Example usage for java.lang Exception getMessage

List of usage examples for java.lang Exception getMessage

Introduction

In this page you can find the example usage for java.lang Exception getMessage.

Prototype

public String getMessage() 

Source Link

Document

Returns the detail message string of this throwable.

Usage

From source file:de.prozesskraft.pkraft.Wrap.java

public static void main(String[] args) throws org.apache.commons.cli.ParseException, IOException {

    //      try/*from w w w  . ja  v  a 2s.  c  o  m*/
    //      {
    //         if (args.length != 3)
    //         {
    //            System.out.println("Please specify processdefinition file (xml) and an outputfilename");
    //         }
    //         
    //      }
    //      catch (ArrayIndexOutOfBoundsException e)
    //      {
    //         System.out.println("***ArrayIndexOutOfBoundsException: Please specify processdefinition.xml, openoffice_template.od*, newfile_for_processdefinitions.odt\n" + e.toString());
    //      }

    /*----------------------------
      get options from ini-file
    ----------------------------*/
    File inifile = new java.io.File(
            WhereAmI.getInstallDirectoryAbsolutePath(Wrap.class) + "/" + "../etc/pkraft-wrap.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 ooutput = OptionBuilder.withArgName("FILE").hasArg()
            .withDescription("[mandatory; default: .] file for generated wrapper process.")
            //            .isRequired()
            .create("output");

    Option odefinition = OptionBuilder.withArgName("FILE").hasArg()
            .withDescription("[mandatory] process definition file.")
            //            .isRequired()
            .create("definition");

    /*----------------------------
      create options object
    ----------------------------*/
    Options options = new Options();

    options.addOption(ohelp);
    options.addOption(ov);
    options.addOption(ooutput);
    options.addOption(odefinition);

    /*----------------------------
      create the parser
    ----------------------------*/
    CommandLineParser parser = new GnuParser();
    try {
        // parse the command line arguments
        commandline = parser.parse(options, args);

    } catch (Exception exp) {
        // oops, something went wrong
        System.err.println("Parsing failed. Reason: " + exp.getMessage());
        exiter();
    }

    /*----------------------------
      usage/help
    ----------------------------*/
    if (commandline.hasOption("help")) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("wrap", options);
        System.exit(0);
    }

    else if (commandline.hasOption("v")) {
        System.out.println("web:     www.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("definition"))) {
        System.err.println("option -definition is mandatory.");
        exiter();
    }

    if (!(commandline.hasOption("output"))) {
        System.err.println("option -output 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
    ----------------------------*/
    Process p1 = new Process();
    java.io.File output = new java.io.File(commandline.getOptionValue("output"));

    if (output.exists()) {
        System.err.println("warn: already exists: " + output.getCanonicalPath());
        exiter();
    }

    p1.setInfilexml(commandline.getOptionValue("definition"));
    System.err.println("info: reading process definition " + commandline.getOptionValue("definition"));

    // dummy process
    Process p2 = null;

    try {
        p2 = p1.readXml();
    } catch (JAXBException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
        System.err.println("error");
        exiter();
    }

    // den wrapper process generieren
    Process p3 = p2.getProcessAsWrapper();
    p3.setOutfilexml(output.getAbsolutePath());

    // den neuen wrap-process rausschreiben
    p3.writeXml();
}

From source file:edu.msu.cme.rdp.classifier.comparison.ComparisonCmd.java

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

    String queryFile1 = null;//from  w w w.  j  ava  2 s.  c o  m
    String queryFile2 = null;
    String class_outputFile = null;
    String compare_outputFile = null;
    String propFile = null;
    ClassificationResultFormatter.FORMAT format = CmdOptions.DEFAULT_FORMAT;
    float conf_cutoff = CmdOptions.DEFAULT_CONF;
    String gene = null;

    try {
        CommandLine line = new PosixParser().parse(options, args);

        if (line.hasOption(QUERYFILE1_SHORT_OPT)) {
            queryFile1 = line.getOptionValue(QUERYFILE1_SHORT_OPT);
        } else {
            throw new Exception("queryFile1 must be specified");
        }
        if (line.hasOption(QUERYFILE2_SHORT_OPT)) {
            queryFile2 = line.getOptionValue(QUERYFILE2_SHORT_OPT);
        } else {
            throw new Exception("queryFile2 must be specified");
        }

        if (line.hasOption(CmdOptions.OUTFILE_SHORT_OPT)) {
            class_outputFile = line.getOptionValue(CmdOptions.OUTFILE_SHORT_OPT);
        } else {
            throw new Exception("outputFile for classification results must be specified");
        }

        if (line.hasOption(COMPARE_OUTFILE_SHORT_OPT)) {
            compare_outputFile = line.getOptionValue(COMPARE_OUTFILE_SHORT_OPT);
        } else {
            throw new Exception("outputFile for comparsion results must be specified");
        }

        if (line.hasOption(CmdOptions.TRAINPROPFILE_SHORT_OPT)) {
            if (gene != null) {
                throw new IllegalArgumentException(
                        "Already specified the gene from the default location. Can not specify train_propfile");
            } else {
                propFile = line.getOptionValue(CmdOptions.TRAINPROPFILE_SHORT_OPT);
            }
        }
        if (line.hasOption(CmdOptions.BOOTSTRAP_SHORT_OPT)) {
            conf_cutoff = Float.parseFloat(line.getOptionValue(CmdOptions.BOOTSTRAP_SHORT_OPT));
        }
        if (line.hasOption(CmdOptions.FORMAT_SHORT_OPT)) {
            String f = line.getOptionValue(CmdOptions.FORMAT_SHORT_OPT);
            if (f.equalsIgnoreCase("allrank")) {
                format = ClassificationResultFormatter.FORMAT.allRank;
            } else if (f.equalsIgnoreCase("fixrank")) {
                format = ClassificationResultFormatter.FORMAT.fixRank;
            } else if (f.equalsIgnoreCase("filterbyconf")) {
                format = ClassificationResultFormatter.FORMAT.filterbyconf;
            } else if (f.equalsIgnoreCase("db")) {
                format = ClassificationResultFormatter.FORMAT.dbformat;
            } else {
                throw new IllegalArgumentException(
                        "Not valid output format, only allrank, fixrank, filterbyconf and db allowed");
            }

        }
        if (line.hasOption(CmdOptions.GENE_SHORT_OPT)) {
            if (propFile != null) {
                throw new IllegalArgumentException(
                        "Already specified train_propfile. Can not specify gene any more");
            }
            gene = line.getOptionValue(CmdOptions.GENE_SHORT_OPT).toLowerCase();

            if (!gene.equals(ClassifierFactory.RRNA_16S_GENE)
                    && !gene.equals(ClassifierFactory.FUNGALLSU_GENE)) {
                throw new IllegalArgumentException(gene + " is NOT valid, only allows "
                        + ClassifierFactory.RRNA_16S_GENE + " and " + ClassifierFactory.FUNGALLSU_GENE);
            }
        }
    } catch (Exception e) {
        System.out.println("Command Error: " + e.getMessage());
        new HelpFormatter().printHelp(120, "ComparisonCmd", "", options, "", true);
        return;
    }

    if (propFile == null && gene == null) {
        gene = ClassifierFactory.RRNA_16S_GENE;
    }

    ComparisonCmd cmd = new ComparisonCmd(propFile, gene);
    cmd.setConfidenceCutoff(conf_cutoff);
    printLicense();

    cmd.doClassify(queryFile1, queryFile2, class_outputFile, compare_outputFile, format);

}

From source file:com.microsoft.azure.management.compute.samples.DeployImageFromContainerRegistryToKubernetes.java

/**
 * Main entry point./*from ww  w  . j a va  2  s  . c  om*/
 *
 * @param args the parameters
 */
public static void main(String[] args) {
    try {
        //=============================================================
        // Authenticate

        final File credFile = new File(System.getenv("AZURE_AUTH_LOCATION"));

        Azure azure = Azure.configure().withLogLevel(LogLevel.BODY).authenticate(credFile)
                .withDefaultSubscription();

        // Print selected subscription
        System.out.println("Selected subscription: " + azure.subscriptionId());

        runSample(azure, "", "");
    } catch (Exception e) {
        System.out.println(e.getMessage());
        e.printStackTrace();
    }
}

From source file:com.genentech.chemistry.tool.SDFSelectivityCalculator.java

/**
 * @param args/*from   ww  w.j  av a  2s  .  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_NUMERATOR, true, "Name of the field containing the numerator value.");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option(OPT_NUMERATOR_OP, true,
            "Name of the field containing the numerator operator."
                    + " If this option is not set it is assumed that the operator" + " is included in the "
                    + OPT_NUMERATOR + " field.");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option(OPT_DENOMINATOR, true, "Name of the field containing the denominator value.");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option(OPT_DENOMINATOR_OP, true,
            "Name of the field containing the denominator operator."
                    + " If this option is not set it is assumed that the operator" + " is included in the "
                    + OPT_DENOMINATOR + " field.");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option(OPT_SELECTIVITY, true, "Name of the field containing the output selectivity value."
            + " If this option is not set, the field name of the denominator" + " is used.");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option(OPT_SELECTIVITY_OP, true,
            "Name of the field containing the output selectivity operator."
                    + " If this option is not set it is assumed that the operator" + " is included in the "
                    + OPT_SELECTIVITY + " field.");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option(OPT_OUTPUT_MODE, true,
            "Valid: separate, combine, combine+op;" + " If not specified, default is combine+op."
                    + " (separate=operator and value in separate fields;"
                    + " combine=operator and value in one field;"
                    + " combine+op=one field with the operator and value and"
                    + " plus one field with only the operator)");
    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 inFile = cmd.getOptionValue(OPT_INFILE);
    String outFile = cmd.getOptionValue(OPT_OUTFILE);
    String outputMode = cmd.getOptionValue(OPT_OUTPUT_MODE);
    String numeratorTag = cmd.getOptionValue(OPT_NUMERATOR);
    String numeratorOPTag = cmd.getOptionValue(OPT_NUMERATOR_OP);
    String denominatorTag = cmd.getOptionValue(OPT_DENOMINATOR);
    String denominatorOPTag = cmd.getOptionValue(OPT_DENOMINATOR_OP);
    String selectivityTag = cmd.getOptionValue(OPT_SELECTIVITY);
    String selectivityOPTag = cmd.getOptionValue(OPT_SELECTIVITY_OP);

    SDFSelectivityCalculator calculator = new SDFSelectivityCalculator(outFile);
    try {
        calculator.setParameters(outputMode, numeratorTag, numeratorOPTag, denominatorTag, denominatorOPTag,
                selectivityTag, selectivityOPTag);
        calculator.run(inFile);
    } catch (IncorrectInputException e) {
        System.err.println(e.getMessage());
        exitWithHelp(options);
    } finally {
        calculator.close();
    }
}

From source file:mx.unam.fesa.isoo.msp.MSPMain.java

/**
 * @param args//from  w w  w . j  av  a  2s .  com
 * @throws Exception
 */
@SuppressWarnings("static-access")
public static void main(String[] args) {

    //
    // creating options
    //

    Options options = new Options();

    // help option
    //
    options.addOption(
            OptionBuilder.withDescription("Prints this message.").withLongOpt("help").create(OPT_HELP));

    // server option
    //
    options.addOption(OptionBuilder.withDescription("The server this MineSweeperPlayer will connect to.")
            .hasArg().withArgName("SERVER").withLongOpt("server").create(OPT_SERVER));

    // port option
    //
    options.addOption(OptionBuilder.withDescription("The port this MineSweeperPlayer will connect to.").hasArg()
            .withType(new Integer(0)).withArgName("PORT").withLongOpt("port").create(OPT_PORT));

    // parsing options
    //
    String hostname = DEFAULT_SERVER;
    int port = DEFAULT_PORT;
    try {
        // using GNU standard
        //
        CommandLine line = new GnuParser().parse(options, args);

        if (line.hasOption(OPT_HELP)) {
            new HelpFormatter().printHelp("msc [options]", options);
            return;
        }

        if (line.hasOption(OPT_PORT)) {
            try {
                port = (Integer) line.getOptionObject(OPT_PORT);
            } catch (Exception e) {
            }
        }

        if (line.hasOption(OPT_SERVER)) {
            hostname = line.getOptionValue(OPT_PORT);
        }
    } catch (ParseException e) {
        System.err.println("Could not parse command line options correctly: " + e.getMessage());
        return;
    }

    //
    // configuring logging services
    //

    try {
        LogManager.getLogManager()
                .readConfiguration(ClassLoader.getSystemResourceAsStream(DEFAULT_LOGGING_CONFIG_FILE));
    } catch (Exception e) {
        throw new Error("Could not load logging properties file.", e);
    }

    //
    // setting up Mine Sweeper client
    //

    try {
        new MSClient(hostname, port);
    } catch (Exception e) {
        System.err.println("Could not execute MineSweeper client: " + e.getMessage());
    }
}

From source file:examples.TelnetClientExample.java

/***
 * Main for the TelnetClientExample.//www . ja  v a  2s  .  c o  m
 ***/
public static void main(String[] args) throws IOException {
    FileOutputStream fout = null;

    if (args.length < 1) {
        System.err.println("Usage: TelnetClientExample1 <remote-ip> [<remote-port>]");
        System.exit(1);
    }

    String remoteip = args[0];

    int remoteport;

    if (args.length > 1) {
        remoteport = (new Integer(args[1])).intValue();
    } else {
        remoteport = 23;
    }

    try {
        fout = new FileOutputStream("spy.log", true);
    } catch (Exception e) {
        System.err.println("Exception while opening the spy file: " + e.getMessage());
    }

    tc = new TelnetClient();

    TerminalTypeOptionHandler ttopt = new TerminalTypeOptionHandler("VT100", false, false, true, false);
    EchoOptionHandler echoopt = new EchoOptionHandler(true, false, true, false);
    SuppressGAOptionHandler gaopt = new SuppressGAOptionHandler(true, true, true, true);

    try {
        tc.addOptionHandler(ttopt);
        tc.addOptionHandler(echoopt);
        tc.addOptionHandler(gaopt);
    } catch (InvalidTelnetOptionException e) {
        System.err.println("Error registering option handlers: " + e.getMessage());
    }

    while (true) {
        boolean end_loop = false;
        try {
            tc.connect(remoteip, remoteport);

            Thread reader = new Thread(new TelnetClientExample());
            tc.registerNotifHandler(new TelnetClientExample());
            System.out.println("TelnetClientExample");
            System.out.println("Type AYT to send an AYT telnet command");
            System.out.println("Type OPT to print a report of status of options (0-24)");
            System.out.println("Type REGISTER to register a new SimpleOptionHandler");
            System.out.println("Type UNREGISTER to unregister an OptionHandler");
            System.out.println("Type SPY to register the spy (connect to port 3333 to spy)");
            System.out.println("Type UNSPY to stop spying the connection");

            reader.start();
            OutputStream outstr = tc.getOutputStream();

            byte[] buff = new byte[1024];
            int ret_read = 0;

            do {
                try {
                    ret_read = System.in.read(buff);
                    if (ret_read > 0) {
                        if ((new String(buff, 0, ret_read)).startsWith("AYT")) {
                            try {
                                System.out.println("Sending AYT");

                                System.out.println("AYT response:" + tc.sendAYT(5000));
                            } catch (Exception e) {
                                System.err.println("Exception waiting AYT response: " + e.getMessage());
                            }
                        } else if ((new String(buff, 0, ret_read)).startsWith("OPT")) {
                            System.out.println("Status of options:");
                            for (int ii = 0; ii < 25; ii++)
                                System.out.println("Local Option " + ii + ":" + tc.getLocalOptionState(ii)
                                        + " Remote Option " + ii + ":" + tc.getRemoteOptionState(ii));
                        } else if ((new String(buff, 0, ret_read)).startsWith("REGISTER")) {
                            StringTokenizer st = new StringTokenizer(new String(buff));
                            try {
                                st.nextToken();
                                int opcode = (new Integer(st.nextToken())).intValue();
                                boolean initlocal = (new Boolean(st.nextToken())).booleanValue();
                                boolean initremote = (new Boolean(st.nextToken())).booleanValue();
                                boolean acceptlocal = (new Boolean(st.nextToken())).booleanValue();
                                boolean acceptremote = (new Boolean(st.nextToken())).booleanValue();
                                SimpleOptionHandler opthand = new SimpleOptionHandler(opcode, initlocal,
                                        initremote, acceptlocal, acceptremote);
                                tc.addOptionHandler(opthand);
                            } catch (Exception e) {
                                if (e instanceof InvalidTelnetOptionException) {
                                    System.err.println("Error registering option: " + e.getMessage());
                                } else {
                                    System.err.println("Invalid REGISTER command.");
                                    System.err.println(
                                            "Use REGISTER optcode initlocal initremote acceptlocal acceptremote");
                                    System.err.println("(optcode is an integer.)");
                                    System.err.println(
                                            "(initlocal, initremote, acceptlocal, acceptremote are boolean)");
                                }
                            }
                        } else if ((new String(buff, 0, ret_read)).startsWith("UNREGISTER")) {
                            StringTokenizer st = new StringTokenizer(new String(buff));
                            try {
                                st.nextToken();
                                int opcode = (new Integer(st.nextToken())).intValue();
                                tc.deleteOptionHandler(opcode);
                            } catch (Exception e) {
                                if (e instanceof InvalidTelnetOptionException) {
                                    System.err.println("Error unregistering option: " + e.getMessage());
                                } else {
                                    System.err.println("Invalid UNREGISTER command.");
                                    System.err.println("Use UNREGISTER optcode");
                                    System.err.println("(optcode is an integer)");
                                }
                            }
                        } else if ((new String(buff, 0, ret_read)).startsWith("SPY")) {
                            try {
                                tc.registerSpyStream(fout);
                            } catch (Exception e) {
                                System.err.println("Error registering the spy");
                            }
                        } else if ((new String(buff, 0, ret_read)).startsWith("UNSPY")) {
                            tc.stopSpyStream();
                        } else {
                            try {
                                outstr.write(buff, 0, ret_read);
                                outstr.flush();
                            } catch (Exception e) {
                                end_loop = true;
                            }
                        }
                    }
                } catch (Exception e) {
                    System.err.println("Exception while reading keyboard:" + e.getMessage());
                    end_loop = true;
                }
            } while ((ret_read > 0) && (end_loop == false));

            try {
                tc.disconnect();
            } catch (Exception e) {
                System.err.println("Exception while connecting:" + e.getMessage());
            }
        } catch (Exception e) {
            System.err.println("Exception while connecting:" + e.getMessage());
            System.exit(1);
        }
    }
}

From source file:net.mitnet.tools.pdf.book.publisher.ui.cli.BookPublisherCLI.java

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

    try {/*from   w  ww .jav  a  2s .c om*/

        BookPublisherCLI cli = new BookPublisherCLI();
        cli.run(args);

    } catch (Exception e) {
        // String msg = "Error publishing book \"" + config.getOutputBookFile() + "\" : " + e.getMessage();
        String msg = "Error publishing book : " + e.getMessage();
        error(msg, e);
        throw new Exception(msg, e);
    }

    System.exit(0);
}

From source file:ch.unizh.ini.jaer.projects.gesture.vlccontrol.TelnetClientExample.java

/***
 * Main for the TelnetClientExample.//from  w w w.  j  av  a  2  s.c o m
 ***/
public static void main(String[] args) throws IOException {
    FileOutputStream fout = null;

    if (args.length < 1) {
        System.err.println("Usage: TelnetClientExample1 <remote-ip> [<remote-port>]");
        System.exit(1);
    }

    String remoteip = args[0];

    int remoteport;

    if (args.length > 1) {
        remoteport = (new Integer(args[1])).intValue();
    } else {
        remoteport = 23;
    }

    try {
        fout = new FileOutputStream("spy.log", true);
    } catch (Exception e) {
        System.err.println("Exception while opening the spy file: " + e.getMessage());
    }

    tc = new TelnetClient();

    TerminalTypeOptionHandler ttopt = new TerminalTypeOptionHandler("VT100", false, false, true, false);
    EchoOptionHandler echoopt = new EchoOptionHandler(true, false, true, false);
    SuppressGAOptionHandler gaopt = new SuppressGAOptionHandler(true, true, true, true);

    try {
        tc.addOptionHandler(ttopt);
        tc.addOptionHandler(echoopt);
        tc.addOptionHandler(gaopt);
    } catch (InvalidTelnetOptionException e) {
        System.err.println("Error registering option handlers: " + e.getMessage());
    }

    while (true) {
        boolean end_loop = false;
        try {
            tc.connect(remoteip, remoteport);

            Thread reader = new Thread(new TelnetClientExample());
            tc.registerNotifHandler(new TelnetClientExample());
            System.out.println("TelnetClientExample");
            System.out.println("Type AYT to send an AYT telnet command");
            System.out.println("Type OPT to print a report of status of options (0-24)");
            System.out.println("Type REGISTER to register a new SimpleOptionHandler");
            System.out.println("Type UNREGISTER to unregister an OptionHandler");
            System.out.println("Type SPY to register the spy (connect to port 3333 to spy)");
            System.out.println("Type UNSPY to stop spying the connection");

            reader.start();
            OutputStream outstr = tc.getOutputStream();

            byte[] buff = new byte[1024];
            int ret_read = 0;

            do {
                try {
                    ret_read = System.in.read(buff);
                    if (ret_read > 0) {
                        if ((new String(buff, 0, ret_read)).startsWith("AYT")) {
                            try {
                                System.out.println("Sending AYT");

                                System.out.println("AYT response:" + tc.sendAYT(5000));
                            } catch (Exception e) {
                                System.err.println("Exception waiting AYT response: " + e.getMessage());
                            }
                        } else if ((new String(buff, 0, ret_read)).startsWith("OPT")) {
                            System.out.println("Status of options:");
                            for (int ii = 0; ii < 25; ii++) {
                                System.out.println("Local Option " + ii + ":" + tc.getLocalOptionState(ii)
                                        + " Remote Option " + ii + ":" + tc.getRemoteOptionState(ii));
                            }
                        } else if ((new String(buff, 0, ret_read)).startsWith("REGISTER")) {
                            StringTokenizer st = new StringTokenizer(new String(buff));
                            try {
                                st.nextToken();
                                int opcode = (new Integer(st.nextToken())).intValue();
                                boolean initlocal = (new Boolean(st.nextToken())).booleanValue();
                                boolean initremote = (new Boolean(st.nextToken())).booleanValue();
                                boolean acceptlocal = (new Boolean(st.nextToken())).booleanValue();
                                boolean acceptremote = (new Boolean(st.nextToken())).booleanValue();
                                SimpleOptionHandler opthand = new SimpleOptionHandler(opcode, initlocal,
                                        initremote, acceptlocal, acceptremote);
                                tc.addOptionHandler(opthand);
                            } catch (Exception e) {
                                if (e instanceof InvalidTelnetOptionException) {
                                    System.err.println("Error registering option: " + e.getMessage());
                                } else {
                                    System.err.println("Invalid REGISTER command.");
                                    System.err.println(
                                            "Use REGISTER optcode initlocal initremote acceptlocal acceptremote");
                                    System.err.println("(optcode is an integer.)");
                                    System.err.println(
                                            "(initlocal, initremote, acceptlocal, acceptremote are boolean)");
                                }
                            }
                        } else if ((new String(buff, 0, ret_read)).startsWith("UNREGISTER")) {
                            StringTokenizer st = new StringTokenizer(new String(buff));
                            try {
                                st.nextToken();
                                int opcode = (new Integer(st.nextToken())).intValue();
                                tc.deleteOptionHandler(opcode);
                            } catch (Exception e) {
                                if (e instanceof InvalidTelnetOptionException) {
                                    System.err.println("Error unregistering option: " + e.getMessage());
                                } else {
                                    System.err.println("Invalid UNREGISTER command.");
                                    System.err.println("Use UNREGISTER optcode");
                                    System.err.println("(optcode is an integer)");
                                }
                            }
                        } else if ((new String(buff, 0, ret_read)).startsWith("SPY")) {
                            try {
                                tc.registerSpyStream(fout);
                            } catch (Exception e) {
                                System.err.println("Error registering the spy");
                            }
                        } else if ((new String(buff, 0, ret_read)).startsWith("UNSPY")) {
                            tc.stopSpyStream();
                        } else {
                            try {
                                outstr.write(buff, 0, ret_read);
                                outstr.flush();
                            } catch (Exception e) {
                                end_loop = true;
                            }
                        }
                    }
                } catch (Exception e) {
                    System.err.println("Exception while reading keyboard:" + e.getMessage());
                    end_loop = true;
                }
            } while ((ret_read > 0) && (end_loop == false));

            try {
                tc.disconnect();
            } catch (Exception e) {
                System.err.println("Exception while connecting:" + e.getMessage());
            }
        } catch (Exception e) {
            System.err.println("Exception while connecting:" + e.getMessage());
            System.exit(1);
        }
    }
}

From source file:apps.quantification.LearnQuantificationSVMLight.java

public static void main(String[] args) throws IOException {
    String cmdLineSyntax = LearnQuantificationSVMLight.class.getName()
            + " [OPTIONS] <path to svm_light_learn> <path to svm_light_classify> <trainingIndexDirectory> <outputDirectory>";

    Options options = new Options();

    OptionBuilder.withArgName("f");
    OptionBuilder.withDescription("Number of folds");
    OptionBuilder.withLongOpt("f");
    OptionBuilder.isRequired(true);/*from  www  .j ava2s.  c o m*/
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("c");
    OptionBuilder.withDescription("The c value for svm_light (default 1)");
    OptionBuilder.withLongOpt("c");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("k");
    OptionBuilder.withDescription("Kernel type (default 0: linear, 1: polynomial, 2: RBF, 3: sigmoid)");
    OptionBuilder.withLongOpt("k");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("t");
    OptionBuilder.withDescription("Path for temporary files");
    OptionBuilder.withLongOpt("t");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("v");
    OptionBuilder.withDescription("Verbose output");
    OptionBuilder.withLongOpt("v");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("s");
    OptionBuilder.withDescription("Don't delete temporary training file in svm_light format (default: delete)");
    OptionBuilder.withLongOpt("s");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

    SvmLightLearnerCustomizer classificationLearnerCustomizer = null;
    SvmLightClassifierCustomizer classificationCustomizer = null;

    int folds = -1;

    GnuParser parser = new GnuParser();
    String[] remainingArgs = null;
    try {
        CommandLine line = parser.parse(options, args);

        remainingArgs = line.getArgs();

        classificationLearnerCustomizer = new SvmLightLearnerCustomizer(remainingArgs[0]);
        classificationCustomizer = new SvmLightClassifierCustomizer(remainingArgs[1]);

        folds = Integer.parseInt(line.getOptionValue("f"));

        if (line.hasOption("c"))
            classificationLearnerCustomizer.setC(Float.parseFloat(line.getOptionValue("c")));

        if (line.hasOption("k")) {
            System.out.println("Kernel type: " + line.getOptionValue("k"));
            classificationLearnerCustomizer.setKernelType(Integer.parseInt(line.getOptionValue("k")));
        }

        if (line.hasOption("v"))
            classificationLearnerCustomizer.printSvmLightOutput(true);

        if (line.hasOption("s"))
            classificationLearnerCustomizer.setDeleteTrainingFiles(false);

        if (line.hasOption("t")) {
            classificationLearnerCustomizer.setTempPath(line.getOptionValue("t"));
            classificationCustomizer.setTempPath(line.getOptionValue("t"));
        }

    } catch (Exception exp) {
        System.err.println("Parsing failed.  Reason: " + exp.getMessage());
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(cmdLineSyntax, options);
        System.exit(-1);
    }

    assert (classificationLearnerCustomizer != null);

    if (remainingArgs.length != 4) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(cmdLineSyntax, options);
        System.exit(-1);
    }

    String indexFile = remainingArgs[2];

    File file = new File(indexFile);

    String indexName = file.getName();
    String indexPath = file.getParent();

    String outputPath = remainingArgs[3];

    SvmLightLearner classificationLearner = new SvmLightLearner();

    classificationLearner.setRuntimeCustomizer(classificationLearnerCustomizer);

    FileSystemStorageManager fssm = new FileSystemStorageManager(indexPath, false);
    fssm.open();

    IIndex training = TroveReadWriteHelper.readIndex(fssm, indexName, TroveContentDBType.Full,
            TroveClassificationDBType.Full);

    final TextualProgressBar progressBar = new TextualProgressBar("Learning the quantifiers");

    IOperationStatusListener status = new IOperationStatusListener() {

        @Override
        public void operationStatus(double percentage) {
            progressBar.signal((int) percentage);
        }
    };

    QuantificationLearner quantificationLearner = new QuantificationLearner(folds, classificationLearner,
            classificationLearnerCustomizer, classificationCustomizer, ClassificationMode.PER_CATEGORY,
            new LogisticFunction(), status);

    IQuantifier[] quantifiers = quantificationLearner.learn(training);

    File executableFile = new File(classificationLearnerCustomizer.getSvmLightLearnPath());
    IDataManager classifierDataManager = new SvmLightDataManager(new SvmLightClassifierCustomizer(
            executableFile.getParentFile().getAbsolutePath() + Os.pathSeparator() + "svm_light_classify"));
    String description = "_SVMLight_C-" + classificationLearnerCustomizer.getC() + "_K-"
            + classificationLearnerCustomizer.getKernelType();
    if (classificationLearnerCustomizer.getAdditionalParameters().length() > 0)
        description += "_" + classificationLearnerCustomizer.getAdditionalParameters();
    String quantifierPrefix = indexName + "_Quantifier-" + folds + description;

    FileSystemStorageManager fssmo = new FileSystemStorageManager(
            outputPath + File.separatorChar + quantifierPrefix, true);
    fssmo.open();
    QuantificationLearner.write(quantifiers, fssmo, classifierDataManager);
    fssmo.close();

    BufferedWriter bfs = new BufferedWriter(
            new FileWriter(outputPath + File.separatorChar + quantifierPrefix + "_rates.txt"));
    TShortDoubleHashMap simpleTPRs = quantificationLearner.getSimpleTPRs();
    TShortDoubleHashMap simpleFPRs = quantificationLearner.getSimpleFPRs();
    TShortDoubleHashMap scaledTPRs = quantificationLearner.getScaledTPRs();
    TShortDoubleHashMap scaledFPRs = quantificationLearner.getScaledFPRs();

    ContingencyTableSet contingencyTableSet = quantificationLearner.getContingencyTableSet();

    short[] cats = simpleTPRs.keys();
    for (int i = 0; i < cats.length; ++i) {
        short cat = cats[i];
        String catName = training.getCategoryDB().getCategoryName(cat);
        ContingencyTable contingencyTable = contingencyTableSet.getCategoryContingencyTable(cat);
        double simpleTPR = simpleTPRs.get(cat);
        double simpleFPR = simpleFPRs.get(cat);
        double scaledTPR = scaledTPRs.get(cat);
        double scaledFPR = scaledFPRs.get(cat);
        String line = quantifierPrefix + "\ttrain\tsimple\t" + catName + "\t" + cat + "\t"
                + contingencyTable.tp() + "\t" + contingencyTable.fp() + "\t" + contingencyTable.fn() + "\t"
                + contingencyTable.tn() + "\t" + simpleTPR + "\t" + simpleFPR + "\n";
        bfs.write(line);
        line = quantifierPrefix + "\ttrain\tscaled\t" + catName + "\t" + cat + "\t" + contingencyTable.tp()
                + "\t" + contingencyTable.fp() + "\t" + contingencyTable.fn() + "\t" + contingencyTable.tn()
                + "\t" + scaledTPR + "\t" + scaledFPR + "\n";
        bfs.write(line);
    }
    bfs.close();
}

From source file:apps.quantification.QuantifySVMLight.java

public static void main(String[] args) throws IOException {
    String cmdLineSyntax = QuantifySVMLight.class.getName()
            + " [OPTIONS] <path to svm_light_classify> <testIndexDirectory> <quantificationModelDirectory>";

    Options options = new Options();

    OptionBuilder.withArgName("d");
    OptionBuilder.withDescription("Dump confidences file");
    OptionBuilder.withLongOpt("d");
    OptionBuilder.isRequired(false);//  w  w w  .  j a v  a2  s . c  o  m
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("t");
    OptionBuilder.withDescription("Path for temporary files");
    OptionBuilder.withLongOpt("t");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("v");
    OptionBuilder.withDescription("Verbose output");
    OptionBuilder.withLongOpt("v");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("s");
    OptionBuilder.withDescription("Don't delete temporary files in svm_light format (default: delete)");
    OptionBuilder.withLongOpt("s");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

    SvmLightClassifierCustomizer customizer = null;

    GnuParser parser = new GnuParser();
    String[] remainingArgs = null;
    try {
        CommandLine line = parser.parse(options, args);

        remainingArgs = line.getArgs();

        customizer = new SvmLightClassifierCustomizer(remainingArgs[0]);

        if (line.hasOption("v"))
            customizer.printSvmLightOutput(true);

        if (line.hasOption("s")) {
            System.out.println("Keeping temporary files.");
            customizer.setDeleteTestFiles(false);
            customizer.setDeletePredictionsFiles(false);
        }

        if (line.hasOption("t"))
            customizer.setTempPath(line.getOptionValue("t"));

    } catch (Exception exp) {
        System.err.println("Parsing failed.  Reason: " + exp.getMessage());
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(cmdLineSyntax, options);
        System.exit(-1);
    }

    if (remainingArgs.length != 3) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(cmdLineSyntax, options);
        System.exit(-1);
    }

    String indexFile = remainingArgs[1];

    File file = new File(indexFile);

    String indexName = file.getName();
    String indexPath = file.getParent();

    String quantifierFilename = remainingArgs[2];

    FileSystemStorageManager indexFssm = new FileSystemStorageManager(indexPath, false);
    indexFssm.open();

    IIndex test = TroveReadWriteHelper.readIndex(indexFssm, indexName, TroveContentDBType.Full,
            TroveClassificationDBType.Full);

    indexFssm.close();

    FileSystemStorageManager quantifierFssm = new FileSystemStorageManager(quantifierFilename, false);
    quantifierFssm.open();

    SvmLightDataManager classifierDataManager = new SvmLightDataManager(customizer);

    FileSystemStorageManager fssm = new FileSystemStorageManager(quantifierFilename, false);
    fssm.open();

    IQuantifier[] quantifiers = QuantificationLearner.read(fssm, classifierDataManager,
            ClassificationMode.PER_CATEGORY);
    fssm.close();

    quantifierFssm.close();

    Quantification ccQuantification = quantifiers[0].quantify(test);
    Quantification paQuantification = quantifiers[1].quantify(test);
    Quantification accQuantification = quantifiers[2].quantify(test);
    Quantification maxQuantification = quantifiers[3].quantify(test);
    Quantification sccQuantification = quantifiers[4].quantify(test);
    Quantification spaQuantification = quantifiers[5].quantify(test);
    Quantification trueQuantification = new Quantification("True", test.getClassificationDB());

    File quantifierFile = new File(quantifierFilename);

    String quantificationName = quantifierFile.getParent() + Os.pathSeparator() + indexName + "_"
            + quantifierFile.getName() + ".txt";

    BufferedWriter writer = new BufferedWriter(new FileWriter(quantificationName));
    IShortIterator iterator = test.getCategoryDB().getCategories();
    while (iterator.hasNext()) {
        short category = iterator.next();
        String prefix = quantifierFile.getName() + "\t" + indexName + "\t"
                + test.getCategoryDB().getCategoryName(category) + "\t" + category + "\t"
                + trueQuantification.getQuantification(category) + "\t";

        writer.write(prefix + ccQuantification.getName() + "\t" + ccQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + paQuantification.getName() + "\t" + paQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + accQuantification.getName() + "\t" + accQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + maxQuantification.getName() + "\t" + maxQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + sccQuantification.getName() + "\t" + sccQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + spaQuantification.getName() + "\t" + spaQuantification.getQuantification(category)
                + "\n");
    }
    writer.close();

    BufferedWriter bfs = new BufferedWriter(new FileWriter(quantifierFile.getParent() + Os.pathSeparator()
            + indexName + "_" + quantifierFile.getName() + "_rates.txt"));
    TShortDoubleHashMap simpleTPRs = ((CCQuantifier) quantifiers[0]).getSimpleTPRs();
    TShortDoubleHashMap simpleFPRs = ((CCQuantifier) quantifiers[0]).getSimpleFPRs();
    TShortDoubleHashMap maxTPRs = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3]).getInternalQuantifier())
            .getSimpleTPRs();
    TShortDoubleHashMap maxFPRs = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3]).getInternalQuantifier())
            .getSimpleFPRs();
    TShortDoubleHashMap scaledTPRs = ((PAQuantifier) quantifiers[1]).getScaledTPRs();
    TShortDoubleHashMap scaledFPRs = ((PAQuantifier) quantifiers[1]).getScaledFPRs();

    ContingencyTableSet simpleContingencyTableSet = ((CCQuantifier) quantifiers[0]).getContingencyTableSet();
    ContingencyTableSet maxContingencyTableSet = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3])
            .getInternalQuantifier()).getContingencyTableSet();

    short[] cats = simpleTPRs.keys();
    for (int i = 0; i < cats.length; ++i) {
        short cat = cats[i];
        String catName = test.getCategoryDB().getCategoryName(cat);
        ContingencyTable simpleContingencyTable = simpleContingencyTableSet.getCategoryContingencyTable(cat);
        ContingencyTable maxContingencyTable = maxContingencyTableSet.getCategoryContingencyTable(cat);
        double simpleTPR = simpleTPRs.get(cat);
        double simpleFPR = simpleFPRs.get(cat);
        double maxTPR = maxTPRs.get(cat);
        double maxFPR = maxFPRs.get(cat);
        double scaledTPR = scaledTPRs.get(cat);
        double scaledFPR = scaledFPRs.get(cat);
        String line = indexName + "_" + quantifierFile.getName() + "\ttest\tsimple\t" + catName + "\t" + cat
                + "\t" + simpleContingencyTable.tp() + "\t" + simpleContingencyTable.fp() + "\t"
                + simpleContingencyTable.fn() + "\t" + simpleContingencyTable.tn() + "\t" + simpleTPR + "\t"
                + simpleFPR + "\n";
        bfs.write(line);
        line = indexName + "_" + quantifierFile.getName() + "\ttest\tmax\t" + catName + "\t" + cat + "\t"
                + maxContingencyTable.tp() + "\t" + maxContingencyTable.fp() + "\t" + maxContingencyTable.fn()
                + "\t" + maxContingencyTable.tn() + "\t" + maxTPR + "\t" + maxFPR + "\n";
        bfs.write(line);
        line = indexName + "_" + quantifierFile.getName() + "\ttest\tscaled\t" + catName + "\t" + cat + "\t"
                + simpleContingencyTable.tp() + "\t" + simpleContingencyTable.fp() + "\t"
                + simpleContingencyTable.fn() + "\t" + simpleContingencyTable.tn() + "\t" + scaledTPR + "\t"
                + scaledFPR + "\n";
        bfs.write(line);
    }
    bfs.close();
}