List of usage examples for java.util.function Consumer Consumer
Consumer
From source file:com.gs.collections.impl.parallel.SerialParallelLazyPerformanceTest.java
private void forEach(FastList<Integer> collection) { MutableList<Runnable> runnables = FastList.newList(); runnables.add(() -> this.basicSerialForEachPerformance(collection, SERIAL_RUN_COUNT)); int cores = Runtime.getRuntime().availableProcessors(); ExecutorService service = Executors.newFixedThreadPool(cores); runnables.add(() -> {//from w w w . j a v a 2s .co m MutableMap<Integer, Boolean> map = new ConcurrentHashMap<>(); this.basicParallelLazyForEachPerformance(collection, "Lambda", item -> map.put(item, Boolean.TRUE), PARALLEL_RUN_COUNT, cores, service); }); runnables.add(() -> { MutableMap<Integer, Boolean> map = new ConcurrentHashMap<>(); this.basicParallelLazyForEachPerformance(collection, "Procedure", new Procedure<Integer>() { @Override public void value(Integer each) { map.put(each, Boolean.TRUE); } }, PARALLEL_RUN_COUNT, cores, service); }); runnables.add(() -> { MutableMap<Integer, Boolean> map = new ConcurrentHashMap<>(); this.basicJava8ParallelLazyForEachPerformance(collection, "Lambda", item -> map.put(item, Boolean.TRUE), PARALLEL_RUN_COUNT); }); List<Integer> arrayList = new ArrayList<>(collection); runnables.add(() -> { MutableMap<Integer, Boolean> map = new ConcurrentHashMap<>(); this.basicJava8ParallelLazyForEachPerformance(arrayList, "Lambda", item -> map.put(item, Boolean.TRUE), PARALLEL_RUN_COUNT); }); runnables.add(() -> { MutableMap<Integer, Boolean> map = new ConcurrentHashMap<>(); this.basicJava8ParallelLazyForEachPerformance(arrayList, "Consumer", new Consumer<Integer>() { @Override public void accept(Integer each) { map.put(each, Boolean.TRUE); } }, PARALLEL_RUN_COUNT); }); this.shuffleAndRun(runnables); service.shutdown(); try { service.awaitTermination(1, TimeUnit.MINUTES); } catch (InterruptedException e) { throw new RuntimeException(e); } }
From source file:com.taobao.android.builder.manager.AtlasAppTaskManager.java
@Override public void runTask() { appExtension.getApplicationVariants().forEach(new Consumer<ApplicationVariant>() { @Override//from w ww . j a va2 s . c om public void accept(ApplicationVariant applicationVariant) { AppVariantContext appVariantContext = AtlasBuildContext.sBuilderAdapter.appVariantContextFactory .getAppVariantContext(project, applicationVariant); if (!AtlasBuildContext.atlasMainDexHelperMap.containsKey(appVariantContext.getVariantName())) { AtlasBuildContext.atlasMainDexHelperMap.put(appVariantContext.getVariantName(), new AtlasMainDexHelper()); } TransformReplacer transformReplacer = new TransformReplacer(appVariantContext); repalceAndroidBuilder(applicationVariant); List<MtlTaskContext> mtlTaskContextList = new ArrayList<MtlTaskContext>(); mtlTaskContextList.add(new MtlTaskContext(appVariantContext.getVariantData().preBuildTask)); mtlTaskContextList.add(new MtlTaskContext(BuildAtlasEnvTask.ConfigAction.class, null)); mtlTaskContextList.add(new MtlTaskContext(ScanDupResTask.ConfigActon.class, null)); mtlTaskContextList.add(new MtlTaskContext(LogDependenciesTask.ConfigAction.class, null)); mtlTaskContextList.add(new MtlTaskContext(PrepareAPTask.ConfigAction.class, null)); mtlTaskContextList.add(new MtlTaskContext(appVariantContext.getVariantData().mergeAssetsTask)); mtlTaskContextList.add(new MtlTaskContext(RenderscriptCompile.class)); mtlTaskContextList.add(new MtlTaskContext(StandardizeLibManifestTask.ConfigAction.class, null)); mtlTaskContextList.add(new MtlTaskContext(PrepareBundleInfoTask.ConfigAction.class, null)); if (!atlasExtension.getTBuildConfig().getClassInject() && atlasExtension.isAtlasEnabled()) { mtlTaskContextList.add(new MtlTaskContext(GenerateAtlasSourceTask.ConfigAction.class, null)); } mtlTaskContextList.add(new MtlTaskContext(PreparePackageIdsTask.ConfigAction.class, null)); mtlTaskContextList.add(new MtlTaskContext(PrepareAaptTask.ConfigAction.class, null)); mtlTaskContextList.add(new MtlTaskContext(AidlCompile.class)); mtlTaskContextList.add(new MtlTaskContext(GenerateBuildConfig.class)); mtlTaskContextList.add(new MtlTaskContext(MergeResAwbsConfigAction.class, null)); mtlTaskContextList.add(new MtlTaskContext(MergeAssetAwbsConfigAction.class, null)); if (null != androidExtension.getDataBinding() && androidExtension.getDataBinding().isEnabled()) { // mtlTaskContextList.add( // new MtlTaskContext(AwbDataBindingProcessLayoutTask.ConfigAction.class, null)); mtlTaskContextList .add(new MtlTaskContext(AwbDataBindingExportBuildInfoTask.ConfigAction.class, null)); mtlTaskContextList .add(new MtlTaskContext(AwbDataBindingMergeArtifactsTask.ConfigAction.class, null)); } mtlTaskContextList.add(new MtlTaskContext(MergeManifests.class)); mtlTaskContextList.add(new MtlTaskContext(MergeManifestAwbsConfigAction.class, null)); //mtlTaskContextList.add(new MtlTaskContext(MergeResV4Dir.ConfigAction.class, null)); mtlTaskContextList.add(new MtlTaskContext(ProcessAndroidResources.class)); ProcessAndroidResources processAndroidResources = appVariantContext.getScope() .getProcessResourcesTask() .get(new TaskContainerAdaptor(appVariantContext.getProject().getTasks())); if (processAndroidResources.isAapt2Enabled()) { processAndroidResources.doLast(new Action<Task>() { @Override public void execute(Task task) { File processResourcePackageOutputDirectory = appVariantContext.getScope() .getProcessResourcePackageOutputDirectory(); File[] files = processResourcePackageOutputDirectory .listFiles((file, name) -> name.endsWith(SdkConstants.DOT_RES)); for (File file : files) { try { ResourcePatch.makePatchable(file); } catch (IOException e) { throw new UncheckedIOException(e); } } } }); } mtlTaskContextList.add(new MtlTaskContext(ProcessResAwbsTask.ConfigAction.class, null)); mtlTaskContextList.add(new MtlTaskContext(JavacAwbsTask.ConfigAction.class, null)); if (null != androidExtension.getDataBinding() && androidExtension.getDataBinding().isEnabled()) { mtlTaskContextList.add(new MtlTaskContext(AwbDataBindingRenameTask.ConfigAction.class, null)); } mtlTaskContextList.add(new MtlTaskContext(TransformTask.class)); mtlTaskContextList.add(new MtlTaskContext(PackageAwbsTask.ConfigAction.class, null)); if (appVariantContext.getAtlasExtension().getTBuildConfig().isIncremental() && (appVariantContext.getBuildType().getPatchConfig() == null || !appVariantContext.getBuildType().getPatchConfig().isCreateTPatch())) { // mtlTaskContextList.add(new MtlTaskContext(PrepareBaseApkTask.ConfigAction.class, null)); final TaskFactory tasks = new TaskContainerAdaptor(project.getTasks()); VariantScope variantScope = appVariantContext.getVariantData().getScope(); // create the stream generated from this task variantScope.getTransformManager() .addStream(OriginalStream.builder(project, applicationVariant.getName()) .addContentType(QualifiedContent.DefaultContentType.RESOURCES) .addScope(QualifiedContent.Scope.PROJECT) .setFolders(new Supplier<Collection<File>>() { @Override public Collection<File> get() { return ImmutableList .of(new File(appVariantContext.apContext.getBaseApk() + "_")); } }).build()); } final TaskFactory tasks = new TaskContainerAdaptor(project.getTasks()); VariantScope variantScope = appVariantContext.getVariantData().getScope(); mtlTaskContextList.add(new MtlTaskContext(PackageApplication.class)); if (appVariantContext.getAtlasExtension().isInstantAppEnabled()) { mtlTaskContextList.add(new MtlTaskContext(AtlasBundleInstantApp.ConfigAction.class, null)); } mtlTaskContextList.add(new MtlTaskContext(ApBuildTask.ConfigAction.class, null)); mtlTaskContextList.add(new MtlTaskContext(DiffBundleInfoTask.ConfigAction.class, null)); mtlTaskContextList.add(new MtlTaskContext(TPatchDiffResAPBuildTask.ConfigAction.class, null)); mtlTaskContextList.add(new MtlTaskContext(TPatchDiffApkBuildTask.ConfigAction.class, null)); mtlTaskContextList.add(new MtlTaskContext(TPatchTask.ConfigAction.class, null)); mtlTaskContextList.add(new MtlTaskContext("assemble")); new MtlTaskInjector(appVariantContext).injectTasks(mtlTaskContextList, tAndroidBuilder); List<MtlTransformContext> mtlTransformContextList = new ArrayList<MtlTransformContext>(); if (atlasExtension.getTBuildConfig().getClassInject()) { mtlTransformContextList.add(new MtlTransformContext(ClassInjectTransform.class, ProGuardTransform.class, DexTransform.class)); } if (!mtlTransformContextList.isEmpty()) { new MtlTransformInjector(appVariantContext).injectTasks(mtlTransformContextList); } Collection<BaseVariantOutput> baseVariantOutputDataList = appVariantContext.getVariantOutputData(); boolean multiDexEnabled = appVariantContext.getVariantData().getVariantConfiguration() .isMultiDexEnabled(); if (atlasExtension.getTBuildConfig().isAtlasMultiDex() && multiDexEnabled) { transformReplacer.replaceMultiDexListTransform(); } transformReplacer.replaceProguardTransform(); transformReplacer.disableCache(); if (variantScope.getGlobalScope().getExtension().getDataBinding().isEnabled()) { transformReplacer.replaceDataBindingMergeArtifactsTransform(); } for (final BaseVariantOutput vod : baseVariantOutputDataList) { transformReplacer.replaceFixStackFramesTransform(vod); transformReplacer.replaceDesugarTransform(vod); transformReplacer.replaceDexArchiveBuilderTransform(vod); transformReplacer.replaceDexExternalLibMerge(vod); transformReplacer.replaceDexMerge(vod); transformReplacer.replaceDexTransform(appVariantContext, vod); transformReplacer.replaceShrinkResourcesTransform(); transformReplacer.replaceMergeJavaResourcesTransform(appVariantContext, vod); if (atlasExtension.getTBuildConfig().isIncremental()) { InstantRunPatchingPolicy patchingPolicy = variantScope.getInstantRunBuildContext() .getPatchingPolicy(); BaseVariantOutputImpl variantOutput = (BaseVariantOutputImpl) vod; ApkData data = ApkDataUtils.get(variantOutput); AtlasDependencyTree atlasDependencyTree = AtlasBuildContext.androidDependencyTrees .get(variantScope.getFullVariantName()); // for (AwbBundle awbBundle : atlasDependencyTree.getAwbBundles()) { // AndroidTask<Dex> dexTask = androidTasks.create(tasks, new Dex.ConfigAction( // appVariantContext.getVariantData().getScope(), appVariantContext.getAppVariantOutputContext(data), awbBundle)); // dexTask.dependsOn(tasks, Iterables // .getLast(TaskQueryHelper.findTask(project, TransformTask.class, appVariantContext.getVariantData()))); // PackagingScope packagingScope = new AwbPackagingScope(appVariantContext.getScope(), appVariantContext, // awbBundle,vod); // AndroidTask<PackageAwb> packageAwb = androidTasks.create(tasks, // new PackageAwb // .StandardConfigAction( // packagingScope, // patchingPolicy)); //// // packageAwb.dependsOn(tasks, dexTask); // PackageAwbsTask packageAwbsTask = Iterators.getOnlyElement( // TaskQueryHelper.findTask(project, PackageAwbsTask.class, appVariantContext.getVariantData()).iterator()); // packageAwbsTask.setEnabled(false); // packageAwbsTask.dependsOn(packageAwb.get(tasks)); // } // AndroidTask<AwoInstallTask> awoInstallTask = androidTasks.create(tasks, // new AwoInstallTask.ConfigAction(appVariantContext, vod)); // awoInstallTask.dependsOn(tasks, variantScope.getPackageApplicationTask().getName()); } } Boolean includeCompileClasspath = appVariantContext.getScope().getVariantConfiguration() .getJavaCompileOptions().getAnnotationProcessorOptions().getIncludeCompileClasspath(); appVariantContext.getVariantData().javaCompilerTask.doFirst(task -> { JavaCompile compile = (JavaCompile) task; Set<File> mainDexFiles = new MainFilesCollection(appVariantContext.getVariantName()).getFiles(); FileCollection mainFiles = appVariantContext.getProject().files(mainDexFiles); FileCollection files = appVariantContext.getScope() .getArtifactFileCollection(ANNOTATION_PROCESSOR, ALL, JAR); FileCollection bootFiles = appVariantContext.getProject().files(appVariantContext.getScope() .getGlobalScope().getAndroidBuilder().getBootClasspath(false)); mainFiles = mainFiles.plus(bootFiles); FileCollection fileCollection = compile.getClasspath(); File kotlinClasses = null; for (File file : fileCollection) { if (file.getAbsolutePath().contains("kotlin-classes")) { mainFiles = mainFiles.plus(appVariantContext.getProject().files(file)); kotlinClasses = file; break; } } compile.setClasspath(mainFiles); if (Boolean.TRUE.equals(includeCompileClasspath)) { compile.getOptions().setAnnotationProcessorPath(files.plus(mainFiles)); } }); appVariantContext.getVariantData().javaCompilerTask.doLast(new Action<Task>() { @Override public void execute(Task task) { JavaCompile compile = (JavaCompile) task; AtlasBuildContext.atlasMainDexHelperMap.get(appVariantContext.getVariantName()) .getInputDirs().add(compile.getDestinationDir()); } }); PackageAndroidArtifact packageAndroidArtifact = appVariantContext.getVariantData() .getTaskByType(PackageAndroidArtifact.class); if (packageAndroidArtifact != null) { ReflectUtils.updateField(packageAndroidArtifact, "javaResourceFiles", new AbstractFileCollection() { @Override public String getDisplayName() { return "java-merge-res.jar"; } @Override public Set<File> getFiles() { if (AtlasBuildContext.atlasMainDexHelperMap .get(packageAndroidArtifact.getVariantName()) .getMainJavaRes() == null) { return Sets.newHashSet(); } return Sets.newHashSet(AtlasBuildContext.atlasMainDexHelperMap .get(packageAndroidArtifact.getVariantName()).getMainJavaRes()); } }); } TaskCollection<ExtractTryWithResourcesSupportJar> taskCollection = appVariantContext.getProject() .getTasks().withType(ExtractTryWithResourcesSupportJar.class); for (ExtractTryWithResourcesSupportJar task : taskCollection) { task.doLast(new Action<Task>() { @Override public void execute(Task task) { ConfigurableFileCollection fileCollection = variantScope .getTryWithResourceRuntimeSupportJar(); for (File file : fileCollection.getFiles()) { if (file.exists()) { AtlasBuildContext.atlasMainDexHelperMap.get(variantScope.getFullVariantName()) .addMainDex(new BuildAtlasEnvTask.FileIdentity( "runtime-deps-try-with-resources", file, false, false)); break; } } } }); } } }); }
From source file:gedi.atac.Atac.java
public static void perChromosomeAndLengthStatistics(GenomicRegionStorage<? extends AlignedReadsData> storage, String chrPath, String lenPath) throws IOException { LineOrientedFile chr = new LineOrientedFile(chrPath); LineOrientedFile len = new LineOrientedFile(lenPath); chr.startWriting();/*from w w w .j av a2s .com*/ len.startWriting(); chr.write("chromosome"); len.write("Length"); for (DynamicObject cond : storage.getMetaData().get("conditions").asArray()) { chr.writef("\t%s", cond.getEntry("name").asString()); len.writef("\t%s", cond.getEntry("name").asString()); } chr.writeLine(); len.writeLine(); IntArrayList[] lenHisto = new IntArrayList[storage.getRandomRecord().getNumConditions()]; for (int i = 0; i < lenHisto.length; i++) lenHisto[i] = new IntArrayList(); for (ReferenceSequence ref : storage.getReferenceSequences()) { MutableMonad<long[]> count = new MutableMonad<long[]>(); storage.iterateMutableReferenceGenomicRegions(ref) .forEachRemaining(new Consumer<MutableReferenceGenomicRegion<? extends AlignedReadsData>>() { @Override public void accept(MutableReferenceGenomicRegion<? extends AlignedReadsData> mrgr) { if (count.Item == null) count.Item = new long[mrgr.getData().getNumConditions()]; for (int d = 0; d < mrgr.getData().getDistinctSequences(); d++) // if (mrgr.getData().getMultiplicity(d)==1) for (int i = 0; i < count.Item.length; i++) { count.Item[i] += mrgr.getData().getCount(d, i) > 0 ? 1 : 0; lenHisto[i].increment(mrgr.getRegion().getTotalLength(), mrgr.getData().getCount(d, i) > 0 ? 1 : 0); } } }); if (count.Item != null) { chr.write(ref.toString()); for (int i = 0; i < count.Item.length; i++) chr.writef("\t%s", count.Item[i]); chr.writeLine(); } } int maxLength = 0; for (int i = 0; i < lenHisto.length; i++) maxLength = Math.max(maxLength, lenHisto[i].size() - 1); for (int l = 1; l <= maxLength; l++) { len.writef("%d", l); for (int i = 0; i < lenHisto.length; i++) len.writef("\t%d", lenHisto[i].getInt(l)); len.writeLine(); } chr.finishWriting(); len.finishWriting(); }
From source file:gov.va.isaac.sync.view.SyncView.java
private Set<String> resolveMergeFailure(MergeFailure mf) throws IllegalArgumentException, IOException { Set<String> changedFiles = mf.getFilesChangedDuringMergeAttempt(); CountDownLatch cdl = new CountDownLatch(1); HashMap<String, MergeFailOption> resolutions = new HashMap<String, MergeFailOption>(); Platform.runLater(() -> {/*from w w w . j a v a 2 s .c o m*/ new ResolveConflicts(root_.getScene().getWindow(), mf.getMergeFailures(), new Consumer<HashMap<String, MergeFailOption>>() { @Override public void accept(HashMap<String, MergeFailOption> t) { resolutions.putAll(t); cdl.countDown(); } }); }); try { cdl.await(); } catch (InterruptedException e) { log.info("Interrupted during wait for resolutions"); } try { syncService_.resolveMergeFailures(resolutions); } catch (MergeFailure nestedMF) { changedFiles.addAll(resolveMergeFailure(nestedMF)); } return changedFiles; }
From source file:module.siadap.domain.Siadap.java
@Atomic public void createCurricularPonderation(SiadapUniverse siadapUniverse, BigDecimal gradeToAssign, Boolean assignedExcellency, String excellencyAwardJustification, String curricularPonderationJustification, Person evaluator) { // let's validate everything if (siadapUniverse == null || assignedExcellency == null || evaluator == null || !SiadapGlobalEvaluation.isValidGrade(gradeToAssign, assignedExcellency.booleanValue()) || (assignedExcellency.booleanValue() && StringUtils.isEmpty(excellencyAwardJustification)) || StringUtils.isEmpty(curricularPonderationJustification)) { throw new SiadapException("invalid.data.for.creation.of.a.curricular.ponderation"); }/*from ww w .j a va 2 s. co m*/ // let's if we don't have an evaluation for the given universe if (getSiadapEvaluationUniverseForSiadapUniverse(siadapUniverse) != null) { throw new SiadapException("error.curricular.ponderation.cannot.have.more.than.one.eval.for.universe"); } SiadapYearConfiguration siadapYearConfiguration = getSiadapYearConfiguration(); Unit siadapSpecialHarmonizationUnit = siadapYearConfiguration.getSiadapSpecialHarmonizationUnit(); if (siadapSpecialHarmonizationUnit == null) { throw new SiadapException("error.must.configure.special.harmonnization.unit.first"); } final AccountabilityType accTypeToReplace; if (siadapUniverse.equals(SiadapUniverse.SIADAP2)) { accTypeToReplace = siadapYearConfiguration.getSiadap2HarmonizationRelation(); } else if (siadapUniverse.equals(SiadapUniverse.SIADAP3)) { accTypeToReplace = siadapYearConfiguration.getSiadap3HarmonizationRelation(); } else { accTypeToReplace = null; } if (accTypeToReplace == null) { throw new SiadapException("error.must.configure.SIADAP.2.and.3.harm.relation.types.first"); } // let's create the new SiadapEvaluationUniverse SiadapEvaluationUniverse siadapEvaluationUniverse = new SiadapEvaluationUniverse(this, siadapUniverse, null, false); CurricularPonderationEvaluationItem curricularPonderationEvaluationItem = new CurricularPonderationEvaluationItem( gradeToAssign, assignedExcellency, excellencyAwardJustification, curricularPonderationJustification, siadapEvaluationUniverse, evaluator); // let's connect this SiadapEvaluationUniverse with the specialunit Person evaluated = getEvaluated(); // let's remove the current accountability that it might have for the // given SiadapUniverse // let's search for the previous accountability evaluated.getParentAccountabilityStream() .filter(a -> accTypeToReplace == null || a.getAccountabilityType() == accTypeToReplace) .filter(a -> a.getParent() instanceof Unit && a.isActive(SiadapMiscUtilClass.lastDayOfYear(getYear()))) .findAny().ifPresent(new Consumer<Accountability>() { @Override public void accept(Accountability t) { throw new SiadapException("already.with.a.curricular.ponderation.attributed"); } }); LocalDate dateToUse = getSiadapYearConfiguration().getLastDayForAccountabilities(); evaluated.addParent(siadapSpecialHarmonizationUnit, accTypeToReplace, dateToUse, SiadapMiscUtilClass.lastDayOfYear(getYear()), null); }
From source file:gedi.atac.Atac.java
public static void lengthPerTypeStatistics(GenomicRegionStorage<? extends AlignedReadsData> storage, String out, String aggOut, String... typePattern) throws IOException { IntArrayList[][] lenHisto = new IntArrayList[typePattern.length][storage.getRandomRecord() .getNumConditions()];//from w w w . j a va2 s . com for (int t = 0; t < lenHisto.length; t++) for (int i = 0; i < lenHisto[t].length; i++) lenHisto[t][i] = new IntArrayList(); Pattern[] types = new Pattern[typePattern.length]; for (int i = 0; i < types.length; i++) types[i] = Pattern.compile(typePattern[i]); for (ReferenceSequence ref : storage.getReferenceSequences()) { int ty = 0; for (; ty < types.length && !types[ty].matcher(ref.toPlusMinusString()).find(); ty++) ; if (ty < types.length) System.out.println(ref + " -> " + types[ty]); else System.out.println("Skipping " + ref); MutableMonad<long[]> count = new MutableMonad<long[]>(); int tyind = ty; if (ty < types.length) storage.iterateMutableReferenceGenomicRegions(ref).forEachRemaining( new Consumer<MutableReferenceGenomicRegion<? extends AlignedReadsData>>() { @Override public void accept(MutableReferenceGenomicRegion<? extends AlignedReadsData> mrgr) { if (count.Item == null) count.Item = new long[mrgr.getData().getNumConditions()]; for (int i = 0; i < count.Item.length; i++) { count.Item[i] += mrgr.getData().getTotalCountForConditionInt(i, ReadCountMode.All); lenHisto[tyind][i].increment(mrgr.getRegion().getTotalLength(), mrgr.getData().getTotalCountForConditionInt(i, ReadCountMode.All)); } } }); } LineOrientedFile o = new LineOrientedFile(out); o.startWriting(); o.write("Type\tLength"); for (DynamicObject cond : storage.getMetaData().get("conditions").asArray()) { o.writef("\t%s", cond.getEntry("name").asString()); } o.writeLine(); int maxLength = 0; for (int t = 0; t < lenHisto.length; t++) for (int i = 0; i < lenHisto.length; i++) maxLength = Math.max(maxLength, lenHisto[t][i].size() - 1); for (int t = 0; t < lenHisto.length; t++) for (int l = 1; l <= maxLength; l++) { o.writef("%s\t%d", typePattern[t], l); for (int i = 0; i < lenHisto[t].length; i++) o.writef("\t%d", lenHisto[t][i].getInt(l)); o.writeLine(); } o.finishWriting(); o = new LineOrientedFile(aggOut); o.startWriting(); o.write("Type"); for (DynamicObject cond : storage.getMetaData().get("conditions").asArray()) { o.writef("\t%s", cond.getEntry("name").asString()); } o.writeLine(); for (int t = 0; t < lenHisto.length; t++) { o.writef("%s", typePattern[t]); for (int i = 0; i < lenHisto[t].length; i++) { long sum = 0; for (int l = 1; l <= maxLength; l++) sum += lenHisto[t][i].getInt(l); o.writef("\t%d", sum); } o.writeLine(); } o.finishWriting(); }
From source file:dk.dma.ais.store.FileExportRest.java
private AisReader aisReadWriter(InputStream in) throws Exception { AisReader r = AisReaders.createReaderFromInputStream(in); r.registerPacketHandler(new Consumer<AisPacket>() { @Override/*www. j ava2 s. c o m*/ public void accept(AisPacket t) { AisMessage message = t.tryGetAisMessage(); // System.out.println(message.toString()); currentTimeStamp = t.getBestTimestamp(); if (lastLoadedTimestamp >= currentTimeStamp) { // System.out.println("Skipping Message!"); return; } if (message == null) { return; } try { sink.process(outputStream, t, counter.incrementAndGet()); if (currentTimeStamp != lastFlushTimestamp && counter.get() % 10000 == 0) { // We have a new timestamp sequence lastFlushTimestamp = currentTimeStamp; writeMetaUpdate(lastFlushTimestamp, counter.get()); // Force flush on both outputStream.flush(); fileOutputStream.flush(); // Write // lastFlushTimestamp // timestamp // if (counter.get() >= 1000) { // System.out.println("Terminating as part of test! Last written timestamp was " + lastFlushTimestamp); // System.exit(0); // } // Update user on progress printDownloadStatus(); } // } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } } }); return r; }
From source file:com.diversityarrays.kdxplore.boxplot.BoxPlotPanel.java
private void setSelectedTraitAndMeasurements() { boolean sync = getSyncWhat().isSync(); PlotsByTraitInstance plotsByTi = sync ? new PlotsByTraitInstance() : null; List<KdxSample> selectedSamples = new ArrayList<>(); if (minSelectedY != null && maxSelectedY != null) { for (Plot plot : plotInfoProvider.getPlots()) { Consumer<KdxSample> visitor = new Consumer<KdxSample>() { @Override//from www . j a va 2 s . co m public void accept(KdxSample s) { TraitInstance ti = plotInfoProvider.getTraitInstanceForSample(s); if (checkIfSelected(s, minSelectedY, maxSelectedY) == AxisType.Y) { selectedSamples.add(s); if (plotsByTi != null) { plotsByTi.addPlot(ti, plot); } } } }; if (usedPlotSpecimens.isEmpty() || usedPlotSpecimens.contains(plot)) { plotInfoProvider.visitSamplesForPlotOrSpecimen(plot, visitor); } } } // TODO review not do it when empty if (plotsByTi != null) { // && ! plotsByTi.isEmpty()) { selectedValueStore.setSelectedPlots(toolPanelId, plotsByTi); } if (curationControls != null) { curationControls.setSamples(selectedSamples); int index = messagesAndCurationTabbedPane.indexOfTab(TAB_CURATION); if (index >= 0) { messagesAndCurationTabbedPane.setSelectedIndex(index); } // Note that curationControls is only non-null if we have ONE TraitInstance // so all of the selectedSampled must be for that TraitInstance curationControls.updateButtons(); } fireSelectionStateChanged(); }
From source file:gedi.atac.Atac.java
public static void normalizationFactors(GenomicRegionStorage<? extends AlignedReadsData> storage, GenomicRegionStorage<?> peaks, String out, String peakout, String detailout, String... typePattern) throws IOException { int cond = storage.getRandomRecord().getNumConditions(); int[][] allCounts = new int[typePattern.length][cond]; int[][] peakCounts = new int[typePattern.length][cond]; Pattern[] types = new Pattern[typePattern.length]; for (int i = 0; i < types.length; i++) types[i] = Pattern.compile(typePattern[i]); new LineOrientedFile(detailout).delete(); Set<ReferenceSequence> refs = new TreeSet<ReferenceSequence>(); for (ReferenceSequence ref : storage.getReferenceSequences()) refs.add(ref.toStrandIndependent()); for (ReferenceSequence ref : refs) { int ty = 0; for (; ty < types.length && !types[ty].matcher(ref.toPlusMinusString()).find(); ty++) ;/* w w w . j a va2s . c om*/ if (ty < types.length) System.out.println(ref + " -> " + types[ty]); else System.out.println("Skipping " + ref); HashMap<ImmutableReferenceGenomicRegion<?>, int[]> detail = new HashMap<ImmutableReferenceGenomicRegion<?>, int[]>(); int tyind = ty; Consumer<MutableReferenceGenomicRegion<? extends AlignedReadsData>> adder = new Consumer<MutableReferenceGenomicRegion<? extends AlignedReadsData>>() { @Override public void accept(MutableReferenceGenomicRegion<? extends AlignedReadsData> mrgr) { int f = GenomicRegionPosition.Start.position(ref, mrgr.getRegion(), 4); int b = GenomicRegionPosition.Stop.position(ref, mrgr.getRegion(), -4); int inpeak = 0; if (StreamSupport.stream(peaks.iterateIntersectingMutableReferenceGenomicRegions( ref.toStrandIndependent(), f, f + 1), false).peek(peak -> { int[] c = detail.computeIfAbsent(peak.toImmutable(), x -> new int[cond]); for (int i = 0; i < c.length; i++) c[i] += mrgr.getData().getTotalCountForConditionInt(i, ReadCountMode.All); }).count() > 0) inpeak++; if (StreamSupport.stream(peaks.iterateIntersectingMutableReferenceGenomicRegions( ref.toStrandIndependent(), b, b + 1), false).peek(peak -> { int[] c = detail.computeIfAbsent(peak.toImmutable(), x -> new int[cond]); for (int i = 0; i < c.length; i++) c[i] += mrgr.getData().getTotalCountForConditionInt(i, ReadCountMode.All); }).count() > 0) inpeak++; for (int i = 0; i < allCounts[tyind].length; i++) { allCounts[tyind][i] += mrgr.getData().getTotalCountForConditionInt(i, ReadCountMode.All); if (inpeak > 0) peakCounts[tyind][i] += mrgr.getData().getTotalCountForConditionInt(i, ReadCountMode.All) * inpeak; } } }; if (ty < types.length) { storage.iterateMutableReferenceGenomicRegions(ref).forEachRemaining(adder); storage.iterateMutableReferenceGenomicRegions(ref.toPlusStrand()).forEachRemaining(adder); storage.iterateMutableReferenceGenomicRegions(ref.toMinusStrand()).forEachRemaining(adder); } LineOrientedFile d = new LineOrientedFile(detailout); if (d.exists()) d.startAppending(); else { d.startWriting(); d.write("Peak\tType"); for (int i = 0; i < cond; i++) d.writef("\t%d", i); d.writeLine(); } for (ImmutableReferenceGenomicRegion<?> peak : detail.keySet()) { int[] count = detail.get(peak); d.writef("%s\t%s", peak.toLocationString(), typePattern[ty]); for (int c = 0; c < cond; c++) d.writef("\t%d", count[c]); d.writeLine(); } d.finishWriting(); } LineOrientedFile o = new LineOrientedFile(out); o.startWriting(); o.write("Type\tCondition Index\tCount\n"); for (int i = 0; i < types.length; i++) { for (int c = 0; c < allCounts[i].length; c++) { o.writef("%s\t%d\t%d\n", typePattern[i], c, allCounts[i][c]); } } o.finishWriting(); o = new LineOrientedFile(peakout); o.startWriting(); o.write("Type\tCondition Index\tCount\n"); for (int i = 0; i < types.length; i++) { for (int c = 0; c < allCounts[i].length; c++) { o.writef("%s\t%d\t%d\n", typePattern[i], c, peakCounts[i][c]); } } o.finishWriting(); }
From source file:pt.ist.expenditureTrackingSystem.domain.organization.Unit.java
public static void getSubUnitsSet(final Set<Unit> result, final Party party) { party.getChildAccountabilityStream().map(a -> a.getChild()).filter(p -> p.isUnit()) .map(p -> (module.organization.domain.Unit) p) .forEach(new Consumer<module.organization.domain.Unit>() { @Override//w w w . j av a 2 s . c om public void accept(final module.organization.domain.Unit u) { if (u.getExpenditureUnit() != null) { result.add(u.getExpenditureUnit()); } else { getSubUnitsSet(result, u); } } }); }