public SelectMany05Bean() {
HobbitBean[] hobbits = {
new HobbitBean("Bilbo", "Ring Finder"),
new HobbitBean("Frodo", "Ring Bearer"),
new HobbitBean("Merry", "Trouble Maker"),
new HobbitBean("Pippin", "Trouble Maker")
};
Set<SelectItem> items = new LinkedHashSet<SelectItem>();
for (HobbitBean hobbit : hobbits) {
items.add(new SelectItem(hobbit.getName()));
}
hobbitCollection = new TreeSet<HobbitBean>();
hobbitCollection.addAll(Arrays.asList(hobbits));
possibleValues = Collections.unmodifiableSet(items);
initialSortedSetValues = new TreeSet<String>(Collections.reverseOrder());
initialSortedSetValues.add("Pippin");
initialSortedSetValues.add("Frodo");
initialCollectionValues = new LinkedHashSet<String>(2);
initialCollectionValues.add("Bilbo");
initialCollectionValues.add("Merry");
initialSetValues = new CopyOnWriteArraySet<String>(); // not Cloneable
initialSetValues.add("Frodo");
initialListValues = new Vector<String>();
initialListValues.add("Bilbo");
initialListValues.add("Pippin");
initialListValues.add("Merry");
hobbitDataModel =
new ListDataModel<HobbitBean>(new ArrayList<HobbitBean>(Arrays.asList(hobbits)));
}
@Test
@SuppressWarnings("unchecked")
public void edit() throws Exception {
final DocumentClass documentClass = new DocumentClass("hello");
final DocumentReference documentReference =
newDocumentReference("hello.txt").withDocumentClass(documentClass).build();
when(documentService.findDocumentReference(1L)).thenReturn(documentReference);
SortedSet<Attribute> attributes = new TreeSet<>();
attributes.add(new Attribute("a", false, AttributeDataType.CURRENCY));
attributes.add(new Attribute("b", false, AttributeDataType.STRING));
when(documentService.findAttributes(documentClass)).thenReturn(attributes);
final ModelAndView modelAndView = controller.editDocument(1L);
assertThat(modelAndView.getViewName(), is("edit.doc"));
assertThat(modelAndView.getModel().size(), is(2));
assertThat(modelAndView.getModel().containsKey("doc"), is(true));
assertThat((DocumentReference) modelAndView.getModel().get("doc"), is(documentReference));
assertThat(modelAndView.getModel().containsKey("attributes"), is(true));
assertThat(((SortedSet<Attribute>) modelAndView.getModel().get("attributes")).size(), is(2));
InOrder order = inOrder(documentService);
order.verify(documentService).findDocumentReference(1L);
order.verify(documentService).findAttributes(documentReference.getDocumentClass());
order.verifyNoMoreInteractions();
}
/**
* 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;
}
@Test
public void getAutoCompletionHintsForMethodWhenJustAfterTheDot() throws Exception {
setupMocks("$key.", createTestVelocityContext("key", new TestClass()));
Hints expectedMethods =
new Hints()
.withHints(
new HintData("doWork", "doWork(...) AncillaryTestClass"),
new HintData("something", "something String"),
new HintData("getSomething", "getSomething(...) String"),
new HintData("method1", "method1(...)"),
new HintData("method2", "method2(...) String"));
setupMethodFinderMock(expectedMethods, "", TestClass.class);
String velocity = "{{velocity}}$key.";
Hints hints =
mocker
.getComponentUnderTest()
.getAutoCompletionHints(velocity.length(), "xwiki/2.0", velocity);
assertEquals(5, hints.getHints().size());
// Verify methods are returned sorted
SortedSet<HintData> expected = new TreeSet<HintData>();
expected.add(new HintData("doWork", "doWork(...) AncillaryTestClass"));
expected.add(new HintData("getSomething", "getSomething(...) String"));
expected.add(new HintData("method1", "method1(...)"));
expected.add(new HintData("method2", "method2(...) String"));
expected.add(new HintData("something", "something String"));
assertEquals(expected, hints.getHints());
}
public void testSetSortedSet() {
Iterator<Integer> i;
SortedSet<Integer> set = new TreeSet<Integer>();
set.add(Integer.valueOf(00));
set.add(Integer.valueOf(10));
set.add(Integer.valueOf(20));
set.add(Integer.valueOf(30));
set.add(Integer.valueOf(40));
this.list.set(set);
i = this.list.iterator();
assertTrue(i.hasNext());
assertEquals(Integer.valueOf(0), i.next());
assertTrue(i.hasNext());
assertEquals(Integer.valueOf(10), i.next());
assertTrue(i.hasNext());
assertEquals(Integer.valueOf(20), i.next());
assertTrue(i.hasNext());
assertEquals(Integer.valueOf(30), i.next());
assertTrue(i.hasNext());
assertEquals(Integer.valueOf(40), i.next());
assertFalse(i.hasNext());
}
public static List<Integer> findMinimumVisits(Interval[] intervals) {
SortedSet<Interval> left = new TreeSet<>(new LeftComp());
SortedSet<Interval> right = new TreeSet<>(new RightComp());
for (Interval interval : intervals) {
left.add(interval);
right.add(interval);
}
List<Integer> s = new ArrayList<>();
while (!left.isEmpty() && !right.isEmpty()) {
int b = right.first().right;
s.add(b);
// Removes the intervals which intersect with R.cbegin().
Iterator<Interval> it = left.iterator();
while (it.hasNext()) {
Interval interval = it.next();
if (interval.left > b) {
break;
}
right.remove(interval);
it.remove();
}
}
return s;
}
Collection<Point2DInt> cutPoints(LineSegmentInt original) {
// Log.println("original=" + original);
// Log.println("inflateX=" + inflateX);
// Log.println("inflateY=" + inflateY);
final SortedSet<Point2DInt> result =
new TreeSet<Point2DInt>(new Point2DIntComparatorDistance(original.getP1()));
if (original.isHorizontal() == false) {
for (InflateData x : inflateX) {
final LineSegmentInt vertical =
new LineSegmentInt(x.getPos(), original.getMinY(), x.getPos(), original.getMaxY());
final Point2DInt inter = original.getSegIntersection(vertical);
if (inter != null) {
result.add(inter);
}
}
}
if (original.isVertical() == false) {
for (InflateData y : inflateY) {
final LineSegmentInt horizontal =
new LineSegmentInt(original.getMinX(), y.getPos(), original.getMaxX(), y.getPos());
final Point2DInt inter = original.getSegIntersection(horizontal);
if (inter != null) {
result.add(inter);
}
}
}
return result;
}
/**
* Visits a class declaration.
*
* @param d the declaration to visit
*/
public void visitClassDeclaration(ClassDeclaration d) {
d.accept(pre);
SortedSet<Declaration> decls = new TreeSet<Declaration>(SourceOrderDeclScanner.comparator);
for (TypeParameterDeclaration tpDecl : d.getFormalTypeParameters()) {
decls.add(tpDecl);
}
for (FieldDeclaration fieldDecl : d.getFields()) {
decls.add(fieldDecl);
}
for (MethodDeclaration methodDecl : d.getMethods()) {
decls.add(methodDecl);
}
for (TypeDeclaration typeDecl : d.getNestedTypes()) {
decls.add(typeDecl);
}
for (ConstructorDeclaration ctorDecl : d.getConstructors()) {
decls.add(ctorDecl);
}
for (Declaration decl : decls) decl.accept(this);
d.accept(post);
}
private SortedSet<String> generateAllPrefixes() {
SortedSet<String> oldPrefs = new TreeSet<String>();
SortedSet<String> newPrefs = new TreeSet<String>();
SortedSet<String> dummySet;
oldPrefs.add("");
Alphabet alph = motifSearchSpace.getAlphabet();
for (int i = 0; i < prefixLength; i++) {
for (Character c : alph) {
for (String s : oldPrefs) {
newPrefs.add(s + c);
}
}
dummySet = oldPrefs;
oldPrefs = newPrefs;
newPrefs = dummySet;
newPrefs.clear();
}
return oldPrefs;
}
private void dispatchForExecution(Schedule schedule) {
long now = System.currentTimeMillis();
synchronized (timingQueue) {
if (timingQueue.size() == 0) {
long nextRun = schedule.nextRun(now);
if (nextRun < 0) {
return;
}
System.out.println("Next run at: " + new DateTime(nextRun));
timingQueue.add(new ScheduleTime(schedule.identity().get(), nextRun));
if (scheduleHandler == null) {
dispatchHandler();
}
} else {
ScheduleTime first = timingQueue.first();
long nextRun = schedule.nextRun(now);
if (nextRun < 0) {
return;
}
System.out.println("Next run at: " + new DateTime(nextRun));
timingQueue.add(new ScheduleTime(schedule.identity().get(), nextRun));
ScheduleTime newFirst = timingQueue.first();
if (!first.equals(newFirst)) {
// We need to restart the managementThread, which is currently waiting for a 'later' event
// to
// occur than the one that was just scheduled.
scheduleHandler.future.cancel(true);
dispatchHandler();
}
}
}
}
protected Map<Individual, SortedSet<Boolean>> getBooleanDatatypeMembersImpl(
DatatypeProperty datatypeProperty) throws ReasoningMethodUnsupportedException {
Map<Individual, SortedSet<Constant>> mapping = getDatatypeMembersImpl(datatypeProperty);
Map<Individual, SortedSet<Boolean>> ret = new TreeMap<Individual, SortedSet<Boolean>>();
for (Entry<Individual, SortedSet<Constant>> e : mapping.entrySet()) {
SortedSet<Constant> values = e.getValue();
SortedSet<Boolean> valuesBoolean = new TreeSet<Boolean>();
for (Constant c : values) {
String s = c.getLiteral();
if (s.equalsIgnoreCase("true")) {
valuesBoolean.add(true);
} else if (s.equalsIgnoreCase("false")) {
valuesBoolean.add(false);
} else {
logger.warn(
"Requested to parse boolean value of property "
+ datatypeProperty
+ ", but "
+ c
+ " could not be parsed successfully.");
}
}
ret.put(e.getKey(), valuesBoolean);
}
return ret;
}
@VisibleForTesting
static StripCapabilitiesResult stripCapabilities(
XmlElement configElement, Set<String> allCapabilitiesFromHello) {
// collect all namespaces
Set<String> foundNamespacesInXML = getNamespaces(configElement);
LOG.trace(
"All capabilities {}\nFound namespaces in XML {}",
allCapabilitiesFromHello,
foundNamespacesInXML);
// required are referenced both in xml and hello
SortedSet<String> requiredCapabilities = new TreeSet<>();
// can be removed
SortedSet<String> obsoleteCapabilities = new TreeSet<>();
for (String capability : allCapabilitiesFromHello) {
String namespace = capability.replaceAll("\\?.*", "");
if (foundNamespacesInXML.contains(namespace)) {
requiredCapabilities.add(capability);
} else {
obsoleteCapabilities.add(capability);
}
}
LOG.trace(
"Required capabilities {}, \nObsolete capabilities {}",
requiredCapabilities,
obsoleteCapabilities);
return new StripCapabilitiesResult(requiredCapabilities, obsoleteCapabilities);
}
@Override
public int complete(String buffer, int cursor, List<CharSequence> candidates) {
Bundle[] bundles = bundleContext.getBundles();
List<Long> bundleIds = new ArrayList<Long>();
for (Bundle b : bundles) {
if (matcher.bundleMatches(b)) {
bundleIds.add(b.getBundleId());
}
}
SortedSet<String> variants = new TreeSet<String>();
if (buffer.matches("^[0-9]+$")) {
for (Long l : bundleIds) {
variants.add(String.valueOf(l));
}
} else {
for (Long l : bundleIds) {
variants.add(bundleContext.getBundle(l).getSymbolicName());
}
}
if (buffer.isEmpty()) {
candidates.addAll(variants);
} else {
for (String match : variants.tailSet(buffer)) {
if (!match.startsWith(buffer)) {
break;
}
candidates.add(match.substring(buffer.length()));
}
}
return candidates.isEmpty() ? -1 : buffer.length();
}
/** @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);
}
private void setProps(ModelNode requestProperties) throws Exception {
props = new TreeSet<RequestProp>();
if (opName.equals("add")) {
UserObject usrObj = (UserObject) node.getUserObject();
props.add(
new RequestProp(
"/" + usrObj.getName() + "=<name>/",
"Resource name for the new " + usrObj.getName(),
true,
ModelType.STRING));
}
if (opName.equals("write-attribute") && node.isLeaf()) {
ModelNode nameNode = requestProperties.get("name");
nameNode
.get("type")
.set(ModelType.UNDEFINED); // undefined type will display as uneditable String
UserObject usrObj = (UserObject) node.getUserObject();
ModelNode nameNodeValue = new ModelNode();
nameNodeValue.set(usrObj.getName());
props.add(new RequestProp("name", requestProperties.get("name"), nameNodeValue));
ModelNode rscDesc =
cliGuiCtx.getExecutor().doCommand(node.addressPath() + ":read-resource-description");
ModelNode valueNode = rscDesc.get("result", "attributes", usrObj.getName());
valueNode.get("required").set(false); // value is never required for write-attribute
ModelNode valueNodeValue = usrObj.getBackingNode().get(usrObj.getName());
props.add(new RequestProp("value", valueNode, valueNodeValue));
return;
}
for (Property prop : requestProperties.asPropertyList()) {
props.add(new RequestProp(prop.getName(), prop.getValue(), null));
}
}
public StringToBoolean() {
$yes.add("yes");
$yes.add("y");
$yes.add("true");
$yes.add("ja");
$yes.add("on");
}
/**
* Saves a given graph to a dot file, it also creates the file, or overwrites the old one
*
* @param g : The jung graph to save
* @param filename : A string that points to the destination of the save
* @param labeler : A node object -> Node name converter object
* @param graphName : The name of the graph to export (usually this is set the project's name)
* @throws IOException On IO error
*/
public void save(Graph<V, E> g, String filename, Transformer<V, String> labeler, String graphName)
throws IOException {
SortedSet<V> nodes = new TreeSet<V>();
Map<V, SortedSet<V>> successors = new HashMap<V, SortedSet<V>>();
for (V source : g.getVertices()) {
Collection<V> actSuccessors = g.getSuccessors(source);
SortedSet<V> successorTree = new TreeSet<V>();
for (V destination : actSuccessors) {
successorTree.add(destination);
}
nodes.add(source);
successors.put(source, successorTree);
}
BufferedWriter writer =
new BufferedWriter(new OutputStreamWriter(new FileOutputStream(filename), "UTF-8"));
writer.write("digraph \"" + graphName + "\" {\n");
for (V from : nodes) {
Collection<V> actSuccessors = successors.get(from);
for (V to : actSuccessors) {
writer.write(
"\t\"" + labeler.transform(from) + "\" -> \"" + labeler.transform(to) + "\";\n");
}
if (g.getPredecessorCount(from) == 0 && actSuccessors.isEmpty()) {
writer.write("\t\"" + labeler.transform(from) + "\";\n");
}
}
writer.write("}");
writer.close();
}
public SortedSet<Grid> children() {
SortedSet<Grid> children = new TreeSet<Grid>();
Grid gridA, gridB;
int t = 0;
gridA = new Grid(this);
for (int i = 0; i < 4; i++) {
while (gridA.moveRight()) {
t++;
gridB = new Grid(gridA);
while (gridB.moveDown()) gridB.down++;
gridB.rotations = i;
gridB.translations = t;
children.add(gridB);
}
while (gridA.moveLeft()) {
t--;
gridB = new Grid(gridA);
while (gridB.moveDown()) gridB.down++;
gridB.rotations = i;
gridB.translations = t;
children.add(gridB);
}
gridA.turnClockwise();
}
return children;
}
/** @see de.interactive_instruments.ShapeChange.Model.ClassInfo#supertypes() */
public SortedSet<String> supertypes() {
// Convert base class object set to base class id set.
SortedSet<String> baseids = new TreeSet<String>();
if (baseclassInfo != null) baseids.add(baseclassInfo.id());
else if (baseclassInfoSet != null)
for (ClassInfoEA bci : baseclassInfoSet) baseids.add(bci.id());
return baseids;
} // supertypes()
/**
* @param version
* @return
* @see
* edu.utah.further.mdr.api.domain.asset.Asset#addVersion(edu.utah.further.mdr.api.domain.asset.Version)
*/
@Override
public void addVersion(final Version version) {
final Long versionId = (version == null) ? null : version.getId();
if (versionId != null) {
versionIdSet.add(versionId);
}
versionSet.add(version);
}
/**
* runs all the internal checks to verify that the job has been initialized
*
* @return true if the job was succesfully initialized
*/
private boolean runJobNotInitializedChecks() {
LOGGER.trace("runJobNotInitializedChecks [in]");
// capture all the start timestamps from the agents
final SortedSet<Timestamp> lStartTimeStamps = new TreeSet<Timestamp>();
// check all the control units
for (ProcessControlUnitWithMonitoring lUnit : mProcessUnits) {
// obtain status first, if the machine address has been set,
// it means it was initialized succesfully
final String lAgentID = lUnit.getAgentId();
LOGGER.trace("Checking machine address for unit [{}]", lAgentID);
if (lUnit.getMachineAddress() == null) {
// one single machine missing means that it hasn't been initialized
LOGGER.trace("Machine address not found found");
return false;
}
LOGGER.trace("[{}] Machine address found [{}]", lAgentID, lUnit.getMachineAddress());
// obtain test duration and start time
final Long lUnitTestDuration = lUnit.getDuration();
if (mTotalJobDuration == null
&& lUnitTestDuration != null) { // do this only if it hasn't been set before
LOGGER.trace("[{}] Setting test duration to [{}]", lAgentID, lUnitTestDuration);
mTotalJobDuration = lUnitTestDuration;
}
final Timestamp lUnitStartTimeStamp = lUnit.getStartTimestamp();
// tree set doesn't handle nulls very well
if (lUnitStartTimeStamp != null) {
LOGGER.trace("[{}] Setting initial timestamp [{}]", lAgentID, lUnitStartTimeStamp);
// add the start timestamp to the set
lStartTimeStamps.add(lUnitStartTimeStamp);
} else if (lUnit.getCurrentUserCount() != null && lUnit.getCurrentUserCount() > 0) {
final Timestamp lInitialTimestamp = new Timestamp(System.currentTimeMillis());
LOGGER.trace("[{}] Default initial timestamp to [{}]", lAgentID, lInitialTimestamp);
// if there are already users created,
// then this means this has already started
lStartTimeStamps.add(lInitialTimestamp);
}
}
// the biggest, or null if we don't have any start time yet
mJobStartTime = lStartTimeStamps.isEmpty() ? null : lStartTimeStamps.last();
mJobInitialized = mJobStartTime != null && mTotalJobDuration != null;
LOGGER.trace("Job has been initialized [{}]", mJobInitialized);
return mJobInitialized;
}
public void endElement(String uri, String name, String qName) {
if (qName.equals("MaxResults")) {
maxResults = Integer.parseInt(currentText.toString().trim());
} else if (qName.equals("Marker")) {
marker = currentText.toString().trim();
marker = (marker.equals("")) ? null : marker;
} else if (qName.equals("Prefix")) {
prefix = currentText.toString().trim();
prefix = (prefix.equals("")) ? null : prefix;
} else if (qName.equals("Delimiter")) {
delimiter = currentText.toString().trim();
delimiter = (delimiter.equals("")) ? null : delimiter;
} else if (qName.equals("NextMarker")) {
nextMarker = currentText.toString().trim();
nextMarker = (nextMarker.equals("")) ? null : nextMarker;
} else if (qName.equals("Blob")) {
ListableBlobProperties md =
new ListableBlobPropertiesImpl(
currentName,
currentUrl,
currentLastModified,
currentETag,
currentSize,
currentContentType,
currentContentEncoding,
currentContentLanguage);
blobMetadata.add(md);
currentName = null;
currentUrl = null;
currentLastModified = null;
currentETag = null;
currentSize = -1;
currentContentType = null;
currentContentEncoding = null;
currentContentLanguage = null;
} else if (qName.equals("Url")) {
currentUrl = URI.create(currentText.toString().trim());
} else if (qName.equals("LastModified")) {
currentLastModified = dateParser.rfc822DateParse(currentText.toString().trim());
} else if (qName.equals("Etag")) {
currentETag = currentText.toString().trim();
} else if (qName.equals("Name")) {
if (inBlob) currentName = currentText.toString().trim();
else if (inBlobPrefix) blobPrefixes.add(currentText.toString().trim());
} else if (qName.equals("Size")) {
currentSize = Long.parseLong(currentText.toString().trim());
} else if (qName.equals("ContentType")) {
currentContentType = currentText.toString().trim();
} else if (qName.equals("ContentEncoding")) {
currentContentEncoding = currentText.toString().trim();
if (currentContentEncoding.equals("")) currentContentEncoding = null;
} else if (qName.equals("ContentLanguage")) {
currentContentLanguage = currentText.toString().trim();
if (currentContentLanguage.equals("")) currentContentLanguage = null;
}
currentText = new StringBuilder();
}
private static void parseHiddenAttributes(
String hide, SortedSet<String> hiddenStrings, SortedSet<String> hiddenPrefixes) {
final StringTokenizer tok = new StringTokenizer(hide);
while (tok.hasMoreTokens()) {
String s = tok.nextToken();
if (s.endsWith("*")) hiddenPrefixes.add(s.substring(0, s.length() - 1));
else hiddenStrings.add(s);
}
}
public static void main(String[] args) {
SortedSet<String> sortedNames = new TreeSet<>();
sortedNames.add("John");
sortedNames.add("Adam");
sortedNames.add("Eve");
sortedNames.add("Donna");
System.out.println(sortedNames);
}
@Test
public void testConvertNetworkMetaAnalysis()
throws Exception, InstantiationException, InvocationTargetException, NoSuchMethodException {
Domain domain = new DomainImpl();
ExampleData.initDefaultData(domain);
String name = "CGI network meta-analysis";
MetaAnalysisWithStudies ma = d_jaxbConverterTest.buildNetworkMetaAnalysis(name);
List<Study> studies = new ArrayList<Study>();
for (org.drugis.addis.entities.data.Study study : ma.d_studies) {
Study studyEnt = JAXBConvertor.convertStudy(study, domain);
domain.getStudies().add(studyEnt);
studies.add(studyEnt);
}
TreatmentDefinition combi =
TreatmentDefinition.createTrivial(
Arrays.asList(ExampleData.buildDrugFluoxetine(), ExampleData.buildDrugSertraline()));
TreatmentDefinition parox =
TreatmentDefinition.createTrivial(ExampleData.buildDrugParoxetine());
TreatmentDefinition sertr =
TreatmentDefinition.createTrivial(ExampleData.buildDrugSertraline());
SortedSet<TreatmentDefinition> alternatives = new TreeSet<TreatmentDefinition>();
alternatives.add(combi);
alternatives.add(parox);
alternatives.add(sertr);
Map<Study, Map<TreatmentDefinition, Arm>> armMap =
new HashMap<Study, Map<TreatmentDefinition, Arm>>();
Map<TreatmentDefinition, Arm> study1map = new HashMap<TreatmentDefinition, Arm>();
study1map.put(combi, studies.get(0).getArms().get(0));
study1map.put(sertr, studies.get(0).getArms().get(1));
armMap.put(studies.get(0), study1map);
Map<TreatmentDefinition, Arm> study2map = new HashMap<TreatmentDefinition, Arm>();
study2map.put(parox, studies.get(1).getArms().get(0));
study2map.put(sertr, studies.get(1).getArms().get(1));
armMap.put(studies.get(1), study2map);
Map<TreatmentDefinition, Arm> study3map = new HashMap<TreatmentDefinition, Arm>();
study3map.put(sertr, studies.get(2).getArms().get(0));
study3map.put(parox, studies.get(2).getArms().get(1));
study3map.put(combi, studies.get(2).getArms().get(2));
armMap.put(studies.get(2), study3map);
Collections.sort(
studies); // So the reading *by definition* puts the studies in their natural order
NetworkMetaAnalysis expected =
new NetworkMetaAnalysis(
name,
ExampleData.buildIndicationDepression(),
ExampleData.buildEndpointCgi(),
studies,
alternatives,
armMap);
assertEntityEquals(expected, NetworkMetaAnalysisConverter.load(ma.d_nwma, domain));
assertEquals(ma.d_nwma, NetworkMetaAnalysisConverter.save(expected));
}
private SortedSet<Package> getInstalledPackages() {
SortedSet<Package> installedPackages = new TreeSet<Package>();
installedPackages.add(PackageBuilder.builder().setName("Package 1").setID("1").build());
installedPackages.add(PackageBuilder.builder().setName("Package 2").setID("2").build());
installedPackages.add(PackageBuilder.builder().setName("Package 3").setID("3").build());
installedPackages.add(PackageBuilder.builder().setName("Package 4").setID("4").build());
installedPackages.add(PackageBuilder.builder().setName("Package 5").setID("5").build());
return installedPackages;
}
private static void applyTiePointGeoCoding(
TiffFileInfo info, double[] tiePoints, Product product) {
final SortedSet<Double> xSet = new TreeSet<>();
final SortedSet<Double> ySet = new TreeSet<>();
for (int i = 0; i < tiePoints.length; i += 6) {
xSet.add(tiePoints[i]);
ySet.add(tiePoints[i + 1]);
}
final double xMin = xSet.first();
final double xMax = xSet.last();
final double xDiff = (xMax - xMin) / (xSet.size() - 1);
final double yMin = ySet.first();
final double yMax = ySet.last();
final double yDiff = (yMax - yMin) / (ySet.size() - 1);
final int width = xSet.size();
final int height = ySet.size();
int idx = 0;
final Map<Double, Integer> xIdx = new HashMap<>();
for (Double val : xSet) {
xIdx.put(val, idx);
idx++;
}
idx = 0;
final Map<Double, Integer> yIdx = new HashMap<>();
for (Double val : ySet) {
yIdx.put(val, idx);
idx++;
}
final float[] lats = new float[width * height];
final float[] lons = new float[width * height];
for (int i = 0; i < tiePoints.length; i += 6) {
final int idxX = xIdx.get(tiePoints[i + 0]);
final int idxY = yIdx.get(tiePoints[i + 1]);
final int arrayIdx = idxY * width + idxX;
lons[arrayIdx] = (float) tiePoints[i + 3];
lats[arrayIdx] = (float) tiePoints[i + 4];
}
String[] names = Utils.findSuitableLatLonNames(product);
final TiePointGrid latGrid =
new TiePointGrid(names[0], width, height, xMin, yMin, xDiff, yDiff, lats);
final TiePointGrid lonGrid =
new TiePointGrid(names[1], width, height, xMin, yMin, xDiff, yDiff, lons);
product.addTiePointGrid(latGrid);
product.addTiePointGrid(lonGrid);
final SortedMap<Integer, GeoKeyEntry> geoKeyEntries = info.getGeoKeyEntries();
final Datum datum = getDatum(geoKeyEntries);
product.setGeoCoding(new TiePointGeoCoding(latGrid, lonGrid, datum));
}
private SortedSet<Package> getAvailablePackages() {
SortedSet<Package> availablePackages = new TreeSet<Package>();
availablePackages.add(PackageBuilder.builder().setName("Package 3").setID("3").build());
availablePackages.add(PackageBuilder.builder().setName("Package 4").setID("4").build());
availablePackages.add(PackageBuilder.builder().setName("Package 5").setID("5").build());
availablePackages.add(PackageBuilder.builder().setName("Package 6").setID("6").build());
availablePackages.add(PackageBuilder.builder().setName("Package 7").setID("7").build());
availablePackages.add(PackageBuilder.builder().setName("Package 8").setID("8").build());
return availablePackages;
}
@Override
public void process(JCas jcas) throws AnalysisEngineProcessException {
// sentenceCount = 0;
tokenCount = 0;
String text = jcas.getDocumentText();
String[] zones = getZoneTypes();
if (isStrictZoning()) {
if (zones == null || zones.length == 0) {
process(jcas, text.substring(0, text.length()), 0);
} else if (zones.length != 1) {
throw new AnalysisEngineProcessException(
new IllegalStateException("Strict zoning cannot use multiple zone types"));
} else {
CAS cas = jcas.getCas();
for (AnnotationFS zone : select(cas, getType(cas, zones[0]))) {
int[] adjusted = limit(text, zone.getBegin(), zone.getEnd());
process(jcas, text.substring(adjusted[0], adjusted[1]), adjusted[0]);
}
}
} else {
// This set collects all zone boundaries.
SortedSet<Integer> boundarySet = new TreeSet<Integer>();
boundarySet.add(0); // Add start boundary
boundarySet.add(text.length()); // Add end boundary
// If zoneTypes have been define then get the boundaries, otherwise we will
// simply have one big zone covering the whole document.
if (zones != null) {
// Iterate over all the zone indices and create sentences respecting
// the zone boundaries. If the zoneTypes overlap... well... bad luck!
for (String zoneName : zones) {
CAS cas = jcas.getCas();
for (AnnotationFS zone : select(cas, getType(cas, zoneName))) {
int[] adjusted = limit(text, zone.getBegin(), zone.getEnd());
boundarySet.add(adjusted[0]);
boundarySet.add(adjusted[1]);
}
}
}
// Now process all zoneTypes. There will be at least two entries in the
// boundary set (see above).
Iterator<Integer> bi = boundarySet.iterator();
int begin = bi.next();
while (bi.hasNext()) {
int end = bi.next();
process(jcas, text.substring(begin, end), begin);
begin = end;
}
}
}
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[] {});
}