/**
* Private helper method for performing fast intersection.
*
* @param <E>
* @param sortedData
* @param sortedQueries
* @param result
*/
private static <E extends Comparable<E>> void fastIntersect(
List<E> sortedData, List<E> sortedQueries, SortedSet<E> result) {
int medianQueryIndex = sortedQueries.size() / 2;
E medianQuery = sortedQueries.get(medianQueryIndex);
int index = Collections.binarySearch(sortedData, medianQuery);
if (index >= 0) {
result.add(medianQuery);
} else {
index = (-1 * index) + 1;
}
if (index - 1 >= 0 && medianQueryIndex - 1 >= 0) {
fastIntersect(
sortedData.subList(0, index), sortedQueries.subList(0, medianQueryIndex), result);
}
if (index + 1 < sortedData.size() && medianQueryIndex + 1 < sortedQueries.size()) {
fastIntersect(
sortedData.subList(index + 1, sortedData.size()),
sortedQueries.subList(medianQueryIndex + 1, sortedQueries.size()),
result);
}
}
/** @tests java.util.TreeSet#add(java.lang.Object) */
public void test_addLjava_lang_Object() {
// Test for method boolean java.util.TreeSet.add(java.lang.Object)
ts.add(new Integer(-8));
assertTrue("Failed to add Object", ts.contains(new Integer(-8)));
ts.add(objArray[0]);
assertTrue("Added existing element", ts.size() == objArray.length + 1);
}
/**
* Takes a potentially non-sequential alignment and guesses a sequential version of it. Residues
* from each structure are sorted sequentially and then compared directly.
*
* <p>The results of this method are consistent with what one might expect from an identity
* function, and are therefore useful with {@link #getSymmetryOrder(Map, Map identity, int,
* float)}.
*
* <ul>
* <li>Perfect self-alignments will have the same pre-image and image, so will map X->X
* <li>Gaps and alignment errors will cause errors in the resulting map, but only locally.
* Errors do not propagate through the whole alignment.
* </ul>
*
* <h4>Example:</h4>
*
* A non sequential alignment, represented schematically as
*
* <pre>
* 12456789
* 78912345</pre>
*
* would result in a map
*
* <pre>
* 12456789
* 12345789</pre>
*
* @param alignment The non-sequential input alignment
* @param inverseAlignment If false, map from structure1 to structure2. If true, generate the
* inverse of that map.
* @return A mapping from sequential residues of one protein to those of the other
* @throws IllegalArgumentException if the input alignment is not one-to-one.
*/
public static Map<Integer, Integer> guessSequentialAlignment(
Map<Integer, Integer> alignment, boolean inverseAlignment) {
Map<Integer, Integer> identity = new HashMap<Integer, Integer>();
SortedSet<Integer> aligned1 = new TreeSet<Integer>();
SortedSet<Integer> aligned2 = new TreeSet<Integer>();
for (Entry<Integer, Integer> pair : alignment.entrySet()) {
aligned1.add(pair.getKey());
if (!aligned2.add(pair.getValue()))
throw new IllegalArgumentException(
"Alignment is not one-to-one for residue "
+ pair.getValue()
+ " of the second structure.");
}
Iterator<Integer> it1 = aligned1.iterator();
Iterator<Integer> it2 = aligned2.iterator();
while (it1.hasNext()) {
if (inverseAlignment) { // 2->1
identity.put(it2.next(), it1.next());
} else { // 1->2
identity.put(it1.next(), it2.next());
}
}
return identity;
}
public static File[] getDirectoryListing(File dir) {
SortedSet<File> dirSet = new TreeSet<File>();
SortedSet<File> fileSet = new TreeSet<File>();
File[] files = dir.listFiles();
for (int i = 0; i < files.length; i++) {
if (files[i].isDirectory()) dirSet.add(files[i]);
else fileSet.add(files[i]);
}
List<File> fileList = new LinkedList<File>();
fileList.addAll(dirSet);
fileList.addAll(fileSet);
return fileList.toArray(new File[] {});
}
public static void main(String[] args) {
System.setProperty("fr.umlv.jbucks.factory", BuckFactoryImpl.class.getName());
BuckFactory factory = BuckFactory.getFactory();
Book book = factory.createBook("test");
System.out.println(book.getName());
book.setUserData("hello-UID", "12345");
System.out.println("hello-UID " + book.getUserDataValue("hello-UID"));
EventManager manager = factory.getEventManager();
manager.addListener(
Book.class,
"accounts",
PropertyEvent.TYPE_PROPERTY_ADDED | PropertyEvent.TYPE_PROPERTY_REMOVED,
new PropertyListener() {
public void propertyChanged(PropertyEvent event) {
System.out.println(event);
}
});
Account account = factory.createAccount(book, "remi");
factory.createAccount(book, "gilles");
List list = book.getAccounts();
System.out.println(list);
SortedSet transactions = account.getTransactions();
manager.addListener(
Account.class,
"transactions",
PropertyEvent.TYPE_PROPERTY_ADDED | PropertyEvent.TYPE_PROPERTY_REMOVED,
new PropertyListener() {
public void propertyChanged(PropertyEvent event) {
System.out.println("transaction " + event);
}
});
Transaction transaction =
factory.createTransaction(new Date().getTime(), Collections.EMPTY_LIST);
transactions.add(transaction);
SortedSet tailSet = transactions.tailSet(transaction);
System.out.println(tailSet);
tailSet.add(factory.createTransaction(transaction.getDate() + 1, Collections.EMPTY_LIST));
}
/**
* Converts the form field values in the <tt>ffValuesIter</tt> into a caps string.
*
* @param ffValuesIter the {@link Iterator} containing the form field values.
* @param capsBldr a <tt>StringBuilder</tt> to which the caps string representing the form field
* values is to be appended
*/
private static void formFieldValuesToCaps(Iterator<String> ffValuesIter, StringBuilder capsBldr) {
SortedSet<String> fvs = new TreeSet<String>();
while (ffValuesIter.hasNext()) fvs.add(ffValuesIter.next());
for (String fv : fvs) capsBldr.append(fv).append('<');
}
/** Set the contents of the field selector list. */
private void setupFieldSelector() {
fieldListModel.clear();
SortedSet<String> contents = new TreeSet<String>();
for (String s : metaData) {
if (s.startsWith(Globals.SELECTOR_META_PREFIX)) {
contents.add(s.substring(Globals.SELECTOR_META_PREFIX.length()));
}
}
if (contents.size() == 0) {
// if nothing was added, put the default fields (as described in the help)
fieldListModel.addElement("author");
fieldListModel.addElement("journal");
fieldListModel.addElement("keywords");
fieldListModel.addElement("publisher");
} else {
for (String s : contents) {
fieldListModel.addElement(s);
}
}
if (currentField == null) {
// if dialog is created for the whole database,
// select the first field to avoid confusions in GUI usage
fieldList.setSelectedIndex(0);
} else {
// a specific field has been chosen at the constructur
// select this field
int i = fieldListModel.indexOf(currentField);
if (i != -1) {
// field has been found in list, select it
fieldList.setSelectedIndex(i);
}
}
}
public static void RetrieveTrainMatrix() {
try {
BufferedReader flrdr =
new BufferedReader(
new FileReader("D:\\IR\\Assignment7\\Pytest\\part2\\output\\train_matrix.txt"));
String line = "";
int doc_count = 0;
while ((line = flrdr.readLine()) != null) {
SortedSet<Integer> word_ids = new TreeSet<Integer>();
int val_count = 0;
String[] key_value = line.split(" :: ");
key_value[1] = key_value[1].substring(1, key_value[1].length() - 2);
String[] values = key_value[1].split(",");
FeatureNode[] node = new FeatureNode[values.length];
for (String val : values) word_ids.add(Integer.parseInt(val.trim()));
for (int val : word_ids) node[val_count++] = new FeatureNode(val, 1);
if (spam_docs.contains(key_value[0].trim())) ylable[doc_count] = 1;
else ylable[doc_count] = 0;
train_matrix[doc_count++] = node;
}
flrdr.close();
} catch (Exception e) {
e.printStackTrace();
System.exit(0);
}
}
private void addRestriction(String name) {
this.rowCount++;
this.slackCount++;
String slackName = "SLC" + slackCount;
columns.add(slackName);
writeToFile(name, slackName, Fraction.ONE);
}
@SuppressWarnings("EmptyCatchBlock")
static void ensureNotDirectlyModifiable(SortedSet<Integer> unmod) {
try {
unmod.add(4);
fail("UnsupportedOperationException expected");
} catch (UnsupportedOperationException expected) {
}
try {
unmod.remove(4);
fail("UnsupportedOperationException expected");
} catch (UnsupportedOperationException expected) {
}
try {
unmod.addAll(Collections.singleton(4));
fail("UnsupportedOperationException expected");
} catch (UnsupportedOperationException expected) {
}
try {
Iterator<Integer> iterator = unmod.iterator();
iterator.next();
iterator.remove();
fail("UnsupportedOperationException expected");
} catch (UnsupportedOperationException expected) {
}
}
public List<Locale> getAvailableLanguages() {
Locale[] locales = Locale.getAvailableLocales();
Map<String, Locale> localeMap = new HashMap<String, Locale>();
// remove all variants
for (Locale locale : locales) {
if (isTranslationsOnly()
&& !ArrayUtils.contains(config.getAvailableTranslations(), locale.getLanguage())) {
continue;
}
if (localeMap.containsKey(locale.getLanguage())
&& locale.getDisplayName().indexOf('(') != -1) {
continue;
}
localeMap.put(locale.getLanguage(), locale);
}
SortedSet<Locale> localeSet =
new TreeSet<Locale>(new LocaleComparator(LocaleComparator.CompareType.LANGUAGE));
for (Locale locale : localeMap.values()) {
localeSet.add(locale);
}
return new ArrayList<Locale>(localeSet);
}
private void calculateArrowsForward(Node x, Node y, Graph graph) {
clearArrow(x, y);
if (!knowledgeEmpty()) {
if (getKnowledge().isForbidden(x.getName(), y.getName())) {
return;
}
}
List<Node> naYX = getNaYX(x, y, graph);
List<Node> t = getTNeighbors(x, y, graph);
DepthChoiceGenerator gen = new DepthChoiceGenerator(t.size(), t.size());
int[] choice;
while ((choice = gen.next()) != null) {
List<Node> s = GraphUtils.asList(choice, t);
if (!knowledgeEmpty()) {
if (!validSetByKnowledge(y, s)) {
continue;
}
}
double bump = insertEval(x, y, s, naYX, graph);
if (bump > 0.0) {
Arrow arrow = new Arrow(bump, x, y, s, naYX);
sortedArrows.add(arrow);
addLookupArrow(x, y, arrow);
}
}
}
public static void main(String[] args) throws Exception {
// TODO Auto-generated method stub
Date startTime = new Date();
String fname = "p079_keylog.txt";
FileReader fr = new FileReader(fname);
BufferedReader br = new BufferedReader(fr);
SortedSet<String> slines = new TreeSet<String>();
String line = "";
while ((line = br.readLine()) != null) {
slines.add(line);
}
String start = slines.first().split("")[0];
String ans = "";
for (String l : slines) {
// System.out.println(l);
for (String l2 : slines) {
if (l2.contains(start) && l2.indexOf(start) > 0) start = l2.split("")[0];
}
}
ans += start;
// System.out.println(ans);
for (int i = 0; i < 10; i++) {
start = (getNext(slines, start));
if (start == null) break;
ans += start;
// System.out.println(ans);
}
Date endTime = new Date();
System.out.println(ans + " in " + (endTime.getTime() - startTime.getTime()) + " ms.");
}
/**
* Gets the unique read groups in the table
*
* @param report the GATKReport containing the table with RecalUtils.READGROUP_REPORT_TABLE_TITLE
* @return the unique read groups
*/
private static SortedSet<String> getReadGroups(final GATKReport report) {
final GATKReportTable reportTable = report.getTable(RecalUtils.READGROUP_REPORT_TABLE_TITLE);
final SortedSet<String> readGroups = new TreeSet<String>();
for (int i = 0; i < reportTable.getNumRows(); i++)
readGroups.add(reportTable.get(i, RecalUtils.READGROUP_COLUMN_NAME).toString());
return readGroups;
}
@SuppressWarnings("unchecked")
public List<ChoiceListValue> getChoiceListValues(
ExtendedPropertyDefinition epd,
String param,
List<ChoiceListValue> values,
Locale locale,
Map<String, Object> context) {
final SortedSet<ChoiceListValue> listValues = new TreeSet<ChoiceListValue>();
if (StringUtils.isEmpty(param)) {
param = "jmix:editorialContent";
}
try {
String includedTypes = StringUtils.substringBefore(param, ";");
Set<String> excludedTypes = new HashSet<String>();
String exclusion = StringUtils.substringAfter(param, ";");
if (StringUtils.isNotBlank(exclusion)) {
excludedTypes.addAll(
CollectionUtils.collect(
Arrays.asList(StringUtils.substringAfter(param, ";").split(",")),
new Transformer() {
public Object transform(Object input) {
return ((String) input).trim();
}
}));
}
for (String nodeTypeName : includedTypes.split(",")) {
nodeTypeName = nodeTypeName.trim();
ExtendedNodeType nodeType = NodeTypeRegistry.getInstance().getNodeType(nodeTypeName);
if (!isExcludedType(nodeType, excludedTypes)) {
listValues.add(new ChoiceListValue(nodeType.getLabel(locale), nodeType.getName()));
}
NodeTypeIterator nti = nodeType.getSubtypes();
while (nti.hasNext()) {
ExtendedNodeType type = (ExtendedNodeType) nti.next();
if (!isExcludedType(type, excludedTypes)) {
listValues.add(new ChoiceListValue(type.getLabel(locale), type.getName()));
}
}
}
} catch (NoSuchNodeTypeException e) {
logger.error("Cannot get type", e);
}
return new LinkedList<ChoiceListValue>(listValues);
}
public void registerValue(String column, String row, double value) {
Fraction fraction = toFraction(value);
if (toReverse.contains(row)) {
fraction = fraction.negate();
}
columns.add(column);
writeToFile(row, column, fraction);
}
static SortedSet<TypeColorEntry> fromPainter(myjava.gui.syntax.Painter painter) {
Token.Type[] types = Token.Type.values();
SortedSet<TypeColorEntry> entries = new TreeSet<>();
for (Token.Type type : types) {
entries.add(new TypeColorEntry(type, painter.fromType(type)));
}
return entries;
}
private Set<Sector> getNeighbors(Sector[] sectors) {
SortedSet<Sector> neighbors = new TreeSet<Sector>(ELEMENT_ORDER);
for (Sector s : sectors) {
if (s != null) {
neighbors.add(s);
}
}
return neighbors;
}
/** @return the repeatable scripts that failed during the last database update */
protected SortedSet<ExecutedScript> getRepeatableScriptsThatFailedDuringLastUpdate() {
SortedSet<ExecutedScript> failedExecutedScripts = new TreeSet<ExecutedScript>();
for (ExecutedScript script : executedScriptInfoSource.getExecutedScripts()) {
if (!script.isSuccessful() && script.getScript().isRepeatable()) {
failedExecutedScripts.add(script);
}
}
return failedExecutedScripts;
}
/**
* Sets up the fixture, for example, open a network connection. This method is called before a
* test is executed.
*/
public void setUp() throws Exception {
super.setUp();
db = newBaseRecordManager();
ts = db.createTreeSet("testBTreeSet");
for (int i = 0; i < objArray.length; i++) {
Object x = objArray[i] = new Integer(i);
ts.add(x);
}
}
@Test
public void simpleQueryWithRangeTombstoneTest() throws Exception {
Table table = Table.open(KSNAME);
ColumnFamilyStore cfs = table.getColumnFamilyStore(CFNAME);
// Inserting data
String key = "k1";
RowMutation rm;
ColumnFamily cf;
rm = new RowMutation(KSNAME, ByteBufferUtil.bytes(key));
for (int i = 0; i < 40; i += 2) add(rm, i, 0);
rm.apply();
cfs.forceBlockingFlush();
rm = new RowMutation(KSNAME, ByteBufferUtil.bytes(key));
cf = rm.addOrGet(CFNAME);
delete(cf, 10, 22, 1);
rm.apply();
cfs.forceBlockingFlush();
rm = new RowMutation(KSNAME, ByteBufferUtil.bytes(key));
for (int i = 1; i < 40; i += 2) add(rm, i, 2);
rm.apply();
cfs.forceBlockingFlush();
rm = new RowMutation(KSNAME, ByteBufferUtil.bytes(key));
cf = rm.addOrGet(CFNAME);
delete(cf, 19, 27, 3);
rm.apply();
// We don't flush to test with both a range tomsbtone in memtable and in sstable
QueryPath path = new QueryPath(CFNAME);
// Queries by name
int[] live = new int[] {4, 9, 11, 17, 28};
int[] dead = new int[] {12, 19, 21, 24, 27};
SortedSet<ByteBuffer> columns = new TreeSet<ByteBuffer>(cfs.getComparator());
for (int i : live) columns.add(b(i));
for (int i : dead) columns.add(b(i));
cf = cfs.getColumnFamily(QueryFilter.getNamesFilter(dk(key), path, columns));
for (int i : live) assert isLive(cf, cf.getColumn(b(i))) : "Column " + i + " should be live";
for (int i : dead)
assert !isLive(cf, cf.getColumn(b(i))) : "Column " + i + " shouldn't be live";
// Queries by slices
cf =
cfs.getColumnFamily(
QueryFilter.getSliceFilter(dk(key), path, b(7), b(30), false, Integer.MAX_VALUE));
for (int i : new int[] {7, 8, 9, 11, 13, 15, 17, 28, 29, 30})
assert isLive(cf, cf.getColumn(b(i))) : "Column " + i + " should be live";
for (int i : new int[] {10, 12, 14, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27})
assert !isLive(cf, cf.getColumn(b(i))) : "Column " + i + " shouldn't be live";
}
/**
* The earliest start date of this research staff.
*
* @return the active date
*/
@Transient
public Date getActiveDate() {
SortedSet<Date> dates = new TreeSet<Date>();
for (SiteResearchStaff srs : this.getSiteResearchStaffs()) {
Date activeDate = srs.getActiveDate();
if (activeDate != null) dates.add(activeDate);
}
if (dates.size() > 0) return dates.first();
else return null;
}
@Override
protected SortedSet<Long> compute() {
SortedSet<Long> index = new TreeSet<>();
try {
if (length < threshold) {
BufferedAccessFile raf = null;
try {
raf = new BufferedAccessFile(file, "r");
raf.seek(start);
// Add the position for 1st line
if (raf.getFilePointer() == 0L) {
index.add(raf.getFilePointer());
}
while (raf.getFilePointer() < end) {
raf.getNextLine();
index.add(raf.getFilePointer());
}
} finally {
if (raf != null) {
raf.close();
}
}
} else {
long start1 = start;
long end1 = start + (length / 2);
long end2 = end;
IndexingTask task1 = new IndexingTask(file, start1, end1, threshold);
task1.fork();
IndexingTask task2 = new IndexingTask(file, end1, end2, threshold);
index.addAll(task2.compute());
index.addAll(task1.join());
}
} catch (IOException ex) {
throw new FileReaderException("Error while index file:" + ex.getMessage(), ex);
}
return index;
}
// assumes o is in satisfiers \ exceptions
private int getIndexInPOPApp(ObjectSet satisfiers, Set exceptions, Object o) {
SortedSet exceptionIndices = new TreeSet();
for (Iterator iter = exceptions.iterator(); iter.hasNext(); ) {
Object exception = iter.next();
exceptionIndices.add(new Integer(satisfiers.indexOf(exception)));
}
int origIndex = satisfiers.indexOf(o);
int numExceptionsBefore = exceptionIndices.headSet(new Integer(origIndex)).size();
return (origIndex - numExceptionsBefore);
}
/** Scratch method for Lane to work on Fast Intersection */
public static void fastIntersection() {
SortedSet<Integer> setA = new TreeSet<Integer>();
SortedSet<Integer> setB = new TreeSet<Integer>();
Random rand = new Random();
for (int i = 0; i < 100000; i++) {
setA.add(rand.nextInt());
}
List<Integer> dataSet = new ArrayList<Integer>(setA);
for (int i = 0; i < 50; i++) {
setB.add(rand.nextInt());
setB.add(dataSet.get(rand.nextInt(setA.size())));
}
List<Integer> querySet = new ArrayList<Integer>(setB);
// for (int i=0, n=dataSet.size(); i < n; i++, n++) dataSet.get(i);
// Calculate intersection
// List<Integer> intersection = new ArrayList<Integer>();
/*
for (int query : querySet) {
//System.out.println("Querying for " + query);
if (Collections.binarySearch(dataSet, query) >= 0) {
intersection.add(query);
}
}
*/
SortedSet<Integer> intersection = new TreeSet<Integer>();
fastIntersect(dataSet, querySet, intersection);
System.out.println(intersection.size());
// int medianQuery = querySet.get(querySet.size()/2);
}
@Test
public void initConstructor() {
WatchListItem watchListItem1 = new WatchListItem("AAPL");
WatchListItem watchListItem2 = new WatchListItem("ORCL");
SortedSet<WatchListItem> techList = new TreeSet<WatchListItem>();
techList.add(watchListItem1);
techList.add(watchListItem2);
WatchList watchList = new WatchList("technology", techList);
watchList.getItems().add(watchListItem1);
watchList.getItems().add(watchListItem2);
}
/**
* Returns all supported sample rates.
*
* @return an array of sample rates, in Hertz, never <code>null</code>.
*/
public Integer[] getSampleRates() {
final String rawValue = this.properties.get(DEVICE_SAMPLERATES);
final String[] values = rawValue.split(",\\s*");
final SortedSet<Integer> result =
new TreeSet<Integer>(
NumberUtils.<Integer>createNumberComparator(false /* aSortAscending */));
for (String value : values) {
result.add(Integer.valueOf(value.trim()));
}
return result.toArray(new Integer[result.size()]);
}
/** @tests java.util.TreeSet#TreeSet(java.util.Comparator) */
public void test_ConstructorLjava_util_Comparator() {
// Test for method java.util.TreeSet(java.util.Comparator)
SortedSet myTreeSet = db.createTreeSet("test", new ReversedIntegerComparator(), null);
assertTrue("Did not construct correct TreeSet", myTreeSet.isEmpty());
myTreeSet.add(new Integer(1));
myTreeSet.add(new Integer(2));
assertTrue(
"Answered incorrect first element--did not use custom comparator ",
myTreeSet.first().equals(new Integer(2)));
assertTrue(
"Answered incorrect last element--did not use custom comparator ",
myTreeSet.last().equals(new Integer(1)));
}
private void storeGraph(Graph graph) {
if (numPatternsToStore < 1) return;
if (topGraphs.isEmpty() || score > topGraphs.first().getScore()) {
Graph graphCopy = new EdgeListGraphSingleConnections(graph);
topGraphs.add(new ScoredGraph(graphCopy, score));
if (topGraphs.size() > getNumPatternsToStore()) {
topGraphs.remove(topGraphs.first());
}
}
}
private void configChanged(String activeConfig) {
DefaultComboBoxModel model = new DefaultComboBoxModel();
model.addElement("");
SortedSet<String> alphaConfigs =
new TreeSet<String>(
new Comparator<String>() {
Collator coll = Collator.getInstance();
public int compare(String s1, String s2) {
return coll.compare(label(s1), label(s2));
}
private String label(String c) {
Map<String, String> m = configs.get(c);
String label = m.get("$label"); // NOI18N
return label != null ? label : c;
}
});
for (Map.Entry<String, Map<String, String>> entry : configs.entrySet()) {
String config = entry.getKey();
if (config != null && entry.getValue() != null) {
alphaConfigs.add(config);
}
}
for (String c : alphaConfigs) {
model.addElement(c);
}
configCombo.setModel(model);
configCombo.setSelectedItem(activeConfig != null ? activeConfig : "");
Map<String, String> m = configs.get(activeConfig);
Map<String, String> def = configs.get(null);
if (m != null) {
// BEGIN Deprecated
if (compProviderDeprecated != null) {
compProviderDeprecated.configUpdated(m);
}
// END Deprecated
for (J2SECategoryExtensionProvider compProvider : compProviders) {
compProvider.configUpdated(m);
}
for (int i = 0; i < data.length; i++) {
String v = m.get(keys[i]);
if (v == null) {
// display default value
v = def.get(keys[i]);
}
data[i].setText(v);
}
} // else ??
configDel.setEnabled(activeConfig != null);
}
