Example usage for java.util TreeSet addAll

List of usage examples for java.util TreeSet addAll

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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.mda.bcb.tcgagsdata.create.ReadPlatform.java

public void readPlatform(String thePlatform) throws IOException, Exception {
    TcgaGSData.printWithFlag("readPlatform for " + thePlatform + " beginning");
    TcgaGSData.printWithFlag("readPlatform can consume excessive amounts of time and memory");
    mNumberOfGenes = 0;/*from   ww w  .  j a v  a2s .c  o m*/
    TreeMap<String, Integer> geneMap = null;
    {
        ReadPlatform_GeneEq lg = new ReadPlatform_GeneEq(mReadPath);
        lg.getNamesGenes(thePlatform);
        mGenes = lg.mGenes;
        geneMap = TcgaGSData.buildIndexMap(lg.mGenes);
        mNumberOfGenes = lg.mSize;
    }
    mNumberOfSamples = 0;
    boolean found = false;
    long start = System.currentTimeMillis();
    TreeSet<File> dataFileList = new TreeSet<>();
    dataFileList.addAll(FileUtils.listFiles(new File(mReadPath, thePlatform),
            new WildcardFileFilter("matrix_data_*.tsv"), TrueFileFilter.INSTANCE));
    for (File input : dataFileList) {
        try (BufferedReader br = Files.newBufferedReader(Paths.get(input.getAbsolutePath()),
                Charset.availableCharsets().get("ISO-8859-1"))) {
            found = true;
            TcgaGSData.printWithFlag("readPlatform file=" + input.getAbsolutePath());
            // first line samples
            String line = br.readLine();
            TreeMap<String, Integer> sampleMap = TcgaGSData
                    .buildIndexMap(GSStringUtils.afterTab(line).split("\t", -1));
            if (0 == mNumberOfSamples) {
                mSamples = GSStringUtils.afterTab(line).split("\t", -1);
                mNumberOfSamples = mSamples.length;
                mGenesBySamplesValues = new double[mNumberOfGenes][mNumberOfSamples];
            } else {
                if (mNumberOfSamples != GSStringUtils.afterTab(line).split("\t", -1).length) {
                    throw new Exception("Expected sample count of " + mNumberOfSamples + " but found different "
                            + input.getAbsolutePath());
                }
            }
            line = br.readLine();
            while (null != line) {
                String gene = GSStringUtils.beforeTab(line);
                Integer intIndex = geneMap.get(gene);
                if (null != intIndex) {
                    int geneIndex = intIndex;
                    double[] valueList = convertToDouble(GSStringUtils.afterTab(line).split("\t", -1));
                    for (int x = 0; x < valueList.length; x++) {
                        int sampleIndex = sampleMap.get(mSamples[x]);
                        mGenesBySamplesValues[geneIndex][sampleIndex] = valueList[x];
                    }
                } else {
                    throw new Exception(
                            "readPlatform for " + thePlatform + " found unexpected 'gene' = " + gene);
                }
                line = br.readLine();
            }
        }
    }
    long finish = System.currentTimeMillis();
    TcgaGSData.printWithFlag(
            "readPlatform for " + thePlatform + " retrieved in " + ((finish - start) / 1000.0) + " seconds");
    if (false == found) {
        throw new Exception("readPlatform for " + thePlatform + " not found");
    } else {
        TcgaGSData.printWithFlag("write " + thePlatform + " to " + mWriteFile);
        writeFile();
    }
}

From source file:org.unitime.timetable.test.StudentSectioningTest.java

private static Course loadCourse(CourseOffering co, long studentId) {
    sLog.debug("  -- loading " + co.getCourseName());
    Offering offering = new Offering(co.getInstructionalOffering().getUniqueId().longValue(),
            co.getInstructionalOffering().getCourseName());
    int projected = (co.getProjectedDemand() == null ? 0 : co.getProjectedDemand().intValue());
    int courseLimit = co.getInstructionalOffering().getLimit().intValue();
    if (co.getReservation() != null)
        courseLimit = co.getReservation();
    Course course = new Course(co.getUniqueId().longValue(), co.getSubjectAreaAbbv(), co.getCourseNbr(),
            offering, courseLimit, projected);
    Hashtable class2section = new Hashtable();
    Hashtable ss2subpart = new Hashtable();
    for (Iterator i = co.getInstructionalOffering().getInstrOfferingConfigs().iterator(); i.hasNext();) {
        InstrOfferingConfig ioc = (InstrOfferingConfig) i.next();
        Config config = new Config(ioc.getUniqueId().longValue(),
                (ioc.isUnlimitedEnrollment() ? -1 : ioc.getLimit()),
                ioc.getCourseName() + " [" + ioc.getName() + "]", offering);
        TreeSet subparts = new TreeSet(new SchedulingSubpartComparator());
        subparts.addAll(ioc.getSchedulingSubparts());
        for (Iterator j = subparts.iterator(); j.hasNext();) {
            SchedulingSubpart ss = (SchedulingSubpart) j.next();
            String sufix = ss.getSchedulingSubpartSuffix();
            Subpart parentSubpart = (ss.getParentSubpart() == null ? null
                    : (Subpart) ss2subpart.get(ss.getParentSubpart()));
            Subpart subpart = new Subpart(ss.getUniqueId().longValue(),
                    ss.getItype().getItype().toString() + sufix,
                    ss.getItypeDesc().trim() + (sufix == null || sufix.length() == 0 ? "" : " (" + sufix + ")"),
                    config, parentSubpart);
            subpart.setAllowOverlap(ss.isStudentAllowOverlap());
            ss2subpart.put(ss, subpart);
            for (Iterator k = ss.getClasses().iterator(); k.hasNext();) {
                Class_ c = (Class_) k.next();
                Assignment a = c.getCommittedAssignment();
                int usedSpace = 0;
                if (studentId >= 0)
                    for (Iterator l = c.getStudentEnrollments().iterator(); l.hasNext();) {
                        StudentClassEnrollment sce = (StudentClassEnrollment) l.next();
                        if (Long.parseLong(sce.getStudent().getExternalUniqueId()) != studentId)
                            usedSpace++;
                    }//from  ww w .  ja va  2 s  .co  m
                /*
                Number usedSpace = (Number)new Class_DAO().getSession().createQuery(
                    "select count(sce) from StudentClassEnrollment sce where " +
                    "sce.clazz.uniqueId=:classId and sce.student.externalUniqueId!=:studentId").
                    setLong("classId", c.getUniqueId()).
                    setLong("studentId", studentId).uniqueResult();
                if (studentId<0) usedSpace = new Integer(0);
                */
                int limit = c.getClassLimit() - usedSpace;
                if (ioc.isUnlimitedEnrollment().booleanValue())
                    limit = -1;
                Section parentSection = (c.getParentClass() == null ? null
                        : (Section) class2section.get(c.getParentClass()));
                Section section = new Section(c.getUniqueId().longValue(), limit, c.getClassLabel(), subpart,
                        (a == null ? null : a.getPlacement()), getInstructorIds(c), getInstructorNames(c),
                        parentSection);
                if (c.getSectioningInfo() != null) {
                    section.setSpaceExpected(c.getSectioningInfo().getNbrExpectedStudents().doubleValue());
                    section.setSpaceHeld(c.getSectioningInfo().getNbrHoldingStudents().doubleValue());
                    section.setPenalty(getPenalty(section, c, studentId));
                }
                class2section.put(c, section);
                sLog.debug("    -- section " + section);
            }
        }
    }
    return course;
}

From source file:controllerTas.actions.gnuplot.ThroughputPlotter.java

public void produceDataFile(PlottableData data, String name, String extension) {
    try {//from   w ww  .  ja  v a  2  s  . co  m
        PrintWriter pw = new PrintWriter(
                new FileWriter(new File(slashedPath(dataPath) + name + "." + extension)));
        String header = header(data.getHeader());
        pw.println(header);
        TreeSet<PlottableDataLine> set = new TreeSet<PlottableDataLine>(new LineComparator());
        set.addAll(data.getLines());
        int lastNodes = -1, newNodes;
        for (PlottableDataLine l : set) {
            newNodes = l.getScale().getNumNodes();
            if (newNodes(lastNodes, newNodes))
                pw.println("");
            lastNodes = newNodes;
            log.trace("Writing " + l.toString());
            pw.println(line(l));
        }
        pw.flush();
        pw.close();
    } catch (IOException e) {
        e.printStackTrace();
    }
}

From source file:org.alfresco.web.forms.xforms.SchemaUtil.java

private static void buildTypeTree(final XSTypeDefinition type, final TreeSet<XSTypeDefinition> descendents,
        final TreeMap<String, TreeSet<XSTypeDefinition>> typeTree) {
    if (type == null) {
        return;/*from  ww  w  .  j  av  a 2  s .  co m*/
    }
    if (LOGGER.isDebugEnabled())
        LOGGER.debug("buildTypeTree(" + type.getName() + ", " + descendents.size() + " descendents)");
    if (descendents.size() > 0) {
        TreeSet<XSTypeDefinition> compatibleTypes = typeTree.get(type.getName());

        if (compatibleTypes == null) {
            if (LOGGER.isDebugEnabled())
                LOGGER.debug("no compatible types found for " + type.getName() + ", creating a new set");
            compatibleTypes = new TreeSet<XSTypeDefinition>(TYPE_EXTENSION_SORTER);
            typeTree.put(type.getName(), compatibleTypes);
        }
        if (LOGGER.isDebugEnabled())
            LOGGER.debug("adding " + descendents.size() + " descendents to " + type.getName());
        compatibleTypes.addAll(descendents);
    }

    final XSTypeDefinition parentType = type.getBaseType();
    if (parentType == null || type.getTypeCategory() != parentType.getTypeCategory()) {
        return;
    }

    if (type != parentType && parentType.getName() != null && !parentType.getName().equals("anyType")) {
        TreeSet<XSTypeDefinition> newDescendents = typeTree.get(parentType.getName());
        if (newDescendents == null) {
            if (LOGGER.isDebugEnabled())
                LOGGER.debug("type tree doesn't contain " + parentType.getName()
                        + ", creating a new descendant set");
            newDescendents = new TreeSet<XSTypeDefinition>(TYPE_EXTENSION_SORTER);
        }
        if (LOGGER.isDebugEnabled())
            LOGGER.debug("adding " + descendents.size() + " descendants to existing " + newDescendents.size()
                    + " descendants of " + parentType.getName());
        newDescendents.addAll(descendents);

        //extension (we only add it to "newDescendants" because we don't want
        //to have a type descendant to itself, but to consider it for the parent
        if (type.getTypeCategory() == XSTypeDefinition.COMPLEX_TYPE) {
            final XSComplexTypeDefinition complexType = (XSComplexTypeDefinition) type;
            if (complexType.getDerivationMethod() == XSConstants.DERIVATION_EXTENSION
                    && !complexType.getAbstract() && !descendents.contains(type)) {
                if (LOGGER.isDebugEnabled())
                    LOGGER.debug("adding " + type.getName() + " to existing " + newDescendents.size()
                            + " descendents of " + parentType.getName());
                newDescendents.add(type);
            }
        }

        //note: extensions are impossible on simpleTypes !
        SchemaUtil.buildTypeTree(parentType, newDescendents, typeTree);
    }
}

From source file:com.webbfontaine.valuewebb.navigation.RetrievedDocuments.java

/**
 * Orders conversations, the last element is the oldest.
 *
 * @return ordered Set where last element is oldest conversation
 * @see org.jboss.seam.faces.Switcher#createSelectItems()
 *///from ww w . java  2 s  . c o  m
public TreeSet<ConversationEntry> order() {
    ConversationEntries conversationEntries = ConversationEntries.getInstance();
    if (conversationEntries == null) {
        return null;
    }

    TreeSet<ConversationEntry> orderedEntries = new TreeSet<ConversationEntry>();
    orderedEntries.addAll(conversationEntries.getConversationEntries());
    return orderedEntries;
}

From source file:net.krautchan.data.KCThread.java

public synchronized Set<KCPosting> getSortedPostings() {
    TreeSet<KCPosting> s = new TreeSet<KCPosting>();
    s.addAll(postings.values());
    return s;/*www  . ja  va 2s .c  om*/
}

From source file:com.samples.platform.service.common.GetServiceStatusOperation.java

/**
 * @param message/*  w w  w .j a v a2 s .  com*/
 *            the {@link JAXBElement} containing a
 *            {@link GetServiceStatusRequestType}.
 * @return the {@link JAXBElement} with a
 *         {@link GetServiceStatusResponseType}.
 */
@InsightEndPoint
@ServiceActivator
public final JAXBElement<GetServiceStatusResponseType> getServiceStatus(
        final JAXBElement<GetServiceStatusRequestType> message) {
    this.logger.debug("+getServiceStatus");
    GetServiceStatusResponseType response = this.of.createGetServiceStatusResponseType();
    try {
        PropertyType p;
        ClassLoader cl;
        URL[] urls;
        ClassLoader sysCl = ClassLoader.getSystemClassLoader();

        response.setStatus("Service is available");

        /* System properties */
        p = new PropertyType();
        p.setName("System Properties");
        response.getDetails().add(p);
        TreeSet<String> propertyNames = new TreeSet<String>();
        propertyNames.addAll(System.getProperties().stringPropertyNames());
        for (String propertyName : propertyNames) {
            p.getValue().add(new StringBuffer(64).append(propertyName).append("=")
                    .append(System.getProperty(propertyName)).toString());
        }

        /* Application properties. */
        p = new PropertyType();
        p.setName("Application loaded properties");
        response.getDetails().add(p);
        propertyNames.clear();
        propertyNames.addAll(this.properties.stringPropertyNames());
        for (String propertyName : propertyNames) {
            p.getValue().add(new StringBuffer(64).append(propertyName).append("=")
                    .append(this.properties.getProperty(propertyName)).toString());
        }

        /* Current lass loader */
        cl = this.getClass().getClassLoader();
        p = new PropertyType();
        p.setName("This ClassLoader");
        response.getDetails().add(p);
        p.getValue().add(cl.getClass().getName());
        if (URLClassLoader.class.isInstance(cl)) {
            urls = ((URLClassLoader) cl).getURLs();
            p.getValue().add(new StringBuffer("Url: ").append(urls.length).toString());
            for (URL url : urls) {
                p.getValue().add(url.toString());
            }
        }
        cl = cl.getParent();
        while (cl != sysCl) {
            p = new PropertyType();
            p.setName("Parent Classloader");
            response.getDetails().add(p);
            p.getValue().add(cl.getClass().getName());
            if (URLClassLoader.class.isInstance(cl)) {
                urls = ((URLClassLoader) cl).getURLs();
                p.getValue().add(new StringBuffer("Url: ").append(urls.length).toString());
                for (URL url : urls) {
                    p.getValue().add(url.toString());
                }
            }
            cl = cl.getParent();
        }

        /* System class loader */
        cl = sysCl;
        p = new PropertyType();
        p.setName("SystemClassLoader");
        response.getDetails().add(p);
        p.getValue().add(cl.getClass().getName());
        if (URLClassLoader.class.isInstance(cl)) {
            urls = ((URLClassLoader) cl).getURLs();
            p.getValue().add(new StringBuffer("Url: ").append(urls.length).toString());
            for (URL url : urls) {
                p.getValue().add(url.toString());
            }
        }
    } catch (Throwable e) {
        this.logger.error(e.getMessage(), e);
    } finally {
        this.logger.debug("-getServiceStatus #{}, #f{}", response/* .get() */ != null ? 1 : 0,
                response.getFailure().size());
    }
    return this.of.createGetServiceStatusResponse(response);
}

From source file:org.jamocha.dn.ConflictSet.java

private TreeSet<RuleAndToken> correctStrategy(final Integer salience, final TreeSet<RuleAndToken> ratSet) {
    if (this.conflictResolutionStrategy == ratSet.comparator())
        return ratSet;
    // if wrong comparator was used, create new set and copy the values
    final TreeSet<RuleAndToken> newRatSet = new TreeSet<>(this.conflictResolutionStrategy);
    newRatSet.addAll(ratSet);
    this.rulesAndTokensBySalience.put(salience, newRatSet);
    return newRatSet;
}

From source file:org.apache.asterix.common.config.ConfigUsageTest.java

protected Set<Section> getSections(ConfigManager configManager) {
    TreeSet<Section> sections = new TreeSet<>(Comparator.comparing(Section::sectionName));
    sections.addAll(configManager.getSections());
    sections.remove(Section.LOCALNC);//from   ww  w  . j  ava 2  s. com
    return sections;
}

From source file:org.apache.axis2.jaxws.runtime.description.marshal.impl.PackageSetBuilder.java

/**
 * @param serviceDescription ServiceDescription
 * @return Set of Packages// w  w w .  j  a va  2 s  .com
 */
public static TreeSet<String> getPackagesFromAnnotations(ServiceDescription serviceDesc,
        MarshalServiceRuntimeDescription msrd) {
    if (log.isDebugEnabled()) {
        log.debug("start getPackagesFromAnnotations");
        log.debug("ServiceDescription = " + serviceDesc.toString());
        log.debug("MarshalServiceRuntimeDescription = " + msrd.toString());
    }
    TreeSet<String> set = new TreeSet<String>();
    Collection<EndpointDescription> endpointDescs = serviceDesc.getEndpointDescriptions_AsCollection();

    // Build a set of packages from all of the endpoints
    if (endpointDescs != null) {
        for (EndpointDescription endpointDesc : endpointDescs) {
            set.addAll(getPackagesFromAnnotations(endpointDesc, msrd));
        }
    }
    if (log.isDebugEnabled()) {
        log.debug("end getPackagesFromAnnotations");
    }
    return set;
}