSet<String> values = new TreeSet<String>(new Comparator<String>() {
            public int compare(String o1, String o2) {
                return o1.length() - o2.length();
            }
        });
        values.addAll(replaceMap.values());

        // find total value characters allowed
        int available = MAX_LENGTH - PROPERTY_NAME_PATTERN.matcher(messageTemplate).replaceAll("").length();

        // fit values from small to large in the allowed size to determine the maximum average
        int averageLength = available / count;
        for (String value : values) {
            final int length = value.length();
            if (length > averageLength) {
                break;
            }
            available -= length;
            count--;
            averageLength = available / count;
        }

        // replace values
        matcher.reset();
        result.delete(0, result.length());
        while (matcher.find()) {
            String value = replaceMap.get(matcher.group(1));
            if (value != null && value.length() > averageLength) {
                value = value.substring(0, averageLength);
            }
            matcher.appendReplacement(result, value != null ? value : matcher.group());
        }
        matcher.appendTail(result);
    }

    return result.toString();
}

---

From source file:org.jenkins.ci.plugins.jobimport.RemoteJobUtils.java

protected static SortedSet<RemoteJob> fromListViewXml(final String xml)
        throws SAXException, IOException, ParserConfigurationException, XPathExpressionException {
    final SortedSet<RemoteJob> remoteJobs = new TreeSet<RemoteJob>();

    if (StringUtils.isEmpty(xml)) {
        return remoteJobs;
    }//from   ww  w .  j  a v  a2  s  .c o m

    if (!xml.startsWith("<listView>")) {
        return remoteJobs;
    }

    final Document document = XPathUtils.parse(xml);

    for (final String jobUrl : XPathUtils.evaluateNodeListTextXPath(document,
            XPATH_EXPRESSION_LIST_VIEW_JOB_URL)) {
        remoteJobs.addAll(fromXml(URLUtils.fetchUrl(jobUrl + "/api/xml")));
    }

    return remoteJobs;
}

---

From source file:com.bluexml.side.form.clazz.utils.ClassDiagramUtils.java

/**
 * Get all class from the model/* ww w  .j  a v a  2 s.  c om*/
 * 
 * @param c
 * @return
 */
public static SortedSet<AbstractClass> getAllClazzs(AbstractClass c) {
    SortedSet<AbstractClass> s = new TreeSet<AbstractClass>(new ClazzComparator());
    List<ClassPackage> l = findAllPackage(c);
    for (ClassPackage p2 : l) {
        EList<Clazz> Clazzs = p2.getClassSet();
        s.addAll(Clazzs);
    }

    return s;
}

---

From source file:org.jasig.schedassist.model.AvailableBlockBuilder.java

/**
 * Expand a {@link Set} of {@link AvailableBlock} into a {@link SortedSet} of {@link AvailableBlock}s with a duration equal
 * to the meetingLengthMinutes argument in minutes.
 * /*from  w w  w .jav a  2 s  . c o m*/
 * @param largeBlocks
 * @return the new set
 */
public static SortedSet<AvailableBlock> expand(Set<AvailableBlock> largeBlocks,
        final int meetingLengthMinutes) {
    SortedSet<AvailableBlock> smallBlocks = new TreeSet<AvailableBlock>();
    for (AvailableBlock sourceBlock : largeBlocks) {
        smallBlocks.addAll(expand(sourceBlock, meetingLengthMinutes));
    }
    return smallBlocks;
}

---

From source file:org.opennms.netmgt.dao.NodeDaoIT.java

private static <T> void assertSetsEqual(Set<T> expectedSet, Set<T> actualSet, String orderProperty,
        AssertEquals<T> comparer) throws Exception {
    SortedSet<T> expectedSorted = new TreeSet<T>(new PropertyComparator(orderProperty));
    expectedSorted.addAll(expectedSet);
    SortedSet<T> actualSorted = new TreeSet<T>(new PropertyComparator(orderProperty));
    actualSorted.addAll(actualSet);//w  w w .java 2  s.  c om

    Iterator<T> expected = expectedSorted.iterator();
    Iterator<T> actual = actualSorted.iterator();

    while (expected.hasNext() && actual.hasNext()) {
        comparer.assertEqual(expected.next(), actual.next());
    }

    if (expected.hasNext())
        fail("Missing item " + expected.next() + " in the actual list");

    if (actual.hasNext())
        fail("Unexpected item " + actual.next() + " in the actual list");
}

---

From source file:gov.nih.nci.cananolab.util.StringUtils.java

/**
 * Parse the text into an array of words using white space as delimiter.
 * Keeping words in quotes together./*from w  ww.  j  av  a  2 s.co  m*/
 *
 * @param texts
 * @return
 */
public static List<String> parseToWords(String text) {
    if (isEmpty(text)) {
        return null;
    }
    SortedSet<String> wordList = new TreeSet<String>();

    // extract words in quotes first
    String patternStr = "\\B[\"']([^\"']*)[\"']\\B";
    String[] nonQuotedTexts = text.split(patternStr);
    for (String txt : nonQuotedTexts) {
        String[] nonQuotedWords = txt.split("\\s");
        wordList.addAll(Arrays.asList(nonQuotedWords));
    }
    Pattern pattern = Pattern.compile(patternStr);
    Matcher matcher = pattern.matcher(text);

    List<String> quotedWords = new ArrayList<String>();
    int start = 0;
    while (matcher.find(start)) {
        String quotedWord = matcher.group(1).trim();
        quotedWords.add(quotedWord);
        start = matcher.end(1);
    }
    wordList.addAll(quotedWords);

    return new ArrayList<String>(wordList);
}

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