@Test
public void testTransformUndef() {
  final RegisterTrackingTransformationProvider transformationProvider =
      new RegisterTrackingTransformationProvider(new RegisterTrackingOptions(false,
          new TreeSet<String>(), false, AnalysisDirection.DOWN));
  final ReilInstruction instruction = ReilHelpers.createUndef(0, OperandSize.DWORD, "eax");
  final Pair<RegisterSetLatticeElement, RegisterSetLatticeElement> transformationResult =
      transformationProvider.transformUndef(instruction, createTaintedState("eax"));

  Assert.assertNull(transformationResult.second());

  transformationResult.first().onInstructionExit();

  Assert.assertTrue(transformationResult.first().getNewlyTaintedRegisters().isEmpty());
  Assert.assertTrue(transformationResult.first().getReadRegisters().isEmpty());
  Assert.assertTrue(transformationResult.first().getTaintedRegisters().isEmpty());
  Assert.assertTrue(transformationResult.first().getUntaintedRegisters().contains("eax"));
  Assert.assertTrue(transformationResult.first().getUpdatedRegisters().isEmpty());
}
 

private Set<String> extractLibJarNamesFromURLs(URL[] urls) {
    if (urls == null) {
        return Collections.emptySet();
    }
    Set<String> libJarNames = new TreeSet<String>(String.CASE_INSENSITIVE_ORDER);
    for (URL url : urls) {
        try {
            String libJarName = extractLibJarName(url);
            if (libJarName.length() > 0) {
                libJarNames.add(libJarName);
            }
        } catch (Exception e) {
            // safety net
            logger.warn("Error extracting library name", e);
        }
    }
    return libJarNames;
}
 

public static String getRequestPrincipals(HttpServletRequest httpRequest)
{
    HttpSession session = httpRequest.getSession(false);
    if (session != null)
    {
        Subject subject = HttpManagementUtil.getAuthorisedSubject(httpRequest);
        if (subject != null)
        {

            Set<Principal> principalSet = subject.getPrincipals();
            if (!principalSet.isEmpty())
            {
                TreeSet<String> principalNames = new TreeSet<>();
                for (Principal principal : principalSet)
                {
                    principalNames.add(principal.getName());
                }
                return principalNames.toString();
            }
        }
    }
    return null;
}
 

@Override
public FloatDataset getUniqueItems() {
	Set<Float> set = new TreeSet<Float>(); // CLASS_TYPE
	IndexIterator it = getIterator();
	while (it.hasNext()) {
		set.add(data[it.index]);
	}

	FloatDataset u = new FloatDataset(set.size()); // CLASS_TYPE
	int i = 0;
	float[] udata = u.getData(); // PRIM_TYPE
	for (Float v : set) { // CLASS_TYPE
		udata[i++] = v;
	}
	return u;
}
 

/**
 * Creates the entries that allow the user to go into the user dictionary for each locale.
 * @param userDictGroup The group to put the settings in.
 */
protected void createUserDictSettings(final PreferenceGroup userDictGroup) {
    final Activity activity = getActivity();
    userDictGroup.removeAll();
    final TreeSet<String> localeSet =
            UserDictionaryList.getUserDictionaryLocalesSet(activity);

    if (localeSet.size() > 1) {
        // Have an "All languages" entry in the languages list if there are two or more active
        // languages
        localeSet.add("");
    }

    if (localeSet.isEmpty()) {
        userDictGroup.addPreference(createUserDictionaryPreference(null));
    } else {
        for (String locale : localeSet) {
            userDictGroup.addPreference(createUserDictionaryPreference(locale));
        }
    }
}
 

private Set<DnsRecord> getDnsRecords(String serviceName) throws Exception {
    Set<DnsRecord> dnsRecords = new TreeSet<DnsRecord>();
    Hashtable<String, String> env = new Hashtable<String, String>();
    env.put(Context.INITIAL_CONTEXT_FACTORY, "com.sun.jndi.dns.DnsContextFactory");
    env.put(Context.PROVIDER_URL, "dns:");
    env.put("com.sun.jndi.dns.recursion", "false");
    // default is one second, but os skydns can be slow
    env.put("com.sun.jndi.dns.timeout.initial", "2000");
    // retries handled by DnsPing
    //env.put("com.sun.jndi.dns.timeout.retries", "4");
    DirContext ctx = new InitialDirContext(env);
    Attributes attrs = ctx.getAttributes("_tcp." + serviceName, new String[]{"SRV"});
    if (attrs == null) {
        return dnsRecords;
    }
    NamingEnumeration<?> servers = attrs.get("SRV").getAll();
    while (servers.hasMore()) {
        DnsRecord record = DnsRecord.fromString((String)servers.next());
        dnsRecords.add(record);
    }
    return dnsRecords;
}
 

public static Mapper getMapper(String... mappingFiles) {
   Set<String> mappingSet = new TreeSet();
   mappingSet.addAll(Arrays.asList(mappingFiles));
   MessageDigest complete = DigestUtils.getMd5Digest();
   Iterator i$ = mappingSet.iterator();

   while(i$.hasNext()) {
      String mapping = (String)i$.next();
      complete.update(mapping.getBytes());
   }

   String key = new String(Base64.encode(complete.digest()));
   if (!cache.containsKey(key)) {
      Map<String, Object> options = new HashMap();
      options.put("be.ehealth.technicalconnector.mapper.configfiles", mappingFiles);

      try {
         cache.put(key, helper.getImplementation(options));
      } catch (TechnicalConnectorException var6) {
         throw new IllegalArgumentException(var6);
      }
   }

   return (Mapper)cache.get(key);
}
 

private void init(String[][][]stringTag,String str) throws Exception{
	ts = new TreeSet<Entity>();
	llis = new LinkedList<Instance>();
	fc = new FormChanger();
	test = new InstanceSet(cl.getPipe());
	test.loadThruPipes(new AR_Reader(stringTag,str));
	for(int i=0;i<test.size();i++){
		String ss = cl.getStringLabel(test.getInstance(i));
		if(ss.equals("1")){
			llis.add(test.getInstance(i));
		}	
	}
	fc.groupToList(llis);
	fc.getLlsb();
	ts = fc.getTs();
}
 

/**
 * This function remove peaks encountered in the lateral of a main peak (currentCandidate) that
 * are considered as garbage, for example FTMS shoulder peaks.
 * 
 * First calculates a peak model (Gauss, Lorenzian, etc) defined by peakModelName parameter, with
 * the same position (m/z) and height (intensity) of the currentCandidate, and the defined
 * resolution (resolution parameter). Second search and remove all the lateral peaks that are
 * under the curve of the modeled peak.
 * 
 */
private static void removeLateralPeaks(DataPoint currentCandidate, TreeSet<DataPoint> candidates,
    PeakModel peakModel, double resolution) {

  // We set our peak model with same position(m/z), height(intensity) and
  // resolution of the current peak
  peakModel.setParameters(currentCandidate.getMZ(), currentCandidate.getIntensity(), resolution);

  // We search over all peak candidates and remove all of them that are
  // under the curve defined by our peak model
  Iterator<DataPoint> candidatesIterator = candidates.iterator();
  while (candidatesIterator.hasNext()) {

    DataPoint lateralCandidate = candidatesIterator.next();

    // Condition in x domain (m/z)
    if ((lateralCandidate.getIntensity() < peakModel.getIntensity(lateralCandidate.getMZ()))) {
      candidatesIterator.remove();
    }
  }

}
 

public String instructorText(String instructorNameFormat, String separator){
	if (getClassInstructors() == null) return "";
	
	TreeSet sortedInstructors = new TreeSet(new InstructorComparator());
	sortedInstructors.addAll(this.getClassInstructors());

	StringBuffer sb = new StringBuffer();
	
	for (Iterator it = sortedInstructors.iterator(); it.hasNext();) {
		ClassInstructor ci = (ClassInstructor) it.next();
		sb.append(ci.getInstructor().getName(instructorNameFormat));
		if (it.hasNext()) sb.append(separator);
	}
	
	return sb.toString();
}
 

/**
 * Returns a new instance that keeps only the percentiles with values
 * falling within the specified range. All new percentiles are adjusted such
 * that the last value has the 100% percentage.
 * 
 * @param range
 *            the range within which the percentiles will be preserved
 * @return a new instance that keeps only the percentiles falling within the
 *         specified range; or <code>null</code> if no such a percentile
 */
public Percentiles percentiles(ConstantRange range) {
	SortedSet<Constant> sorted = values();
	SortedSet<Constant> contained = new TreeSet<Constant>();
	Constant prev = null;
	for (Constant pct : sorted) {
		if (range.contains(pct)) {
			contained.add(pct);
		} else if (contained.isEmpty())
			prev = pct;
	}
	if (contained.isEmpty())
		return null;
	double prevPercent = prev == null ? 0.0 : pcts.get(prev);
	double totalPercent = pcts.get(contained.last()) - prevPercent;
	Map<Constant, Double> newPcts = new HashMap<Constant, Double>();
	for (Constant p : contained)
		newPcts.put(p, (pcts.get(p) - prevPercent) / totalPercent);
	return new Percentiles(newPcts);
}
 

@Override
public boolean onOptionsItemSelected(MenuItem item) {
    // Handle action bar item clicks here. The action bar will
    // automatically handle clicks on the Home/Up button, so long
    // as you specify a parent activity in AndroidManifest.xml.
    int id = item.getItemId();
    if (id == R.id.action_remove) {
        if (agv.getCount() >= 6) {
            TreeSet<Integer> row = new TreeSet<Integer>();
            row.add(0);
            agv.animateDeleteRow(row, 200);
        }

        return true;
    } else if (id == R.id.action_add) {
        LinkedList<Object> items = new LinkedList<Object>();
        items.add(1);
        items.add(2);
        items.add(3);
        items.add(4);
        items.add(5);
        items.add(6);
        agv.animateAddCells(items, 200);
    }
    return super.onOptionsItemSelected(item);
}
 

/**
 * Gets an array of unit dimensions for all currently selected variables.
 *
 * @return array of unit dimensions
 */
private String[] getCurrentDimensions() {
  TTrack track = TTrack.getTrack(trackID);
  if (track==null) return new String[0];
  Class<? extends TTrack> trackType = getTrackType(track);
	TreeSet<String> dimensions = new TreeSet<String>(); 
int[] indices = variableList.getSelectedIndices();
Object[] selected = new Object[indices.length];
for (int j=0; j<indices.length; j++) {
	selected[j] = displayedNames[indices[j]];
}
for (Object displayedName : selected) {
	String name = realNames.get(displayedName.toString());
		String dim = getVariableDimensions(trackType, name);
		if (dim!=null) {
			dimensions.add(dim);
		}
}
return dimensions.toArray(new String[dimensions.size()]);
}
 

@Override
public boolean addInputFile(InputFile inputFile) throws UnusableFileException {
    String path = inputFile.getDirectory();
    long slice = util.getBucket(grouping, path);
    // we should never use default...
    String folder = "default";
    for (String string : folders) {
        if (path.contains(string)) {
            folder = string;
            break;
        }
    }
    DFKey bucket = new DFKey(slice, folder);
    Set<InputFile> bucketList = buckets.get(bucket);
    if (bucketList == null) {
        bucketList = new TreeSet<>(fc.isLifo() ? InputFile.LIFO : InputFile.FIFO);
        buckets.put(bucket, bucketList);
    }
    return bucketList.add(inputFile);
}
 

private DependencyNode(Artifact artifact, NodeResolution resolution, String effectiveVersion) {
  if (artifact == null) {
    throw new NullPointerException("Artifact must not be null");
  }

  this.effectiveVersion = effectiveVersion;
  this.scopes = new TreeSet<>();
  this.classifiers = new TreeSet<>();
  this.types = new TreeSet<>();
  this.artifact = artifact;
  this.resolution = resolution;
  if (artifact.getScope() != null) {
    this.scopes.add(artifact.getScope());
  }
  this.types.add(artifact.getType());

  if (!isNullOrEmpty(artifact.getClassifier())) {
    this.classifiers.add(artifact.getClassifier());
  }
}
 

/**
 * Finds all the resource names contained in this file system folder.
 *
 * @param scanRootLocation
 *            The root location of the scan on disk.
 * @param folder
 *            The folder to look for resources under on disk.
 * @return The resource names;
 * @throws IOException
 *             when the folder could not be read.
 */
private Set<String> findResourceNamesFromFileSystem(String scanRootLocation, File folder) throws IOException {
    LOG.debug("Scanning for resources in path: " + folder.getPath() + " (" + scanRootLocation + ")");

    Set<String> resourceNames = new TreeSet<String>();

    File[] files = folder.listFiles();
    for (File file : files) {
        if (file.canRead()) {
            if (file.isDirectory()) {
                resourceNames.addAll(findResourceNamesFromFileSystem(scanRootLocation, file));
            } else {
                resourceNames.add(file.getPath());
            }
        }
    }

    return resourceNames;
}
 

@Test
public void testTransformSubIdenticalInput() {
  final RegisterTrackingTransformationProvider transformationProvider =
      new RegisterTrackingTransformationProvider(new RegisterTrackingOptions(false,
          new TreeSet<String>(), false, AnalysisDirection.DOWN));
  final ReilInstruction instruction =
      ReilHelpers.createSub(0, OperandSize.DWORD, "ecx", OperandSize.DWORD, "ecx",
          OperandSize.DWORD, "eax");
  final Pair<RegisterSetLatticeElement, RegisterSetLatticeElement> transformationResult =
      transformationProvider.transformSub(instruction, createTaintedState("ecx", "eax"));

  Assert.assertNull(transformationResult.second());

  transformationResult.first().onInstructionExit();

  Assert.assertTrue(transformationResult.first().getNewlyTaintedRegisters().isEmpty());
  Assert.assertTrue(transformationResult.first().getReadRegisters().isEmpty());
  Assert.assertFalse(transformationResult.first().getTaintedRegisters().contains("eax"));
  Assert.assertTrue(transformationResult.first().getTaintedRegisters().contains("ecx"));
  Assert.assertTrue(transformationResult.first().getUntaintedRegisters().contains("eax"));
  Assert.assertTrue(transformationResult.first().getUpdatedRegisters().isEmpty());
}
 

private static SortedSet<MethodDescriptor> getSortedMethods(final Class<?> type) {
  SortedSet<MethodDescriptor> methods = new TreeSet<MethodDescriptor>(METHOD_COMPARATOR);

  if (type == null) {
    return methods;
  }

  final Method[] declaredMethods = type.getDeclaredMethods();

  if (declaredMethods.length > 256) {
    throw new IllegalArgumentException("Can't proxy that many methods on a single instance!");
  }

  for (Method declaredMethod : declaredMethods) {
    methods.add(MethodDescriptor.of(declaredMethod));
  }

  if (methods.size() != declaredMethods.length) {
    throw new AssertionError("Ouch... looks like that didn't work!");
  }
  return methods;
}
 

@Override
protected void prepare() {
    super.prepare();

    // Initialize everything
    closed = new TCustomHashSet<int[]>(new ArrayHashingStrategy()); // Parent set already seen
    open = new TreeSet<OpenParentSet>(); // Parent set to evaluate

    if (max_pset_size <= 1) {
        return;
    }

    // Consider all two-parent set for evaluation
    for (int i = 0; i < parents.length; i++) {
        for (int j = i + 1; j < parents.length; j++) {

            addParentSetToEvaluate(new int[] { parents[i]}, parents[j],
                    null);
        }
    }

}
 

@Test
public void testDifferentGroup() {
    Node n1 = new Node(ip1, port1);
    Node n2 = new Node(ip1, port2);

    Node n3 = new Node(ip1, port1);
    Node n4 = new Node(ip1, "3002");

    TreeSet<Node> set = new TreeSet<>();
    TreeSet<Node> set2 = new TreeSet<>();
    set.add(n1);
    set.add(n2);
    set2.add(n3);
    set2.add(n4);
    Group g1 = new Group(new Configuration(), n1, n2);
    Group g2 = new Group(new Configuration(), n3, n4);
    Assert.assertTrue(n1.equals(n3));
    Assert.assertTrue(g1.hashCode() != g2.hashCode());
    Assert.assertTrue(!g1.equals(g2));
}
 

SerialCenterIntensity(RadiusNeighbors nbrs) {
	
	LogTimer timer;
	
	// Now get single seed members
	MeanShiftSeed sd;
	this.computedSeeds = new TreeSet<>();
	final double[][] X = data.getData();
	
	int idx = 0;
	for(double[] seed: seeds) {
		idx++;
		timer = new LogTimer();
		sd = singleSeed(seed, nbrs, X, maxIter);
		
		if(null == sd)
			continue;
		
		computedSeeds.add(sd);
		itrz = FastMath.max(itrz, sd.iterations);
		
		// If it actually converged, add the summary
		summaries.add(new SummaryLite(
			"Kernel "+(idx - 1), sd.iterations, 
			timer.formatTime(), timer.wallTime()
		));
	}
}
 

/**
 * @see HttpServlet#doGet(HttpServletRequest request, HttpServletResponse response)
 */
protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
	HttpSession session = ((HttpServletRequest)request).getSession(true);
	synchronized (session) {
		session.setMaxInactiveInterval(300);
		
		String url = ((HttpServletRequest)request).getRequestURL().toString();
		String font = url.substring(url.lastIndexOf("/") + 1).replace('_', ' ');

		int substr_end= font.indexOf(";jsessionid", 0);
		if(substr_end > -1){
			//Trim off jsessionid if present
			font = font.substring(0, substr_end);
		}
		if(expectedFonts.contains(font)){
			//System.out.println("Requested: " + font);
			TreeSet<String> fontsNotRequested = (TreeSet<String>)session.getAttribute("fontsNotRequested");
			if(fontsNotRequested == null){
				fontsNotRequested = new TreeSet<String>(expectedFonts);
				session.setAttribute("fontsNotRequested", fontsNotRequested);
			}
			
			fontsNotRequested.remove(font);
		}
		response.sendError(404);
	}
}
 

@Override
public String getLSTformat(boolean useAny)
{
	Set<PrimitiveCollection<? super T>> sortSet = new TreeSet<>(PrimitiveUtilities.COLLECTION_SORTER);
	sortSet.addAll(filterSet);
	return "ALL|!" + PrimitiveUtilities.joinLstFormat(sortSet, "|!", useAny);
}
 

/** Requests the domain assignments for the current PDB IDs from the PDB.
 * @throws IOException if the server cannot be reached
 *
 */
private void loadRepresentativeDomainAssignments() throws IOException {
	AssignmentXMLSerializer results = null;
	try {
		URL u = new URL(url + "getRepresentativeDomains");
		logger.info("Fetching {}",u);
		InputStream response = URLConnectionTools.getInputStream(u);
		String xml = JFatCatClient.convertStreamToString(response);
		results  = AssignmentXMLSerializer.fromXML(xml);

		Map<String,String> data = results.getAssignments();
		logger.info("got {} ranges from server.",data.size());
		for (String key: data.keySet()){
			String range = data.get(key);

			// work around list in results;

			String[] spl = range.split(",");
			SortedSet<String> value = new TreeSet<String>();

			for (String s : spl){
				value.add(s);

			}
			serializedCache.put(key, value);
		}

	} catch (MalformedURLException e){
		logger.error("Malformed Domain server: "+url,e);
		throw new IllegalArgumentException("Invalid Server: "+url, e);
	}
}
 

/**
 * Creates a MetadataImpl.
 *
 * @param sqlParser Parser
 */
public MetadataImpl(SqlAbstractParserImpl sqlParser) {
  initList(sqlParser, reservedFunctionNames, "ReservedFunctionName");
  initList(sqlParser, contextVariableNames, "ContextVariable");
  initList(sqlParser, nonReservedKeyWordSet, "NonReservedKeyWord");
  tokenList = ImmutableList.copyOf(tokenSet);
  sql92ReservedWords = constructSql92ReservedWordList();
  Set<String> reservedWordSet = new TreeSet<>();
  reservedWordSet.addAll(tokenSet);
  reservedWordSet.removeAll(nonReservedKeyWordSet);
  reservedWords.addAll(reservedWordSet);
}
 

private static SortedSet<Map.Entry<List<String>, List<Double>>> sortByValue(
                                                                            Map<List<String>, List<Double>> mapForSort,
                                                                            List<SortOption> sortOptions) {
    SortedSet<Map.Entry<List<String>, List<Double>>> sortedEntries = new TreeSet<Map.Entry<List<String>, List<Double>>>(
        new MapEntryComparator(sortOptions));
    sortedEntries.addAll(mapForSort.entrySet());
    return sortedEntries;
}
 

/**
 * generate report
 * @param assignment current assignment
 * @return resultant report
 */
public CSVFile report(Assignment<Exam, ExamPlacement> assignment) {
    CSVFile csv = new CSVFile();
    csv.setHeader(new CSVField[] { new CSVField("Exam"), new CSVField("Enrl"), new CSVField("Period"),
            new CSVField("Date"), new CSVField("Time"), new CSVField("Room 1"), new CSVField("Cap 1"),
            new CSVField("Room 2"), new CSVField("Cap 2"), new CSVField("Room 3"), new CSVField("Cap 3"),
            new CSVField("Room 4"), new CSVField("Cap 4") });
    for (Exam exam : iModel.variables()) {
        ExamPlacement placement = assignment.getValue(exam);
        if (placement == null || placement.getRoomPlacements().size() <= 1)
            continue;
        List<CSVField> fields = new ArrayList<CSVField>();
        fields.add(new CSVField(exam.getName()));
        fields.add(new CSVField(exam.getStudents().size()));
        fields.add(new CSVField(placement.getPeriod().getIndex() + 1));
        fields.add(new CSVField(placement.getPeriod().getDayStr()));
        fields.add(new CSVField(placement.getPeriod().getTimeStr()));
        TreeSet<ExamRoomPlacement> rooms = new TreeSet<ExamRoomPlacement>(new ExamRoomComparator(exam, false));
        rooms.addAll(placement.getRoomPlacements());
        for (ExamRoomPlacement room : rooms) {
            fields.add(new CSVField(room.getName()));
            fields.add(new CSVField(room.getSize(exam.hasAltSeating())));
        }
        csv.addLine(fields);
    }
    return csv;
}
 

public void printReport(ExamInstructorInfo instructor) throws DocumentException {
    TreeSet<ExamAssignmentInfo> exams = new TreeSet();
    for (ExamAssignmentInfo exam:getExams()) {
        if (exam.getPeriod()==null) continue;
        if (exam.getInstructors().contains(instructor));
    }
    if (exams.isEmpty()) return;
    printHeader();
    printReport(instructor, exams);
    lastPage();
}
 

public Set<String> getTableBlackList(String username, Set<String> groups) {
    Set<String> tableBlackList = new TreeSet<>(String.CASE_INSENSITIVE_ORDER);
    tableBlackList.addAll(userTableBlackList.getTableBlackList(username));
    //if user is in group, add group's black list
    for (String group : groups) {
        tableBlackList.addAll(groupTableBlackList.getTableBlackList(group));
    }
    return tableBlackList;
}
 

private void getTestsOnly(String dir, Node root, Document doc, String type, ConnectorHelper ch) {
   	
       List myTests = null;
       String siteId = null;
    	String[] f = dir.split("/");
      	siteId = f[2];

SortedSet<Element> sortedItems = new TreeSet<Element>(new SortElementsForDisplay());

       Element assessments=doc.createElement("Assessments");
       root.appendChild(assessments);
       myTests = ch.getPublishedAssements(siteId);
       Iterator assessmentIterator = myTests.iterator();
       while(assessmentIterator.hasNext()){
     	  String[] thisAssessmentReference = (String[]) assessmentIterator.next();
      	   	Element element=doc.createElement("Assessment");
        	   	element.setAttribute("name",thisAssessmentReference[0]);
        	   	element.setAttribute("url",serverUrlPrefix + thisAssessmentReference[1]);
        	   	element.setAttribute("size", "0");
        	   	sortedItems.add(element);           	  
       }

for (Element item: sortedItems) {
	assessments.appendChild(item);
}

   }