List of usage examples for org.apache.commons.cli Options addOption
public Options addOption(Option opt)
From source file:edu.umd.ujjwalgoel.AnalyzePMI.java
@SuppressWarnings({ "static-access" })
public static void main(String[] args) {
Options options = new Options();
options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("input path").create(INPUT));
CommandLine cmdline = null;/* w ww . j a v a 2 s .co m*/
CommandLineParser parser = new GnuParser();
try {
cmdline = parser.parse(options, args);
} catch (ParseException exp) {
System.err.println("Error parsing command line: " + exp.getMessage());
System.exit(-1);
}
if (!cmdline.hasOption(INPUT)) {
System.out.println("args: " + Arrays.toString(args));
HelpFormatter formatter = new HelpFormatter();
formatter.setWidth(120);
formatter.printHelp(AnalyzePMI.class.getName(), options);
ToolRunner.printGenericCommandUsage(System.out);
System.exit(-1);
}
String inputPath = cmdline.getOptionValue(INPUT);
System.out.println("input path: " + inputPath);
BufferedReader br = null;
int countPairs = 0;
List<PairOfWritables<PairOfStrings, FloatWritable>> pmis = new ArrayList<PairOfWritables<PairOfStrings, FloatWritable>>();
List<PairOfWritables<PairOfStrings, FloatWritable>> cloudPmis = new ArrayList<PairOfWritables<PairOfStrings, FloatWritable>>();
List<PairOfWritables<PairOfStrings, FloatWritable>> lovePmis = new ArrayList<PairOfWritables<PairOfStrings, FloatWritable>>();
PairOfWritables<PairOfStrings, FloatWritable> highestPMI = null;
PairOfWritables<PairOfStrings, FloatWritable> highestCloudPMI = null;
PairOfWritables<PairOfStrings, FloatWritable> highestCloudPMI2 = null;
PairOfWritables<PairOfStrings, FloatWritable> highestCloudPMI3 = null;
PairOfWritables<PairOfStrings, FloatWritable> highestLovePMI = null;
PairOfWritables<PairOfStrings, FloatWritable> highestLovePMI2 = null;
PairOfWritables<PairOfStrings, FloatWritable> highestLovePMI3 = null;
try {
FileSystem fs = FileSystem.get(new Configuration());
FileStatus[] status = fs.listStatus(new Path(inputPath));
//PairOfStrings pair = new PairOfStrings();
for (int i = 0; i < status.length; i++) {
br = new BufferedReader(new InputStreamReader(fs.open(status[i].getPath())));
String line = br.readLine();
while (line != null) {
String[] words = line.split("\\t");
float value = Float.parseFloat(words[1].trim());
String[] wordPair = words[0].replaceAll("\\(", "").replaceAll("\\)", "").split(",");
PairOfStrings pair = new PairOfStrings();
pair.set(wordPair[0].trim(), wordPair[1].trim());
if (wordPair[0].trim().equals("cloud")) {
PairOfWritables<PairOfStrings, FloatWritable> cloudPmi = new PairOfWritables<PairOfStrings, FloatWritable>();
cloudPmi.set(pair, new FloatWritable(value));
cloudPmis.add(cloudPmi);
if ((highestCloudPMI == null)
|| (highestCloudPMI.getRightElement().compareTo(cloudPmi.getRightElement()) < 0)) {
highestCloudPMI = cloudPmi;
} else if ((highestCloudPMI2 == null)
|| (highestCloudPMI2.getRightElement().compareTo(cloudPmi.getRightElement()) < 0)) {
highestCloudPMI2 = cloudPmi;
} else if ((highestCloudPMI3 == null)
|| (highestCloudPMI3.getRightElement().compareTo(cloudPmi.getRightElement()) < 0)) {
highestCloudPMI3 = cloudPmi;
}
}
if (wordPair[0].trim().equals("love")) {
PairOfWritables<PairOfStrings, FloatWritable> lovePmi = new PairOfWritables<PairOfStrings, FloatWritable>();
lovePmi.set(pair, new FloatWritable(value));
lovePmis.add(lovePmi);
if ((highestLovePMI == null)
|| (highestLovePMI.getRightElement().compareTo(lovePmi.getRightElement()) < 0)) {
highestLovePMI = lovePmi;
} else if ((highestLovePMI2 == null)
|| (highestLovePMI2.getRightElement().compareTo(lovePmi.getRightElement()) < 0)) {
highestLovePMI2 = lovePmi;
} else if ((highestLovePMI3 == null)
|| (highestLovePMI3.getRightElement().compareTo(lovePmi.getRightElement()) < 0)) {
highestLovePMI3 = lovePmi;
}
}
PairOfWritables<PairOfStrings, FloatWritable> pmi = new PairOfWritables<PairOfStrings, FloatWritable>();
pmi.set(pair, new FloatWritable(value));
pmis.add(pmi);
if (highestPMI == null) {
highestPMI = pmi;
} else if (highestPMI.getRightElement().compareTo(pmi.getRightElement()) < 0) {
highestPMI = pmi;
}
countPairs++;
line = br.readLine();
}
}
} catch (Exception ex) {
System.out.println("ERROR" + ex.getMessage());
}
/*Collections.sort(pmis, new Comparator<PairOfWritables<PairOfStrings, FloatWritable>>() {
public int compare(PairOfWritables<PairOfStrings, FloatWritable> e1,
PairOfWritables<PairOfStrings, FloatWritable> e2) {
/*if (e2.getRightElement().compareTo(e1.getRightElement()) == 0) {
return e1.getLeftElement().getLeftElement().compareTo(e2.getLeftElement().getLeftElement());
}
return e2.getRightElement().compareTo(e1.getRightElement());
}
});
Collections.sort(cloudPmis, new Comparator<PairOfWritables<PairOfStrings, FloatWritable>>() {
public int compare(PairOfWritables<PairOfStrings, FloatWritable> e1,
PairOfWritables<PairOfStrings, FloatWritable> e2) {
if (e2.getRightElement().compareTo(e1.getRightElement()) == 0) {
return e1.getLeftElement().getLeftElement().compareTo(e2.getLeftElement().getLeftElement());
}
return e2.getRightElement().compareTo(e1.getRightElement());
}
});
Collections.sort(lovePmis, new Comparator<PairOfWritables<PairOfStrings, FloatWritable>>() {
public int compare(PairOfWritables<PairOfStrings, FloatWritable> e1,
PairOfWritables<PairOfStrings, FloatWritable> e2) {
if (e2.getRightElement().compareTo(e1.getRightElement()) == 0) {
return e1.getLeftElement().getLeftElement().compareTo(e2.getLeftElement().getLeftElement());
}
return e2.getRightElement().compareTo(e1.getRightElement());
}
});
PairOfWritables<PairOfStrings, FloatWritable> highestPMI = pmis.get(0);
PairOfWritables<PairOfStrings, FloatWritable> highestCloudPMI = cloudPmis.get(0); PairOfWritables<PairOfStrings, FloatWritable> highestCloudPMI2 = cloudPmis.get(1);
PairOfWritables<PairOfStrings, FloatWritable> highestCloudPMI3 = cloudPmis.get(2);
PairOfWritables<PairOfStrings, FloatWritable> highestLovePMI = lovePmis.get(0); PairOfWritables<PairOfStrings, FloatWritable> highestLovePMI2 = lovePmis.get(1);
PairOfWritables<PairOfStrings, FloatWritable> highestLovePMI3 = lovePmis.get(2);*/
System.out.println("Total Distinct Pairs : " + countPairs);
System.out.println("Pair with highest PMI : (" + highestPMI.getLeftElement().getLeftElement() + ", "
+ highestPMI.getLeftElement().getRightElement());
System.out
.println("Word with highest PMI with Cloud : " + highestCloudPMI.getLeftElement().getRightElement()
+ " with value : " + highestCloudPMI.getRightElement().get());
System.out.println(
"Word with second highest PMI with Cloud : " + highestCloudPMI2.getLeftElement().getRightElement()
+ " with value : " + highestCloudPMI2.getRightElement().get());
System.out.println(
"Word with third highest PMI with Cloud : " + highestCloudPMI3.getLeftElement().getRightElement()
+ " with value : " + highestCloudPMI3.getRightElement().get());
System.out.println("Word with highest PMI with Love : " + highestLovePMI.getLeftElement().getRightElement()
+ " with value : " + highestLovePMI.getRightElement().get());
System.out.println(
"Word with second highest PMI with Love : " + highestLovePMI2.getLeftElement().getRightElement()
+ " with value : " + highestLovePMI2.getRightElement().get());
System.out.println(
"Word with third highest PMI with Love : " + highestLovePMI3.getLeftElement().getRightElement()
+ " with value : " + highestLovePMI3.getRightElement().get());
}
From source file:com.khubla.jvmbasic.jvmbasicc.JVMBasic.java
/** * start here//from w w w . j av a 2 s . c om * <p> * -file src\test\resources\bas\easy\print.bas -verbose true * </p> */ public static void main(String[] args) { try { System.out.println("khubla.com jvmBASIC Compiler"); /* * options */ final Options options = new Options(); Option oo = Option.builder().argName(OUTPUT_OPTION).longOpt(OUTPUT_OPTION).type(String.class).hasArg() .required(false).desc("target directory to output to").build(); options.addOption(oo); oo = Option.builder().argName(FILE_OPTION).longOpt(FILE_OPTION).type(String.class).hasArg() .required(true).desc("file to compile").build(); options.addOption(oo); oo = Option.builder().argName(VERBOSE_OPTION).longOpt(VERBOSE_OPTION).type(String.class).hasArg() .required(false).desc("verbose output").build(); options.addOption(oo); /* * parse */ final CommandLineParser parser = new DefaultParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (final Exception e) { e.printStackTrace(); final HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("posix", options); System.exit(0); } /* * verbose output? */ final Boolean verbose = Boolean.parseBoolean(cmd.getOptionValue(VERBOSE_OPTION)); /* * get the file */ final String filename = cmd.getOptionValue(FILE_OPTION); final String outputDirectory = cmd.getOptionValue(OUTPUT_OPTION); if (null != filename) { /* * filename */ final String basFileName = System.getProperty("user.dir") + "/" + filename; final File fl = new File(basFileName); if (true == fl.exists()) { /* * show the filename */ System.out.println("Compiling: " + fl.getCanonicalFile()); /* * compiler */ final JVMBasicCompiler jvmBasicCompiler = new JVMBasicCompiler(); /* * compile */ jvmBasicCompiler.compileToClassfile(basFileName, null, outputDirectory, verbose, true, true); } else { throw new Exception("Unable to find: '" + basFileName + "'"); } } else { throw new Exception("File was not supplied"); } } catch (final Exception e) { e.printStackTrace(); } }
From source file:de.prozesskraft.pkraft.Clone.java
public static void main(String[] args) throws org.apache.commons.cli.ParseException, IOException { /*---------------------------- get options from ini-file/*from w ww.ja v a2 s . c o m*/ ----------------------------*/ java.io.File inifile = new java.io.File( WhereAmI.getInstallDirectoryAbsolutePath(Clone.class) + "/" + "../etc/pkraft-clone.ini"); if (inifile.exists()) { try { ini = new Ini(inifile); } catch (InvalidFileFormatException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } catch (IOException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } } else { System.err.println("ini file does not exist: " + inifile.getAbsolutePath()); System.exit(1); } /*---------------------------- create boolean options ----------------------------*/ Option ohelp = new Option("help", "print this message"); Option ov = new Option("v", "prints version and build-date"); /*---------------------------- create argument options ----------------------------*/ Option oinstance = OptionBuilder.withArgName("File").hasArg() .withDescription("[mandatory] process you want to clone.") // .isRequired() .create("instance"); Option obasedir = OptionBuilder.withArgName("DIR").hasArg().withDescription( "[optional, default: <basedirOfInstance>] base directory you want to place the root directory of the clone. this directory must exist at call time.") // .isRequired() .create("basedir"); /*---------------------------- create options object ----------------------------*/ Options options = new Options(); options.addOption(ohelp); options.addOption(ov); options.addOption(oinstance); options.addOption(obasedir); /*---------------------------- create the parser ----------------------------*/ CommandLineParser parser = new GnuParser(); // parse the command line arguments commandline = parser.parse(options, args); /*---------------------------- usage/help ----------------------------*/ if (commandline.hasOption("help")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("clone", options); System.exit(0); } if (commandline.hasOption("v")) { System.out.println("author: alexander.vogel@prozesskraft.de"); System.out.println("version: [% version %]"); System.out.println("date: [% date %]"); System.exit(0); } /*---------------------------- ueberpruefen ob eine schlechte kombination von parametern angegeben wurde ----------------------------*/ if (!(commandline.hasOption("instance"))) { System.err.println("option -instance is mandatory"); exiter(); } /*---------------------------- die lizenz ueberpruefen und ggf abbrechen ----------------------------*/ // check for valid license ArrayList<String> allPortAtHost = new ArrayList<String>(); allPortAtHost.add(ini.get("license-server", "license-server-1")); allPortAtHost.add(ini.get("license-server", "license-server-2")); allPortAtHost.add(ini.get("license-server", "license-server-3")); MyLicense lic = new MyLicense(allPortAtHost, "1", "user-edition", "0.1"); // lizenz-logging ausgeben for (String actLine : (ArrayList<String>) lic.getLog()) { System.err.println(actLine); } // abbruch, wenn lizenz nicht valide if (!lic.isValid()) { System.exit(1); } /*---------------------------- die eigentliche business logic ----------------------------*/ String pathToInstance = commandline.getOptionValue("instance"); java.io.File fileInstance = new java.io.File(pathToInstance); java.io.File fileBaseDir = null; // wenn es nicht vorhanden ist, dann mit fehlermeldung abbrechen if (!fileInstance.exists()) { System.err.println("instance file does not exist."); exiter(); } // testen ob eventuell vorhandene angaben basedir if (commandline.hasOption("basedir")) { fileBaseDir = new java.io.File(commandline.getOptionValue("basedir")); if (!fileBaseDir.exists()) { System.err.println("error: -basedir: directory does not exist"); exiter(); } if (!fileBaseDir.isDirectory()) { System.err.println("error: -basedir: is not a directory"); exiter(); } } // den main-prozess trotzdem nochmal einlesen um subprozesse extrahieren zu koennen Process p1 = new Process(); p1.setInfilebinary(pathToInstance); Process process = p1.readBinary(); // directories setzen, falls angegeben if (fileBaseDir != null) { process.setBaseDir(fileBaseDir.getCanonicalPath()); } // den main-prozess ueber die static function klonen Process clonedProcess = cloneProcess(process, null); // alle steps durchgehen und falls subprocesses existieren auch fuer diese ein cloning durchfuehren for (Step actStep : process.getStep()) { if (actStep.getSubprocess() != null) { Process pDummy = new Process(); pDummy.setInfilebinary(actStep.getAbsdir() + "/process.pmb"); Process processInSubprocess = pDummy.readBinary(); // System.err.println("info: reading process freshly from file: " + actStep.getAbsdir() + "/process.pmb"); if (processInSubprocess != null) { cloneProcess(processInSubprocess, clonedProcess); } } } }
From source file:com.act.reachables.CladeTraversal.java
public static void main(String[] args) throws Exception { Options opts = new Options(); for (Option.Builder b : OPTION_BUILDERS) { opts.addOption(b.build()); }/*from w ww .j a v a2s .c om*/ CommandLine cl = null; try { CommandLineParser parser = new DefaultParser(); cl = parser.parse(opts, args); } catch (ParseException e) { System.err.format("Argument parsing failed: %s\n", e.getMessage()); HELP_FORMATTER.printHelp(CladeTraversal.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } if (cl.hasOption("help")) { HELP_FORMATTER.printHelp(CladeTraversal.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); return; } String targetInchi = cl.getOptionValue(OPTION_TARGET_INCHI, PABA_INCHI); String inchiFileName = cl.getOptionValue(OPTION_OUTPUT_INCHI_FILE_NAME, DEFAULT_INCHI_FILE); String reactionsFileName = cl.getOptionValue(OPTION_OUTPUT_REACTION_FILE_NAME, DEFAULT_REACTIONS_FILE); String reactionDirectory = cl.getOptionValue(OPTION_OUTPUT_FAILED_REACTIONS_DIR_NAME, "/"); String actDataFile = cl.getOptionValue(OPTION_ACT_DATA_FILE, DEFAULT_ACTDATA_FILE); runCladeExpansion(actDataFile, targetInchi, inchiFileName, reactionsFileName, reactionDirectory); }
From source file:com.genentech.chemistry.openEye.apps.SDFMDLSSSMatcher.java
public static void main(String... args) throws IOException, InterruptedException { oechem.OEUseJavaHeap(false);//from w ww . ja va 2 s.c o m // create command line Options object Options options = new Options(); Option opt = new Option("in", true, "input file [.sdf,...]"); opt.setRequired(true); options.addOption(opt); opt = new Option("out", true, "output file oe-supported"); opt.setRequired(false); options.addOption(opt); opt = new Option("ref", true, "refrence file with MDL query molecules"); opt.setRequired(true); options.addOption(opt); opt = new Option("anyMatch", false, "if set all matches are reported not just the first."); opt.setRequired(false); options.addOption(opt); opt = new Option("printAll", false, "if set even compounds that do not macht are outputted."); opt.setRequired(false); options.addOption(opt); opt = new Option("nCpu", true, "number of CPU's used in parallel, dafault 1"); opt.setRequired(false); 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 > 0) { exitWithHelp("Unknown param: " + args[0], options); } if (cmd.hasOption("d")) { System.err.println("Start debugger and press return:"); new BufferedReader(new InputStreamReader(System.in)).readLine(); } int nCpu = 1; boolean firstMatch = !cmd.hasOption("anyMatch"); boolean printAll = cmd.hasOption("printAll"); String d = cmd.getOptionValue("nCpu"); if (d != null) nCpu = Integer.parseInt(d); String inFile = cmd.getOptionValue("in"); String outFile = cmd.getOptionValue("out"); String refFile = cmd.getOptionValue("ref"); SDFMDLSSSMatcher matcher = new SDFMDLSSSMatcher(refFile, outFile, firstMatch, printAll, nCpu); matcher.run(inFile); matcher.close(); }
From source file:fr.tpt.s3.mcdag.scheduling.Main.java
public static void main(String[] args) throws IOException, InterruptedException { /* Command line options */ Options options = new Options(); Option input = new Option("i", "input", true, "MC-DAG XML Models"); input.setRequired(true);// w w w . j a v a 2 s .c o m input.setArgs(Option.UNLIMITED_VALUES); // Sets maximum number of threads to be launched options.addOption(input); Option outSched = new Option("os", "out-scheduler", false, "Write the scheduling tables into a file."); outSched.setRequired(false); options.addOption(outSched); Option outPrism = new Option("op", "out-prism", false, "Write PRISM model into a file."); outPrism.setRequired(false); options.addOption(outPrism); Option jobs = new Option("j", "jobs", true, "Number of threads to be launched."); jobs.setRequired(false); options.addOption(jobs); Option debugOpt = new Option("d", "debug", false, "Enabling debug."); debugOpt.setRequired(false); options.addOption(debugOpt); Option preemptOpt = new Option("p", "preempt", false, "Count for preemptions."); preemptOpt.setRequired(false); options.addOption(preemptOpt); CommandLineParser parser = new DefaultParser(); HelpFormatter formatter = new HelpFormatter(); CommandLine cmd; try { cmd = parser.parse(options, args); } catch (ParseException e) { System.err.println(e.getMessage()); formatter.printHelp("MC-DAG framework", options); System.exit(1); return; } String inputFilePath[] = cmd.getOptionValues("input"); boolean bOutSched = cmd.hasOption("out-scheduler"); boolean bOutPrism = cmd.hasOption("out-prism"); boolean debug = cmd.hasOption("debug"); boolean preempt = cmd.hasOption("preempt"); boolean levels = cmd.hasOption("n-levels"); int nbFiles = inputFilePath.length; int nbJobs = 1; if (cmd.hasOption("jobs")) nbJobs = Integer.parseInt(cmd.getOptionValue("jobs")); if (debug) System.out.println("[DEBUG] Launching " + inputFilePath.length + " thread(s)."); int i_files = 0; ExecutorService executor = Executors.newFixedThreadPool(nbJobs); /* Launch threads to solve allocation */ while (i_files != nbFiles) { SchedulingThread ft = new SchedulingThread(inputFilePath[i_files], bOutSched, bOutPrism, debug, preempt); ft.setLevels(levels); executor.execute(ft); i_files++; } executor.shutdown(); executor.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS); System.out.println("[FRAMEWORK Main] DONE"); }
From source file:es.tid.fiware.fiwareconnectors.cygnus.nodes.CygnusApplication.java
/** * Main application to be run when this CygnusApplication is invoked. The only differences with the original one * are the CygnusApplication is used instead of the Application one, and the Management Interface port option in * the command line.//from www .j a va 2 s . c om * @param args */ public static void main(String[] args) { try { Options options = new Options(); Option option = new Option("n", "name", true, "the name of this agent"); option.setRequired(true); options.addOption(option); option = new Option("f", "conf-file", true, "specify a conf file"); option.setRequired(true); options.addOption(option); option = new Option(null, "no-reload-conf", false, "do not reload " + "conf file if changed"); options.addOption(option); option = new Option("h", "help", false, "display help text"); options.addOption(option); option = new Option("p", "mgmt-if-port", true, "the management interface port"); option.setRequired(false); options.addOption(option); CommandLineParser parser = new GnuParser(); CommandLine commandLine = parser.parse(options, args); File configurationFile = new File(commandLine.getOptionValue('f')); String agentName = commandLine.getOptionValue('n'); boolean reload = !commandLine.hasOption("no-reload-conf"); if (commandLine.hasOption('h')) { new HelpFormatter().printHelp("flume-ng agent", options, true); return; } // if int mgmtIfPort = 8081; // default value if (commandLine.hasOption('p')) { mgmtIfPort = new Integer(commandLine.getOptionValue('p')).intValue(); } // if // the following is to ensure that by default the agent will fail on startup if the file does not exist if (!configurationFile.exists()) { // if command line invocation, then need to fail fast if (System.getProperty(Constants.SYSPROP_CALLED_FROM_SERVICE) == null) { String path = configurationFile.getPath(); try { path = configurationFile.getCanonicalPath(); } catch (IOException ex) { logger.error("Failed to read canonical path for file: " + path, ex); } // try catch throw new ParseException("The specified configuration file does not exist: " + path); } // if } // if List<LifecycleAware> components = Lists.newArrayList(); CygnusApplication application; if (reload) { EventBus eventBus = new EventBus(agentName + "-event-bus"); PollingPropertiesFileConfigurationProvider configurationProvider = new PollingPropertiesFileConfigurationProvider( agentName, configurationFile, eventBus, 30); components.add(configurationProvider); application = new CygnusApplication(components, mgmtIfPort); eventBus.register(application); } else { PropertiesFileConfigurationProvider configurationProvider = new PropertiesFileConfigurationProvider( agentName, configurationFile); application = new CygnusApplication(mgmtIfPort); application.handleConfigurationEvent(configurationProvider.getConfiguration()); } // if else application.start(); final CygnusApplication appReference = application; Runtime.getRuntime().addShutdownHook(new Thread("agent-shutdown-hook") { @Override public void run() { appReference.stop(); } // run }); } catch (Exception e) { logger.error("A fatal error occurred while running. Exception follows.", e); } // try catch }
From source file:fr.tpt.s3.mcdag.generator.MainGenerator.java
/** * Main method for the generator: it launches a given number of threads with the parameters * given/*w ww. ja v a 2 s . c o m*/ * @param args */ public static void main(String[] args) { /* ============================ Command line ================= */ Options options = new Options(); Option o_hi = new Option("mu", "max_utilization", true, "Upper bound utilization"); o_hi.setRequired(true); options.addOption(o_hi); Option o_tasks = new Option("nt", "nb_tasks", true, "Number of tasks for the system"); o_tasks.setRequired(true); options.addOption(o_tasks); Option o_eprob = new Option("e", "eprobability", true, "Probability of edges"); o_eprob.setRequired(true); options.addOption(o_eprob); Option o_levels = new Option("l", "levels", true, "Number of criticality levels"); o_levels.setRequired(true); options.addOption(o_levels); Option o_para = new Option("p", "parallelism", true, "Max parallelism for the DAGs"); o_para.setRequired(true); options.addOption(o_para); Option o_nbdags = new Option("nd", "num_dags", true, "Number of DAGs"); o_nbdags.setRequired(true); options.addOption(o_nbdags); Option o_nbfiles = new Option("nf", "num_files", true, "Number of files"); o_nbfiles.setRequired(true); options.addOption(o_nbfiles); Option o_rfactor = new Option("rf", "reduc_factor", true, "Reduction factor for criticality modes"); o_rfactor.setRequired(false); options.addOption(o_rfactor); Option o_out = new Option("o", "output", true, "Output file for the DAG"); o_out.setRequired(true); options.addOption(o_out); Option graphOpt = new Option("g", "graphviz", false, "Generate a graphviz DOT file"); graphOpt.setRequired(false); options.addOption(graphOpt); Option debugOpt = new Option("d", "debug", false, "Enabling debug"); debugOpt.setRequired(false); options.addOption(debugOpt); Option jobsOpt = new Option("j", "jobs", true, "Number of jobs"); jobsOpt.setRequired(false); options.addOption(jobsOpt); CommandLineParser parser = new DefaultParser(); HelpFormatter formatter = new HelpFormatter(); CommandLine cmd; try { cmd = parser.parse(options, args); } catch (ParseException e) { System.out.println(e.getMessage()); formatter.printHelp("DAG Generator", options); System.exit(1); return; } double maxU = Double.parseDouble(cmd.getOptionValue("max_utilization")); int edgeProb = Integer.parseInt(cmd.getOptionValue("eprobability")); int levels = Integer.parseInt(cmd.getOptionValue("levels")); int nbDags = Integer.parseInt(cmd.getOptionValue("num_dags")); int nbFiles = Integer.parseInt(cmd.getOptionValue("num_files")); int para = Integer.parseInt(cmd.getOptionValue("parallelism")); int nbTasks = Integer.parseInt(cmd.getOptionValue("nb_tasks")); boolean graph = cmd.hasOption("graphviz"); boolean debug = cmd.hasOption("debug"); String output = cmd.getOptionValue("output"); int nbJobs = 1; if (cmd.hasOption("jobs")) nbJobs = Integer.parseInt(cmd.getOptionValue("jobs")); double rfactor = 2.0; if (cmd.hasOption("reduc_factor")) rfactor = Double.parseDouble(cmd.getOptionValue("reduc_factor")); /* ============================= Generator parameters ============================= */ if (nbFiles < 0 || nbDags < 0 || nbJobs < 0) { System.err.println("[ERROR] Generator: Number of files & DAGs need to be positive."); formatter.printHelp("DAG Generator", options); System.exit(1); return; } Thread threads[] = new Thread[nbJobs]; int nbFilesCreated = 0; int count = 0; while (nbFilesCreated != nbFiles) { int launched = 0; for (int i = 0; i < nbJobs && count < nbFiles; i++) { String outFile = output.substring(0, output.lastIndexOf('.')).concat("-" + count + ".xml"); GeneratorThread gt = new GeneratorThread(maxU, nbTasks, edgeProb, levels, para, nbDags, rfactor, outFile, graph, debug); threads[i] = new Thread(gt); threads[i].setName("GeneratorThread-" + i); launched++; count++; threads[i].start(); } for (int i = 0; i < launched; i++) { try { threads[i].join(); nbFilesCreated++; } catch (InterruptedException e) { e.printStackTrace(); } } } }
From source file:com.genentech.struchk.sdfNormalizer.java
public static void main(String[] args) { long start = System.currentTimeMillis(); int nMessages = 0; int nErrors = 0; int nStruct = 0; // create command line Options object Options options = new Options(); Option opt = new Option("in", true, "input file [.ism,.sdf,...]"); opt.setRequired(true);/*from w ww.j av a 2 s . c om*/ options.addOption(opt); opt = new Option("out", true, "output file"); opt.setRequired(true); options.addOption(opt); opt = new Option("mol", true, "molFile used for output: ORIGINAL(def)|NORMALIZED|TAUTOMERIC"); opt.setRequired(false); options.addOption(opt); opt = new Option("shortMessage", false, "Limit message to first 80 characters to conform with sdf file specs."); opt.setRequired(false); options.addOption(opt); CommandLineParser parser = new PosixParser(); CommandLine cmd; try { cmd = parser.parse(options, args); } catch (ParseException e) { exitWithHelp(options, e.getMessage()); throw new Error(e); // avoid compiler errors } args = cmd.getArgs(); if (args.length != 0) { System.err.print("Unknown options: " + args + "\n\n"); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("sdfNormalizer", options); System.exit(1); } String molOpt = cmd.getOptionValue("mol"); OUTMolFormat outMol = OUTMolFormat.ORIGINAL; if (molOpt == null || "original".equalsIgnoreCase(molOpt)) outMol = OUTMolFormat.ORIGINAL; else if ("NORMALIZED".equalsIgnoreCase(molOpt)) outMol = OUTMolFormat.NORMALIZED; else if ("TAUTOMERIC".equalsIgnoreCase(molOpt)) outMol = OUTMolFormat.TAUTOMERIC; else { System.err.printf("Unkown option for -mol: %s\n", molOpt); System.exit(1); } String inFile = cmd.getOptionValue("in"); String outFile = cmd.getOptionValue("out"); boolean limitMessage = cmd.hasOption("shortMessage"); try { oemolistream ifs = new oemolistream(inFile); oemolostream ofs = new oemolostream(outFile); URL cFile = OEStruchk.getResourceURL(OEStruchk.class, "Struchk.xml"); // create OEStruchk from config file OEStruchk strchk = new OEStruchk(cFile, CHECKConfig.ASSIGNStructFlag, false); OEGraphMol mol = new OEGraphMol(); StringBuilder sb = new StringBuilder(2000); while (oechem.OEReadMolecule(ifs, mol)) { if (!strchk.applyRules(mol, null)) nErrors++; switch (outMol) { case NORMALIZED: mol.Clear(); oechem.OEAddMols(mol, strchk.getTransformedMol("parent")); break; case TAUTOMERIC: mol.Clear(); oechem.OEAddMols(mol, strchk.getTransformedMol(null)); break; case ORIGINAL: break; } oechem.OESetSDData(mol, "CTISMILES", strchk.getTransformedIsoSmiles(null)); oechem.OESetSDData(mol, "CTSMILES", strchk.getTransformedSmiles(null)); oechem.OESetSDData(mol, "CISMILES", strchk.getTransformedIsoSmiles("parent")); oechem.OESetSDData(mol, "Strutct_Flag", strchk.getStructureFlag().getName()); List<Message> msgs = strchk.getStructureMessages(null); nMessages += msgs.size(); for (Message msg : msgs) sb.append(String.format("\t%s:%s", msg.getLevel(), msg.getText())); if (limitMessage) sb.setLength(Math.min(sb.length(), 80)); oechem.OESetSDData(mol, "NORM_MESSAGE", sb.toString()); oechem.OEWriteMolecule(ofs, mol); sb.setLength(0); nStruct++; } strchk.delete(); mol.delete(); ifs.close(); ifs.delete(); ofs.close(); ofs.delete(); } catch (Exception e) { throw new Error(e); } finally { System.err.printf("sdfNormalizer: Checked %d structures %d errors, %d messages in %dsec\n", nStruct, nErrors, nMessages, (System.currentTimeMillis() - start) / 1000); } }
From source file:act.installer.pubchem.PubchemSynonymFinder.java
public static void main(String[] args) throws Exception { org.apache.commons.cli.Options opts = new org.apache.commons.cli.Options(); for (Option.Builder b : OPTION_BUILDERS) { opts.addOption(b.build()); }/*from www. j av a 2 s .c om*/ CommandLine cl = null; try { CommandLineParser parser = new DefaultParser(); cl = parser.parse(opts, args); } catch (ParseException e) { System.err.format("Argument parsing failed: %s\n", e.getMessage()); HELP_FORMATTER.printHelp(PubchemSynonymFinder.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } if (cl.hasOption("help")) { HELP_FORMATTER.printHelp(PubchemSynonymFinder.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); return; } File rocksDBFile = new File(cl.getOptionValue(OPTION_INDEX_PATH)); if (!rocksDBFile.isDirectory()) { System.err.format("Index directory does not exist or is not a directory at '%s'", rocksDBFile.getAbsolutePath()); HELP_FORMATTER.printHelp(PubchemSynonymFinder.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } List<String> compoundIds = null; if (cl.hasOption(OPTION_PUBCHEM_COMPOUND_ID)) { compoundIds = Collections.singletonList(cl.getOptionValue(OPTION_PUBCHEM_COMPOUND_ID)); } else if (cl.hasOption(OPTION_IDS_FILE)) { File idsFile = new File(cl.getOptionValue(OPTION_IDS_FILE)); if (!idsFile.exists()) { System.err.format("Cannot find Pubchem CIDs file at %s", idsFile.getAbsolutePath()); HELP_FORMATTER.printHelp(PubchemSynonymFinder.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } compoundIds = getCIDsFromFile(idsFile); if (compoundIds.size() == 0) { System.err.format("Found zero Pubchem CIDs to process in file at '%s', exiting", idsFile.getAbsolutePath()); HELP_FORMATTER.printHelp(PubchemSynonymFinder.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } } else { System.err.format("Must specify one of '%s' or '%s'; index is too big to print all synonyms.", OPTION_PUBCHEM_COMPOUND_ID, OPTION_IDS_FILE); HELP_FORMATTER.printHelp(PubchemSynonymFinder.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } // Run a quick check to warn users of malformed ids. compoundIds.forEach(x -> { if (!PC_CID_PATTERN.matcher(x).matches()) { // Use matches() for complete matching. LOGGER.warn("Specified compound id does not match expected format: %s", x); } }); LOGGER.info("Opening DB and searching for %d Pubchem CIDs", compoundIds.size()); Pair<RocksDB, Map<PubchemTTLMerger.COLUMN_FAMILIES, ColumnFamilyHandle>> dbAndHandles = null; Map<String, PubchemSynonyms> results = new LinkedHashMap<>(compoundIds.size()); try { dbAndHandles = PubchemTTLMerger.openExistingRocksDB(rocksDBFile); RocksDB db = dbAndHandles.getLeft(); ColumnFamilyHandle cidToSynonymsCfh = dbAndHandles.getRight() .get(PubchemTTLMerger.COLUMN_FAMILIES.CID_TO_SYNONYMS); for (String cid : compoundIds) { PubchemSynonyms synonyms = null; byte[] val = db.get(cidToSynonymsCfh, cid.getBytes(UTF8)); if (val != null) { ObjectInputStream oi = new ObjectInputStream(new ByteArrayInputStream(val)); // We're relying on our use of a one-value-type per index model here so we can skip the instanceof check. synonyms = (PubchemSynonyms) oi.readObject(); } else { LOGGER.warn("No synonyms available for compound id '%s'", cid); } results.put(cid, synonyms); } } finally { if (dbAndHandles != null) { dbAndHandles.getLeft().close(); } } try (OutputStream outputStream = cl.hasOption(OPTION_OUTPUT) ? new FileOutputStream(cl.getOptionValue(OPTION_OUTPUT)) : System.out) { OBJECT_MAPPER.writerWithDefaultPrettyPrinter().writeValue(outputStream, results); new OutputStreamWriter(outputStream).append('\n'); } LOGGER.info("Done searching for Pubchem synonyms"); }