List of usage examples for org.apache.commons.lang ArrayUtils toPrimitive
public static boolean[] toPrimitive(Boolean[] array)
Converts an array of object Booleans to primitives.
From source file:aldenjava.opticalmapping.data.data.OptMapDataReader.java
private DataNode parseFA01() throws IOException { if (nextline == null) return null; String name = nextline.substring(1); StringBuilder zeroOneString = new StringBuilder(); String s;/*from ww w.j a v a 2s .c om*/ while ((s = br.readLine()) != null) { if (s.startsWith(">")) { nextline = s; break; } else zeroOneString = zeroOneString.append(s); } if (zeroOneString.length() == 0) return null; else { long ref_size = zeroOneString.length(); long zero = 0; List<Long> refl = new ArrayList<Long>(); List<Long> refp = new ArrayList<Long>(); for (long i = 0; i < ref_size; i++) { if (zeroOneString.charAt((int) i) == '0') zero++; else if (zeroOneString.charAt((int) i) == '1') { refl.add(zero); refp.add(i); zero = 0; } } refl.add(zero); return new DataNode(name, zeroOneString.length(), ArrayUtils.toPrimitive(refp.toArray(new Long[refp.size()]))); } }
From source file:com.runwaysdk.generation.loader.RunwayClassLoader.java
/** * *///from w w w. j a v a2 s . c o m protected Class<?> findClass(final String name) throws ClassNotFoundException { String mod = name.replace('.', '/') + ".class"; URL res = this.findResource(mod); if (res != null) { try { Class<?> clazz = null; Byte[] objectArray = FileIO.getBytesFromStream(res.openStream()); byte[] classBytes = ArrayUtils.toPrimitive(objectArray); if (implementsReloadable(classBytes)) { clazz = defineClass(name, classBytes, 0, classBytes.length); classes.put(name, clazz); return clazz; } } catch (IOException e1) { throw new ClassNotFoundException("Error reading class " + name); } // throw new ClassNotFoundException("Unable to find class " + name); } return null; }
From source file:edu.isi.misd.scanner.network.modules.master.processors.glore.GloreAggregateProcessor.java
/** * Camel {@link org.apache.camel.Processor} implementation -- * the majority of the work is handled in this function implementation. *//*from w w w. j a v a 2 s .c om*/ @Override public void process(Exchange exchange) throws Exception { // creates the aggregate ServiceResponses object super.process(exchange); // fail fast - treating GLORE as transactional for now, // so if any part of the request fails, the entire request fails. List<ServiceResponse> errorResponses = getErrorResponses(exchange); if (!errorResponses.isEmpty()) { ServiceResponses responses = new ServiceResponses(); responses.getServiceResponse().addAll(errorResponses); exchange.getIn().setBody(responses); // signal complete exchange.setProperty("status", "complete"); return; } List<GloreLogisticRegressionRequest> gloreRequestList = getTypedResponses(exchange, GloreLogisticRegressionRequest.class); if (gloreRequestList.isEmpty()) { ErrorUtils.setHttpError(exchange, new NullPointerException("Null Glore aggregate results"), 500); return; } GloreLogisticRegressionRequest request = gloreRequestList.get(0); GloreData gloreData = request.getGloreData(); if (gloreData == null) { ErrorUtils.setHttpError(exchange, new NullPointerException("Null Glore state data"), 500); return; } // replace the getFeatures with the standardized input parameters LogisticRegressionInputParameters params = request.getLogisticRegressionInput().getInputParameters(); ArrayList<String> independentVariables = new ArrayList<>(params.getIndependentVariableName()); int features = independentVariables.size() + 1; int iter = gloreData.getIteration(); Matrix beta0, beta1; if ("computeCovarianceMatrix".equalsIgnoreCase(gloreData.getState())) { if (log.isDebugEnabled()) { log.debug("Compute covariance matrix"); } ArrayList<double[][]> D_values = new ArrayList<double[][]>(); for (GloreLogisticRegressionRequest gloreRequest : gloreRequestList) { Matrix D = GloreUtils.convertMatrixTypeToMatrix(gloreRequest.getGloreData().getD()); D_values.add(D.getArray()); } Matrix temp_b = new Matrix(row_sums_two_dim(D_values, features)); Matrix temp_c = diag(0.0000001, features); temp_b = temp_b.plus(temp_c); Matrix cov_matrix = temp_b.inverse(); if (log.isDebugEnabled()) { log.debug("Covariance matrix:" + GloreUtils.matrixToString(cov_matrix, 8, 6)); } gloreData.setCovarianceMatrix(GloreUtils.convertMatrixToMatrixType(cov_matrix)); gloreData.setState("computeSDMatrix"); } else if ("computeSDMatrix".equalsIgnoreCase(gloreData.getState())) { if (log.isDebugEnabled()) { log.debug("Compute SD matrix"); } Matrix cov_matrix = GloreUtils.convertMatrixTypeToMatrix(gloreData.getCovarianceMatrix()); Matrix SD = new Matrix(1, features); for (int i = 0; i < features; i++) { SD.set(0, i, Math.sqrt(cov_matrix.get(i, i))); } if (log.isDebugEnabled()) { log.debug("SD Matrix: " + GloreUtils.matrixToString(SD, 8, 6)); } int totalRows = 0; double[] M = new double[features]; double[] STD = new double[features]; for (GloreLogisticRegressionRequest gloreRequest : gloreRequestList) { double[] tempM = ArrayUtils.toPrimitive(gloreRequest.getGloreData().getM().toArray(new Double[0])); double[] tempSTD = ArrayUtils .toPrimitive(gloreRequest.getGloreData().getSTD().toArray(new Double[0])); int tempRows = gloreRequest.getGloreData().getRows(); M[0] = 0; STD[0] = 0; for (int i = 1; i < features; i++) { M[i] = M[i] + tempM[i]; STD[i] = STD[i] + tempSTD[i]; totalRows = totalRows + tempRows; } } for (int i = 0; i < features; i++) { M[i] = M[i] / totalRows; STD[i] = Math.sqrt(STD[i] / totalRows - Math.pow(M[i], 2)); } gloreData.setState("complete"); // prepare GLORE outputs GloreLogisticRegressionResponse gloreResponse = new GloreLogisticRegressionResponse(); LogisticRegressionResponse lrResponse = new LogisticRegressionResponse(); LogisticRegressionOutput output = new LogisticRegressionOutput(); // need to decide how best to handle the DataSetID //response.setDataSetID("GLORE server"); lrResponse.setInput(request.getLogisticRegressionInput()); lrResponse.getOutput().add(output); List<Coefficient> target = output.getCoefficient(); Matrix fBeta = GloreUtils.convertMatrixTypeToMatrix(gloreData.getBeta()); // set intercept Coefficient coefficient = new Coefficient(); coefficient.setB(GloreUtils.df(fBeta.get(0, 0))); coefficient.setSE(GloreUtils.df(SD.get(0, 0))); coefficient.setTStatistics(GloreUtils.df(fBeta.get(0, 0) / SD.get(0, 0))); coefficient.setDegreeOfFreedom(1); coefficient.setPValue(GloreUtils.df(ztest(fBeta.get(0, 0) / SD.get(0, 0)))); coefficient.setName("Intercept"); //add two more attributes coefficient.setM(GloreUtils.df(M[0])); coefficient.setSTD(GloreUtils.df(STD[0])); target.add(coefficient); //set the rest of the attributes for (int i = 1; i < fBeta.getColumnPackedCopy().length; i++) { coefficient = new Coefficient(); coefficient.setB(GloreUtils.df(fBeta.get(i, 0))); coefficient.setSE(GloreUtils.df(SD.get(0, i))); coefficient.setTStatistics(GloreUtils.df(fBeta.get(i, 0) / SD.get(0, i))); coefficient.setDegreeOfFreedom(1); coefficient.setPValue(GloreUtils.df(ztest(fBeta.get(i, 0) / SD.get(0, i)))); coefficient.setName(independentVariables.get(i - 1)); //add two more attributes coefficient.setM(GloreUtils.df(M[i - 1])); coefficient.setSTD(GloreUtils.df(STD[i - 1])); target.add(coefficient); } gloreResponse.setLogisticRegressionResponse(lrResponse); // format the service response objects and set as the result body ServiceResponseData responseData = new ServiceResponseData(); responseData.setAny(gloreResponse); ServiceResponse response = new ServiceResponse(); response.setServiceResponseData(responseData); Calendar start = exchange.getProperty(BaseConstants.EXECUTION_START, Calendar.class); Calendar end = Calendar.getInstance(); ServiceResponseMetadata responseMetadata = MessageUtils.createServiceResponseMetadata(exchange, ServiceRequestStateType.COMPLETE, "The distributed GLORE analysis completed successfully.", MessageUtils.formatEventDuration(start, end)); response.setServiceResponseMetadata(responseMetadata); ServiceResponses responses = new ServiceResponses(); responses.getServiceResponse().add(response); exchange.getIn().setBody(responses); // signal complete exchange.setProperty("status", "complete"); return; } else { if (iter == 0) { if (log.isDebugEnabled()) { log.debug("Primary iteration phase"); } // init beta vectors beta0 = new Matrix(features, 1, -1.0); beta1 = new Matrix(features, 1, 0.0); if (log.isDebugEnabled()) { log.debug("Initial iteration value: " + GloreUtils.max_abs((beta1.minus(beta0)).getArray())); } gloreData.setState("iteration"); } else { beta1 = GloreUtils.convertMatrixTypeToMatrix(gloreData.getBeta()); } beta0 = beta1.copy(); /* beta1<-beta0+solve(rowSums(d,dims=2)+ diag(0.0000001,m))%*%(rowSums(e,dims=2)) */ ArrayList<double[]> E_values = new ArrayList<double[]>(); for (GloreLogisticRegressionRequest gloreRequest : gloreRequestList) { Matrix E = GloreUtils.convertMatrixTypeToMatrix(gloreRequest.getGloreData().getE()); double[] e = new double[features]; for (int i = 0; i < features; i++) { e[i] = E.get(i, 0); } E_values.add(e); } Matrix temp_a = new Matrix(row_sums_one_dim(E_values, features)); ArrayList<double[][]> D_values = new ArrayList<double[][]>(); for (GloreLogisticRegressionRequest gloreRequest : gloreRequestList) { Matrix D = GloreUtils.convertMatrixTypeToMatrix(gloreRequest.getGloreData().getD()); D_values.add(D.getArray()); } Matrix temp_b = new Matrix(row_sums_two_dim(D_values, features)); Matrix temp_c = diag(0.0000001, features); temp_b = temp_b.plus(temp_c); temp_b = temp_b.inverse(); temp_b = temp_b.times(temp_a); beta1 = beta0.plus(temp_b); if (log.isDebugEnabled()) { log.debug("beta1:" + GloreUtils.matrixToString(beta1, 10, 12)); } gloreData.setBeta(GloreUtils.convertMatrixToMatrixType(beta1)); if (log.isDebugEnabled()) { log.debug("Iteration " + iter + " value: " + GloreUtils.max_abs((beta1.minus(beta0)).getArray())); } if (iter > 0) { if ((GloreUtils.max_abs((beta1.minus(beta0)).getArray()) < epsilon) || (iter >= max_iter)) { if (iter >= max_iter) { log.info("Hit maximum number of iterations (" + max_iter + ") without converging, iterations stopped."); } if (log.isDebugEnabled()) { log.debug("Iteration final value: " + GloreUtils.max_abs((beta1.minus(beta0)).getArray())); } gloreData.setState("computeCovarianceMatrix"); } } gloreData.setIteration(iter + 1); } exchange.getIn().setBody(request); }
From source file:au.org.ala.delta.intkey.ui.MultiStateInputDialog.java
/** * ctor//from w ww . j a v a 2s.c o m * * @param owner * Owner frame of dialog * @param ch * the character whose states are being set * @param initialSelectedStates * initial states that should be selected in the dialog. In * general this should be any states already set for the * character. In the case that this is a controlling character * being set before its dependent character, all states that make * the dependent character applicable should be selected. * @param dependentCharacter * the dependent character - if the dialog is being used to set a * controlling character before its dependent character, this * argument should be a reference to the dependent character. In * all other cases it should be null. * @param imageSettings * image settings * @param displayNumbering * true if numbering should be displayed * @param enableImagesButton * the if the images button should be enabled * @param imagesStartScaled * true if images should start scaled. */ public MultiStateInputDialog(Frame owner, MultiStateCharacter ch, Set<Integer> initialSelectedStates, au.org.ala.delta.model.Character dependentCharacter, ImageSettings imageSettings, boolean displayNumbering, boolean enableImagesButton, boolean imagesStartScaled, boolean advancedMode) { super(owner, ch, imageSettings, displayNumbering, enableImagesButton, imagesStartScaled, advancedMode); ResourceMap resourceMap = Application.getInstance().getContext() .getResourceMap(MultiStateInputDialog.class); resourceMap.injectFields(this); setTitle(title); setPreferredSize(new Dimension(600, 350)); if (dependentCharacter != null) { _pnlControllingCharacterMessage = new JPanel(); _pnlControllingCharacterMessage.setFocusable(false); _pnlControllingCharacterMessage.setBorder(new EmptyBorder(5, 0, 0, 0)); _pnlMain.add(_pnlControllingCharacterMessage, BorderLayout.SOUTH); _pnlControllingCharacterMessage.setLayout(new BorderLayout(0, 0)); _lblWarningIcon = new JLabel(""); _lblWarningIcon.setFocusable(false); _lblWarningIcon.setIcon(UIManager.getIcon("OptionPane.warningIcon")); _pnlControllingCharacterMessage.add(_lblWarningIcon, BorderLayout.WEST); _txtControllingCharacterMessage = new JTextArea(); _txtControllingCharacterMessage.setText(MessageFormat.format(setControllingCharacterMessage, _formatter.formatCharacterDescription(dependentCharacter), _formatter.formatCharacterDescription(ch))); _txtControllingCharacterMessage.setFocusable(false); _txtControllingCharacterMessage.setBorder(new EmptyBorder(0, 5, 0, 0)); _txtControllingCharacterMessage.setEditable(false); _pnlControllingCharacterMessage.add(_txtControllingCharacterMessage); _txtControllingCharacterMessage.setWrapStyleWord(true); _txtControllingCharacterMessage.setFont(UIManager.getFont("Button.font")); _txtControllingCharacterMessage.setLineWrap(true); _txtControllingCharacterMessage.setBackground(SystemColor.control); } _scrollPane = new JScrollPane(); _pnlMain.add(_scrollPane, BorderLayout.CENTER); _list = new JList(); _scrollPane.setViewportView(_list); _listModel = new DefaultListModel(); for (int i = 0; i < ch.getNumberOfStates(); i++) { _listModel.addElement(_formatter.formatState(ch, i + 1)); } _list.setModel(_listModel); _list.addMouseListener(new MouseAdapter() { @Override public void mouseClicked(MouseEvent e) { if (e.getClickCount() > 1) { // Treat double click on a list item as the ok button being // pressed. _okPressed = true; handleBtnOKClicked(); } } }); // Select the list items that correspond to the initial selected states. if (initialSelectedStates != null) { List<Integer> listIndiciesToSelect = new ArrayList<Integer>(); for (int stateNumber : new ArrayList<Integer>(initialSelectedStates)) { listIndiciesToSelect.add(stateNumber - 1); } Integer[] wrappedPrimitivesList = listIndiciesToSelect .toArray(new Integer[initialSelectedStates.size()]); _list.setSelectedIndices(ArrayUtils.toPrimitive(wrappedPrimitivesList)); } _inputData = new HashSet<Integer>(); }
From source file:com.kylinolap.job.engine.JobEngine.java
public double getPercentileJobStepDuration(double percentile) { Collection<Double> values = JOB_DURATION.values(); Double[] all = (Double[]) values.toArray(new Double[values.size()]); Percentile p = new Percentile(percentile); return p.evaluate(ArrayUtils.toPrimitive(all)); }
From source file:de.codesourcery.eve.skills.ui.model.FilteringTreeModel.java
@Override public void addChildren(ITreeNode parent, Collection<ITreeNode> nodes) { delegate.addChildren(parent, nodes); if (!isPathToRootVisible(parent)) { // children cannot be visible if their parent is hidden return;/*from ww w . j a va2 s . c o m*/ } final List<Integer> childIndices = new ArrayList<Integer>(); final List<ITreeNode> children = new ArrayList<ITreeNode>(); for (ITreeNode child : nodes) { if (isHidden(child)) { continue; } childIndices.add(getIndexOfChild(parent, child)); children.add(child); } if (!childIndices.isEmpty()) { final int[] indices = ArrayUtils.toPrimitive(childIndices.toArray(new Integer[childIndices.size()])); final Object[] childs = children.toArray(new ITreeNode[children.size()]); fireEvent(EventType.ADDED, new TreeModelEvent(this, parent.getPathToRoot(), indices, childs)); } }
From source file:edu.harvard.iq.dvn.ingest.statdataio.impl.plugins.util.StatHelper.java
/** * Returns a new double array of nulls and non-Double.NaN values only * * @param x a double array// w w w. j ava2s .c om * @return a double array */ private static double[] removeInvalidValues(Double[] x) { List<Double> dl = new ArrayList<Double>(); for (Double d : x) { if (d != null && !Double.isNaN(d)) { dl.add(d); } } return ArrayUtils.toPrimitive(dl.toArray(new Double[dl.size()])); }
From source file:com.ec.android.module.bluetooth40.base.BaseBluetoothControlActivity.java
protected void writeContent(Byte[] bytes) { if (mWriteCharacteristic != null) { mWriteCharacteristic.setValue(ArrayUtils.toPrimitive(bytes)); mBluetoothLeService.writeCharacteristic(mWriteCharacteristic); }//from ww w . j a va 2 s.co m }
From source file:com.google.gwt.benchmark.dashboard.server.controller.BenchmarkController.java
private BenchmarkResultsTable createResponse(String benchmarkName, List<BenchmarkGraph> graphs, int week, int year) { Collections.sort(graphs, new Comparator<BenchmarkGraph>() { @Override/* ww w .j a v a 2s . co m*/ public int compare(BenchmarkGraph o1, BenchmarkGraph o2) { return o1.getRunnerId().compareTo(o2.getRunnerId()); } }); String weekName = String.format("Week: %d Year: %d", week, year); List<String> allRunnerIds = new ArrayList<String>(); List<String> commitIds = new ArrayList<String>(); List<double[]> runnerResultList = new ArrayList<>(); boolean first = true; for (BenchmarkGraph benchmarkGraph : graphs) { if (first) { commitIds.addAll(benchmarkGraph.getCommitIds()); first = false; } else { // if an update is in progress some graph entities might have been updated // and some not. In this case we are just going to return an empty response if (commitIds.size() != benchmarkGraph.getCommitIds().size()) { return BenchmarkResultsTable.create(benchmarkName, weekName, year, week, Collections.<String>emptyList(), Collections.<String>emptyList(), Collections.<double[]>emptyList()); } } allRunnerIds.add(benchmarkGraph.getRunnerId()); Double[] runsPerSecond = benchmarkGraph.getRunsPerSecond().toArray(new Double[] {}); double[] runs = ArrayUtils.toPrimitive(runsPerSecond); runnerResultList.add(runs); } return BenchmarkResultsTable.create(benchmarkName, weekName, year, week, commitIds, allRunnerIds, runnerResultList); }
From source file:io.joynr.util.JoynrUtil.java
public static void writeResource(Byte[] byteResource, String fileName) throws IOException { writeResource(ArrayUtils.toPrimitive(byteResource), fileName); }