Example usage for java.lang String String

List of usage examples for java.lang String String

Introduction

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

Prototype

public String() 

Source Link

Document

Initializes a newly created String object so that it represents an empty character sequence.

Usage

From source file:GetMethod.java

public static void main(String[] args) {
    Method[] ms = String.class.getMethods();
    for (int i = 0; i < ms.length; i++) {
        // System.out.println(ms[i].getName());
    }/*from w  w  w. ja  v  a  2  s  . com*/
    Method[] ims = XMLReader.class.getMethods();
    for (int i = 0; i < ims.length; i++) {
        // System.out.println(ims[i].getName());
    }
    Method[] sms = Size.class.getMethods();
    for (int i = 0; i < sms.length; i++) {
        // System.out.println(sms[i].getName());
    }
    String pc = new String();
    try {
        Method setCpu = String.class.getMethod("toString", String.class);
        setCpu.invoke(pc, "Intel 3.0");
        System.out.println(pc.toString());
    } catch (Exception e) {
        e.printStackTrace();
    }
}

From source file:Main.java

static public void main(String args[]) throws Exception {
    URL myurl[] = { new URL("file:///C:/CH3/ClassLoader/web/"), new URL("http://www.java2s.edu/~xyx/test/") };
    URLClassLoader x = new URLClassLoader(myurl);
    Class c = x.loadClass("TestURL");

    Class getArg1[] = { (new String[1]).getClass() };
    Method m = c.getMethod("main", getArg1);
    String[] my1 = { "arg1 passed", "arg2 passed" };
    Object myarg1[] = { my1 };/*from  www  . ja  va  2 s.  c o  m*/
    m.invoke(null, myarg1);

    Object ob = c.newInstance();
    Class arg2[] = {};
    Method m2 = c.getMethod("tt", arg2);
    m2.invoke(ob, null);

    Class arg3[] = { (new String()).getClass(), int.class };
    Method m3 = c.getMethod("tt", arg3);
    Object myarg2[] = { "Arg1", new Integer(100) };
    m3.invoke(ob, myarg2);
}

From source file:SampleModifier.java

public static void main(String[] args) {
    String s = new String();
    printModifiers(s);
}

From source file:implementation.java

public static void main(String[] args) throws IOException {
    // Network Variables
    KUSOCKET ClientSocket = new KUSOCKET();
    ENDPOINT ClientAddress = new ENDPOINT("0.0.0.0", 0);
    ENDPOINT BroadcastAddress = new ENDPOINT("255.255.255.255", TokenAccess.SERVER_PORT_NUMBER);
    ENDPOINT AnyAddress = new ENDPOINT("0.0.0.0", 0);

    ENDPOINT ServerAddress = new ENDPOINT();
    MESSAGE OutgoingMessage = new MESSAGE();
    MESSAGE IncomingMessage = new MESSAGE();

    // Output variables         
    int CommentLength = TokenAccess.COMMENT_LENGTH;
    String Comment = new String();

    // Protocol variables
    Timer firstnode = new Timer();
    Timer tokentimer = new Timer();
    Timer tokenlost = new Timer();
    Timer exit = new Timer();
    int DialogueNumber = 0;
    int numRetries = 0;
    Integer addressIP[] = new Integer[2];
    int trigger = 0;
    String lanAddress = "192.168.1.67";
    // Create socket and await connection ///////////////////////////////////////

    // --------------------------------------------------------------------------
    // FINITE STATE MACHINE
    // --------------------------------------------------------------------------

    System.err.println("FSM Started ===================" + '\n');

    // FSM variables
    TokenAccess.STATES state = TokenAccess.STATES.STATE_INITIAL; // Initial STATE
    TokenAccess.STATES lastState = state; // Last STATE
    boolean bContinueEventWait = false;
    boolean bContinueStateLoop = true;
    String last = null;//from  ww  w  .  j  a  v a2  s.  c  om
    ClientSocket.CreateUDPSocket(ClientAddress);
    while (bContinueStateLoop) {

        switch (state) {
        case STATE_INITIAL:

            firstnode.Start(TokenAccess.firstnode);
            state = TokenAccess.STATES.STATE_STARTED;
            bContinueEventWait = false; // Stop Events loop
            break;

        case STATE_STARTED:

            ClientSocket.MakeConnection(AnyAddress);

            if (firstnode.isExpired()) {
                tokentimer.Start(TokenAccess.tokentimer);

                System.out.println("implementation.main()");
                // adding  local host ip to array
                String t = InetAddress.getLocalHost().getHostAddress();
                String[] split = t.split("\\.");
                addressIP[0] = Integer.parseInt(split[3]);
                System.out.println(split[3]);
                state = TokenAccess.STATES.STATE_TOKENED;
                bContinueEventWait = false;// Stop Events loop

            }
            boolean isMessageQueued = false;

            isMessageQueued = ClientSocket.RetrieveQueuedMessage(TokenAccess.READ_INTERVAL, IncomingMessage,
                    ServerAddress);

            if (isMessageQueued && (IncomingMessage.Type == TokenAccess.PDU_CONNECT)) {
                System.out.println("ring exists");
                //pdu_connect used instead of ring exisits 
                state = TokenAccess.STATES.STATE_tokenLess;
                bContinueEventWait = false;

            }

        case STATE_tokenLess:
            ClientSocket.MakeConnection(AnyAddress);
            while (state == TokenAccess.STATES.STATE_tokenLess) {
                // Instructs the socket to accept

                // building ip address message
                OutgoingMessage.BuildMessage(++DialogueNumber, TokenAccess.PDU_CONNECT,
                        InetAddress.getLocalHost().getHostAddress(),
                        InetAddress.getLocalHost().getHostAddress().length());
                //broadcasting ip address
                ClientSocket.DeliverMessage(OutgoingMessage, BroadcastAddress);
                //     System.out.println("broadcasting address");

                isMessageQueued = ClientSocket.RetrieveQueuedMessage(TokenAccess.READ_INTERVAL, IncomingMessage,
                        ServerAddress);

                //will trigger if used on a 192 network i didnt know how to use regex for any number and a dot
                if (isMessageQueued == true && (IncomingMessage.Type == TokenAccess.PDU_CLOSE)) {
                    System.out.println("pdu close");
                    String ipaddress = IncomingMessage.Buffer;

                    for (int n : addressIP) {
                        if (addressIP[n] == Integer.parseInt(ipaddress)) {
                            String a;
                            a = Integer.toString(addressIP[n]);
                            OutgoingMessage.BuildMessage(++DialogueNumber, TokenAccess.PDU_ACK,
                                    InetAddress.getLocalHost().getHostAddress(),
                                    InetAddress.getLocalHost().getHostAddress().length());
                            ENDPOINT exitAddress = new ENDPOINT(a, TokenAccess.SERVER_PORT_NUMBER);

                            ClientSocket.DeliverMessage(OutgoingMessage, exitAddress);
                            addressIP = ArrayUtils.removeElement(addressIP, n);
                        }

                    }
                }

                if (last != null && tokenlost.bRunning == false) {
                    tokenlost.Start(TokenAccess.tokenlost);
                    last = null;
                    System.out.println("token lost timer started");
                }

                if (isMessageQueued == true && (IncomingMessage.Type == TokenAccess.CMD_CONNECT)) {
                    System.out.println("token lost timer stopped");
                    tokenlost.Stop();
                }

                if (tokenlost.isExpired()) {

                    System.out.println("token lost");

                    for (int n = 0; n < addressIP.length; n++) {
                        String ipaddress = InetAddress.getLocalHost().toString();
                        int lastdot = ipaddress.lastIndexOf(".") + 1;
                        ipaddress = ipaddress.substring(lastdot, ipaddress.length());
                        System.out.println(n);
                        if (addressIP[n] == null) {

                        } else {
                            if (addressIP[n] == Integer.parseInt(ipaddress)) {

                                String a;
                                a = Integer.toString(addressIP[n]);
                                System.out.println("variable a " + a);
                                OutgoingMessage.BuildMessage(++DialogueNumber, TokenAccess.PDU_ACK,
                                        InetAddress.getLocalHost().getHostAddress(),
                                        InetAddress.getLocalHost().getHostAddress().length());
                                ENDPOINT exitAddress = new ENDPOINT(lanAddress, TokenAccess.SERVER_PORT_NUMBER);

                                ClientSocket.DeliverMessage(OutgoingMessage, exitAddress);

                                OutgoingMessage.BuildMessage(++DialogueNumber, TokenAccess.PDU_TOKEN,
                                        InetAddress.getLocalHost().getHostAddress(),
                                        InetAddress.getLocalHost().getHostAddress().length());
                                String b = Integer.toString(addressIP[n]);
                                b = lanAddress;
                                System.out.println(b);

                                ENDPOINT exitAddresss = new ENDPOINT(b, TokenAccess.SERVER_PORT_NUMBER);
                                ClientSocket.DeliverMessage(OutgoingMessage, exitAddresss);

                            }
                        }
                    }

                }

                if (exit.isExpired()) {
                    OutgoingMessage.BuildMessage(++DialogueNumber, TokenAccess.PDU_CLOSE,
                            InetAddress.getLocalHost().getHostAddress(),
                            InetAddress.getLocalHost().getHostAddress().length());
                    exit.Start(30);
                }

                if (isMessageQueued && (IncomingMessage.Type == TokenAccess.PDU_TOKEN)) {
                    tokenlost.Stop();
                    System.out.println(IncomingMessage.Type);
                    state = TokenAccess.STATES.STATE_TOKENED;
                    tokentimer.Start(TokenAccess.tokentimer);
                    break;
                }

            }

        case STATE_TOKENED:
            while (state == TokenAccess.STATES.STATE_TOKENED) {

                //send data
                OutgoingMessage.BuildMessage(0, 0, "ALIVE", CommentLength);
                ClientSocket.DeliverMessage(OutgoingMessage, BroadcastAddress);
                tokenlost.Stop();
                while (trigger == 0) {
                    System.out.println("TOKENED");
                    trigger++;
                }

                if (tokentimer.isExpired()) {
                    trigger = 0;
                    System.out.println("token expired");
                    String ipaddress = InetAddress.getLocalHost().toString();
                    //  System.out.println( "System name : "+ipaddress);

                    for (int n = 0; n < addressIP.length; n++) {
                        // System.out.println(n);
                        int lastdot = ipaddress.lastIndexOf(".") + 1;
                        ipaddress = ipaddress.substring(lastdot, ipaddress.length());
                        // System.out.println("IP address: "+ipaddress);
                        int address1 = Integer.parseInt(ipaddress);

                        System.out.println("made it to line 214");
                        System.out.println(n);
                        System.out.println(addressIP[0]);

                        if (addressIP[n] == address1) {
                            String a;
                            a = Integer.toString(addressIP[n]);
                            System.out.println("variable a = " + a);

                            String ip = InetAddress.getLocalHost().getHostAddress();
                            System.out.println("line 226");
                            System.out.println(ip);

                            OutgoingMessage.BuildMessage(++DialogueNumber, TokenAccess.PDU_TOKEN,
                                    InetAddress.getLocalHost().getHostAddress(),
                                    InetAddress.getLocalHost().getHostAddress().length());
                            String b;

                            System.out.println("line 222");
                            if (n + 1 >= addressIP.length) {
                                b = (ip);
                                //   System.out.println(b);
                            } else {
                                b = ip;

                            }

                            System.out.println(b);

                            //b = InetAddress.getLocalHost().toString().substring(0, lastdot); 
                            // int slash =   b.indexOf("/");
                            System.out.println(b);
                            ENDPOINT exitAddresss = new ENDPOINT(b, TokenAccess.SERVER_PORT_NUMBER);
                            ClientSocket.DeliverMessage(OutgoingMessage, exitAddresss);
                            System.out.println("exiting tokened state");
                            state = TokenAccess.STATES.STATE_tokenLess;
                            last = "1";
                        }
                        break;
                    }
                }
            }

        case STATE_EXIT:
            while (state == TokenAccess.STATES.STATE_EXIT) {
                System.exit(0);

            }

        }

    }

}

From source file:com.opengsn.controller.client.ControllerClient.java

/**
 * @param args//from   ww w . j  av  a2s .com
 */
public static void main(String[] args) {
    ControllerClient client = new ControllerClient();

    String arguments = new String();
    for (int i = 0; i < args.length; i++) {
        arguments = args[i] + " ";
    }
    System.out.println("Arguments: " + arguments);

    if (args.length < 1) {
        client.usage(null);
        System.exit(1);
    }
    client.process(args);
}

From source file:guardar.en.base.de.datos.MainServidor.java

public static void main(String[] args)
        throws ParserConfigurationException, SAXException, IOException, ClassNotFoundException {

    Mongo mongo = new Mongo("localhost", 27017);

    // nombre de la base de datos
    DB database = mongo.getDB("paginas");
    // coleccion de la db
    DBCollection collection = database.getCollection("indice");
    DBCollection collection_textos = database.getCollection("tabla");
    ArrayList<String> lista_textos = new ArrayList();

    try {/*from   ww w .  j a  v a  2 s  . c  o m*/
        ServerSocket servidor = new ServerSocket(4545); // Crear un servidor en pausa hasta que un cliente llegue.
        while (true) {
            String aux = new String();
            lista_textos.clear();
            Socket clienteNuevo = servidor.accept();// Si llega se acepta.
            // Queda en pausa otra vez hasta que un objeto llegue.
            ObjectInputStream entrada = new ObjectInputStream(clienteNuevo.getInputStream());

            JSONObject request = (JSONObject) entrada.readObject();
            String b = (String) request.get("id");
            //hacer una query a la base de datos con la palabra que se quiere obtener

            BasicDBObject query = new BasicDBObject("palabra", b);
            DBCursor cursor = collection.find(query);
            ArrayList<DocumentosDB> lista_doc = new ArrayList<>();
            // de la query tomo el campo documentos y los agrego a una lista
            try {
                while (cursor.hasNext()) {
                    //System.out.println(cursor.next());
                    BasicDBList campo_documentos = (BasicDBList) cursor.next().get("documentos");
                    // en el for voy tomando uno por uno los elementos en el campo documentos
                    for (Iterator<Object> it = campo_documentos.iterator(); it.hasNext();) {
                        BasicDBObject dbo = (BasicDBObject) it.next();
                        //DOC tiene id y frecuencia
                        DocumentosDB doc = new DocumentosDB();
                        doc.makefn2(dbo);
                        //int id = (int)doc.getId_documento();
                        //int f = (int)doc.getFrecuencia();

                        lista_doc.add(doc);

                        //*******************************************

                        //********************************************

                        //QUERY A LA COLECCION DE TEXTOS
                        /* BasicDBObject query_textos = new BasicDBObject("id", doc.getId_documento());//query
                         DBCursor cursor_textos = collection_textos.find(query_textos);
                         try {
                        while (cursor_textos.hasNext()) {
                                    
                                    
                            DBObject obj = cursor_textos.next();
                                
                            String titulo = (String) obj.get("titulo");
                            titulo = titulo + "\n\n";
                            String texto = (String) obj.get("texto");
                                
                            String texto_final = titulo + texto;
                            aux = texto_final;
                            lista_textos.add(texto_final);
                        }
                         } finally {
                        cursor_textos.close();
                         }*/
                        //System.out.println(doc.getId_documento());
                        //System.out.println(doc.getFrecuencia());

                    } // end for

                } //end while query

            } finally {
                cursor.close();
            }

            // ordeno la lista de menor a mayor
            Collections.sort(lista_doc, new Comparator<DocumentosDB>() {

                @Override
                public int compare(DocumentosDB o1, DocumentosDB o2) {
                    //throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
                    return o1.getFrecuencia().compareTo(o2.getFrecuencia());
                }
            });
            int tam = lista_doc.size() - 1;
            for (int j = tam; j >= 0; j--) {

                BasicDBObject query_textos = new BasicDBObject("id",
                        (int) lista_doc.get(j).getId_documento().intValue());//query
                DBCursor cursor_textos = collection_textos.find(query_textos);// lo busco
                try {
                    while (cursor_textos.hasNext()) {

                        DBObject obj = cursor_textos.next();
                        String titulo = "*******************************";
                        titulo += (String) obj.get("titulo");
                        int f = (int) lista_doc.get(j).getFrecuencia().intValue();
                        String strinf = Integer.toString(f);
                        titulo += "******************************* frecuencia:" + strinf;
                        titulo = titulo + "\n\n";

                        String texto = (String) obj.get("texto");

                        String texto_final = titulo + texto + "\n\n";
                        aux = aux + texto_final;
                        //lista_textos.add(texto_final);
                    }
                } finally {
                    cursor_textos.close();
                }

            }

            //actualizar el cache
            try {
                Socket cliente_cache = new Socket("localhost", 4500); // nos conectamos con el servidor
                ObjectOutputStream mensaje_cache = new ObjectOutputStream(cliente_cache.getOutputStream()); // get al output del servidor, que es cliente : socket del cliente q se conecto al server
                JSONObject actualizacion_cache = new JSONObject();
                actualizacion_cache.put("actualizacion", 1);
                actualizacion_cache.put("busqueda", b);
                actualizacion_cache.put("respuesta", aux);
                mensaje_cache.writeObject(actualizacion_cache); // envio el msj al servidor
            } catch (Exception ex) {

            }

            //RESPONDER DESDE EL SERVIDORIndex al FRONT
            ObjectOutputStream resp = new ObjectOutputStream(clienteNuevo.getOutputStream());// obtengo el output del cliente para mandarle un msj
            resp.writeObject(aux);
            System.out.println("msj enviado desde el servidor");

        }
    } catch (IOException ex) {
        Logger.getLogger(MainServidor.class.getName()).log(Level.SEVERE, null, ex);
    }

}

From source file:edu.usc.pgroup.floe.client.commands.SwitchAlternate.java

/**
 * Entry point for Scale command.//from www.  j av  a  2s  .c  o m
 * @param args command line arguments sent by the floe.py script.
 */
public static void main(final String[] args) {

    Options options = new Options();

    Option appOption = OptionBuilder.withArgName("name").hasArg().isRequired()
            .withDescription("Application Name").create("app");

    Option pelletNameOption = OptionBuilder.withArgName("name").hasArg().isRequired()
            .withDescription("Pellet Name").create("pellet");

    Option alternateOption = OptionBuilder.withArgName("alternate").hasArg().withType(new String())
            .withDescription("The new alternate to switch to.").create("alternate");

    options.addOption(appOption);
    options.addOption(pelletNameOption);
    options.addOption(alternateOption);

    CommandLineParser parser = new BasicParser();
    CommandLine line;

    try {
        line = parser.parse(options, args);

    } catch (ParseException e) {
        LOGGER.error("Invalid command: " + e.getMessage());
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("scale options", options);
        return;
    }

    String app = line.getOptionValue("app");
    String pellet = line.getOptionValue("pellet");
    String alternate = line.getOptionValue("alternate");

    LOGGER.info("Application: {}", app);
    LOGGER.info("Pellet: {}", pellet);
    LOGGER.info("alternate: {}", alternate);

    try {

        FloeClient.getInstance().getClient().switchAlternate(app, pellet, alternate);
    } catch (TException e) {
        LOGGER.error("Error while connecting to the coordinator: {}", e);
    }
}

From source file:edu.usc.pgroup.floe.client.commands.Signal.java

/**
 * Entry point for Scale command.//ww w .ja  va 2  s .c  o m
 * @param args command line arguments sent by the floe.py script.
 */
public static void main(final String[] args) {

    Options options = new Options();

    Option appOption = OptionBuilder.withArgName("name").hasArg().isRequired()
            .withDescription("Application Name").create("app");

    Option pelletNameOption = OptionBuilder.withArgName("name").hasArg().isRequired()
            .withDescription("Pellet Name").create("pellet");

    Option signalOption = OptionBuilder.withArgName("data").hasArg().withType(new String())
            .withDescription("signal data to send to the pellet").create("data");

    options.addOption(appOption);
    options.addOption(pelletNameOption);
    options.addOption(signalOption);

    CommandLineParser parser = new BasicParser();
    CommandLine line;

    try {
        line = parser.parse(options, args);

    } catch (ParseException e) {
        LOGGER.error("Invalid command: " + e.getMessage());
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("scale options", options);
        return;
    }

    String app = line.getOptionValue("app");
    String pellet = line.getOptionValue("pellet");
    String data = line.getOptionValue("data");

    LOGGER.info("Application: {}", app);
    LOGGER.info("Pellet: {}", pellet);
    LOGGER.info("data: {}", data);

    byte[] datab = Utils.serialize(data);
    try {
        TSignal signal = new TSignal();
        signal.set_destApp(app);
        signal.set_destPellet(pellet);
        signal.set_data(datab);
        FloeClient.getInstance().getClient().signal(signal);
    } catch (TException e) {
        LOGGER.error("Error while connecting to the coordinator: {}", e);
    }
}

From source file:edu.usc.pgroup.floe.client.commands.Scale.java

/**
 * Entry point for Scale command./*  w w  w  .  j  a v a2  s.c  o  m*/
 * @param args command line arguments sent by the floe.py script.
 */
public static void main(final String[] args) {

    Options options = new Options();

    Option dirOption = OptionBuilder.withArgName("direction").hasArg().isRequired()
            .withDescription("Scale Direction.").create("dir");

    Option appOption = OptionBuilder.withArgName("name").hasArg().isRequired()
            .withDescription("Application Name").create("app");

    Option pelletNameOption = OptionBuilder.withArgName("name").hasArg().isRequired()
            .withDescription("Pellet Name").create("pellet");

    Option cntOption = OptionBuilder.withArgName("num").hasArg().withType(new String())
            .withDescription("Number of instances to scale up/down").create("cnt");

    options.addOption(dirOption);
    options.addOption(appOption);
    options.addOption(pelletNameOption);
    options.addOption(cntOption);

    CommandLineParser parser = new BasicParser();
    CommandLine line;

    try {
        line = parser.parse(options, args);

    } catch (ParseException e) {
        LOGGER.error("Invalid command: " + e.getMessage());
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("scale options", options);
        return;
    }

    String dir = line.getOptionValue("dir");
    String app = line.getOptionValue("app");
    String pellet = line.getOptionValue("pellet");
    String cnt = line.getOptionValue("cnt");

    LOGGER.info("direction: {}", dir);
    LOGGER.info("Application: {}", app);
    LOGGER.info("Pellet: {}", pellet);
    LOGGER.info("count: {}", cnt);

    ScaleDirection direction = Enum.valueOf(ScaleDirection.class, dir);
    int count = Integer.parseInt(cnt);
    try {
        FloeClient.getInstance().getClient().scale(direction, app, pellet, count);
    } catch (TException e) {
        LOGGER.error("Error while connecting to the coordinator: {}", e);
    }
}

From source file:com.github.codingtogenomic.CodingToGenomic.java

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

    //parse commandline
    Options options = new Options();
    CommandLineParser parser = new PosixParser();
    String gene = new String();
    String transcript = new String();
    String species = "human";
    boolean mapCdna = false;
    String coordinate = new String();
    StringBuilder errorMsg = new StringBuilder();
    try {//from  www  .  j  ava 2  s.co m
        options = getOptions(args);
    } catch (org.apache.commons.cli.ParseException ex) {
        System.err.println("Parsing failed.  Reason: " + ex.getMessage());
        System.exit(1);
    }
    CommandLine line = parser.parse(options, args);
    if (line.hasOption("help")) {
        showHelp(options);
    }
    if (line.hasOption("gene")) {
        gene = line.getOptionValue("gene");
    } else {
        if (!line.hasOption("transcript")) {
            errorMsg.append("Either --gene or --transcript argument is required\n");
        }
    }
    if (line.hasOption("transcript")) {
        if (line.hasOption("gene")) {
            errorMsg.append("Please specify only one of " + "--gene or --transcript arguments, not both\n");
        } else {
            transcript = line.getOptionValue("transcript");
            if (line.hasOption("species")) {
                System.out.println("Ignoring --species option when using --transcript argument");
            }
        }
    }
    if (line.hasOption("coordinate")) {
        coordinate = line.getOptionValue("coordinate");
    } else {
        errorMsg.append("--coordinate argument is required\n");
    }
    if (line.hasOption("species")) {
        species = line.getOptionValue("species").replaceAll("\\s+", "_");
    }
    if (line.hasOption("b37")) {
        if (species.equalsIgnoreCase("human") || species.equalsIgnoreCase("homo sapiens")) {
            SERVER = GRCh37Server;
        } else {
            System.out.println("--b37 argument will be ignored - it can only be "
                    + "used when human is the species of interest. Current species" + " is " + species + ".\n");
        }
    }
    if (line.hasOption("noncoding")) {
        mapCdna = true;
    }

    if (errorMsg.length() > 0) {
        showHelp(options, errorMsg.toString(), 2);
    }
    int c = 0;
    boolean threePrimeUtr = false;
    String prefix = "c.";
    if (mapCdna) {
        prefix = "n.";
        try {
            c = Integer.parseInt(coordinate);
        } catch (NumberFormatException ex) {
            showHelp(options,
                    "--coordinate argument '" + coordinate + "' could not " + "be parsed as an integer", 2);
        }
    } else if (coordinate.startsWith("*")) {
        threePrimeUtr = true;
        prefix = "c.*";
        String coord = coordinate.replaceFirst("\\*", "");
        try {
            c = Integer.parseInt(coord);
        } catch (NumberFormatException ex) {
            showHelp(options, "--coordinate argument '" + coordinate + "' could not "
                    + "be parsed as an integer or UTR coordinate", 2);
        }
    } else {
        try {
            c = Integer.parseInt(coordinate);
        } catch (NumberFormatException ex) {
            showHelp(options,
                    "--coordinate argument '" + coordinate + "' could not " + "be parsed as an integer", 2);
        }
    }
    //got arguments
    String result;
    String header = "Input\tSymbol\tEnsemblGene\tEnsemblTranscript\tGenomicCoordinate";
    if (!gene.isEmpty()) {
        IdParser idParser = new IdParser(gene);
        System.out.println("Interpretting " + gene + " as of type " + idParser.getIdentifierType());
        if (idParser.isEnsemblId()) {
            if (line.hasOption("species")) {
                System.out.println("Ignoring --species option when searching Ensembl ID.");
            }
            if (idParser.isTranscript()) {
                result = codingToGenomicTranscript(gene, c, threePrimeUtr, mapCdna);
            } else if (idParser.isEnsp()) {
                result = codingToGenomicEnsp(gene, c, threePrimeUtr, mapCdna);
            } else {
                result = codingToGenomicId(gene, c, threePrimeUtr, mapCdna);
            }
        } else {
            if (idParser.isTranscript()) {
                //append user input to beginning
                result = codingToGenomicXrefTranscript(species, gene, c, threePrimeUtr, mapCdna);
            } else {
                result = codingToGenomicXref(species, gene, c, threePrimeUtr, mapCdna);
            }
        }
        if (idParser.isTranscript() || idParser.isEnsp()) {

            result = gene + ":" + prefix + c + "\t" + result;
        } else {
            result = convertGeneResult(result, gene, c, prefix);
        }

    } else {
        System.out.println("Searching for " + transcript + " as Ensembl transcript ID");
        result = codingToGenomicTranscript(transcript, c, threePrimeUtr, mapCdna);
        //append user input to beginning
        result = transcript + ":" + prefix + c + "\t" + result;
    }

    System.out.println(header);
    System.out.println(result);

}