List of usage examples for com.google.common.collect Lists newArrayListWithExpectedSize
@GwtCompatible(serializable = true) public static <E> ArrayList<E> newArrayListWithExpectedSize(int estimatedSize)
From source file:com.android.tools.idea.navigator.nodes.AndroidResFolderTypeNode.java
@NotNull @Override/*from w ww .j a v a 2 s .co m*/ public Collection<? extends AbstractTreeNode> getChildren() { // all resource folders of a given folder type List<PsiDirectory> folders = getValue(); Multimap<String, PsiFile> multimap = HashMultimap.create(); for (PsiDirectory res : folders) { for (PsiFile file : res.getFiles()) { String resName = file.getName(); multimap.put(resName, file); } } List<AbstractTreeNode> children = Lists.newArrayListWithExpectedSize(multimap.size()); for (String resName : multimap.keySet()) { List<PsiFile> files = Lists.newArrayList(multimap.get(resName)); if (files.size() > 1) { children.add(new AndroidResGroupNode(myProject, myFacet, files, resName, getSettings())); } else { children.add(new AndroidResFileNode(myProject, files.get(0), getSettings(), myFacet)); } } return children; }
From source file:com.isotrol.impe3.web20.client.content.counter.GreatestHitsComponent.java
public ComponentResponse execute() { final Pagination pag = new Pagination(config.pageSize(), null); listing = ContentListingPage.empty(pag); // Fetch resources final CounterFilterDTO filter = new CounterFilterDTO(); filter.setCounterType(config.counterType()); List<ResourceCounterDTO> resources; try {//from ww w . j a v a 2 s .co m resources = service.getGreatestHits("", filter, Math.max(1, config.pageSize())); } catch (ServiceException e) { // TODO log return ComponentResponse.OK; } if (resources == null || resources.isEmpty()) { // Nothing to do return ComponentResponse.OK; } // Turn resources into keys final List<ContentKey> keys = Lists.newArrayListWithExpectedSize(resources.size()); for (ResourceCounterDTO resource : Iterables.filter(resources, Predicates.notNull())) { final ContentKey ck = r2ck(resource.getResource()); if (ck != null) { keys.add(ck); } } if (keys.isEmpty()) { // Nothing to do return ComponentResponse.OK; } // Perform the search ContentCriteria cc = loader.newCriteria(); cc.setBytes(true); Map<ContentKey, Content> map = loader.newCriteria().setBytes(true).getContents(keys); if (map.isEmpty()) { // Nothing found return ComponentResponse.OK; } // Turn to listing final List<Content> contents = Lists.newArrayListWithExpectedSize(keys.size()); for (ContentKey ck : keys) { final Content c = map.get(ck); if (c != null) { contents.add(c); } } listing = new ContentListingPage(null, pag, contents); return ComponentResponse.OK; }
From source file:org.apache.phoenix.mapreduce.index.DirectHTableWriter.java
public void write(List<Mutation> mutations) throws IOException, InterruptedException { Object[] results = new Object[mutations.size()]; String txnIdStr = conf.get(PhoenixConfigurationUtil.TX_SCN_VALUE); if (txnIdStr == null) { table.batch(mutations, results); } else {//from ww w . ja v a 2s.com long ts = Long.parseLong(txnIdStr); PhoenixTransactionProvider provider = TransactionFactory.Provider.getDefault().getTransactionProvider(); String txnProviderStr = conf.get(PhoenixConfigurationUtil.TX_PROVIDER); if (txnProviderStr != null) { provider = TransactionFactory.Provider.valueOf(txnProviderStr).getTransactionProvider(); } List<Mutation> shadowedMutations = Lists.newArrayListWithExpectedSize(mutations.size()); for (Mutation m : mutations) { if (m instanceof Put) { shadowedMutations.add(provider.markPutAsCommitted((Put) m, ts, ts)); } } table.batch(shadowedMutations, results); } }
From source file:com.twitter.distributedlog.impl.ZKLogMetadataStore.java
@Override public Future<Iterator<String>> getLogs() { final Promise<Iterator<String>> promise = new Promise<Iterator<String>>(); final String nsRootPath = namespace.getPath(); try {//ww w . j av a 2 s . c o m final ZooKeeper zk = zkc.get(); zk.sync(nsRootPath, new AsyncCallback.VoidCallback() { @Override public void processResult(int syncRc, String syncPath, Object ctx) { if (KeeperException.Code.OK.intValue() == syncRc) { zk.getChildren(nsRootPath, false, new AsyncCallback.Children2Callback() { @Override public void processResult(int rc, String path, Object ctx, List<String> children, Stat stat) { if (KeeperException.Code.OK.intValue() == rc) { List<String> results = Lists.newArrayListWithExpectedSize(children.size()); for (String child : children) { if (!isReservedStreamName(child)) { results.add(child); } } promise.setValue(results.iterator()); } else if (KeeperException.Code.NONODE.intValue() == rc) { List<String> streams = Lists.newLinkedList(); promise.setValue(streams.iterator()); } else { promise.setException(new ZKException("Error reading namespace " + nsRootPath, KeeperException.Code.get(rc))); } } }, null); } else if (KeeperException.Code.NONODE.intValue() == syncRc) { List<String> streams = Lists.newLinkedList(); promise.setValue(streams.iterator()); } else { promise.setException(new ZKException("Error reading namespace " + nsRootPath, KeeperException.Code.get(syncRc))); } } }, null); zkc.get(); } catch (ZooKeeperClient.ZooKeeperConnectionException e) { promise.setException(e); } catch (InterruptedException e) { promise.setException(e); } return promise; }
From source file:ch.ethz.bsse.quasirecomb.model.Preprocessing.java
/** * Entry point. Forwards invokes of the specified workflow. * * @param input path to the fasta file//from w ww . j a v a 2 s. c o m * @param Kmin minimal amount of generators * @param Kmax minimal amount of generators */ public static void workflow(String input, int Kmin, int Kmax) { Utils.mkdir(Globals.getINSTANCE().getSAVEPATH() + "support"); //parse file StatusUpdate.getINSTANCE().print("Parsing"); Read[] reads = Utils.parseInput(input); int L = fixAlignment(reads); if (L > 300 && Globals.getINSTANCE().getINTERPOLATE_MU() > 0) { Globals.getINSTANCE().setINTERPOLATE_MU(.5); } int[][] alignment = computeAlignment(reads, L); StatusUpdate.getINSTANCE().println("Paired reads\t" + Globals.getINSTANCE().getPAIRED_COUNT()); computeInsertDist(reads); StatusUpdate.getINSTANCE().println("Merged reads\t" + Globals.getINSTANCE().getMERGED() + "\n"); printAlignment(reads); circos(L, alignment); if (Globals.getINSTANCE().isDEBUG()) { new File(Globals.getINSTANCE().getSAVEPATH() + "support/log/").mkdirs(); } int n = countChars(reads); Globals.getINSTANCE().setTAU_OMEGA(reads, L); int N = 0; for (Read r : reads) { if (r.getWatsonLength() > 0) { N += r.getCount(); } } plot(); if (Globals.getINSTANCE().isBOOTSTRAP()) { String[] truth = FastaParser.parseFarFile(Globals.getINSTANCE().getPRIOR()); Multimap<Integer, Double> bics = ArrayListMultimap.create(); List<Read> readList = Lists.newArrayListWithExpectedSize(N); int x = 0; for (Read r : reads) { int count = r.getCount(); for (int i = 0; i < count; i++) { readList.add(new Read(r)); } // r.setCount(1); } // for (Read r : reads) { // Utils.appendFile(Globals.getINSTANCE().getSAVEPATH() + "pi_bootstrap_original.txt", + r.getCount() + "\n"); // } Read[] readArray = readList.toArray(new Read[readList.size()]); for (int i = 0; i < 100; i++) { StatusUpdate.getINSTANCE().println("Bootstrap " + i + "\n"); Map<Integer, Read> hashed = new HashMap<>(); Random rnd = new Random(); for (int y = 0; y < N; y++) { Read r = readArray[rnd.nextInt(N)]; int hash = r.hashCode(); if (hashed.containsKey(hash)) { hashed.get(hash).incCount(); } else { hashed.put(r.hashCode(), r); } } // for (Read r : reads) { // Utils.appendFile(Globals.getINSTANCE().getSAVEPATH() + "pi_bootstrap_" + i + ".txt", (hashed.get(r.hashCode()) == null ? 0 : hashed.get(r.hashCode()).getCount()) + "\n"); // } Read[] rs = hashed.values().toArray(new Read[hashed.size()]); ModelSelection ms = new ModelSelection(rs, Kmin, Kmax, L, n); OptimalResult or = ms.getOptimalResult(); double[] pi = new double[or.getPi()[0].length]; double piSum = 0; for (int j = 0; j < or.getPi().length; j++) { for (int k = 0; k < or.getPi()[j].length; k++) { pi[k] += or.getPi()[j][k]; piSum += or.getPi()[j][k]; } } StringBuilder piSB = new StringBuilder(); piSB.append(pi[0] / piSum); for (int k = 1; k < pi.length; k++) { piSB.append("\t"); piSB.append(pi[k] / piSum); } new File(Globals.getINSTANCE().getSAVEPATH() + i).mkdirs(); ModelSampling modelSampling = new ModelSampling(or, Globals.getINSTANCE().getSAVEPATH() + i + File.separator); modelSampling.save(); Map<String, Double> quasispecies = FastaParser.parseQuasispeciesFile( Globals.getINSTANCE().getSAVEPATH() + i + File.separator + "quasispecies.fasta"); double[] frequencies = new double[truth.length]; for (Map.Entry<String, Double> e : quasispecies.entrySet()) { int distance = Integer.MAX_VALUE; int index = -1; for (int t = 0; t < truth.length; t++) { int hamming = DistanceUtils.calcHamming(e.getKey(), truth[t]); if (hamming < distance) { index = t; distance = hamming; } } frequencies[index] += e.getValue(); } StringBuilder fSB = new StringBuilder(); fSB.append(frequencies[0]); for (int f = 1; f < frequencies.length; f++) { fSB.append("\t"); fSB.append(frequencies[f]); } Utils.appendFile(Globals.getINSTANCE().getSAVEPATH() + "bootstrap.txt", fSB.toString() + "\n"); Utils.appendFile(Globals.getINSTANCE().getSAVEPATH() + "pi_bootstrap.txt", piSB.toString() + "\n"); bics.putAll(ms.getMsTemp().getMaxBICs()); } System.exit(0); StringBuilder sb = new StringBuilder(); int bootstraps = bics.asMap().values().iterator().next().size(); Set<Integer> keySet = bics.keySet(); for (int i : keySet) { sb.append(i).append("\t"); } sb.setLength(sb.length() - 1); sb.append("\n"); for (int l = 0; l < bootstraps; l++) { for (int i : keySet) { ArrayList arrayList = new ArrayList(bics.get(i)); if (l < arrayList.size()) { sb.append(arrayList.get(l)); } sb.append("\t"); } sb.setLength(sb.length() - 1); sb.append("\n"); } Utils.saveFile(Globals.getINSTANCE().getSAVEPATH() + "support" + File.separator + "bics.txt", sb.toString()); StatusUpdate.getINSTANCE().println(""); ModelSelectionBootstrapStorage msbt = new ModelSelectionBootstrapStorage(bics); Kmin = msbt.getBestK(); Kmax = Kmin; Globals.getINSTANCE().setBOOTSTRAP(false); } ModelSelection ms = null; // if (Globals.getINSTANCE().isSUBSAMPLE()) { // shuffleArray(reads); // List<Read> subsample = new LinkedList<>(); // Map<String, Integer> generators = new HashMap<>(); // Globals.getINSTANCE().setDESIRED_REPEATS(0); // for (int i = 0; i < reads.length; i++) { // if (subsample.size() < reads.length / 10 || i + reads.length / 10 > reads.length) { // subsample.add(reads[i]); // } else { // Read[] readsSubsample = subsample.toArray(new Read[subsample.size()]); // ModelSelection msSubsample = new ModelSelection(readsSubsample, Kmin, Kmax, L, n); // subsample.clear(); // saveSubSample(msSubsample.getOptimalResult().getMu(), generators, L); // } // } // for (Map.Entry<String, Integer> e : generators.entrySet()) { // System.out.println(e.getValue() + "\t" + e.getKey()); // } // } else { ms = new ModelSelection(reads, Kmin, Kmax, L, n); if (!Globals.getINSTANCE().isNOSAMPLE()) { ModelSampling modelSampling = new ModelSampling(ms.getOptimalResult(), Globals.getINSTANCE().getSAVEPATH()); modelSampling.save(); System.out .println("\nQuasispecies saved: " + Globals.getINSTANCE().getSAVEPATH() + "quasispecies.fasta"); } if (!Globals.getINSTANCE().isDEBUG()) { deleteDirectory( new File(Globals.getINSTANCE().getSAVEPATH() + "support" + File.separator + "snapshots")); } // } // errorCorrection(ms, reads); }
From source file:org.apache.distributedlog.feature.DynamicConfigurationFeatureProvider.java
@Override public void start() throws IOException { List<FileConfigurationBuilder> fileConfigBuilders = Lists.newArrayListWithExpectedSize(2); String baseConfigPath = conf.getFileFeatureProviderBaseConfigPath(); checkNotNull(baseConfigPath);//from www. ja v a 2 s. c o m File baseConfigFile = new File(baseConfigPath); FileConfigurationBuilder baseProperties = new PropertiesConfigurationBuilder( baseConfigFile.toURI().toURL()); fileConfigBuilders.add(baseProperties); String overlayConfigPath = conf.getFileFeatureProviderOverlayConfigPath(); if (null != overlayConfigPath) { File overlayConfigFile = new File(overlayConfigPath); FileConfigurationBuilder overlayProperties = new PropertiesConfigurationBuilder( overlayConfigFile.toURI().toURL()); fileConfigBuilders.add(overlayProperties); } try { this.featuresConfSubscription = new ConfigurationSubscription(this.featuresConf, fileConfigBuilders, executorService, conf.getDynamicConfigReloadIntervalSec(), TimeUnit.SECONDS); } catch (ConfigurationException e) { throw new IOException("Failed to register subscription on features configuration"); } this.featuresConfSubscription.registerListener(this); }
From source file:com.android.tools.lint.client.api.OtherFileVisitor.java
/** Analyze other files in the given project */ void scan(@NonNull LintDriver driver, @NonNull Project project, @Nullable Project main) { // Collect all project files File projectFolder = project.getDir(); EnumSet<Scope> scopes = EnumSet.noneOf(Scope.class); for (Detector detector : mDetectors) { OtherFileScanner fileScanner = (OtherFileScanner) detector; EnumSet<Scope> applicable = fileScanner.getApplicableFiles(); if (applicable.contains(Scope.OTHER)) { scopes = Scope.ALL;//from w w w . ja v a 2 s . c om break; } scopes.addAll(applicable); } List<File> subset = project.getSubset(); if (scopes.contains(Scope.RESOURCE_FILE)) { if (subset != null && !subset.isEmpty()) { List<File> files = new ArrayList<File>(subset.size()); for (File file : subset) { if (SdkUtils.endsWith(file.getPath(), DOT_XML) && !file.getName().equals(ANDROID_MANIFEST_XML)) { files.add(file); } } if (!files.isEmpty()) { mFiles.put(Scope.RESOURCE_FILE, files); } } else { List<File> files = Lists.newArrayListWithExpectedSize(100); for (File res : project.getResourceFolders()) { collectFiles(files, res); } File assets = new File(projectFolder, FD_ASSETS); if (assets.exists()) { collectFiles(files, assets); } if (!files.isEmpty()) { mFiles.put(Scope.RESOURCE_FILE, files); } } } if (scopes.contains(Scope.JAVA_FILE)) { if (subset != null && !subset.isEmpty()) { List<File> files = new ArrayList<File>(subset.size()); for (File file : subset) { if (file.getPath().endsWith(DOT_JAVA)) { files.add(file); } } if (!files.isEmpty()) { mFiles.put(Scope.JAVA_FILE, files); } } else { List<File> files = Lists.newArrayListWithExpectedSize(100); for (File srcFolder : project.getJavaSourceFolders()) { collectFiles(files, srcFolder); } if (!files.isEmpty()) { mFiles.put(Scope.JAVA_FILE, files); } } } if (scopes.contains(Scope.CLASS_FILE)) { if (subset != null && !subset.isEmpty()) { List<File> files = new ArrayList<File>(subset.size()); for (File file : subset) { if (file.getPath().endsWith(DOT_CLASS)) { files.add(file); } } if (!files.isEmpty()) { mFiles.put(Scope.CLASS_FILE, files); } } else { List<File> files = Lists.newArrayListWithExpectedSize(100); for (File classFolder : project.getJavaClassFolders()) { collectFiles(files, classFolder); } if (!files.isEmpty()) { mFiles.put(Scope.CLASS_FILE, files); } } } if (scopes.contains(Scope.MANIFEST)) { if (subset != null && !subset.isEmpty()) { List<File> files = new ArrayList<File>(subset.size()); for (File file : subset) { if (file.getName().equals(ANDROID_MANIFEST_XML)) { files.add(file); } } if (!files.isEmpty()) { mFiles.put(Scope.MANIFEST, files); } } else { List<File> manifestFiles = project.getManifestFiles(); if (manifestFiles != null) { mFiles.put(Scope.MANIFEST, manifestFiles); } } } for (Map.Entry<Scope, List<File>> entry : mFiles.entrySet()) { Scope scope = entry.getKey(); List<File> files = entry.getValue(); List<Detector> applicable = new ArrayList<Detector>(mDetectors.size()); for (Detector detector : mDetectors) { OtherFileScanner fileScanner = (OtherFileScanner) detector; EnumSet<Scope> appliesTo = fileScanner.getApplicableFiles(); if (appliesTo.contains(Scope.OTHER) || appliesTo.contains(scope)) { applicable.add(detector); } } if (!applicable.isEmpty()) { for (File file : files) { Context context = new Context(driver, project, main, file); for (Detector detector : applicable) { detector.beforeCheckFile(context); detector.run(context); detector.afterCheckFile(context); } if (driver.isCanceled()) { return; } } } } }
From source file:org.nmdp.ngs.align.BiojavaPairwiseAlignment.java
@Override public Iterable<AlignmentPair> global(final List<Sequence> queries, final List<Sequence> subjects, final GapPenalties gapPenalties) { checkNotNull(queries);/*from www. j av a2s . com*/ checkNotNull(subjects); checkNotNull(gapPenalties); if (queries.isEmpty() || subjects.isEmpty()) { return Collections.<AlignmentPair>emptyList(); } NeedlemanWunsch needlemanWunsch = new NeedlemanWunsch(gapPenalties.match(), gapPenalties.replace(), gapPenalties.insert(), gapPenalties.delete(), gapPenalties.extend(), getSubstitutionMatrix()); List<AlignmentPair> alignmentPairs = Lists.newArrayListWithExpectedSize(queries.size() * subjects.size()); for (Sequence query : queries) { for (Sequence subject : subjects) { try { AlignmentPair alignmentPair = needlemanWunsch.pairwiseAlignment(query, subject); alignmentPairs.add(alignmentPair); } catch (BioException e) { // todo } } } return alignmentPairs; }
From source file:org.spongepowered.common.data.processor.data.tileentity.SignDataProcessor.java
@Override public Optional<SignData> from(DataHolder dataHolder) { if (dataHolder instanceof TileEntitySign) { final SignData signData = new SpongeSignData(); final IChatComponent[] rawLines = ((TileEntitySign) dataHolder).signText; final List<Text> signLines = Lists.newArrayListWithExpectedSize(4); for (int i = 0; i < rawLines.length; i++) { signLines.add(i, SpongeTexts.toText(rawLines[i])); }// w w w.j a v a 2 s. c o m return Optional.of(signData.set(Keys.SIGN_LINES, signLines)); } else if (dataHolder instanceof ItemStack) { if (!((ItemStack) dataHolder).hasTagCompound()) { return Optional.empty(); } else { final NBTTagCompound mainCompound = ((ItemStack) dataHolder).getTagCompound(); if (!mainCompound.hasKey(NbtDataUtil.BLOCK_ENTITY_TAG, NbtDataUtil.TAG_COMPOUND) || !mainCompound .getCompoundTag(NbtDataUtil.BLOCK_ENTITY_TAG).hasKey(NbtDataUtil.BLOCK_ENTITY_ID)) { return Optional.empty(); } final NBTTagCompound tileCompound = mainCompound.getCompoundTag(NbtDataUtil.BLOCK_ENTITY_TAG); final String id = tileCompound.getString(NbtDataUtil.BLOCK_ENTITY_ID); if (!id.equalsIgnoreCase(NbtDataUtil.SIGN)) { return Optional.empty(); } final List<Text> texts = Lists.newArrayListWithCapacity(4); texts.add(Texts.legacy().fromUnchecked(tileCompound.getString("Text1"))); texts.add(Texts.legacy().fromUnchecked(tileCompound.getString("Text2"))); texts.add(Texts.legacy().fromUnchecked(tileCompound.getString("Text3"))); texts.add(Texts.legacy().fromUnchecked(tileCompound.getString("Text4"))); return Optional.of(new SpongeSignData(texts)); } } return Optional.empty(); }
From source file:com.yahoo.yqlplus.engine.internal.source.InsertMethod.java
private OperatorNode<PhysicalExprOperator> createInvocation(Location location, OperatorNode<PhysicalExprOperator> source, ContextPlanner planner, OperatorNode<PhysicalExprOperator> recordOrRecords) { List<OperatorNode<PhysicalExprOperator>> callArgs = Lists.newArrayListWithExpectedSize(2); callArgs.add(source);/*from w w w.j a v a 2 s . c o m*/ callArgs.add(OperatorNode.create(PhysicalExprOperator.CURRENT_CONTEXT)); callArgs.add(recordOrRecords); OperatorNode<PhysicalExprOperator> invocation = OperatorNode.create(location, invoker.getReturnType().isPromise() ? PhysicalExprOperator.ASYNC_INVOKE : PhysicalExprOperator.INVOKE, invoker, callArgs); if (minimumBudget > 0 || maximumBudget > 0) { OperatorNode<PhysicalExprOperator> ms = planner.constant(TimeUnit.MILLISECONDS); OperatorNode<PhysicalExprOperator> subContext = OperatorNode.create(PhysicalExprOperator.TIMEOUT_GUARD, planner.constant(minimumBudget), ms, planner.constant(maximumBudget), ms); return OperatorNode.create(PhysicalExprOperator.WITH_CONTEXT, subContext, OperatorNode.create(PhysicalExprOperator.ENFORCE_TIMEOUT, invocation)); } return invocation; }