Example usage for java.io InputStreamReader InputStreamReader

List of usage examples for java.io InputStreamReader InputStreamReader

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Introduction

In this page you can find the example usage for java.io InputStreamReader InputStreamReader.

Prototype

public InputStreamReader(InputStream in)

Source Link

Document

Creates an InputStreamReader that uses the default charset.

Usage

From source file:com.act.biointerpretation.BiointerpretationDriver.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.ja  va2 s  .c  o m*/
    }

    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(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        System.exit(1);
    }

    if (cl.hasOption("help")) {
        HELP_FORMATTER.printHelp(ReactionDesalter.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        return;
    }

    if (cl.hasOption(OPTION_CONFIGURATION_FILE)) {
        List<BiointerpretationStep> steps;
        File configFile = new File(cl.getOptionValue(OPTION_CONFIGURATION_FILE));
        if (!configFile.exists()) {
            String msg = String.format("Cannot find configuration file at %s", configFile.getAbsolutePath());
            LOGGER.error(msg);
            throw new RuntimeException(msg);
        }
        // Read the whole config file.
        try (InputStream is = new FileInputStream(configFile)) {
            steps = OBJECT_MAPPER.readValue(is, new TypeReference<List<BiointerpretationStep>>() {
            });
        } catch (IOException e) {
            LOGGER.error("Caught IO exception when attempting to read configuration file: %s", e.getMessage());
            throw e; // Crash after logging if the config file can't be read.
        }

        // Ask for explicit confirmation before dropping databases.
        LOGGER.info("Biointerpretation plan:");
        for (BiointerpretationStep step : steps) {
            crashIfInvalidDBName(step.getReadDBName());
            crashIfInvalidDBName(step.getWriteDBName());
            LOGGER.info("%s: %s -> %s", step.getOperation(), step.getReadDBName(), step.getWriteDBName());
        }
        LOGGER.warn("WARNING: each DB to be written will be dropped before the writing step commences");
        LOGGER.info("Proceed? [y/n]");
        String readLine;
        try (BufferedReader reader = new BufferedReader(new InputStreamReader(System.in))) {
            readLine = reader.readLine();
        }
        readLine.trim();
        if ("y".equalsIgnoreCase(readLine) || "yes".equalsIgnoreCase(readLine)) {
            LOGGER.info("Biointerpretation plan confirmed, commencing");
            for (BiointerpretationStep step : steps) {
                performOperation(step, true);
            }
            LOGGER.info("Biointerpretation plan completed");
        } else {
            LOGGER.info("Biointerpretation plan not confirmed, exiting");
        }
    } else if (cl.hasOption(OPTION_SINGLE_OPERATION)) {
        if (!cl.hasOption(OPTION_SINGLE_READ_DB) || !cl.hasOption(OPTION_SINGLE_WRITE_DB)) {
            String msg = "Must specify read and write DB names when performing a single operation";
            LOGGER.error(msg);
            throw new RuntimeException(msg);
        }
        BiointerpretationOperation operation;
        try {
            operation = BiointerpretationOperation.valueOf(cl.getOptionValue(OPTION_SINGLE_OPERATION));
        } catch (IllegalArgumentException e) {
            LOGGER.error("Caught IllegalArgumentException when trying to parse operation '%s': %s",
                    cl.getOptionValue(OPTION_SINGLE_OPERATION), e.getMessage());
            throw e; // Crash if we can't interpret the operation.
        }
        String readDB = crashIfInvalidDBName(cl.getOptionValue(OPTION_SINGLE_READ_DB));
        String writeDB = crashIfInvalidDBName(cl.getOptionValue(OPTION_SINGLE_WRITE_DB));

        performOperation(new BiointerpretationStep(operation, readDB, writeDB), false);
    } else {
        String msg = "Must specify either a config file or a single operation to perform.";
        LOGGER.error(msg);
        throw new RuntimeException(msg);
    }
}

From source file:com.aestel.chemistry.openEye.fp.Fingerprinter.java

public static void main(String... args) throws IOException {
    long start = System.currentTimeMillis();
    long iCounter = 0;

    // create command line Options object
    Options options = new Options();
    Option opt = new Option("in", true, "input file [.ism,.sdf,...]");
    opt.setRequired(true);//  w w  w .j  ava  2s.c o m
    options.addOption(opt);

    opt = new Option("out", true, "output file .tsv or oe-supported");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option("idTag", true, "field with ID (default title)");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option("fpType", true, "fingerPrintType: maccs|linear7|linear7*4|HashLinear7*4\n"
            + "   maccs: generate maccs keys\n"
            + "   linear7 generate 7 bonds long linear fingerprints (210k known rest hashed)\n"
            + "   linear7*4 linear 7 bonds if more than 4 atoms code atoms as * (5.1k known rest hashed)\n"
            + "   HashLinear7*4: as linear7*4 but hashed to 16k");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option("format", true,
            "folded512|folded2048|bitList|fragList|none\n" + "   folded512/2048: hex encoded 512/2048 bits\n"
                    + "   bitList: list of bitpositions\n" + "   none: no fp output for use with writeCodeMap");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option("writeCodeMap", false, "Overwrite the codeMap file at the end of processing");
    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 (cmd.hasOption("d")) {
        System.err.println("Start debugger and press return:");
        new BufferedReader(new InputStreamReader(System.in)).readLine();
    }

    String idTag = null;
    if (cmd.hasOption("idTag"))
        idTag = cmd.getOptionValue("idTag");

    String outformat = cmd.getOptionValue("format").toLowerCase().intern();
    if (args.length != 0) {
        exitWithHelp(options);
    }

    String type = cmd.getOptionValue("fpType");
    boolean updateDictionaryFile = cmd.hasOption("writeCodeMap");
    boolean hashUnknownFrag = true;
    if (type.equals("HashLinear7*4"))
        hashUnknownFrag = false;
    if (type.equals("maccs"))
        hashUnknownFrag = false;
    if (updateDictionaryFile)
        hashUnknownFrag = false;
    Fingerprinter fprinter = createFingerprinter(type, updateDictionaryFile, hashUnknownFrag);
    OEMolBase mol = new OEGraphMol();

    String inFile = cmd.getOptionValue("in");
    String outFile = cmd.getOptionValue("out");
    oemolistream ifs = new oemolistream(inFile);

    Runtime rt = Runtime.getRuntime();
    Outputter out;
    if (outFile.endsWith(".txt") || outFile.endsWith(".tab"))
        out = new TabOutputter(fprinter.getMapper(), outFile, outformat);
    else
        out = new OEOutputter(fprinter.getMapper(), outFile, type, outformat);

    while (oechem.OEReadMolecule(ifs, mol)) {
        iCounter++;
        Fingerprint fp = fprinter.getFingerprint(mol);

        String id;
        if (idTag == null)
            id = mol.GetTitle();
        else
            id = oechem.OEGetSDData(mol, idTag);

        if (iCounter % 100 == 0)
            System.err.print(".");
        if (iCounter % 4000 == 0) {
            System.err.printf(" %d %dsec\tt=%d f=%d u=%d m=%d tf=%d\n", iCounter,
                    (System.currentTimeMillis() - start) / 1000, rt.totalMemory() / 1024,
                    rt.freeMemory() / 1024, (rt.totalMemory() - rt.freeMemory()) / 1024, rt.maxMemory() / 1024,
                    (rt.freeMemory() + (rt.maxMemory() - rt.totalMemory())) / 1024);
        }

        out.output(id, mol, fp);
    }

    System.err.printf("Fingerprinter: Read %d structures in %d sec\n", iCounter,
            (System.currentTimeMillis() - start) / 1000);

    if (updateDictionaryFile)
        fprinter.writeDictionary();
    out.close();
    fprinter.close();
}

From source file:com.splout.db.dnode.TCPStreamer.java

/**
 * This main method can be used for testing the TCP interface directly to a
 * local DNode. Will ask for protocol input from Stdin and print output to
 * Stdout//from w w  w. ja  v a 2s  . c  om
 */
public static void main(String[] args) throws UnknownHostException, IOException, SerializationException {
    SploutConfiguration config = SploutConfiguration.get();
    Socket clientSocket = new Socket("localhost", config.getInt(DNodeProperties.STREAMING_PORT));

    DataInputStream inFromServer = new DataInputStream(new BufferedInputStream(clientSocket.getInputStream()));
    DataOutputStream outToServer = new DataOutputStream(
            new BufferedOutputStream(clientSocket.getOutputStream()));

    BufferedReader reader = new BufferedReader(new InputStreamReader(System.in));
    System.out.println("Enter tablespace: ");
    String tablespace = reader.readLine();

    System.out.println("Enter version number: ");
    long versionNumber = Long.parseLong(reader.readLine());

    System.out.println("Enter partition: ");
    int partition = Integer.parseInt(reader.readLine());

    System.out.println("Enter query: ");
    String query = reader.readLine();

    outToServer.writeUTF(tablespace);
    outToServer.writeLong(versionNumber);
    outToServer.writeInt(partition);
    outToServer.writeUTF(query);

    outToServer.flush();

    byte[] buffer = new byte[0];
    boolean read;
    do {
        read = false;
        int nBytes = inFromServer.readInt();
        if (nBytes > 0) {
            buffer = new byte[nBytes];
            int inRead = inFromServer.read(buffer);
            if (inRead > 0) {
                Object[] res = ResultSerializer.deserialize(ByteBuffer.wrap(buffer), Object[].class);
                read = true;
                System.out.println(Arrays.toString(res));
            }
        }
    } while (read);

    clientSocket.close();
}

From source file:edu.cmu.lti.oaqa.knn4qa.apps.ExtractDataAndQueryAsSparseVectors.java

public static void main(String[] args) {
    String optKeys[] = { CommonParams.MAX_NUM_QUERY_PARAM, MAX_NUM_DATA_PARAM, CommonParams.MEMINDEX_PARAM,
            IN_QUERIES_PARAM, OUT_QUERIES_PARAM, OUT_DATA_PARAM, TEXT_FIELD_PARAM, TEST_QTY_PARAM, };
    String optDescs[] = { CommonParams.MAX_NUM_QUERY_DESC, MAX_NUM_DATA_DESC, CommonParams.MEMINDEX_DESC,
            IN_QUERIES_DESC, OUT_QUERIES_DESC, OUT_DATA_DESC, TEXT_FIELD_DESC, TEST_QTY_DESC };
    boolean hasArg[] = { true, true, true, true, true, true, true, true };

    ParamHelper prmHlp = null;/*from w  w  w . j  av a  2 s .  com*/

    try {

        prmHlp = new ParamHelper(args, optKeys, optDescs, hasArg);

        CommandLine cmd = prmHlp.getCommandLine();
        Options opt = prmHlp.getOptions();

        int maxNumQuery = Integer.MAX_VALUE;

        String tmpn = cmd.getOptionValue(CommonParams.MAX_NUM_QUERY_PARAM);
        if (tmpn != null) {
            try {
                maxNumQuery = Integer.parseInt(tmpn);
            } catch (NumberFormatException e) {
                UsageSpecify(CommonParams.MAX_NUM_QUERY_PARAM, opt);
            }
        }

        int maxNumData = Integer.MAX_VALUE;
        tmpn = cmd.getOptionValue(MAX_NUM_DATA_PARAM);
        if (tmpn != null) {
            try {
                maxNumData = Integer.parseInt(tmpn);
            } catch (NumberFormatException e) {
                UsageSpecify(MAX_NUM_DATA_PARAM, opt);
            }
        }
        String memIndexPref = cmd.getOptionValue(CommonParams.MEMINDEX_PARAM);
        if (null == memIndexPref) {
            UsageSpecify(CommonParams.MEMINDEX_PARAM, opt);
        }
        String textField = cmd.getOptionValue(TEXT_FIELD_PARAM);
        if (null == textField) {
            UsageSpecify(TEXT_FIELD_PARAM, opt);
        }

        textField = textField.toLowerCase();
        int fieldId = -1;
        for (int i = 0; i < FeatureExtractor.mFieldNames.length; ++i)
            if (FeatureExtractor.mFieldNames[i].compareToIgnoreCase(textField) == 0) {
                fieldId = i;
                break;
            }
        if (-1 == fieldId) {
            Usage("Wrong field index, should be one of the following: "
                    + String.join(",", FeatureExtractor.mFieldNames), opt);
        }

        InMemForwardIndex indx = new InMemForwardIndex(
                FeatureExtractor.indexFileName(memIndexPref, FeatureExtractor.mFieldNames[fieldId]));

        BM25SimilarityLucene bm25simil = new BM25SimilarityLucene(FeatureExtractor.BM25_K1,
                FeatureExtractor.BM25_B, indx);

        String inQueryFile = cmd.getOptionValue(IN_QUERIES_PARAM);
        String outQueryFile = cmd.getOptionValue(OUT_QUERIES_PARAM);
        if ((inQueryFile == null) != (outQueryFile == null)) {
            Usage("You should either specify both " + IN_QUERIES_PARAM + " and " + OUT_QUERIES_PARAM
                    + " or none of them", opt);
        }
        String outDataFile = cmd.getOptionValue(OUT_DATA_PARAM);

        tmpn = cmd.getOptionValue(TEST_QTY_PARAM);
        int testQty = 0;
        if (tmpn != null) {
            try {
                testQty = Integer.parseInt(tmpn);
            } catch (NumberFormatException e) {
                UsageSpecify(TEST_QTY_PARAM, opt);
            }
        }

        ArrayList<DocEntry> testDocEntries = new ArrayList<DocEntry>();
        ArrayList<DocEntry> testQueryEntries = new ArrayList<DocEntry>();
        ArrayList<TrulySparseVector> testDocVectors = new ArrayList<TrulySparseVector>();
        ArrayList<TrulySparseVector> testQueryVectors = new ArrayList<TrulySparseVector>();

        if (outDataFile != null) {
            BufferedWriter out = new BufferedWriter(
                    new OutputStreamWriter(CompressUtils.createOutputStream(outDataFile)));

            ArrayList<DocEntryExt> docEntries = indx.getDocEntries();

            for (int id = 0; id < Math.min(maxNumData, docEntries.size()); ++id) {
                DocEntry e = docEntries.get(id).mDocEntry;
                TrulySparseVector v = bm25simil.getDocSparseVector(e, false);
                if (id < testQty) {
                    testDocEntries.add(e);
                    testDocVectors.add(v);
                }
                outputVector(out, v);
            }

            out.close();

        }

        Splitter splitOnSpace = Splitter.on(' ').trimResults().omitEmptyStrings();

        if (outQueryFile != null) {
            BufferedReader inpText = new BufferedReader(
                    new InputStreamReader(CompressUtils.createInputStream(inQueryFile)));
            BufferedWriter out = new BufferedWriter(
                    new OutputStreamWriter(CompressUtils.createOutputStream(outQueryFile)));

            String queryText = XmlHelper.readNextXMLIndexEntry(inpText);

            for (int queryQty = 0; queryText != null && queryQty < maxNumQuery; queryText = XmlHelper
                    .readNextXMLIndexEntry(inpText), queryQty++) {
                Map<String, String> queryFields = null;
                // 1. Parse a query

                try {
                    queryFields = XmlHelper.parseXMLIndexEntry(queryText);
                } catch (Exception e) {
                    System.err.println("Parsing error, offending QUERY:\n" + queryText);
                    throw new Exception("Parsing error.");
                }

                String fieldText = queryFields.get(FeatureExtractor.mFieldsSOLR[fieldId]);

                if (fieldText == null) {
                    fieldText = "";
                }

                ArrayList<String> tmpa = new ArrayList<String>();
                for (String s : splitOnSpace.split(fieldText))
                    tmpa.add(s);

                DocEntry e = indx.createDocEntry(tmpa.toArray(new String[tmpa.size()]));

                TrulySparseVector v = bm25simil.getDocSparseVector(e, true);
                if (queryQty < testQty) {
                    testQueryEntries.add(e);
                    testQueryVectors.add(v);
                }
                outputVector(out, v);
            }

            out.close();
        }

        int testedQty = 0, diffQty = 0;
        // Now let's do some testing
        for (int iq = 0; iq < testQueryEntries.size(); ++iq) {
            DocEntry queryEntry = testQueryEntries.get(iq);
            TrulySparseVector queryVector = testQueryVectors.get(iq);
            for (int id = 0; id < testDocEntries.size(); ++id) {
                DocEntry docEntry = testDocEntries.get(id);
                TrulySparseVector docVector = testDocVectors.get(id);
                float val1 = bm25simil.compute(queryEntry, docEntry);
                float val2 = TrulySparseVector.scalarProduct(queryVector, docVector);
                ++testedQty;
                if (Math.abs(val1 - val2) > 1e5) {
                    System.err.println(
                            String.format("Potential mismatch BM25=%f <-> scalar product=%f", val1, val2));
                    ++diffQty;
                }
            }
        }
        if (testedQty > 0)
            System.out.println(String.format("Tested %d Mismatched %d", testedQty, diffQty));

    } catch (ParseException e) {
        Usage("Cannot parse arguments: " + e, prmHlp != null ? prmHlp.getOptions() : null);
        e.printStackTrace();
    } catch (Exception e) {
        e.printStackTrace();
        System.err.println("Terminating due to an exception: " + e);
        System.exit(1);
    }
}

From source file:licenseUtil.LicenseUtil.java

public static void main(String[] args) throws IOException, IncompleteLicenseObjectException {
    if (args.length == 0) {
        logger.error("Missing parameters. Use --help to get a list of the possible options.");
    } else if (args[0].equals("--addPomToTsv")) {
        if (args.length < 4)
            logger.error(//from  ww w  .j ava  2  s. co  m
                    "Missing arguments for option --addPomToTsv. Please specify <pomFileName> <licenses.stub.tsv> <currentVersion> or use the option --help for further information.");
        String pomFN = args[1];
        String spreadSheetFN = args[2];
        String currentVersion = args[3];

        MavenProject project = null;
        try {
            project = Utils.readPom(new File(pomFN));
        } catch (XmlPullParserException e) {
            logger.error("Could not parse pom file: \"" + pomFN + "\"");
        }
        LicensingList licensingList = new LicensingList();
        File f = new File(spreadSheetFN);
        if (f.exists() && !f.isDirectory()) {
            licensingList.readFromSpreadsheet(spreadSheetFN);
        }

        licensingList.addMavenProject(project, currentVersion);
        licensingList.writeToSpreadsheet(spreadSheetFN);
    } else if (args[0].equals("--writeLicense3rdParty")) {
        if (args.length < 4)
            logger.error(
                    "Missing arguments for option --writeLicense3rdParty. Please provide <licenses.enhanced.tsv> <processModule> <currentVersion> [and <targetDir>] or use the option --help for further information.");
        String spreadSheetFN = args[1];
        String processModule = args[2];
        String currentVersion = args[3];

        HashMap<String, String> targetDirs = new HashMap<>();
        if (args.length > 4) {
            File targetDir = new File(args[4]);
            logger.info("scan pom files in direct subdirectories of \"" + targetDir.getPath()
                    + "\" to obtain target locations for 3rd party license files...");
            File[] subdirs = targetDir.listFiles((FileFilter) DirectoryFileFilter.DIRECTORY);
            for (File subdir : subdirs) {
                File pomFile = new File(subdir.getPath() + File.separator + POM_FN);
                if (!pomFile.exists())
                    continue;
                MavenProject mavenProject;
                try {
                    mavenProject = Utils.readPom(pomFile);
                } catch (Exception e) {
                    logger.warn("Could not read from pom file: \"" + pomFile.getPath() + "\" because of "
                            + e.getMessage());
                    continue;
                }
                targetDirs.put(mavenProject.getModel().getArtifactId(), subdir.getAbsolutePath());
            }
        }

        LicensingList licensingList = new LicensingList();
        licensingList.readFromSpreadsheet(spreadSheetFN);
        if (processModule.toUpperCase().equals("ALL")) {
            for (String module : licensingList.getNonFixedHeaders()) {
                try {
                    writeLicense3rdPartyFile(module, licensingList, currentVersion, targetDirs.get(module));
                } catch (NoLicenseTemplateSetException e) {
                    logger.error("Could not write file for module \"" + module
                            + "\". There is no template specified for \"" + e.getLicensingObject()
                            + "\". Please add an existing template filename to the column \""
                            + LicensingObject.ColumnHeader.LICENSE_TEMPLATE.value() + "\" of \"" + spreadSheetFN
                            + "\".");
                }
            }
        } else {
            try {
                writeLicense3rdPartyFile(processModule, licensingList, currentVersion,
                        targetDirs.get(processModule));
            } catch (NoLicenseTemplateSetException e) {
                logger.error("Could not write file for module \"" + processModule
                        + "\". There is no template specified for \"" + e.getLicensingObject()
                        + "\". Please add an existing template filename to the column \""
                        + LicensingObject.ColumnHeader.LICENSE_TEMPLATE.value() + "\" of \"" + spreadSheetFN
                        + "\".");
            }
        }
    } else if (args[0].equals("--buildEffectivePom")) {
        Utils.writeEffectivePom(new File(args[1]), (new File(EFFECTIVE_POM_FN)).getAbsolutePath());
    } else if (args[0].equals("--updateTsvWithProjectsInFolder")) {
        if (args.length < 4)
            logger.error(
                    "Missing arguments for option --processProjectsInFolder. Please provide <superDirectory> <licenses.stub.tsv> and <currentVersion> or use the option --help for further information.");
        File directory = new File(args[1]);
        String spreadSheetFN = args[2];
        String currentVersion = args[3];
        LicensingList licensingList = new LicensingList();
        File f = new File(spreadSheetFN);
        if (f.exists() && !f.isDirectory()) {
            licensingList.readFromSpreadsheet(spreadSheetFN);
        }
        licensingList.addAll(processProjectsInFolder(directory, currentVersion, false));
        licensingList.writeToSpreadsheet(spreadSheetFN);

    } else if (args[0].equals("--purgeTsv")) {
        if (args.length < 3)
            logger.error(
                    "Missing arguments for option --purgeTsv. Please provide <spreadSheetIN.tsv>, <spreadSheetOUT.tsv> and <currentVersion> or use the option --help for further information.");
        String spreadSheetIN = args[1];
        String spreadSheetOUT = args[2];
        String currentVersion = args[3];

        LicensingList licensingList = new LicensingList();
        licensingList.readFromSpreadsheet(spreadSheetIN);
        licensingList.purge(currentVersion);
        licensingList.writeToSpreadsheet(spreadSheetOUT);

    } else if (args[0].equals("--help")) {
        InputStream in = LicenseUtil.class.getClassLoader().getResourceAsStream(README_PATH);
        BufferedReader reader = new BufferedReader(new InputStreamReader(in));
        String line;
        while ((line = reader.readLine()) != null) {
            System.out.println(line);
        }
    } else {
        logger.error("Unknown parameter: " + args[0] + ". Use --help to get a list of the possible options.");
    }
}

From source file:com.genentech.chemistry.tool.mm.SDFMMMinimize.java

/**
 * Main function for running on the command line
 * @param args//from  w  ww  .jav  a  2  s.co  m
 */
public static void main(String... args) throws IOException {
    // Get the available options from the programs
    Map<String, List<String>> allowedProgramsAndForceFields = getAllowedProgramsAndForceFields();
    Map<String, List<String>> allowedProgramsAndSolvents = getAllowedProgramsAndSolvents();

    // 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);

    StringBuilder programOptions = new StringBuilder("Program to use for minimization.  Choices are\n");

    for (String program : allowedProgramsAndForceFields.keySet()) {
        programOptions.append("\n***   -program " + program + "   ***\n");
        String forcefields = "";
        for (String option : allowedProgramsAndForceFields.get(program)) {
            forcefields += option + " ";
        }
        programOptions.append("-forcefield " + forcefields + "\n");

        String solvents = "";
        for (String option : allowedProgramsAndSolvents.get(program)) {
            solvents += option + " ";
        }
        programOptions.append("-solvent " + solvents + "\n");
    }

    opt = new Option(OPT_PROGRAM, true, programOptions.toString());
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option(OPT_FORCEFIELD, true, "Forcefield options.  See -program for choices");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option(OPT_SOLVENT, true, "Solvent options.  See -program for choices");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option(OPT_FIXED_ATOM_TAG, true, "SD tag name which contains the atom numbers to be held fixed.");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option(OPT_FIX_TORSION, true,
            "true/false. if true, the atoms in fixedAtomTag contains 4 indices of atoms defining a torsion angle to be held fixed");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option(OPT_WORKING_DIR, true, "Working directory to put files.");
    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) {
        System.err.println("Unknown arguments" + args);
        exitWithHelp(options);
    }

    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 fixedAtomTag = cmd.getOptionValue(OPT_FIXED_ATOM_TAG);
    boolean fixTorsion = (cmd.getOptionValue(OPT_FIX_TORSION) != null
            && cmd.getOptionValue(OPT_FIX_TORSION).equalsIgnoreCase("true"));
    String programName = cmd.getOptionValue(OPT_PROGRAM);
    String forcefield = cmd.getOptionValue(OPT_FORCEFIELD);
    String solvent = cmd.getOptionValue(OPT_SOLVENT);
    String workDir = cmd.getOptionValue(OPT_WORKING_DIR);

    if (workDir == null || workDir.trim().length() == 0)
        workDir = ".";

    // Create a minimizer 
    SDFMMMinimize minimizer = new SDFMMMinimize();
    minimizer.setMethod(programName, forcefield, solvent);
    minimizer.run(inFile, outFile, fixedAtomTag, fixTorsion, workDir);
    minimizer.close();
    System.err.println("Minimization complete.");
}

From source file:eu.scape_project.tb.chutney.ChutneyDriver.java

/**
 * This main runs only on the local machine when the job is initiated
 * //from   w w w . j ava  2s.c  om
 * @param args command line arguments
 * @throws ParseException command line parse issue
 */
@SuppressWarnings("unused")
public static void main(String[] args) throws ParseException {

    System.out.println(Settings.JOB_NAME + "v" + Settings.VERSION);

    //warning code
    if (true) {
        String yes = "YeS";
        System.out.println(
                "WARNING: this code has not been fully tested and it may delete/modify/alter your systems");
        System.out.println("You run this development code at your own risk, no liability is assumed");
        System.out.print("To continue, type \"" + yes + "\": ");
        try {
            String input = new BufferedReader(new InputStreamReader(System.in)).readLine();
            if (!input.equals(yes)) {
                return;
            }
        } catch (IOException e1) {
            return;
        }
    }
    //end of warning code

    try {
        ToolRunner.run(new Configuration(), new ChutneyDriver(), args);
    } catch (Exception e) {
        e.printStackTrace();
    }

}

From source file:io.tempra.AppServer.java

public static void main(String[] args) throws Exception {

    try {/*w  ww  .  j av  a  2  s.c o  m*/
        // String dir = getProperty("storageLocal");//
        // System.getProperty("user.home");
        String arch = "Win" + System.getProperty("sun.arch.data.model");
        System.out.println("sun.arch.data.model " + arch);

        // Sample to force java load dll or so on a filesystem
        // InputStream in = AppServer.class.getResourceAsStream("/dll/" +
        // arch + "/RechargeRPC.dll");
        //
        // File jCliSiTefI = new File(dir + "/" + "RechargeRPC.dll");
        // System.out.println("Writing dll to: " +
        // jCliSiTefI.getAbsolutePath());
        // OutputStream os = new FileOutputStream(jCliSiTefI);
        // byte[] buffer = new byte[4096];
        // int length;
        // while ((length = in.read(buffer)) > 0) {
        // os.write(buffer, 0, length);
        // }
        // os.close();
        // in.close();
        // System.load(jCliSiTefI.toString());
        // addLibraryPath(dir);

    } catch (Exception e) {
        e.printStackTrace();
    }

    ServletContextHandler context = new ServletContextHandler(ServletContextHandler.SESSIONS);
    context.setContextPath("/");

    Server jettyServer = new Server(Integer.parseInt(getProperty("localport")));
    // security configuration
    // FilterHolder holder = new FilterHolder(CrossOriginFilter.class);
    // holder.setInitParameter(CrossOriginFilter.ALLOWED_ORIGINS_PARAM,
    // "*");
    // holder.setInitParameter("allowCredentials", "true");
    // holder.setInitParameter(
    // CrossOriginFilter.ACCESS_CONTROL_ALLOW_ORIGIN_HEADER, "*");
    // holder.setInitParameter(CrossOriginFilter.ALLOWED_METHODS_PARAM,
    // "GET,POST,HEAD");
    // holder.setInitParameter(CrossOriginFilter.ALLOWED_HEADERS_PARAM,
    // "X-Requested-With,Content-Type,Accept,Origin");
    // holder.setName("cross-origin");

    // context.addFilter(holder, fm);

    ResourceHandler resource_handler = new ResourceHandler();

    // add application on embedded server
    boolean servApp = true;
    boolean quioskMode = false;

    // if (System.getProperty("noServApp") != null )
    // if (System.getProperty("noServApp").equalsIgnoreCase("true"))
    // servApp = false;
    if (servApp) {
        //   ProtectionDomain domain = AppServer.class.getProtectionDomain();
        String webDir = AppServer.class.getResource("/webapp").toExternalForm();
        System.out.println("Jetty WEB DIR >>>>" + webDir);
        resource_handler.setDirectoriesListed(true);
        resource_handler.setWelcomeFiles(new String[] { "index.html" });
        resource_handler.setResourceBase(webDir); //
        // "C:/git/tsAgenciaVirtual/www/");
        // resource_handler.setResourceBase("C:/git/tsAgenciaVirtual/www/");

        // copyJarResourceToFolder((JarURLConnection) AppServer.class
        // .getResource("/app").openConnection(), createTempDir("app"));

        // resource_handler.setResourceBase(System
        // .getProperty("java.io.tmpdir") + "/app");
    }
    // sample to add rest services on container
    context.addServlet(FileUploadServlet.class, "/upload");
    ServletHolder jerseyServlet = context.addServlet(ServletContainer.class, "/services/*");
    jerseyServlet.setInitOrder(0);

    jerseyServlet.setInitParameter("jersey.config.server.provider.classnames",
            RestServices.class.getCanonicalName() + "," + RestServices.class.getCanonicalName());

    HandlerList handlers = new HandlerList();
    // context.addFilter(holder, "/*", EnumSet.of(DispatcherType.REQUEST));

    handlers.setHandlers(new Handler[] { resource_handler, context,

            // wscontext,
            new DefaultHandler() });
    jettyServer.setHandler(handlers);
    try {
        // Initialize javax.websocket layer
        ServerContainer wscontainer = WebSocketServerContainerInitializer.configureContext(context);
        wscontainer.setDefaultMaxSessionIdleTimeout(TimeUnit.HOURS.toMillis(1000));

        // Add WebSocket endpoint to javax.websocket layer
        wscontainer.addEndpoint(FileUpload.class);

    } catch (Throwable t) {
        t.printStackTrace(System.err);
    }

    // try {
    jettyServer.start();
    jettyServer.dump(System.err);

    if (servApp && quioskMode) {
        try {
            Process process = new ProcessBuilder(
                    "C:\\Program Files (x86)\\Google\\Chrome\\Application\\chrome.exe", "--kiosk",
                    "--kiosk-printing", "--auto", "--disable-pinch", "--incognito",
                    "--disable-session-crashed-bubble", "--overscroll-history-navigation=0",
                    "http://localhost:" + getProperty("localport")).start();
            // Process process =
            // Runtime.getRuntime().exec(" -kiosk http://localhost:8080");
            InputStream is = process.getInputStream();
            InputStreamReader isr = new InputStreamReader(is);
            BufferedReader br = new BufferedReader(isr);
            String line;

            System.out.printf("Output of running %s is:", Arrays.toString(args));
            while ((line = br.readLine()) != null) {
                System.out.println(line);
            }
        }

        catch (Exception e) {
            // TODO: handle exception
            e.printStackTrace();
        }
    }
    // } finally {
    // jettyServer.destroy();
    // }//}

    jettyServer.join();
}

From source file:com.bluemarsh.jswat.console.Main.java

/**
 * Kicks off the application./*from w w  w  .  ja v  a  2s . co  m*/
 *
 * @param  args  the command line arguments.
 */
public static void main(String[] args) {
    //
    // An attempt was made early on to use the Console class in java.io,
    // but that is not designed to handle asynchronous output from
    // multiple threads, so we just use the usual System.out for output
    // and System.in for input. Note that automatic flushing is used to
    // ensure output is shown in a timely fashion.
    //

    //
    // Where console mode seems to work:
    // - bash
    // - emacs
    //
    // Where console mode does not seem to work:
    // - NetBeans: output from event listeners is never shown and the
    //   cursor sometimes lags behind the output
    //

    // Turn on flushing so printing the prompt will flush
    // all buffered output generated from other threads.
    PrintWriter output = new PrintWriter(System.out, true);

    // Make sure we have the JPDA classes.
    try {
        Bootstrap.virtualMachineManager();
    } catch (NoClassDefFoundError ncdfe) {
        output.println(NbBundle.getMessage(Main.class, "MSG_Main_NoJPDA"));
        System.exit(1);
    }

    // Ensure we can create the user directory by requesting the
    // platform service. Simply asking for it has the desired effect.
    PlatformProvider.getPlatformService();

    // Define the logging configuration.
    LogManager manager = LogManager.getLogManager();
    InputStream is = Main.class.getResourceAsStream("logging.properties");
    try {
        manager.readConfiguration(is);
    } catch (IOException ioe) {
        ioe.printStackTrace();
        System.exit(1);
    }

    // Print out some useful debugging information.
    logSystemDetails();

    // Add a shutdown hook to make sure we exit cleanly.
    Runtime.getRuntime().addShutdownHook(new Thread(new Runnable() {

        @Override
        public void run() {
            // Save the command aliases.
            CommandParser parser = CommandProvider.getCommandParser();
            parser.saveSettings();
            // Save the runtimes to persistent storage.
            RuntimeManager rm = RuntimeProvider.getRuntimeManager();
            rm.saveRuntimes();
            // Save the sessions to persistent storage and have them
            // close down in preparation to exit.
            SessionManager sm = SessionProvider.getSessionManager();
            sm.saveSessions(true);
        }
    }));

    // Initialize the command parser and load the aliases.
    CommandParser parser = CommandProvider.getCommandParser();
    parser.loadSettings();
    parser.setOutput(output);

    // Create an OutputAdapter to display debuggee output.
    OutputAdapter adapter = new OutputAdapter(output);
    SessionManager sessionMgr = SessionProvider.getSessionManager();
    sessionMgr.addSessionManagerListener(adapter);
    // Create a SessionWatcher to monitor the session status.
    SessionWatcher swatcher = new SessionWatcher();
    sessionMgr.addSessionManagerListener(swatcher);
    // Create a BreakpointWatcher to monitor the breakpoints.
    BreakpointWatcher bwatcher = new BreakpointWatcher();
    sessionMgr.addSessionManagerListener(bwatcher);

    // Add the watchers and adapters to the open sessions.
    Iterator<Session> iter = sessionMgr.iterateSessions();
    while (iter.hasNext()) {
        Session s = iter.next();
        s.addSessionListener(adapter);
        s.addSessionListener(swatcher);
    }

    // Find and run the RC file.
    try {
        runStartupFile(parser, output);
    } catch (IOException ioe) {
        logger.log(Level.SEVERE, null, ioe);
    }

    // Process command line arguments.
    try {
        processArguments(args);
    } catch (ParseException pe) {
        // Report the problem and keep going.
        System.err.println("Option parsing failed: " + pe.getMessage());
        logger.log(Level.SEVERE, null, pe);
    }

    // Display a helpful greeting.
    output.println(NbBundle.getMessage(Main.class, "MSG_Main_Welcome"));
    if (jdbEmulationMode) {
        output.println(NbBundle.getMessage(Main.class, "MSG_Main_Jdb_Emulation"));
    }

    // Enter the main loop of processing user input.
    BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
    while (true) {
        // Keep the prompt format identical to jdb for compatibility
        // with emacs and other possible wrappers.
        output.print("> ");
        output.flush();
        try {
            String command = input.readLine();
            // A null value indicates end of stream.
            if (command != null) {
                performCommand(output, parser, command);
            }
            // Sleep briefly to give the event processing threads,
            // and the automatic output flushing, a chance to catch
            // up before printing the input prompt again.
            Thread.sleep(250);
        } catch (InterruptedException ie) {
            logger.log(Level.WARNING, null, ie);
        } catch (IOException ioe) {
            logger.log(Level.SEVERE, null, ioe);
            output.println(NbBundle.getMessage(Main.class, "ERR_Main_IOError", ioe));
        } catch (Exception x) {
            // Don't ever let an internal bug (e.g. in the command parser)
            // hork the console, as it really irritates people.
            logger.log(Level.SEVERE, null, x);
            output.println(NbBundle.getMessage(Main.class, "ERR_Main_Exception", x));
        }
    }
}

From source file:com.vmware.photon.controller.core.Main.java

public static void main(String[] args) throws Throwable {
    try {//from   w ww. j a  v a 2 s .co m
        LoggingFactory.bootstrap();

        logger.info("args: " + Arrays.toString(args));

        ArgumentParser parser = ArgumentParsers.newArgumentParser("PhotonControllerCore").defaultHelp(true)
                .description("Photon Controller Core");
        parser.addArgument("config-file").help("photon controller configuration file");
        parser.addArgument("--manual").type(Boolean.class).setDefault(false)
                .help("If true, create default deployment.");

        Namespace namespace = parser.parseArgsOrFail(args);

        PhotonControllerConfig photonControllerConfig = getPhotonControllerConfig(namespace);
        DeployerConfig deployerConfig = photonControllerConfig.getDeployerConfig();

        new LoggingFactory(photonControllerConfig.getLogging(), "photon-controller-core").configure();

        SSLContext sslContext;
        if (deployerConfig.getDeployerContext().isAuthEnabled()) {
            sslContext = SSLContext.getInstance(KeyStoreUtils.THRIFT_PROTOCOL);
            TrustManagerFactory tmf = null;

            tmf = TrustManagerFactory.getInstance(TrustManagerFactory.getDefaultAlgorithm());
            KeyStore keyStore = KeyStore.getInstance("JKS");
            InputStream in = FileUtils
                    .openInputStream(new File(deployerConfig.getDeployerContext().getKeyStorePath()));
            keyStore.load(in, deployerConfig.getDeployerContext().getKeyStorePassword().toCharArray());
            tmf.init(keyStore);
            sslContext.init(null, tmf.getTrustManagers(), null);
        } else {
            KeyStoreUtils.generateKeys("/thrift/");
            sslContext = KeyStoreUtils.acceptAllCerts(KeyStoreUtils.THRIFT_PROTOCOL);
        }

        ThriftModule thriftModule = new ThriftModule(sslContext);
        PhotonControllerXenonHost xenonHost = startXenonHost(photonControllerConfig, thriftModule,
                deployerConfig, sslContext);

        if ((Boolean) namespace.get("manual")) {
            DefaultDeployment.createDefaultDeployment(photonControllerConfig.getXenonConfig().getPeerNodes(),
                    deployerConfig, xenonHost);
        }

        // Creating a temp configuration file for apife with modification to some named sections in photon-controller-config
        // so that it can match the Configuration class of dropwizard.
        File apiFeTempConfig = File.createTempFile("apiFeTempConfig", ".tmp");
        File source = new File(args[0]);
        FileInputStream fis = new FileInputStream(source);
        BufferedReader in = new BufferedReader(new InputStreamReader(fis));

        FileWriter fstream = new FileWriter(apiFeTempConfig, true);
        BufferedWriter out = new BufferedWriter(fstream);

        String aLine = null;
        while ((aLine = in.readLine()) != null) {
            if (aLine.equals("apife:")) {
                aLine = aLine.replace("apife:", "server:");
            }
            out.write(aLine);
            out.newLine();
        }
        in.close();
        out.close();

        // This approach can be simplified once the apife container is gone, but for the time being
        // it expects the first arg to be the string "server".
        String[] apiFeArgs = new String[2];
        apiFeArgs[0] = "server";
        apiFeArgs[1] = apiFeTempConfig.getAbsolutePath();
        ApiFeService.setupApiFeConfigurationForServerCommand(apiFeArgs);
        ApiFeService.addServiceHost(xenonHost);
        ApiFeService.setSSLContext(sslContext);

        ApiFeService apiFeService = new ApiFeService();
        apiFeService.run(apiFeArgs);
        apiFeTempConfig.deleteOnExit();

        LocalApiClient localApiClient = apiFeService.getInjector().getInstance(LocalApiClient.class);
        xenonHost.setApiClient(localApiClient);

        // in the non-auth enabled scenario we need to be able to accept any self-signed certificate
        if (!deployerConfig.getDeployerContext().isAuthEnabled()) {
            KeyStoreUtils.acceptAllCerts(KeyStoreUtils.THRIFT_PROTOCOL);
        }

        Runtime.getRuntime().addShutdownHook(new Thread() {
            @Override
            public void run() {
                logger.info("Shutting down");
                xenonHost.stop();
                logger.info("Done");
                LoggingFactory.detachAndStop();
            }
        });
    } catch (Exception e) {
        logger.error("Failed to start photon controller ", e);
        throw e;
    }
}