List of usage examples for java.lang Double parseDouble
public static double parseDouble(String s) throws NumberFormatException
From source file:gamlss.algorithm.Gamlss.java
/** * Main method.//from w ww . j a v a 2 s . c o m * @param args - command-line arguments */ public static void main(final String[] args) { //String fileName = "Data/dataReduced.csv"; String fileName = "Data/oil.csv"; // String fileName = "Data/sp.csv"; //String fileName = "Data/dataReduced.csv"; CSVFileReader readData = new CSVFileReader(fileName); readData.readFile(); ArrayList<String> data = readData.storeValues; ArrayRealVector y = new ArrayRealVector(data.size()); BlockRealMatrix muX = new BlockRealMatrix(data.size(), 1); BlockRealMatrix sigmaX = new BlockRealMatrix(data.size(), 1); BlockRealMatrix nuX = new BlockRealMatrix(data.size(), 1); BlockRealMatrix tauX = new BlockRealMatrix(data.size(), 1); ArrayRealVector w = new ArrayRealVector(data.size()); BlockRealMatrix muS = new BlockRealMatrix(data.size(), 1); BlockRealMatrix sigmaS = new BlockRealMatrix(data.size(), 1); BlockRealMatrix nuS = new BlockRealMatrix(data.size(), 1); BlockRealMatrix tauS = new BlockRealMatrix(data.size(), 1); for (int i = 0; i < data.size(); i++) { String[] line = data.get(i).split(","); y.setEntry(i, Double.parseDouble(line[0])); muX.setEntry(i, 0, Double.parseDouble(line[1])); muS.setEntry(i, 0, Double.parseDouble(line[1])); sigmaX.setEntry(i, 0, Double.parseDouble(line[1])); sigmaS.setEntry(i, 0, Double.parseDouble(line[1])); nuX.setEntry(i, 0, Double.parseDouble(line[1])); nuS.setEntry(i, 0, Double.parseDouble(line[1])); tauX.setEntry(i, 0, Double.parseDouble(line[1])); tauS.setEntry(i, 0, Double.parseDouble(line[1])); } Hashtable<Integer, BlockRealMatrix> designMatrices = new Hashtable<Integer, BlockRealMatrix>(); designMatrices.put(DistributionSettings.MU, muX); designMatrices.put(DistributionSettings.SIGMA, sigmaX); designMatrices.put(DistributionSettings.NU, nuX); designMatrices.put(DistributionSettings.TAU, tauX); HashMap<Integer, BlockRealMatrix> smoothMatrices = new HashMap<Integer, BlockRealMatrix>(); smoothMatrices.put(DistributionSettings.MU, muS); smoothMatrices.put(DistributionSettings.SIGMA, sigmaS); smoothMatrices.put(DistributionSettings.NU, nuS); smoothMatrices.put(DistributionSettings.TAU, tauS); //smoothMatrices.put(DistributionSettings.MU, null); //smoothMatrices.put(DistributionSettings.SIGMA, null); //smoothMatrices.put(DistributionSettings.NU, null); //smoothMatrices.put(DistributionSettings.TAU, null); DistributionSettings.DISTR = DistributionSettings.SST; Controls.GLOB_DEVIANCE_TOL = 5500; Controls.INTER = 50;//only for the PB smoother Controls.SMOOTHER = Controls.PB; //or PB Controls.IS_SVD = true; Controls.BIG_DATA = true; Controls.JAVA_OPTIMIZATION = false; Controls.GAMLSS_NUM_CYCLES = 50; //Gamlss gamlss = new Gamlss(y, designMatrices, null); Gamlss gamlss = new Gamlss(y, designMatrices, null); //Gamlss gamlss = new Gamlss(y, null, smoothMatrices); gamlss.saveFittedDistributionParameters("Data/oilresults.csv"); }
From source file:edu.duke.igsp.gkde.Main.java
public static void main(String[] argv) throws Exception { Options opts = new Options(); opts.addOption("s", true, "wiggle track step (default=1)"); opts.addOption("l", true, "feature length (default=600)"); opts.addOption("f", true, "fragment size (default=estimated from data)"); // opts.addOption("b", true, "bandwidth (default=200)"); // opts.addOption("w", true, "window (default=3800"); opts.addOption("wg", true, "wg threshold set (defualt = calculated)"); opts.addOption("c", true, "genomic total read weight (defualt = calculated)"); opts.addOption("h", false, "print usage"); opts.addOption(OptionBuilder.withArgName("input dir").hasArg() .withDescription("input directory (default=current directory)").isRequired(false).create("d")); opts.addOption(OptionBuilder.withArgName("output dir").hasArg() .withDescription("output directory (default=current directory)").isRequired(false).create("o")); opts.addOption(OptionBuilder.withArgName("background dir").hasArg() .withDescription("background directory (default=none)").isRequired(false).create("b")); opts.addOption(OptionBuilder.withArgName("ploidy dir").hasArg() .withDescription("ploidy/input directory (default=none)").isRequired(false).create("p")); opts.addOption(OptionBuilder.withArgName("wig | bed | npf").hasArg() .withDescription("output format (default wig)").isRequired(false).create("of")); opts.addOption(OptionBuilder.withArgName("dnase | chip | faire | atac").hasArg() .withDescription("input data").isRequired(true).create("in")); opts.addOption(OptionBuilder.withArgName("weight clip").hasArg() .withDescription("weight clip value (default none)").isRequired(false).create("wc")); opts.addOption("t", true, "threshold (standard deviations) (default=4.0)"); // opts.addOption("r", true, "background ratio (default=2.0)"); opts.addOption("v", false, "verbose output"); CommandLineParser parser = new GnuParser(); int fragment_size = -1; int fragment_offset = 0; long featureLength = 600l; // float thresh = 2; float threshold = KDEChromosome.Settings.DEFAULT_THRESHOLD; int step = 1; boolean showHelp = false; boolean verbose = false; String inputDirectory = null; String backgroundDirectory = null; String ploidyDirectory = null; String[] files = null;/*w w w. ja v a 2s . c om*/ String[] bgfiles = {}; String[] ipfiles = {}; String outputFormat = "wig"; String inputDataType = "dnase"; File outputDirectory = new File(System.getProperty("user.dir")); long bandwidth = 0l; long window = 0l; double ncuts = 0.0d; float temp_threshold = 0f; int weight_clip = 0; System.out.println("F-Seq Version 1.85"); try { CommandLine cmd = parser.parse(opts, argv); showHelp = (cmd.hasOption("h")); verbose = (cmd.hasOption("v")); if (cmd.hasOption("s")) step = Integer.parseInt(cmd.getOptionValue("s")); if (cmd.hasOption("f")) fragment_size = Integer.parseInt(cmd.getOptionValue("f")); if (cmd.hasOption("d")) //input directory inputDirectory = cmd.getOptionValue("d"); if (cmd.hasOption("b")) //background directory backgroundDirectory = cmd.getOptionValue("b"); if (cmd.hasOption("p")) //ploidy|input directory ploidyDirectory = cmd.getOptionValue("p"); if (cmd.hasOption("l")) // bandwidth featureLength = Long.parseLong(cmd.getOptionValue("l")); if (cmd.hasOption("of")) { // output format outputFormat = cmd.getOptionValue("of"); if (!outputFormat.equals("wig") && !outputFormat.equals("bed") && !outputFormat.equals("npf")) { System.out.println("Parameter error: output format must be 'wig' or 'bed'."); showHelp = true; } } if (cmd.hasOption("in")) { // input data type inputDataType = cmd.getOptionValue("in"); if (!inputDataType.equals("dnase") && !inputDataType.equals("chip") && !inputDataType.equals("faire") && !inputDataType.equals("atac")) { System.out.println( "Parameter error: input data type must be 'dnase', 'chip', 'faire', or 'atac'."); showHelp = true; } } if (cmd.hasOption("wc")) { // weight clip weight_clip = Integer.parseInt(cmd.getOptionValue("wc")); } if (cmd.hasOption("t")) { // threshold (standard deviations) threshold = Float.parseFloat(cmd.getOptionValue("t")); } if (cmd.hasOption("o")) { // output directory String out = cmd.getOptionValue("o"); outputDirectory = new File(out); if (!outputDirectory.exists() && !outputDirectory.isDirectory()) { System.out.println("Output directory '" + out + "' is not a valid directory."); showHelp = true; } } if (cmd.hasOption("wg")) temp_threshold = Float.parseFloat(cmd.getOptionValue("wg")); if (cmd.hasOption("c")) ncuts = Double.parseDouble(cmd.getOptionValue("c")); // TESTING ONLY // if(cmd.hasOption("w")) // window // window = Long.parseLong(cmd.getOptionValue("w")); //if(cmd.hasOption("b")) // window // bandwidth = Long.parseLong(cmd.getOptionValue("b")); files = cmd.getArgs(); // input files //bgfiles = cmd.getArgs(); // background files } catch (Exception e) { System.out.println("Error parsing arguments: " + e.getMessage()); e.printStackTrace(); showHelp = true; } if (showHelp || (inputDirectory == null && files.length == 0)) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("fseq [options]... [file(s)]...", opts); System.exit(1); } File[] pfiles = getFiles(inputDirectory, files); File[] background_files = getFiles(backgroundDirectory, bgfiles); File[] ploidy_files = getFiles(ploidyDirectory, ipfiles); KDEChromosome[] chrs = null; // assume all files are of the same type, if not we'll get parsing errors String path = pfiles[0].getPath(); String extension = path.substring(path.lastIndexOf('.')).toLowerCase(); System.out.println("Path: " + path + ", extension: " + extension); if (extension.equals(".bed")) { System.out.println("Parsing BED file."); chrs = BedReader.read(pfiles); } else if (extension.equals(".sam") || extension.equals(".bam")) { System.out.println("Parsing SAM/BAM file."); chrs = SamReader.read(pfiles, weight_clip); } //KDEChromosome[] input = BedReader.read(ifiles); //compute fragment offset if (fragment_size == -1) { fragment_size = wgShiftCalc(chrs); } fragment_offset = (int) (fragment_size / 2); if (ncuts == 0.0d) { for (int i = 0; i < chrs.length; ++i) { // computes the total read weight of all cuts on a chromosome ncuts += chrs[i].getTotalWeight(); } } KDEChromosome.Settings settings = null; if (bandwidth > 0 || window > 0) { settings = new KDEChromosome.Settings(bandwidth, window, threshold, fragment_offset, ncuts, inputDataType); } else { settings = new KDEChromosome.Settings(featureLength, threshold, fragment_offset, ncuts, inputDataType); } float wg_threshold = wgThreshold(settings, chrs); if (temp_threshold != 0f) { wg_threshold = temp_threshold; } //KDEChromosome.Settings bg_settings = null; //bg_settings = new KDEChromosome.Settings(featureLength*2, threshold, fragment_offset); //int background_size = 0; //int input_size = 0; //float bg_ratio = 0; //float sd = 0; if (verbose) { System.out.println("Settings: "); System.out.println("\twindow=" + (settings.window * 2)); System.out.println("\tbandwidth=" + (settings.bandwidth)); //System.out.println("\tfragment offset=" + (settings.offset)); System.out.println("\tthreshold = " + wg_threshold); System.out.println("\test. fragment size = " + fragment_size); System.out.println("\tsequence length = " + chrs[0].getSequenceLength()); } // if(backgroundDirectory != null) { // for(int i = 0; i < input.length; ++i) { // background_size += input[i].getLength(); // } // for(int i = 0; i < chrs.length; ++i) { // input_size += chrs[i].getLength(); // } // bg_ratio = (float)input_size/(float)background_size; // sd = computeSD(bg_settings, input); // //System.out.println("Sample Ratio: " + bg_ratio); // //System.out.println("Input Size: " + input_size); // //System.out.println("Background Size: " + background_size); // //System.out.println("Input standard deviation: " + (settings.threshold * (float)Math.sqrt((double)bg_ratio * (double)sd * (double)sd))); // //System.out.println("Data standard deviation: " + settings.threshold * computeSD(settings, chrs)); // } for (int i = 0; i < chrs.length; ++i) { if (chrs[i].getFirstPos() == chrs[i].getLastPos()) { System.out.println("Warning: " + chrs[i].getChromosome() + " has size zero. Skipping."); continue; } File ofile = Util.makeUniqueFileWithExtension(outputDirectory, chrs[i].getChromosome(), outputFormat); DensityWriter dw = null; if (outputFormat.equals("wig")) { dw = new WiggleDensityWriter(ofile, chrs[i].getChromosome(), chrs[i].getFirstPos(), step); } else { if (outputFormat.equals("npf")) { dw = new NpfDensityWriter(ofile, chrs[i].getChromosome(), chrs[i].getFirstPos(), step); } else { dw = new BedDensityWriter(ofile, chrs[i].getChromosome(), chrs[i].getFirstPos(), step); } } //Function takes all? or new function for each? // if(backgroundDirectory != null) { // boolean hit = false; // for(int j = 0; j < background_files.length; ++j) { // if(background_files[j].getName().equals(chrs[i].getChromosome() + ".bff")) { // System.out.println("Running background on Chromosome " + chrs[i].getChromosome()); // chrs[i].runBG(settings, dw, verbose, wg_threshold, background_files[j]); // hit = true; // } // } // if(!hit) // System.out.println("No background for Chromosome " + chrs[i].getChromosome()); // } else { // if(ploidyDirectory !=) // chrs[i].run(settings, dw, verbose, wg_threshold); // } chrs[i].run(settings, dw, verbose, wg_threshold, background_files, ploidy_files); dw.close(); } //kde.showGraph(); }
From source file:com.genentech.chemistry.openEye.apps.enumerate.SDFEnumerator.java
public static void main(String... args) throws IOException { Options options = new Options(); Option opt = new Option("out", true, "output file oe-supported"); opt.setRequired(true);//from ww w.j av a 2s .c o m options.addOption(opt); opt = new Option("hydrogenExplicit", false, "Use explicit hydrogens"); options.addOption(opt); opt = new Option("correctValences", false, "Correct valences after the enumeration"); options.addOption(opt); opt = new Option("regenerate2D", false, "Regenerate 2D coordinates for the products"); options.addOption(opt); opt = new Option("reactAllSites", false, "Generate a product for each match in a reagent."); options.addOption(opt); opt = new Option("randomFraction", true, "Only output a fraction of the products."); options.addOption(opt); opt = new Option("maxAtoms", true, "Only output products with <= maxAtoms."); options.addOption(opt); opt = new Option("notReacted", true, "Output file for reagents that didn't produce at leaste one output molecule, useful for debugging SMIRKS."); options.addOption(opt); CommandLineParser parser = new PosixParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (Exception e) { System.err.println(e.getMessage()); exitWithHelp("", options); } args = cmd.getArgs(); if (args.length < 2) { exitWithHelp("Transformation and/or reagentFiles missing", options); } String smirks = args[0]; if (new File(smirks).canRead()) smirks = IOUtil.fileToString(smirks).trim(); if (!smirks.contains(">>")) smirks = scaffoldToSmirks(smirks); String[] reagentSmiOrFiles = Arrays.copyOfRange(args, 1, args.length); if (cmd.hasOption("d")) { System.err.println("Start debugger and press return:"); new BufferedReader(new InputStreamReader(System.in)).readLine(); } String outFile = cmd.getOptionValue("out"); OELibraryGen lg = new OELibraryGen(); lg.Init(smirks); if (!lg.IsValid()) exitWithHelp("Invalid Transform: " + smirks, options); lg.SetExplicitHydrogens(cmd.hasOption("hydrogenExplicit")); lg.SetValenceCorrection(cmd.hasOption("correctValences")); lg.SetRemoveUnmappedFragments(true); boolean regenerate2D = cmd.hasOption("regenerate2D"); boolean reactAllSites = cmd.hasOption("reactAllSites"); String unreactedFile = null; if (cmd.hasOption("notReacted")) { unreactedFile = cmd.getOptionValue("notReacted"); } double randomFract = 2; if (cmd.hasOption("randomFraction")) randomFract = Double.parseDouble(cmd.getOptionValue("randomFraction")); int maxAtoms = 0; if (cmd.hasOption("maxAtoms")) maxAtoms = Integer.parseInt(cmd.getOptionValue("maxAtoms")); SDFEnumerator en = new SDFEnumerator(lg, reactAllSites, reagentSmiOrFiles); en.generateLibrary(outFile, maxAtoms, randomFract, regenerate2D, unreactedFile); en.delete(); }
From source file:com.twentyn.bioreactor.pH.ControlSystem.java
public static void main(String[] args) throws Exception { Options opts = new Options(); for (Option.Builder b : OPTION_BUILDERS) { opts.addOption(b.build());//from ww w .j a va 2 s . co m } CommandLine cl = null; try { CommandLineParser parser = new DefaultParser(); cl = parser.parse(opts, args); } catch (ParseException e) { LOGGER.error(String.format("Argument parsing failed: %s\n", e.getMessage())); HELP_FORMATTER.printHelp(ControlSystem.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } if (cl.hasOption("help")) { HELP_FORMATTER.printHelp(ControlSystem.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); return; } SOLUTION solution = null; String acidOrBase = cl.getOptionValue(OPTION_CONTROL_SOLUTION); if (acidOrBase.equals(SOLUTION.ACID.name())) { solution = SOLUTION.ACID; } if (acidOrBase.equals(SOLUTION.BASE.name())) { solution = SOLUTION.BASE; } if (solution == null) { LOGGER.error("Input solution is neither %s or %s", SOLUTION.ACID.name(), SOLUTION.BASE.name()); return; } Double targetPH = Double.parseDouble(cl.getOptionValue(OPTION_TARGET_PH)); File sensorReadingDataFile = new File( cl.getOptionValue(OPTION_SENSOR_READING_FILE_LOCATION, SENSOR_READING_FILE_LOCATION)); MotorPinConfiguration motorPinConfiguration = new MotorPinConfiguration( MotorPinConfiguration.PinNumberingScheme.BOARD); motorPinConfiguration.initializeGPIOPinsAndSetConfigToStartState(); ControlSystem controlSystem = new ControlSystem(motorPinConfiguration, solution, targetPH, sensorReadingDataFile); controlSystem.registerModuleForObjectMapper(new JodaModule()); try { controlSystem.run(); } finally { LOGGER.info("Shutting down"); controlSystem.shutdownFermentation(); } }
From source file:com.jug.MotherMachine.java
/** * PROJECT MAIN/*from w w w. j a va2 s . com*/ * ============ * * @param args * muh! */ public static void main(final String[] args) { try { final MotherMachine main = new MotherMachine(); guiFrame = new JFrame("Interactive MotherMachine"); main.initMainWindow(guiFrame); props = main.loadParams(); BGREM_TEMPLATE_XMIN = Integer .parseInt(props.getProperty("BGREM_TEMPLATE_XMIN", Integer.toString(BGREM_TEMPLATE_XMIN))); BGREM_TEMPLATE_XMAX = Integer .parseInt(props.getProperty("BGREM_TEMPLATE_XMAX", Integer.toString(BGREM_TEMPLATE_XMAX))); BGREM_X_OFFSET = Integer .parseInt(props.getProperty("BGREM_X_OFFSET", Integer.toString(BGREM_X_OFFSET))); GL_OFFSET_BOTTOM = Integer .parseInt(props.getProperty("GL_OFFSET_BOTTOM", Integer.toString(GL_OFFSET_BOTTOM))); GL_OFFSET_TOP = Integer.parseInt(props.getProperty("GL_OFFSET_TOP", Integer.toString(GL_OFFSET_TOP))); GL_OFFSET_LATERAL = Integer .parseInt(props.getProperty("GL_OFFSET_LATERAL", Integer.toString(GL_OFFSET_LATERAL))); MIN_CELL_LENGTH = Integer .parseInt(props.getProperty("MIN_CELL_LENGTH", Integer.toString(MIN_CELL_LENGTH))); MIN_GAP_CONTRAST = Double .parseDouble(props.getProperty("MIN_GAP_CONTRAST", Double.toString(MIN_GAP_CONTRAST))); SIGMA_PRE_SEGMENTATION_X = Double.parseDouble( props.getProperty("SIGMA_PRE_SEGMENTATION_X", Double.toString(SIGMA_PRE_SEGMENTATION_X))); SIGMA_PRE_SEGMENTATION_Y = Double.parseDouble( props.getProperty("SIGMA_PRE_SEGMENTATION_Y", Double.toString(SIGMA_PRE_SEGMENTATION_Y))); SIGMA_GL_DETECTION_X = Double .parseDouble(props.getProperty("SIGMA_GL_DETECTION_X", Double.toString(SIGMA_GL_DETECTION_X))); SIGMA_GL_DETECTION_Y = Double .parseDouble(props.getProperty("SIGMA_GL_DETECTION_Y", Double.toString(SIGMA_GL_DETECTION_Y))); DEFAULT_PATH = props.getProperty("DEFAULT_PATH", DEFAULT_PATH); GUI_POS_X = Integer.parseInt(props.getProperty("GUI_POS_X", Integer.toString(DEFAULT_GUI_POS_X))); GUI_POS_Y = Integer.parseInt(props.getProperty("GUI_POS_Y", Integer.toString(DEFAULT_GUI_POS_X))); GUI_WIDTH = Integer.parseInt(props.getProperty("GUI_WIDTH", Integer.toString(GUI_WIDTH))); GUI_HEIGHT = Integer.parseInt(props.getProperty("GUI_HEIGHT", Integer.toString(GUI_HEIGHT))); GUI_CONSOLE_WIDTH = Integer .parseInt(props.getProperty("GUI_CONSOLE_WIDTH", Integer.toString(GUI_CONSOLE_WIDTH))); // Iterate over all currently attached monitors and check if sceen position is actually possible, // otherwise fall back to the DEFAULT values and ignore the ones coming from the properties-file. boolean pos_ok = false; final GraphicsEnvironment ge = GraphicsEnvironment.getLocalGraphicsEnvironment(); final GraphicsDevice[] gs = ge.getScreenDevices(); for (int i = 0; i < gs.length; i++) { final DisplayMode dm = gs[i].getDisplayMode(); if (gs[i].getDefaultConfiguration().getBounds() .contains(new java.awt.Point(GUI_POS_X, GUI_POS_Y))) { pos_ok = true; } } // None of the screens contained the top-left window coordinates --> fall back onto default values... if (!pos_ok) { GUI_POS_X = DEFAULT_GUI_POS_X; GUI_POS_Y = DEFAULT_GUI_POS_Y; } String path = props.getProperty("import_path", System.getProperty("user.home")); final File fPath = main.showStartupDialog(guiFrame, path); path = fPath.getAbsolutePath(); props.setProperty("import_path", fPath.getAbsolutePath()); // Setting up console window and window snapper... main.initConsoleWindow(); main.showConsoleWindow(); final JFrameSnapper snapper = new JFrameSnapper(); snapper.addFrame(main.frameConsoleWindow); snapper.addFrame(guiFrame); // --------------------------------------------------- main.processDataFromFolder(path); // --------------------------------------------------- System.out.print("Build and show GUI..."); // show loaded and annotated data ImageJFunctions.show(main.imgRaw, "Rotated & cropped raw data"); ImageJFunctions.show(main.imgTemp, "Temporary"); ImageJFunctions.show(main.imgAnnotated, "Annotated ARGB data"); final MotherMachineGui gui = new MotherMachineGui(new MotherMachineModel(main)); gui.setVisible(true); main.ij = new ImageJ(); guiFrame.add(gui); guiFrame.setSize(GUI_WIDTH, GUI_HEIGHT); guiFrame.setLocation(GUI_POS_X, GUI_POS_Y); guiFrame.setVisible(true); SwingUtilities.invokeLater(new Runnable() { @Override public void run() { snapper.snapFrames(main.frameConsoleWindow, guiFrame, JFrameSnapper.EAST); } }); System.out.println(" done!"); } catch (final UnsatisfiedLinkError ulr) { JOptionPane.showMessageDialog(MotherMachine.guiFrame, "Could initialize Gurobi.\n" + "You might not have installed Gurobi properly or you miss a valid license.\n" + "Please visit 'www.gurobi.com' for further information.\n\n" + ulr.getMessage(), "Gurobi Error?", JOptionPane.ERROR_MESSAGE); } }
From source file:net.myrrix.online.eval.ParameterOptimizer.java
public static void main(String[] args) throws Exception { if (args.length < 4) { System.err.println(//from www.j av a 2 s.c o m "Usage: dataDirectory numSteps evaluationPercentage property=min:max [property2=min2:max2 ...]"); return; } final File dataDir = new File(args[0]); Preconditions.checkArgument(dataDir.exists() && dataDir.isDirectory(), "Not a directory: %s", dataDir); Preconditions.checkArgument(dataDir.listFiles().length > 0, "No files in: %s", dataDir); int numSteps = Integer.parseInt(args[1]); Preconditions.checkArgument(numSteps >= 2, "# steps must be at least 2: %s", numSteps); final double evaluationPercentage = Double.parseDouble(args[2]); Preconditions.checkArgument(evaluationPercentage > 0.0 && evaluationPercentage <= 1.0, "evaluationPercentage must be in (0,1]: %s", evaluationPercentage); Map<String, ParameterRange> parameterRanges = Maps.newHashMapWithExpectedSize(args.length); for (int i = 3; i < args.length; i++) { String[] propValue = EQUALS.split(args[i]); String systemProperty = propValue[0]; String[] minMax = COLON.split(propValue[1]); ParameterRange range; try { int min = Integer.parseInt(minMax[0]); int max = Integer.parseInt(minMax.length == 1 ? minMax[0] : minMax[1]); range = new ParameterRange(min, max); } catch (NumberFormatException ignored) { double min = Double.parseDouble(minMax[0]); double max = Double.parseDouble(minMax.length == 1 ? minMax[0] : minMax[1]); range = new ParameterRange(min, max); } parameterRanges.put(systemProperty, range); } Callable<Number> evaluator = new Callable<Number>() { @Override public Number call() throws IOException, TasteException, InterruptedException { MyrrixIRStatistics stats = (MyrrixIRStatistics) new PrecisionRecallEvaluator().evaluate(dataDir, 0.9, evaluationPercentage, null); return stats == null ? null : stats.getMeanAveragePrecision(); } }; ParameterOptimizer optimizer = new ParameterOptimizer(parameterRanges, numSteps, evaluator, false); Map<String, Number> optimalValues = optimizer.findGoodParameterValues(); System.out.println(optimalValues); }
From source file:com.genentech.chemistry.openEye.apps.SdfRMSDSphereExclusion.java
/** * @param args/* w ww. j a va2s . c o m*/ */ public static void main(String... args) throws IOException { // create command line Options object Options options = new Options(); Option opt = new Option(OPT_INFILE, true, "input file oe-supported Use .sdf|.smi to specify the file type."); opt.setRequired(true); options.addOption(opt); opt = new Option(OPT_OUTFILE, true, "output file oe-supported. Use .sdf|.smi to specify the file type."); opt.setRequired(true); options.addOption(opt); opt = new Option(OPT_REFFILE, true, "Reference file of molecules which define pre-existign exclusion spheres."); options.addOption(opt); opt = new Option(OPT_RADIUS, true, "Radius of exclusion spehre in A2."); opt.setRequired(true); options.addOption(opt); opt = new Option(OPT_GROUPBY, true, "Group by fieldname, run sphere exclusion for consecutive groups of records with same value for this field."); options.addOption(opt); opt = new Option(OPT_DONotOpt, false, "If specified the RMSD is computed without trying to optimize the alignment."); options.addOption(opt); opt = new Option(OPT_PRINT_All, false, "print all molecule, check includeIdx tag"); options.addOption(opt); opt = new Option(OPT_MIRROR, false, "For non-chiral molecules also try mirror image"); options.addOption(opt); CommandLineParser parser = new PosixParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (Exception e) { System.err.println(e.getMessage()); exitWithHelp(options); } args = cmd.getArgs(); if (cmd.hasOption("d")) { System.err.println("Start debugger and press return:"); new BufferedReader(new InputStreamReader(System.in)).readLine(); } String inFile = cmd.getOptionValue(OPT_INFILE); String outFile = cmd.getOptionValue(OPT_OUTFILE); String refFile = cmd.getOptionValue(OPT_REFFILE); String groupBy = cmd.getOptionValue(OPT_GROUPBY); boolean doOptimize = !cmd.hasOption(OPT_DONotOpt); double radius = Double.parseDouble(cmd.getOptionValue(OPT_RADIUS)); boolean printAll = cmd.hasOption(OPT_PRINT_All); boolean doMirror = cmd.hasOption(OPT_MIRROR); SdfRMSDSphereExclusion sphereExclusion = new SdfRMSDSphereExclusion(refFile, outFile, radius, printAll, doMirror, doOptimize, groupBy); sphereExclusion.run(inFile); sphereExclusion.close(); }
From source file:com.oltpbenchmark.multitenancy.MuTeBench.java
/** * @param args/*from www . j a v a 2 s . c o m*/ * @throws Exception */ public static void main(String[] args) throws Exception { String duration = null; String scenarioFile = null; // ------------------------------------------------------------------- // INITIALIZE LOGGING // ------------------------------------------------------------------- String log4jPath = System.getProperty("log4j.configuration"); if (log4jPath != null) { org.apache.log4j.PropertyConfigurator.configure(log4jPath); } else { throw new RuntimeException("Missing log4j.properties file"); } // ------------------------------------------------------------------- // PARSE COMMAND LINE PARAMETERS // ------------------------------------------------------------------- CommandLineParser parser = new PosixParser(); XMLConfiguration pluginConfig = null; try { pluginConfig = new XMLConfiguration("config/plugin.xml"); } catch (ConfigurationException e1) { LOG.info("Plugin configuration file config/plugin.xml is missing"); e1.printStackTrace(); } pluginConfig.setExpressionEngine(new XPathExpressionEngine()); Options options = new Options(); options.addOption("s", "scenario", true, "[required] Workload scenario file"); options.addOption("a", "analysis-buckets", true, "sampling buckets for result aggregation"); options.addOption("r", "runtime", true, "maximum runtime (no events will be started after finishing runtime)"); options.addOption("v", "verbose", false, "Display Messages"); options.addOption("g", "gui", false, "Show controlling GUI"); options.addOption("h", "help", false, "Print this help"); options.addOption("o", "output", true, "Output file (default System.out)"); options.addOption("b", "baseline", true, "Output files of previous baseline run"); options.addOption(null, "histograms", false, "Print txn histograms"); options.addOption("d", "dialects-export", true, "Export benchmark SQL to a dialects file"); // parse the command line arguments CommandLine argsLine = parser.parse(options, args); if (argsLine.hasOption("h")) { printUsage(options); return; } else if (!argsLine.hasOption("scenario")) { INIT_LOG.fatal("Missing scenario description file"); System.exit(-1); } else scenarioFile = argsLine.getOptionValue("scenario"); if (argsLine.hasOption("r")) duration = argsLine.getOptionValue("r"); if (argsLine.hasOption("runtime")) duration = argsLine.getOptionValue("runtime"); // ------------------------------------------------------------------- // CREATE TENANT SCHEDULE // ------------------------------------------------------------------- INIT_LOG.info("Create schedule"); Schedule schedule = new Schedule(duration, scenarioFile); HashMap<Integer, ScheduleEvents> tenantEvents = schedule.getTenantEvents(); ArrayList<Integer> tenantList = schedule.getTenantList(); List<BenchmarkModule> benchList = new ArrayList<BenchmarkModule>(); for (int tenInd = 0; tenInd < tenantList.size(); tenInd++) { int tenantID = tenantList.get(tenInd); for (int tenEvent = 0; tenEvent < tenantEvents.get(tenantID).size(); tenEvent++) { BenchmarkSettings benchmarkSettings = (BenchmarkSettings) tenantEvents.get(tenantID) .getBenchmarkSettings(tenEvent); // update benchmark Settings benchmarkSettings.setTenantID(tenantID); // ------------------------------------------------------------------- // GET PLUGIN LIST // ------------------------------------------------------------------- String plugins = benchmarkSettings.getBenchmark(); String[] pluginList = plugins.split(","); String configFile = benchmarkSettings.getConfigFile(); XMLConfiguration xmlConfig = new XMLConfiguration(configFile); xmlConfig.setExpressionEngine(new XPathExpressionEngine()); int lastTxnId = 0; for (String plugin : pluginList) { // ---------------------------------------------------------------- // WORKLOAD CONFIGURATION // ---------------------------------------------------------------- String pluginTest = ""; pluginTest = "[@bench='" + plugin + "']"; WorkloadConfiguration wrkld = new WorkloadConfiguration(); wrkld.setTenantId(tenantID); wrkld.setBenchmarkName(setTenantIDinString(plugin, tenantID)); wrkld.setXmlConfig(xmlConfig); wrkld.setDBType(DatabaseType.get(setTenantIDinString(xmlConfig.getString("dbtype"), tenantID))); wrkld.setDBDriver(setTenantIDinString(xmlConfig.getString("driver"), tenantID)); wrkld.setDBConnection(setTenantIDinString(xmlConfig.getString("DBUrl"), tenantID)); wrkld.setDBName(setTenantIDinString(xmlConfig.getString("DBName"), tenantID)); wrkld.setDBUsername(setTenantIDinString(xmlConfig.getString("username"), tenantID)); wrkld.setDBPassword(setTenantIDinString(xmlConfig.getString("password"), tenantID)); String terminalString = setTenantIDinString(xmlConfig.getString("terminals[not(@bench)]", "0"), tenantID); int terminals = Integer.parseInt(xmlConfig.getString("terminals" + pluginTest, terminalString)); wrkld.setTerminals(terminals); int taSize = Integer.parseInt(xmlConfig.getString("taSize", "1")); if (taSize < 0) INIT_LOG.fatal("taSize must not be negative!"); wrkld.setTaSize(taSize); wrkld.setProprietaryTaSyntax(xmlConfig.getBoolean("proprietaryTaSyntax", false)); wrkld.setIsolationMode(setTenantIDinString( xmlConfig.getString("isolation", "TRANSACTION_SERIALIZABLE"), tenantID)); wrkld.setScaleFactor(Double .parseDouble(setTenantIDinString(xmlConfig.getString("scalefactor", "1.0"), tenantID))); wrkld.setRecordAbortMessages(xmlConfig.getBoolean("recordabortmessages", false)); int size = xmlConfig.configurationsAt("/works/work").size(); for (int i = 1; i < size + 1; i++) { SubnodeConfiguration work = xmlConfig.configurationAt("works/work[" + i + "]"); List<String> weight_strings; // use a workaround if there multiple workloads or // single // attributed workload if (pluginList.length > 1 || work.containsKey("weights[@bench]")) { weight_strings = get_weights(plugin, work); } else { weight_strings = work.getList("weights[not(@bench)]"); } int rate = 1; boolean rateLimited = true; boolean disabled = false; // can be "disabled", "unlimited" or a number String rate_string; rate_string = setTenantIDinString(work.getString("rate[not(@bench)]", ""), tenantID); rate_string = setTenantIDinString(work.getString("rate" + pluginTest, rate_string), tenantID); if (rate_string.equals(RATE_DISABLED)) { disabled = true; } else if (rate_string.equals(RATE_UNLIMITED)) { rateLimited = false; } else if (rate_string.isEmpty()) { LOG.fatal(String.format( "Tenant " + tenantID + ": Please specify the rate for phase %d and workload %s", i, plugin)); System.exit(-1); } else { try { rate = Integer.parseInt(rate_string); if (rate < 1) { LOG.fatal("Tenant " + tenantID + ": Rate limit must be at least 1. Use unlimited or disabled values instead."); System.exit(-1); } } catch (NumberFormatException e) { LOG.fatal(String.format( "Tenant " + tenantID + ": Rate string must be '%s', '%s' or a number", RATE_DISABLED, RATE_UNLIMITED)); System.exit(-1); } } Phase.Arrival arrival = Phase.Arrival.REGULAR; String arrive = setTenantIDinString(work.getString("@arrival", "regular"), tenantID); if (arrive.toUpperCase().equals("POISSON")) arrival = Phase.Arrival.POISSON; int activeTerminals; activeTerminals = Integer.parseInt(setTenantIDinString( work.getString("active_terminals[not(@bench)]", String.valueOf(terminals)), tenantID)); activeTerminals = Integer.parseInt(setTenantIDinString( work.getString("active_terminals" + pluginTest, String.valueOf(activeTerminals)), tenantID)); if (activeTerminals > terminals) { LOG.fatal("Tenant " + tenantID + ": Configuration error in work " + i + ": number of active terminals" + "" + "is bigger than the total number of terminals"); System.exit(-1); } wrkld.addWork(Integer.parseInt(setTenantIDinString(work.getString("/time"), tenantID)), rate, weight_strings, rateLimited, disabled, activeTerminals, arrival); } // FOR int numTxnTypes = xmlConfig .configurationsAt("transactiontypes" + pluginTest + "/transactiontype").size(); if (numTxnTypes == 0 && pluginList.length == 1) { // if it is a single workload run, <transactiontypes /> // w/o attribute is used pluginTest = "[not(@bench)]"; numTxnTypes = xmlConfig .configurationsAt("transactiontypes" + pluginTest + "/transactiontype").size(); } wrkld.setNumTxnTypes(numTxnTypes); // CHECKING INPUT PHASES int j = 0; for (Phase p : wrkld.getAllPhases()) { j++; if (p.getWeightCount() != wrkld.getNumTxnTypes()) { LOG.fatal(String.format("Tenant " + tenantID + ": Configuration files is inconsistent, phase %d contains %d weights but you defined %d transaction types", j, p.getWeightCount(), wrkld.getNumTxnTypes())); System.exit(-1); } } // FOR // Generate the dialect map wrkld.init(); assert (wrkld.getNumTxnTypes() >= 0); assert (xmlConfig != null); // ---------------------------------------------------------------- // BENCHMARK MODULE // ---------------------------------------------------------------- String classname = pluginConfig.getString("/plugin[@name='" + plugin + "']"); if (classname == null) { throw new ParseException("Plugin " + plugin + " is undefined in config/plugin.xml"); } BenchmarkModule bench = ClassUtil.newInstance(classname, new Object[] { wrkld }, new Class<?>[] { WorkloadConfiguration.class }); assert (benchList.get(0) != null); Map<String, Object> initDebug = new ListOrderedMap<String, Object>(); initDebug.put("Benchmark", String.format("%s {%s}", plugin.toUpperCase(), classname)); initDebug.put("Configuration", configFile); initDebug.put("Type", wrkld.getDBType()); initDebug.put("Driver", wrkld.getDBDriver()); initDebug.put("URL", wrkld.getDBConnection()); initDebug.put("Isolation", setTenantIDinString( xmlConfig.getString("isolation", "TRANSACTION_SERIALIZABLE [DEFAULT]"), tenantID)); initDebug.put("Scale Factor", wrkld.getScaleFactor()); INIT_LOG.info(SINGLE_LINE + "\n\n" + StringUtil.formatMaps(initDebug)); INIT_LOG.info(SINGLE_LINE); // Load TransactionTypes List<TransactionType> ttypes = new ArrayList<TransactionType>(); // Always add an INVALID type for Carlo ttypes.add(TransactionType.INVALID); int txnIdOffset = lastTxnId; for (int i = 1; i < wrkld.getNumTxnTypes() + 1; i++) { String key = "transactiontypes" + pluginTest + "/transactiontype[" + i + "]"; String txnName = setTenantIDinString(xmlConfig.getString(key + "/name"), tenantID); int txnId = i + 1; if (xmlConfig.containsKey(key + "/id")) { txnId = Integer .parseInt(setTenantIDinString(xmlConfig.getString(key + "/id"), tenantID)); } ttypes.add(bench.initTransactionType(txnName, txnId + txnIdOffset)); lastTxnId = i; } // FOR TransactionTypes tt = new TransactionTypes(ttypes); wrkld.setTransTypes(tt); if (benchmarkSettings.getBenchmarkSlaFile() != null) wrkld.setSlaFromFile(benchmarkSettings.getBenchmarkSlaFile()); LOG.debug("Tenant " + tenantID + ": Using the following transaction types: " + tt); bench.setTenantOffset(tenantEvents.get(tenantID).getTime(tenEvent)); bench.setTenantID(tenantID); bench.setBenchmarkSettings(benchmarkSettings); benchList.add(bench); } } } // create result collector ResultCollector rCollector = new ResultCollector(tenantList); // execute benchmarks in parallel ArrayList<Thread> benchThreads = new ArrayList<Thread>(); for (BenchmarkModule benchmark : benchList) { BenchmarkExecutor benchThread = new BenchmarkExecutor(benchmark, argsLine); Thread t = new Thread(benchThread); t.start(); benchThreads.add(t); benchmark.getWorkloadConfiguration().setrCollector(rCollector); } // waiting for completion of all benchmarks for (Thread t : benchThreads) { t.join(); } // print statistics int analysisBuckets = -1; if (argsLine.hasOption("analysis-buckets")) analysisBuckets = Integer.parseInt(argsLine.getOptionValue("analysis-buckets")); String output = null; if (argsLine.hasOption("o")) output = argsLine.getOptionValue("o"); String baseline = null; if (argsLine.hasOption("b")) baseline = argsLine.getOptionValue("b"); rCollector.printStatistics(output, analysisBuckets, argsLine.hasOption("histograms"), baseline); // create GUI if (argsLine.hasOption("g") && (!rCollector.getAllResults().isEmpty())) { try { Gui gui = new Gui(Integer.parseInt(argsLine.getOptionValue("analysis-buckets", "10")), rCollector, output); } catch (Exception e) { e.printStackTrace(); } } }
From source file:Main.java
public static double AmountShowBug(String sum) { return Double.parseDouble(sum.replace(",", "")); }
From source file:Main.java
public static double getCashSum(String cashFlowSum) { return Double.parseDouble(cashFlowSum); }