List of usage examples for com.google.common.collect Sets newTreeSet
public static <E extends Comparable> TreeSet<E> newTreeSet()
From source file:org.jclouds.s3.domain.AccessControlList.java
/** * @return an unmodifiable set of grantees who have been assigned permissions in this ACL. *//*from w ww . ja v a 2 s.c o m*/ public Set<Grantee> getGrantees() { Set<Grantee> grantees = Sets.newTreeSet(); for (Grant grant : getGrants()) { grantees.add(grant.getGrantee()); } return Collections.unmodifiableSet(grantees); }
From source file:org.gbif.refine.datasets.taibif.FishAssemblages.java
/** * Iterates over original source file and does the following: * i) cleans it (e.g. maps column header names to DwC term names, converts dates to ISO format, etc) * ii) augments it (e.g. adds new columns for sample size, higher taxonomy, etc) * iii) transforms it into star format (core file events.txt is list of unique sampling events, and extension file * occurrence.txt is a list of all observations derived from all sampling events) * * @param output directory to write files to * * @throws IOException if method fails//w w w . j a va 2 s. c o m */ public static void processFish(File output) throws IOException { // load the original source file to process InputStream fis = FishAssemblages.class.getResourceAsStream("/datasets/taibif/1987-1990_UTF8.txt"); // create an iterator on the file CSVReader reader = CSVReaderFactory.build(fis, "UTF-8", "\t", null, 1); // get header row for the new event and occurrence files that this method will output String[] header = getHeader(); // sampling events file Writer writerEvents = FileUtils.startEventsFile(output, header); // observations file Writer writerOccs = FileUtils.startOccurrencesFile(output, header); // to capture all unique eventIDs Set<String> events = Sets.newHashSet(); // to capture bad names Set<String> namesNotFound = Sets.newTreeSet(); ClosableReportingIterator<String[]> iter = null; int line = 0; try { iter = reader.iterator(); while (iter.hasNext()) { line++; String[] record = iter.next(); if (record == null || record.length == 0) { continue; } // create new augmented record String[] modifiedRecord = Arrays.copyOf(record, header.length); // convert year and month into ISO format String year = modifiedRecord[1]; String month = modifiedRecord[2]; if (year.length() == 4 && month.length() == 3) { String concatenatedDate = year + "-" + month; DateFormat concatenatedDf = new SimpleDateFormat("yy-MMM", Locale.ENGLISH); Date concatenatedEventDate = concatenatedDf.parse(concatenatedDate); String concatenatedIsoDate = Constants.ISO_DF_SHORT.format(concatenatedEventDate); // quality control: ensure year and month are same as eventDate (if eventDate provided) String verbatimEventDate = modifiedRecord[3]; if (!verbatimEventDate.isEmpty()) { // convert event date (e.g. 1987/03/) into ISO format (e.g. 1987-03) DateFormat df = new SimpleDateFormat("yy/MM/", Locale.ENGLISH); Date eventDate = df.parse(verbatimEventDate); String isoDate = Constants.ISO_DF_SHORT.format(eventDate); if (!isoDate.equals(concatenatedIsoDate)) { LOG.error("Skipping record: year " + year + " & month " + month + " don't match eventDate " + isoDate); continue; } } modifiedRecord[3] = concatenatedIsoDate; } else { LOG.error("Skipping record: invalid year (" + year + ") and month (" + month + ")"); continue; } modifiedRecord[4] = modifiedRecord[4].toUpperCase(); // occurrenceStatus (present vs absent) // TODO: confirm there are absence records! Indeed there are records missing individualCount if (modifiedRecord[10].isEmpty()) { modifiedRecord[16] = Constants.ABSENT; } else { modifiedRecord[16] = TermUtils.getOccurrenceStatus(Integer.valueOf(modifiedRecord[10])) .toString().toLowerCase(); } // add static values modifiedRecord[17] = "Taiwan"; // country modifiedRecord[18] = "TW"; // countryCode // static values, based on which nuclear power plant it is: N1 or N2 if (modifiedRecord[4].equals("N1")) { modifiedRecord[19] = "Nuclear Power Plant at Shihmen"; // locality modifiedRecord[20] = "25 17 9 N, 121 35 10 E"; // verbatimCoordinates modifiedRecord[21] = "25.28583"; // decimalLatitude modifiedRecord[22] = "121.5861"; // decimalLongitude } else { modifiedRecord[19] = "Nuclear Power Plant at Yehliu"; // locality modifiedRecord[20] = "25 12 10 N, 121 39 45 E"; // verbatimCoordinates modifiedRecord[21] = "25.20278"; // decimalLatitude modifiedRecord[22] = "121.6625"; // decimalLongitude } modifiedRecord[23] = "fish samples were collected monthly from the intake screens at nuclear power plant for 24h (from 9 AM to 9 AM) on the date chosen by a systematic sampling method (Cochran, W. G. Sampling Techniques. 3rd ed. (John Wiley & Sons, 1977)"; // samplingProtocol modifiedRecord[24] = "24"; // sampleSizeValue modifiedRecord[25] = "hour"; // sampleSizeUnit modifiedRecord[26] = "24hr"; // samplingEffort modifiedRecord[27] = "http://creativecommons.org/publicdomain/zero/1.0/legalcode"; // license modifiedRecord[28] = "Event"; // type modifiedRecord[29] = "Chen H, Liao Y, Chen C, Tsai J, Chen L, Shao K"; // rightsHolder modifiedRecord[31] = "MaterialSample"; // basisOfRecord modifiedRecord[32] = "Dr. Kwang-Tsao Shao and the senior laboratory members"; // identifiedBy modifiedRecord[33] = "Identification done using plenty of handbooks of field guide and identification keys."; // identifiedBy modifiedRecord[35] = "individuals"; // organismQuantityType modifiedRecord[36] = "Animalia"; // kingdom modifiedRecord[37] = "Chordata"; // phylum // store organismQuantity modifiedRecord[34] = modifiedRecord[11]; // same as individualCount // construct unique eventID for this sampling period // Format: "urn:[institutionID]:[eventDate]:[locationID]" // Example: "urn:taibif:1987-08:N2" modifiedRecord[0] = "urn:taibif:" + modifiedRecord[3] + ":" + modifiedRecord[4]; // verify taxonomy String name = modifiedRecord[8].trim(); // for more accurate match, we take higher taxonomy into consideration LinneanClassification cl = new NameUsage(); cl.setFamily(modifiedRecord[6]); // only if binomial, set species if (name.split(" ").length == 2 && !name.endsWith("spp.")) { cl.setSpecies(name); // lowest rank specified Rank rank = TermUtils.lowestRank(cl); if (rank != null) { modifiedRecord[43] = rank.toString().toLowerCase(); } // verify name, and add higher taxonomy NameUsageMatch match = MATCHING_SERVICE.match(name, rank, cl, false, false); if (match.getMatchType().equals(NameUsageMatch.MatchType.EXACT)) { modifiedRecord[36] = match.getKingdom(); modifiedRecord[37] = match.getPhylum(); modifiedRecord[38] = match.getClazz(); modifiedRecord[39] = match.getOrder(); modifiedRecord[40] = match.getFamily(); modifiedRecord[41] = match.getGenus(); modifiedRecord[42] = match.getScientificName(); modifiedRecord[43] = match.getRank().toString(); modifiedRecord[44] = match.getUsageKey().toString(); modifiedRecord[45] = match.getStatus().toString(); } else { if (!namesNotFound.contains(name)) { LOG.error(match.getMatchType().toString() + " match for: " + name + " (with rank " + rank + ") to: " + match.getScientificName() + " (with rank " + match.getRank() + ")" + ". See example record with eventDate: " + modifiedRecord[0]); namesNotFound.add(name); } } } else { namesNotFound.add(name); } // construct unique occurrenceID for this abundance record: // Format: "urn:[institutionCode]:[eventDate]:[locationID]:[taxonID]" // Example: "urn:taibif:1994-08:N2:1301" modifiedRecord[30] = modifiedRecord[0] + modifiedRecord[44]; // always output line to new occurrences file String row = FileUtils.tabRow(modifiedRecord); writerOccs.write(row); // only output line to events file if event hasn't been included yet String eventID = modifiedRecord[0]; if (!events.contains(eventID)) { writerEvents.write(row); events.add(eventID); } } LOG.info("Iterated over " + line + " rows."); LOG.info("Found " + events.size() + " unique events."); LOG.warn("***** " + namesNotFound.size() + " names not found in taxa list: "); for (String notFound : namesNotFound) { LOG.warn(notFound); } } catch (Exception e) { // some error validating this file, report LOG.error("Exception caught while iterating over file", e); } finally { if (iter != null) { iter.close(); } reader.close(); writerEvents.close(); writerOccs.close(); } }
From source file:uk.ac.ebi.atlas.experimentpage.context.DifferentialRequestContextBuilder.java
Set<Contrast> getSelectedQueryContrasts(DifferentialExperiment experiment) {
if (CollectionUtils.isEmpty(getRequestPreferences().getQueryFactorValues())) {
return Sets.newHashSet();
}//ww w.j a va 2s. c o m
SortedSet<Contrast> selectedQueryContrasts = Sets.newTreeSet();
for (String queryContrastId : getRequestPreferences().getQueryFactorValues()) {
try {
Contrast contrast = experiment.getContrast(queryContrastId);
selectedQueryContrasts.add(contrast);
} catch (IllegalArgumentException e) {
throw new ResourceNotFoundException(e);
}
}
return selectedQueryContrasts;
}
From source file:symbolicexecutor.SymbolicExecutor.java
private SymbolicExecutor(String source, FileLoader loader, NewInputGenerator newInputGenerator, Input arguments, int maxNumInputs) { this.jsSource = source; this.loader = loader; this.newInputGenerator = newInputGenerator; this.maxNumInputs = maxNumInputs; this.inputs = Sets.newTreeSet(); this.inputs.add(arguments); }
From source file:blackboard.plugin.hayabusa.provider.LanguagePackProvider.java
@Override public Iterable<Command> getCommands() { Iterator<LocalePickerOption> ll = getLocaleList().iterator(); Set<Command> commands = Sets.newTreeSet(); Context bbCtxt = ContextManagerFactory.getInstance().getContext(); while (ll.hasNext()) { LocalePickerOption option = ll.next(); HashMap<String, String> params = new HashMap<String, String>(); params.put("top_Submit", "Submit"); params.put("target", "/webapps/portal/frameset.jsp"); params.put("locale", option.getLocaleLocale()); params.put("showInstructions", "true"); params.put(NonceUtil.NONCE_KEY, NonceUtil.create(bbCtxt.getSession(), NONCE_ID, NONCE_CONTEXT)); commands.add(new PostCommand(option.getLocaleName(), "/webapps/blackboard/execute/personalSettings?command=save", Category.LANGUAGE_PACK, params)); }/*from w w w . ja v a 2 s .co m*/ return commands; }
From source file:org.geogit.api.plumbing.merge.CheckMergeScenarioOp.java
@Override public Boolean call() { if (commits.size() < 2) { return Boolean.FALSE; }// w w w .jav a 2 s.c om Optional<RevCommit> ancestor = command(FindCommonAncestor.class).setLeft(commits.get(0)) .setRight(commits.get(1)).call(); Preconditions.checkState(ancestor.isPresent(), "No ancestor commit could be found."); for (int i = 2; i < commits.size(); i++) { ancestor = command(FindCommonAncestor.class).setLeft(commits.get(i)).setRight(ancestor.get()).call(); Preconditions.checkState(ancestor.isPresent(), "No ancestor commit could be found."); } Map<String, List<DiffEntry>> diffs = Maps.newHashMap(); Set<String> removedPaths = Sets.newTreeSet(); // we organize the changes made for each path for (RevCommit commit : commits) { Iterator<DiffEntry> toMergeDiffs = command(DiffTree.class).setReportTrees(true) .setOldTree(ancestor.get().getId()).setNewTree(commit.getId()).call(); while (toMergeDiffs.hasNext()) { DiffEntry diff = toMergeDiffs.next(); String path = diff.oldPath() == null ? diff.newPath() : diff.oldPath(); if (diffs.containsKey(path)) { diffs.get(path).add(diff); } else { diffs.put(path, Lists.newArrayList(diff)); } if (ChangeType.REMOVED.equals(diff.changeType())) { removedPaths.add(path); } } } // now we check that, for any path, changes are compatible Collection<List<DiffEntry>> values = diffs.values(); for (List<DiffEntry> list : values) { for (int i = 0; i < list.size(); i++) { for (int j = i + 1; j < list.size(); j++) { if (hasConflicts(list.get(i), list.get(j))) { return true; } } if (!ChangeType.REMOVED.equals(list.get(i).changeType())) { if (removedPaths.contains(list.get(i).getNewObject().getParentPath())) { return true; } } } } return false; }
From source file:com.google.gerrit.testutil.InMemoryRepositoryManager.java
@Override public SortedSet<Project.NameKey> list() { SortedSet<Project.NameKey> names = Sets.newTreeSet(); for (DfsRepository repo : repos.values()) { names.add(new Project.NameKey(repo.getDescription().getRepositoryName())); }// ww w . j ava2 s . co m return ImmutableSortedSet.copyOf(names); }
From source file:com.google.devtools.j2objc.gen.ObjectiveCImplementationGenerator.java
private void printImports() { Set<String> includeFiles = Sets.newTreeSet(); includeFiles.add("J2ObjC_source.h"); includeFiles.add(getGenerationUnit().getOutputPath() + ".h"); for (GeneratedType generatedType : getOrderedTypes()) { for (Import imp : generatedType.getImplementationIncludes()) { if (!isLocalType(imp.getTypeName())) { includeFiles.add(imp.getImportFileName()); }//www . jav a 2 s. co m } } newline(); for (String header : includeFiles) { printf("#include \"%s\"\n", header); } for (String code : getGenerationUnit().getNativeImplementationBlocks()) { print(code); } Set<String> seenTypes = Sets.newHashSet(); Set<Import> forwardDecls = Sets.newHashSet(); for (GeneratedType generatedType : getOrderedTypes()) { String name = generatedType.getTypeName(); seenTypes.add(name); for (Import imp : generatedType.getImplementationForwardDeclarations()) { // Only need to forward declare private local types. All else is handled // by imports. GeneratedType localType = getLocalType(imp.getTypeName()); if (!seenTypes.contains(imp.getTypeName()) && localType != null && localType.isPrivate()) { forwardDecls.add(imp); } } } printForwardDeclarations(forwardDecls); }
From source file:org.codeqinvest.investment.QualityInvestmentPlanService.java
public QualityInvestmentPlan computeInvestmentPlan(QualityAnalysis analysis, String basePackage, int investmentInMinutes) { Multimap<Double, QualityViolation> violationsByProfit = ArrayListMultimap.create(); for (QualityViolation violation : filterViolationsByArtefactNameStartingWith(basePackage, analysis.getViolations())) { double profit = profitCalculator.calculateProfit(violation); if (Math.round(profit) > 0) { violationsByProfit.put(profit, violation); }/*from w w w .j a v a 2 s. c o m*/ } List<Double> allProfits = new ArrayList<Double>(); for (Double profit : violationsByProfit.keySet()) { int numberOfViolations = violationsByProfit.get(profit).size(); for (int i = 0; i < numberOfViolations; i++) { allProfits.add(profit); } } Collections.sort(allProfits, new DescendingComparator<Double>()); Set<QualityInvestmentPlanEntry> investmentPlanEntries = Sets.newTreeSet(); int toInvest = investmentInMinutes; int invested = 0; for (double profit : allProfits) { List<QualityViolation> violations = new ArrayList<QualityViolation>(violationsByProfit.get(profit)); Collections.sort(violations, new ViolationByRemediationCostsComparator()); for (QualityViolation violation : violations) { int remediationCost = violation.getRemediationCosts(); if (remediationCost <= toInvest) { invested += remediationCost; toInvest -= remediationCost; QualityRequirement requirement = violation.getRequirement(); investmentPlanEntries.add(new QualityInvestmentPlanEntry(requirement.getMetricIdentifier(), requirement.getOperator() + " " + requirement.getThreshold(), violation.getArtefact().getName(), violation.getArtefact().getShortClassName(), (int) Math.round(profit), remediationCost)); } } } final int overallProfit = calculateOverallProfit(investmentPlanEntries); return new QualityInvestmentPlan(basePackage, invested, overallProfit, calculateRoi(investmentPlanEntries, overallProfit), investmentPlanEntries); }
From source file:org.incode.eurocommercial.contactapp.dom.number.ContactNumberRepository.java
@Programmatic public Set<String> existingTypes() { final Set<String> types = Sets.newTreeSet(); types.addAll(ContactNumberType.titles()); types.addAll(FluentIterable.from(listAll()).transform(ContactNumber::getType).toSet()); return types; }