private Set<Vertex> computeMinVertexCover(Set<Vertex> side1, Set<Vertex> side2) {
Set<Vertex> konigSet = new HashSet<Vertex>();
Set<Vertex> unmatched = new TreeSet<Vertex>(side1);
unmatched.removeAll(matches);
// System.out.println("Matches: " + matches);
// System.out.println("side 1 unmatched set: " + unmatched);
for (Vertex v : unmatched) {
konigDFS(konigSet, v, false);
}
// System.out.println("Konig set: " + konigSet);
Set<Vertex> result = new HashSet<Vertex>(side2);
result.retainAll(konigSet);
// System.out.println("side 2 intersect konigSet: " + result);
Set<Vertex> side1notInKonigSet = new HashSet<Vertex>(side1);
side1notInKonigSet.removeAll(konigSet);
// System.out.println("side 1 not in Konig set: " + side1notInKonigSet);
result.addAll(side1notInKonigSet);
return result;
}
public static Set<RepairedCell> getRepairFalse(Set<RepairedCell> truth, Set<RepairedCell> found) {
Set<RepairedCell> rst = new HashSet<RepairedCell>();
if (found.size() != 0) {
rst.addAll(found);
rst.removeAll(truth);
}
return rst;
}
/** Asserts that this file contains exactly the given set of descendants. */
public TestFile assertHasDescendants(String... descendants) {
Set<String> actual = new TreeSet<String>();
assertIsDir();
visit(actual, "", this);
Set<String> expected = new TreeSet<String>(Arrays.asList(descendants));
Set<String> extras = new TreeSet<String>(actual);
extras.removeAll(expected);
Set<String> missing = new TreeSet<String>(expected);
missing.removeAll(actual);
assertEquals(
String.format(
"For dir: %s, extra files: %s, missing files: %s, expected: %s",
this, extras, missing, expected),
expected,
actual);
return this;
}
private void updateInSelectionHighlighters() {
if (mySearchResults.getEditor() == null) return;
final SelectionModel selectionModel = mySearchResults.getEditor().getSelectionModel();
int[] starts = selectionModel.getBlockSelectionStarts();
int[] ends = selectionModel.getBlockSelectionEnds();
final HashSet<RangeHighlighter> toRemove = new HashSet<RangeHighlighter>();
Set<RangeHighlighter> toAdd = new HashSet<RangeHighlighter>();
for (RangeHighlighter highlighter : myHighlighters) {
boolean intersectsWithSelection = false;
for (int i = 0; i < starts.length; ++i) {
TextRange selectionRange = new TextRange(starts[i], ends[i]);
intersectsWithSelection =
selectionRange.intersects(highlighter.getStartOffset(), highlighter.getEndOffset())
&& selectionRange.getEndOffset() != highlighter.getStartOffset()
&& highlighter.getEndOffset() != selectionRange.getStartOffset();
if (intersectsWithSelection) break;
}
final Object userData = highlighter.getUserData(IN_SELECTION_KEY);
if (userData != null) {
if (!intersectsWithSelection) {
if (userData == IN_SELECTION2) {
HighlightManager.getInstance(mySearchResults.getProject())
.removeSegmentHighlighter(mySearchResults.getEditor(), highlighter);
toRemove.add(highlighter);
} else {
highlighter.putUserData(IN_SELECTION_KEY, null);
}
}
} else if (intersectsWithSelection) {
TextRange cursor = mySearchResults.getCursor();
if (cursor != null
&& highlighter.getStartOffset() == cursor.getStartOffset()
&& highlighter.getEndOffset() == cursor.getEndOffset()) continue;
final RangeHighlighter toAnnotate =
highlightRange(
new TextRange(highlighter.getStartOffset(), highlighter.getEndOffset()),
new TextAttributes(null, null, Color.WHITE, EffectType.ROUNDED_BOX, 0),
toAdd);
highlighter.putUserData(IN_SELECTION_KEY, IN_SELECTION1);
toAnnotate.putUserData(IN_SELECTION_KEY, IN_SELECTION2);
}
}
myHighlighters.removeAll(toRemove);
myHighlighters.addAll(toAdd);
}
private void clearUnusedHightlighters() {
Set<RangeHighlighter> unused = new com.intellij.util.containers.HashSet<RangeHighlighter>();
for (RangeHighlighter highlighter : myHighlighters) {
if (highlighter.getUserData(MARKER_USED) == null) {
unused.add(highlighter);
} else {
highlighter.putUserData(MARKER_USED, null);
}
}
myHighlighters.removeAll(unused);
Project project = mySearchResults.getProject();
if (!project.isDisposed()) {
for (RangeHighlighter highlighter : unused) {
HighlightManager.getInstance(project)
.removeSegmentHighlighter(mySearchResults.getEditor(), highlighter);
}
}
}
private Set<Document> getDocsWithNoEmotions(
Indexer indexer, Collection<Document> docs, boolean originalContentOnly) {
Set<Document> result = new LinkedHashSet<Document>(docs);
result.removeAll(getDocsWithAnyEmotions(indexer, docs, originalContentOnly));
return result;
}
/** Return the difference of two sets, a - b. */
<T> Set<T> diff(Set<T> a, Set<T> b) {
if (b.isEmpty()) return a;
Set<T> result = new LinkedHashSet<T>(a);
result.removeAll(b);
return result;
}
/**
* Runs ConflictTreeSimulatedSession with calculated diagnoses
*
* @param matchingsDir
* @param ontologyDir
* @param files
* @param map
* @throws SolverException
* @throws InconsistentTheoryException
* @throws OWLOntologyCreationException
*/
private void runOaeiConferenceTests(
String matchingsDir,
String ontologyDir,
Set<File> files,
Map<File, String> map,
int numberOfConflicts)
throws SolverException, InconsistentTheoryException, OWLOntologyCreationException {
OAEI11ConferenceSession conferenceSession = new OAEI11ConferenceSession();
QSSType[] qssTypes = new QSSType[] {QSSType.MINSCORE};
// QSSType[] qssTypes = new QSSType[]{QSSType.MINSCORE, QSSType.SPLITINHALF,
// QSSType.DYNAMICRISK};
TargetSource targetSource = TargetSource.FROM_30_DIAGS;
for (File file : files) {
logger.info("processing " + file.getName());
String out = "STAT, " + file;
// file parameter
String fileName = file.getName();
StringTokenizer t = new StringTokenizer(fileName, "-");
String matcher = t.nextToken();
String o1 = t.nextToken();
String o2 = t.nextToken();
o2 = o2.substring(0, o2.length() - 4);
String n = file.getName().substring(0, file.getName().length() - 4);
Set<FormulaSet<OWLLogicalAxiom>> targetDgSet =
getRandomDiagSet(matchingsDir, ontologyDir, map, file, o1, o2, n, conferenceSession);
logger.info("number of found diagnoses (max. 30): " + targetDgSet.size());
/*
TODO: for each ontology always the same "randomly" chosen diagnosis is calculated, dependent
from the size of the targetDgSet -> change to a real random selection
*/
Random random = new Random(12311);
int randomNr = conferenceSession.chooseRandomNum(targetDgSet, random);
Set<OWLLogicalAxiom> targetDg =
conferenceSession.chooseRandomDiag(targetDgSet, file, randomNr);
OWLOntology inconsOntology =
loadOntology(matchingsDir, ontologyDir, map, conferenceSession, file, o1, o2, n);
// OWLTheory faultyTheory = getExtendTheory(inconsOntology, false);
OWLTheory faultyTheory = loadTheory(inconsOntology, ontologyDir, o1, o2);
Set<OWLLogicalAxiom> rem = validateMinimality(targetDg, faultyTheory);
if (!rem.isEmpty()) {
targetDg.removeAll(rem);
assertTrue(validateMinimality(targetDg, faultyTheory).isEmpty());
}
Map<QSSType, DurationStat> ctTimes = new HashMap<QSSType, DurationStat>();
Map<QSSType, List<Double>> ctQueries = new HashMap<QSSType, List<Double>>();
for (QSSType qssType : qssTypes) {
String message =
"act,"
+ file.getName()
+ ","
+ map.get(file)
+ ","
+ targetSource
+ ","
+ qssType
+ ","
+ randomNr;
long preprocessModulExtract = System.currentTimeMillis();
OWLOntology ontology =
loadOntology(matchingsDir, ontologyDir, map, conferenceSession, file, o1, o2, n);
ctTheory = loadTheory(ontology, ontologyDir, o1, o2);
preprocessModulExtract = System.currentTimeMillis() - preprocessModulExtract;
message += "," + preprocessModulExtract;
// Define Treesearch here
TreeSearch<FormulaSet<OWLLogicalAxiom>, OWLLogicalAxiom> search =
getUniformCostSearch(ctTheory, false);
Map<OWLLogicalAxiom, BigDecimal> map1 =
conferenceSession.readRdfMapping(matchingsDir + map.get(file), n + ".rdf");
OWLAxiomCostsEstimator es = new OWLAxiomCostsEstimator(ctTheory, map1);
search.setCostsEstimator(es);
search.reset();
// set for all found diagnoses during search
foundDiagnoses = new LinkedHashSet<OWLLogicalAxiom>();
ctTimes.put(qssType, new DurationStat());
ctQueries.put(qssType, new LinkedList<Double>());
// calculation part
ConflictTreeSession conflictTreeSearch = new ConflictTreeSession(this, ctTheory, search);
if (numberOfConflicts > 0) {
conflictTreeSearch.setMaximumNumberOfConflicts(numberOfConflicts);
}
conflictTreeSearch.setOutputString(out);
conflictTreeSearch.setMessageString(message);
FormulaSet<OWLLogicalAxiom> targetD =
new FormulaSetImpl<OWLLogicalAxiom>(new BigDecimal(1), targetDg, null);
long completeTime = conflictTreeSearch.search(targetD, ctQueries, qssType, true);
ctTimes.get(qssType).add(completeTime);
out += conflictTreeSearch.getOutputString();
foundDiagnoses = conflictTreeSearch.getDiagnosis();
logger.info("targetD: " + targetD.size() + ", " + CalculateDiagnoses.renderAxioms(targetD));
logger.info(
"foundD: "
+ foundDiagnoses.size()
+ ", "
+ CalculateDiagnoses.renderAxioms(foundDiagnoses));
faultyTheory
.getReasoner()
.addFormulasToCache(faultyTheory.getKnowledgeBase().getFaultyFormulas());
assertFalse(faultyTheory.verifyConsistency());
Set<OWLLogicalAxiom> removedFound = validateMinimality(foundDiagnoses, faultyTheory);
// assertTrue(removed.isEmpty());
Set<OWLLogicalAxiom> removedTarget = validateMinimality(targetD, faultyTheory);
assertTrue(removedTarget.isEmpty());
assertTrue(targetD.containsAll(foundDiagnoses));
// TODO uncomment later
// assertTrue(foundDiagnoses.containsAll(targetD));
resetTheoryTests(ctTheory);
search.reset();
}
logger.info(out);
}
}
public void setLabels(Collection<BxZoneLabel> labels) {
ignoredLabels.addAll(EnumSet.allOf(BxZoneLabel.class));
ignoredLabels.removeAll(labels);
}
/**
* @param packageNames Packages to be reindexd if version has changed or package has been
* installed since last indexing run.If non are provided all packages will be refreshed.
*/
public boolean refreshIndex(String... packageNames) {
RHelperUtil.runHelperWithArgs(RHelperUtil.R_HELPER_INSTALL_TIDYVERSE);
Set<RPackage> installedPackages = LocalRUtil.getInstalledPackages();
// remove packages from index that are no longer present
if (packageNames.length == 0) {
Sets.SetView<RPackage> noLongerInstalled = Sets.difference(allPackages, installedPackages);
allPackages.removeAll(noLongerInstalled);
}
// cut down packges to be refreshed to speed up calculations
// if(packageNames.length>0){
// installedPackages = installedPackages.stream().
// filter(p -> Arrays.asList(packageNames).contains(p.getName())).
// collect(Collectors.toSet());
// }
ExecutorService executorService = Executors.newFixedThreadPool(8);
final boolean[] hasChanged = {false};
for (final RPackage rPackage : installedPackages) {
final RPackage indexPackage = getByName(rPackage.getName());
if (indexPackage != null
&& ObjectUtils.equals(indexPackage.getVersion(), rPackage.getVersion())) {
continue;
}
executorService.submit(
new Runnable() {
@Override
public void run() {
reindexPackage(rPackage, indexPackage);
hasChanged[0] = true;
}
});
}
executorService.shutdown();
try {
executorService.awaitTermination(1, TimeUnit.DAYS);
} catch (InterruptedException e) {
e.printStackTrace();
}
// allPackages.clear();
// allPackages.addAll(installedPackages);
if (hasChanged[0]) {
if (ApplicationManager.getApplication() != null) {
Project[] projects = ProjectManager.getInstance().getOpenProjects();
for (Project project : projects) {
if (project.isInitialized() && project.isOpen() && !project.isDefault()) {
SpellCheckerManager spellCheckerManager = SpellCheckerManager.getInstance(project);
EditableDictionary dictionary = spellCheckerManager.getUserDictionary();
for (RPackage rPackage : RPackageService.getInstance().allPackages) {
dictionary.addToDictionary(rPackage.getName());
dictionary.addToDictionary(rPackage.getFunctionNames());
}
DaemonCodeAnalyzer.getInstance(project).restart();
}
}
}
}
return hasChanged[0];
}