Example usage for java.io BufferedReader readLine

Introduction

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

Prototype

public String readLine() throws IOException 

Source Link

Document

Reads a line of text.

Usage

From source file:com.mycompany.mavenproject4.NewMain.java

/**
 * @param args the command line arguments
 *///  w  w w .ja  v a2s . c o m
public static void main(String[] args) {
    System.out.println("Enter your choice do you want to work with 1.postgre 2.Redis 3.Mongodb");
    InputStreamReader IORdatabase = new InputStreamReader(System.in);
    BufferedReader BIOdatabase = new BufferedReader(IORdatabase);
    String databasechoice = null;
    try {
        databasechoice = BIOdatabase.readLine();
    } catch (Exception E7) {
        System.out.println(E7.getMessage());
    }

    // loading data from the CSV file 

    CsvReader Employees = null;

    try {
        Employees = new CsvReader("CSVFile\\Employees.csv");
    } catch (FileNotFoundException EB) {
        System.out.println(EB.getMessage());
    }
    int ColumnCount = 3;
    int RowCount = 100;
    int iloop = 0;

    try {
        Employees = new CsvReader("CSVFile\\Employees.csv");
    } catch (FileNotFoundException E) {
        System.out.println(E.getMessage());
    }

    String[][] Dataarray = new String[RowCount][ColumnCount];
    try {
        while (Employees.readRecord()) {
            String v;
            String[] x;
            v = Employees.getRawRecord();
            x = v.split(",");
            for (int j = 0; j < ColumnCount; j++) {
                String value = null;
                int z = j;
                value = x[z];
                try {
                    Dataarray[iloop][j] = value;
                } catch (Exception E) {
                    System.out.println(E.getMessage());
                }
                // System.out.println(Dataarray[iloop][j]);
            }
            iloop = iloop + 1;
        }
    } catch (IOException Em) {
        System.out.println(Em.getMessage());
    }

    Employees.close();

    // connection to Database 
    switch (databasechoice) {
    // postgre code goes here 
    case "1":

        Connection Conn = null;
        Statement Stmt = null;
        URI dbUri = null;
        String choice = null;
        InputStreamReader objin = new InputStreamReader(System.in);
        BufferedReader objbuf = new BufferedReader(objin);
        try {
            Class.forName("org.postgresql.Driver");
        } catch (Exception E1) {
            System.out.println(E1.getMessage());
        }
        String username = "ldoiarosfrzrua";
        String password = "HBkE_pJpK5mMIg3p2q1_odmEFX";
        String dbUrl = "jdbc:postgresql://ec2-54-83-53-120.compute-1.amazonaws.com:5432/d6693oljh5cco4?ssl=true&sslfactory=org.postgresql.ssl.NonValidatingFactory";

        // now update data in the postgress Database 

        // for(int i=0;i<RowCount;i++)
        // {
        //       try 
        //          {

        //         Conn= DriverManager.getConnection(dbUrl, username, password);    
        //           Stmt = Conn.createStatement();
        //           String Connection_String = "insert into EmployeeDistinct (name,jobtitle,department) values (' "+ Dataarray[i][0]+" ',' "+ Dataarray[i][1]+" ',' "+ Dataarray[i][2]+" ')";
        //         Stmt.executeUpdate(Connection_String);
        //       
        //        }
        //        catch(SQLException E4)
        //         {
        //             System.out.println(E4.getMessage());
        //          }
        // }

        // Quering with the Database 

        System.out.println("1. Display Data ");
        System.out.println("2. Select data based on primary key");
        System.out.println("3. Select data based on Other attributes e.g Name");
        System.out.println("Enter your Choice ");
        try {
            choice = objbuf.readLine();
        } catch (IOException E) {
            System.out.println(E.getMessage());
        }
        switch (choice) {
        case "1":
            try {
                Conn = DriverManager.getConnection(dbUrl, username, password);
                Stmt = Conn.createStatement();
                String Connection_String = " Select * from EmployeeDistinct;";
                ResultSet objRS = Stmt.executeQuery(Connection_String);
                while (objRS.next()) {
                    System.out.println("Employee ID: " + objRS.getInt("EmployeeID"));
                    System.out.println("Employee Name: " + objRS.getString("Name"));
                    System.out.println("Employee City: " + objRS.getString("Jobtitle"));
                    System.out.println("Employee City: " + objRS.getString("Department"));
                }

            } catch (Exception E2) {
                System.out.println(E2.getMessage());
            }

            break;

        case "2":

            System.out.println("Enter the Primary Key");
            InputStreamReader objkey = new InputStreamReader(System.in);
            BufferedReader objbufkey = new BufferedReader(objkey);
            int key = 0;
            try {
                key = Integer.parseInt(objbufkey.readLine());
            } catch (IOException E) {
                System.out.println(E.getMessage());
            }
            try {
                Conn = DriverManager.getConnection(dbUrl, username, password);
                Stmt = Conn.createStatement();
                String Connection_String = " Select * from EmployeeDistinct where EmployeeID=" + key + ";";
                ResultSet objRS = Stmt.executeQuery(Connection_String);
                while (objRS.next()) {
                    System.out.println("Employee Name: " + objRS.getString("Name"));
                    System.out.println("Employee City: " + objRS.getString("Jobtitle"));
                    System.out.println("Employee City: " + objRS.getString("Department"));
                }

            } catch (Exception E2) {
                System.out.println(E2.getMessage());
            }
            break;

        case "3":
            String Name = null;
            System.out.println("Enter Name to find the record");
            InputStreamReader objname = new InputStreamReader(System.in);
            BufferedReader objbufname = new BufferedReader(objname);

            try {
                Name = (objbufname.readLine()).toString();
            } catch (IOException E) {
                System.out.println(E.getMessage());
            }
            try {
                Conn = DriverManager.getConnection(dbUrl, username, password);
                Stmt = Conn.createStatement();
                String Connection_String = " Select * from EmployeeDistinct where Name=" + "'" + Name + "'"
                        + ";";

                ResultSet objRS = Stmt.executeQuery(Connection_String);
                while (objRS.next()) {
                    System.out.println("Employee ID: " + objRS.getInt("EmployeeID"));
                    System.out.println("Employee City: " + objRS.getString("Jobtitle"));
                    System.out.println("Employee City: " + objRS.getString("Department"));
                }

            } catch (Exception E2) {
                System.out.println(E2.getMessage());
            }
            break;
        }
        try {
            Conn.close();
        } catch (SQLException E6) {
            System.out.println(E6.getMessage());
        }
        break;

    // Redis code goes here 

    case "2":
        int Length = 0;
        String ID = null;
        Length = 100;

        // Connection to Redis 
        Jedis jedis = new Jedis("pub-redis-18017.us-east-1-4.6.ec2.redislabs.com", 18017);
        jedis.auth("7EFOisRwMu8zvhin");
        System.out.println("Connected to Redis");

        // Storing values in the database 

        //  System.out.println("Storing values in the Database might take a minute ");

        // for(int i=0;i<Length;i++)
        // { 
        // Store data in redis 
        //     int j=i+1;
        //  jedis.hset("Employe:" + j , "Name", Dataarray[i][0]);
        //   jedis.hset("Employe:" + j , "Jobtitle ", Dataarray[i][1]);
        //  jedis.hset("Employe:" + j , "Department", Dataarray[i][2]);

        //  }

        System.out.println("Search by 1.primary key,2.Name 3.display first 20");
        InputStreamReader objkey = new InputStreamReader(System.in);
        BufferedReader objbufkey = new BufferedReader(objkey);
        String interimChoice1 = null;
        try {
            interimChoice1 = objbufkey.readLine();
        } catch (IOException E) {
            System.out.println(E.getMessage());
        }
        switch (interimChoice1) {
        case "1":
            System.out.print("Get details using the primary Key");
            InputStreamReader IORKey = new InputStreamReader(System.in);
            BufferedReader BIORKey = new BufferedReader(IORKey);
            String ID1 = null;
            try {
                ID1 = BIORKey.readLine();
            } catch (IOException E3) {
                System.out.println(E3.getMessage());
            }

            Map<String, String> properties = jedis.hgetAll("Employe:" + Integer.parseInt(ID1));
            for (Map.Entry<String, String> entry : properties.entrySet()) {
                System.out.println("Name:" + jedis.hget("Employee:" + Integer.parseInt(ID1), "Name"));
                System.out.println("Jobtitle:" + jedis.hget("Employee:" + Integer.parseInt(ID1), "Jobtitle"));
                System.out
                        .println("Department:" + jedis.hget("Employee:" + Integer.parseInt(ID1), "Department"));
            }
            break;

        case "2":
            System.out.print("Get details using Department");
            InputStreamReader IORName1 = new InputStreamReader(System.in);
            BufferedReader BIORName1 = new BufferedReader(IORName1);

            String ID2 = null;
            try {
                ID2 = BIORName1.readLine();
            } catch (IOException E3) {
                System.out.println(E3.getMessage());
            }
            for (int i = 0; i < 100; i++) {
                Map<String, String> properties3 = jedis.hgetAll("Employe:" + i);
                for (Map.Entry<String, String> entry : properties3.entrySet()) {
                    String value = entry.getValue();
                    if (entry.getValue().equals(ID2)) {
                        System.out.println("Name:" + jedis.hget("Employee:" + i, "Name"));
                        System.out.println("Jobtitle:" + jedis.hget("Employee:" + i, "Jobtitle"));
                        System.out.println("Department:" + jedis.hget("Employee:" + i, "Department"));
                    }

                }
            }

            //for (Map.Entry<String, String> entry : properties1.entrySet())
            //{
            //System.out.println(entry.getKey() + "---" + entry.getValue());
            // }
            break;

        case "3":
            for (int i = 1; i < 21; i++) {
                Map<String, String> properties3 = jedis.hgetAll("Employe:" + i);
                for (Map.Entry<String, String> entry : properties3.entrySet()) {

                    // System.out.println(jedis.hget("Employee:" + i,"Name"));
                    System.out.println("Name:" + jedis.hget("Employee:" + i, "Name"));
                    System.out.println("Jobtitle:" + jedis.hget("Employee:" + i, "Jobtitle"));
                    System.out.println("Department:" + jedis.hget("Employee:" + i, "Department"));

                }
            }
            break;
        }

        break;

    // mongo db code goes here 

    case "3":
        MongoClient mongo = new MongoClient(
                new MongoClientURI("mongodb://root2:12345@ds055564.mongolab.com:55564/heroku_766dnj8c"));
        DB db;
        db = mongo.getDB("heroku_766dnj8c");
        // storing values in the database 
        //  for(int i=0;i<100;i++)
        // {
        //     BasicDBObject document = new BasicDBObject();
        //    document.put("_id", i+1);
        //    document.put("Name", Dataarray[i][0]);
        //    document.put("Jobtitle", Dataarray[i][1]);    
        //    document.put("Department", Dataarray[i][2]);    
        //    db.getCollection("EmployeeRaw").insert(document);

        // }
        System.out.println("Search by 1.primary key,2.Name 3.display first 20");
        InputStreamReader objkey6 = new InputStreamReader(System.in);
        BufferedReader objbufkey6 = new BufferedReader(objkey6);
        String interimChoice = null;
        try {
            interimChoice = objbufkey6.readLine();
        } catch (IOException E) {
            System.out.println(E.getMessage());
        }
        switch (interimChoice) {
        case "1":
            System.out.println("Enter the Primary Key");
            InputStreamReader IORPkey = new InputStreamReader(System.in);
            BufferedReader BIORPkey = new BufferedReader(IORPkey);
            int Pkey = 0;
            try {
                Pkey = Integer.parseInt(BIORPkey.readLine());
            } catch (IOException E) {
                System.out.println(E.getMessage());
            }
            BasicDBObject inQuery = new BasicDBObject();
            inQuery.put("_id", Pkey);
            DBCursor cursor = db.getCollection("EmployeeRaw").find(inQuery);
            while (cursor.hasNext()) {
                // System.out.println(cursor.next());
                System.out.println(cursor.next());
            }
            break;
        case "2":
            System.out.println("Enter the Name to Search");
            InputStreamReader objName = new InputStreamReader(System.in);
            BufferedReader objbufName = new BufferedReader(objName);
            String Name = null;
            try {
                Name = objbufName.readLine();
            } catch (IOException E) {
                System.out.println(E.getMessage());
            }
            BasicDBObject inQuery1 = new BasicDBObject();
            inQuery1.put("Name", Name);
            DBCursor cursor1 = db.getCollection("EmployeeRaw").find(inQuery1);
            while (cursor1.hasNext()) {
                // System.out.println(cursor.next());
                System.out.println(cursor1.next());
            }
            break;

        case "3":
            for (int i = 1; i < 21; i++) {
                BasicDBObject inQuerya = new BasicDBObject();
                inQuerya.put("_id", i);
                DBCursor cursora = db.getCollection("EmployeeRaw").find(inQuerya);
                while (cursora.hasNext()) {
                    // System.out.println(cursor.next());
                    System.out.println(cursora.next());
                }
            }
            break;
        }
        break;

    }

}

---

From source file:bluevia.examples.MODemo.java

/**
 * @param args//from   w  w w. ja v a  2s.  co m
 */
public static void main(String[] args) throws IOException {

    BufferedReader iReader = null;
    String apiDataFile = "API-AccessToken.ini";

    String consumer_key;
    String consumer_secret;
    String registrationId;

    OAuthConsumer apiConsumer = null;
    HttpURLConnection request = null;
    URL moAPIurl = null;

    Logger logger = Logger.getLogger("moSMSDemo.class");
    int i = 0;
    int rc = 0;

    Thread mThread = Thread.currentThread();

    try {
        System.setProperty("debug", "1");

        iReader = new BufferedReader(new FileReader(apiDataFile));

        // Private data: consumer info + access token info + phone info
        consumer_key = iReader.readLine();
        consumer_secret = iReader.readLine();
        registrationId = iReader.readLine();

        // Set up the oAuthConsumer
        while (true) {
            try {

                logger.log(Level.INFO, String.format("#%d: %s\n", ++i, "Requesting messages..."));

                apiConsumer = new DefaultOAuthConsumer(consumer_key, consumer_secret);

                apiConsumer.setMessageSigner(new HmacSha1MessageSigner());

                moAPIurl = new URL("https://api.bluevia.com/services/REST/SMS/inbound/" + registrationId
                        + "/messages?version=v1&alt=json");

                request = (HttpURLConnection) moAPIurl.openConnection();
                request.setRequestMethod("GET");

                apiConsumer.sign(request);

                StringBuffer doc = new StringBuffer();
                BufferedReader br = null;

                rc = request.getResponseCode();
                if (rc == HttpURLConnection.HTTP_OK) {
                    br = new BufferedReader(new InputStreamReader(request.getInputStream()));

                    String line = br.readLine();
                    while (line != null) {
                        doc.append(line);
                        line = br.readLine();
                    }

                    System.out.printf("Output message: %s\n", doc.toString());
                    try {
                        JSONObject apiResponse1 = new JSONObject(doc.toString());
                        String aux = apiResponse1.getString("receivedSMS");
                        if (aux != null) {
                            String szMessage;
                            String szOrigin;
                            String szDate;

                            JSONObject smsPool = apiResponse1.getJSONObject("receivedSMS");
                            JSONArray smsInfo = smsPool.optJSONArray("receivedSMS");
                            if (smsInfo != null) {
                                for (i = 0; i < smsInfo.length(); i++) {
                                    szMessage = smsInfo.getJSONObject(i).getString("message");
                                    szOrigin = smsInfo.getJSONObject(i).getJSONObject("originAddress")
                                            .getString("phoneNumber");
                                    szDate = smsInfo.getJSONObject(i).getString("dateTime");
                                    System.out.printf("#%d %s\n - from %s\n - message:%s\n", i, szDate,
                                            szOrigin, szMessage);
                                }
                            } else {
                                JSONObject sms = smsPool.getJSONObject("receivedSMS");
                                szMessage = sms.getString("message");
                                szOrigin = sms.getJSONObject("originAddress").getString("phoneNumber");
                                szDate = sms.getString("dateTime");
                                System.out.printf("#%d %s\n - from %s\n - message:%s\n", i, szDate, szOrigin,
                                        szMessage);
                            }
                        }
                    } catch (JSONException e) {
                        System.err.println("JSON error: " + e.getMessage());
                    }

                } else if (rc == HttpURLConnection.HTTP_NO_CONTENT)
                    System.out.printf("No content\n");
                else
                    System.err.printf("Error: %d:%s\n", rc, request.getResponseMessage());

                request.disconnect();

            } catch (Exception e) {
                System.err.println("Exception: " + e.getMessage());
            }
            mThread.sleep(15000);
        }
    } catch (Exception e) {
        System.err.println("Exception: " + e.getMessage());
    }
}

---

From source file:com.era7.bioinfo.annotation.AutomaticQualityControl.java

public static void main(String[] args) {

    if (args.length != 4) {
        System.out.println("This program expects four parameters: \n" + "1. Gene annotation XML filename \n"
                + "2. Reference protein set (.fasta)\n" + "3. Output TXT filename\n"
                + "4. Initial Blast XML results filename (the one used at the very beginning of the semiautomatic annotation process)\n");
    } else {/*from   w  w w .  j  av a  2 s. c o m*/

        BufferedWriter outBuff = null;

        try {

            File inFile = new File(args[0]);
            File fastaFile = new File(args[1]);
            File outFile = new File(args[2]);
            File blastFile = new File(args[3]);

            //Primero cargo todos los datos del archivo xml del blast
            BufferedReader buffReader = new BufferedReader(new FileReader(blastFile));
            StringBuilder stBuilder = new StringBuilder();
            String line = null;

            while ((line = buffReader.readLine()) != null) {
                stBuilder.append(line);
            }

            buffReader.close();
            System.out.println("Creating blastoutput...");
            BlastOutput blastOutput = new BlastOutput(stBuilder.toString());
            System.out.println("BlastOutput created! :)");
            stBuilder.delete(0, stBuilder.length());

            HashMap<String, String> blastProteinsMap = new HashMap<String, String>();
            ArrayList<Iteration> iterations = blastOutput.getBlastOutputIterations();
            for (Iteration iteration : iterations) {
                blastProteinsMap.put(iteration.getQueryDef().split("\\|")[1].trim(), iteration.toString());
            }
            //freeing some memory
            blastOutput = null;
            //------------------------------------------------------------------------

            //Initializing writer for output file
            outBuff = new BufferedWriter(new FileWriter(outFile));

            //reading gene annotation xml file.....
            buffReader = new BufferedReader(new FileReader(inFile));
            stBuilder = new StringBuilder();
            line = null;
            while ((line = buffReader.readLine()) != null) {
                stBuilder.append(line);
            }
            buffReader.close();

            XMLElement genesXML = new XMLElement(stBuilder.toString());
            //freeing some memory I don't need anymore
            stBuilder.delete(0, stBuilder.length());

            //reading file with the reference proteins set
            ArrayList<String> proteinsReferenceSet = new ArrayList<String>();
            buffReader = new BufferedReader(new FileReader(fastaFile));
            while ((line = buffReader.readLine()) != null) {
                if (line.charAt(0) == '>') {
                    proteinsReferenceSet.add(line.split("\\|")[1]);
                }
            }
            buffReader.close();

            Element pGenes = genesXML.asJDomElement().getChild(PredictedGenes.TAG_NAME);

            List<Element> contigs = pGenes.getChildren(ContigXML.TAG_NAME);

            System.out.println("There are " + contigs.size() + " contigs to be checked... ");

            outBuff.write("There are " + contigs.size() + " contigs to be checked... \n");
            outBuff.write("Proteins reference set: \n");
            for (String st : proteinsReferenceSet) {
                outBuff.write(st + ",");
            }
            outBuff.write("\n");

            for (Element elem : contigs) {
                ContigXML contig = new ContigXML(elem);

                //escribo el id del contig en el que estoy
                outBuff.write("Checking contig: " + contig.getId() + "\n");
                outBuff.flush();

                List<XMLElement> geneList = contig.getChildrenWith(PredictedGene.TAG_NAME);
                System.out.println("geneList.size() = " + geneList.size());

                int numeroDeGenesParaAnalizar = geneList.size() / FACTOR;
                if (numeroDeGenesParaAnalizar == 0) {
                    numeroDeGenesParaAnalizar++;
                }

                ArrayList<Integer> indicesUtilizados = new ArrayList<Integer>();

                outBuff.write("\nThe contig has " + geneList.size() + " predicted genes, let's analyze: "
                        + numeroDeGenesParaAnalizar + "\n");

                for (int j = 0; j < numeroDeGenesParaAnalizar; j++) {
                    int geneIndex;

                    boolean geneIsDismissed = false;
                    do {
                        geneIsDismissed = false;
                        geneIndex = (int) Math.round(Math.floor(Math.random() * geneList.size()));
                        PredictedGene tempGene = new PredictedGene(geneList.get(geneIndex).asJDomElement());
                        if (tempGene.getStatus().equals(PredictedGene.STATUS_DISMISSED)) {
                            geneIsDismissed = true;
                        }
                    } while (indicesUtilizados.contains(new Integer(geneIndex)) && geneIsDismissed);

                    indicesUtilizados.add(geneIndex);
                    System.out.println("geneIndex = " + geneIndex);

                    //Ahora hay que sacar el gen correspondiente al indice y hacer el control de calidad
                    PredictedGene gene = new PredictedGene(geneList.get(geneIndex).asJDomElement());

                    outBuff.write("\nAnalyzing gene with id: " + gene.getId() + " , annotation uniprot id: "
                            + gene.getAnnotationUniprotId() + "\n");
                    outBuff.write("eValue: " + gene.getEvalue() + "\n");

                    //--------------PETICION POST HTTP BLAST----------------------
                    PostMethod post = new PostMethod(BLAST_URL);
                    post.addParameter("program", "blastx");
                    post.addParameter("sequence", gene.getSequence());
                    post.addParameter("database", "uniprotkb");
                    post.addParameter("email", "ppareja@era7.com");
                    post.addParameter("exp", "1e-10");
                    post.addParameter("stype", "dna");

                    // execute the POST
                    HttpClient client = new HttpClient();
                    int status = client.executeMethod(post);
                    System.out.println("status post = " + status);
                    InputStream inStream = post.getResponseBodyAsStream();

                    String fileName = "jobid.txt";
                    FileOutputStream outStream = new FileOutputStream(new File(fileName));
                    byte[] buffer = new byte[1024];
                    int len;

                    while ((len = inStream.read(buffer)) != -1) {
                        outStream.write(buffer, 0, len);
                    }
                    outStream.close();

                    //Once the file is created I just have to read one line in order to extract the job id
                    buffReader = new BufferedReader(new FileReader(new File(fileName)));
                    String jobId = buffReader.readLine();
                    buffReader.close();

                    System.out.println("jobId = " + jobId);

                    //--------------HTTP CHECK JOB STATUS REQUEST----------------------
                    GetMethod get = new GetMethod(CHECK_JOB_STATUS_URL + jobId);
                    String jobStatus = "";
                    do {

                        try {
                            Thread.sleep(1000);//sleep for 1000 ms                                
                        } catch (InterruptedException ie) {
                            //If this thread was intrrupted by nother thread
                        }

                        status = client.executeMethod(get);
                        //System.out.println("status get = " + status);

                        inStream = get.getResponseBodyAsStream();

                        fileName = "jobStatus.txt";
                        outStream = new FileOutputStream(new File(fileName));

                        while ((len = inStream.read(buffer)) != -1) {
                            outStream.write(buffer, 0, len);
                        }
                        outStream.close();

                        //Once the file is created I just have to read one line in order to extract the job id
                        buffReader = new BufferedReader(new FileReader(new File(fileName)));
                        jobStatus = buffReader.readLine();
                        //System.out.println("jobStatus = " + jobStatus);
                        buffReader.close();

                    } while (!jobStatus.equals(FINISHED_JOB_STATUS));

                    //Once I'm here the blast should've already finished

                    //--------------JOB RESULTS HTTP REQUEST----------------------
                    get = new GetMethod(JOB_RESULT_URL + jobId + "/out");

                    status = client.executeMethod(get);
                    System.out.println("status get = " + status);

                    inStream = get.getResponseBodyAsStream();

                    fileName = "jobResults.txt";
                    outStream = new FileOutputStream(new File(fileName));

                    while ((len = inStream.read(buffer)) != -1) {
                        outStream.write(buffer, 0, len);
                    }
                    outStream.close();

                    //--------parsing the blast results file-----

                    TreeSet<GeneEValuePair> featuresBlast = new TreeSet<GeneEValuePair>();

                    buffReader = new BufferedReader(new FileReader(new File(fileName)));
                    while ((line = buffReader.readLine()) != null) {
                        if (line.length() > 3) {
                            String prefix = line.substring(0, 3);
                            if (prefix.equals("TR:") || prefix.equals("SP:")) {
                                String[] columns = line.split(" ");
                                String id = columns[1];
                                //System.out.println("id = " + id);

                                String e = "";

                                String[] arraySt = line.split("\\.\\.\\.");
                                if (arraySt.length > 1) {
                                    arraySt = arraySt[1].trim().split(" ");
                                    int contador = 0;
                                    for (int k = 0; k < arraySt.length && contador <= 2; k++) {
                                        String string = arraySt[k];
                                        if (!string.equals("")) {
                                            contador++;
                                            if (contador == 2) {
                                                e = string;
                                            }
                                        }

                                    }
                                } else {
                                    //Number before e-
                                    String[] arr = arraySt[0].split("e-")[0].split(" ");
                                    String numeroAntesE = arr[arr.length - 1];
                                    String numeroDespuesE = arraySt[0].split("e-")[1].split(" ")[0];
                                    e = numeroAntesE + "e-" + numeroDespuesE;
                                }

                                double eValue = Double.parseDouble(e);
                                //System.out.println("eValue = " + eValue);
                                GeneEValuePair g = new GeneEValuePair(id, eValue);
                                featuresBlast.add(g);
                            }
                        }
                    }

                    GeneEValuePair currentGeneEValuePair = new GeneEValuePair(gene.getAnnotationUniprotId(),
                            gene.getEvalue());

                    System.out.println("currentGeneEValuePair.id = " + currentGeneEValuePair.id);
                    System.out.println("currentGeneEValuePair.eValue = " + currentGeneEValuePair.eValue);
                    boolean blastContainsGene = false;
                    for (GeneEValuePair geneEValuePair : featuresBlast) {
                        if (geneEValuePair.id.equals(currentGeneEValuePair.id)) {
                            blastContainsGene = true;
                            //le pongo la e que tiene en el wu-blast para poder comparar
                            currentGeneEValuePair.eValue = geneEValuePair.eValue;
                            break;
                        }
                    }

                    if (blastContainsGene) {
                        outBuff.write("The protein was found in the WU-BLAST result.. \n");
                        //Una vez que se que esta en el blast tengo que ver que sea la mejor
                        GeneEValuePair first = featuresBlast.first();
                        outBuff.write("Protein with best eValue according to the WU-BLAST result: " + first.id
                                + " , " + first.eValue + "\n");
                        if (first.id.equals(currentGeneEValuePair.id)) {
                            outBuff.write("Proteins with best eValue match up \n");
                        } else {
                            if (first.eValue == currentGeneEValuePair.eValue) {
                                outBuff.write(
                                        "The one with best eValue is not the same protein but has the same eValue \n");
                            } else if (first.eValue > currentGeneEValuePair.eValue) {
                                outBuff.write(
                                        "The one with best eValue is not the same protein but has a worse eValue :) \n");
                            } else {
                                outBuff.write(
                                        "The best protein from BLAST has an eValue smaller than ours, checking if it's part of the reference set...\n");
                                //System.exit(-1);
                                if (proteinsReferenceSet.contains(first.id)) {
                                    //The protein is in the reference set and that shouldn't happen
                                    outBuff.write(
                                            "The protein was found on the reference set, checking if it belongs to the same contig...\n");
                                    String iterationSt = blastProteinsMap.get(gene.getAnnotationUniprotId());
                                    if (iterationSt != null) {
                                        outBuff.write(
                                                "The protein was found in the BLAST used at the beginning of the annotation process.\n");
                                        Iteration iteration = new Iteration(iterationSt);
                                        ArrayList<Hit> hits = iteration.getIterationHits();
                                        boolean contigFound = false;
                                        Hit errorHit = null;
                                        for (Hit hit : hits) {
                                            if (hit.getHitDef().indexOf(contig.getId()) >= 0) {
                                                contigFound = true;
                                                errorHit = hit;
                                                break;
                                            }
                                        }
                                        if (contigFound) {
                                            outBuff.write(
                                                    "ERROR: A hit from the same contig was find in the Blast file: \n"
                                                            + errorHit.toString() + "\n");
                                        } else {
                                            outBuff.write("There is no hit with the same contig! :)\n");
                                        }
                                    } else {
                                        outBuff.write(
                                                "The protein is NOT in the BLAST used at the beginning of the annotation process.\n");
                                    }

                                } else {
                                    //The protein was not found on the reference set so everything's ok
                                    outBuff.write(
                                            "The protein was not found on the reference, everything's ok :)\n");
                                }
                            }
                        }

                    } else {
                        outBuff.write("The protein was NOT found on the WU-BLAST !! :( \n");

                        //System.exit(-1);
                    }

                }

            }

        } catch (Exception ex) {
            ex.printStackTrace();
        } finally {
            try {
                //closing outputfile
                outBuff.close();
            } catch (IOException ex) {
                Logger.getLogger(AutomaticQualityControl.class.getName()).log(Level.SEVERE, null, ex);
            }
        }

    }
}

---

From source file:eu.skqs.bertie.standalone.BertieStandalone.java

public static void main(String[] args) {

    // Options/*from  w  w  w. j av a2  s .com*/
    Option file = OptionBuilder.withArgName("file").withLongOpt("file").hasArg()
            .withDescription("File to annotate").create("f");

    Option directory = OptionBuilder.withArgName("directory").withLongOpt("directory").hasArg()
            .withDescription("Directory to annotate").create("d");

    Option owl = OptionBuilder.withArgName("owl").withLongOpt("owl").hasArg()
            .withDescription("OWL file to use in annotation").create("o");

    Option plain = OptionBuilder.withLongOpt("plain").withDescription("Plain text file format").create("p");

    Option tei = OptionBuilder.withLongOpt("tei").withDescription("TEI file format").create("t");

    Option mode = OptionBuilder.withArgName("extract|minimal|maximal|prosody").withLongOpt("mode").hasArg()
            .withDescription("Mode to operate in").create("m");

    Option clean = OptionBuilder.withArgName("T0,T1,T3").withLongOpt("clean").hasArg()
            .withDescription("Remove gives types, MUST START UPPERCASE").create("c");

    Options options = new Options();
    options.addOption(file);
    options.addOption(directory);
    options.addOption(owl);
    options.addOption(plain);
    options.addOption(tei);
    options.addOption(mode);
    options.addOption(clean);

    CommandLineParser parser = new GnuParser();
    HelpFormatter formatter = new HelpFormatter();
    CommandLine cmdline = null;

    try {
        cmdline = parser.parse(options, args);
    } catch (ParseException e) {
        e.printStackTrace();
        System.exit(-1);
    }

    BertieStandalone standalone = new BertieStandalone();
    String documentPath = null;

    // Check for custom OWL
    if (cmdline.hasOption("owl")) {
        owlPath = cmdline.getOptionValue("owl");
    }

    // Check for clean
    if (cmdline.hasOption("clean")) {
        typesToRemove = cmdline.getOptionValue("clean");
    }

    // Check for mode
    if (cmdline.hasOption("mode")) {
        String currentMode = cmdline.getOptionValue("mode");

        if (currentMode.equals("extract")) {
            extractMode = true;
        } else if (currentMode.equals("poetry")) {
            poetryMode = true;
        }

        analysisMode = currentMode;
    }

    // Check for directory option
    if (cmdline.hasOption("directory")) {
        // We support TEI directorys only
        if (!cmdline.hasOption("tei")) {
            logger.log(Level.WARNING, "TEI file format must be selected with directory argument");
            System.exit(-1);
        }

        String directoryPath = cmdline.getOptionValue("directory");

        if (extractMode) {
            try {
                standalone.extractWithCollectionReader(directoryPath);
            } catch (Exception e) {
            }

            System.exit(0);
        }

        try {
            standalone.processWithCollectionReader(directoryPath);
        } catch (Exception e) {
            e.printStackTrace();
            System.exit(-1);
        }

        System.exit(0);
    }

    // Check for file option
    if (cmdline.hasOption("file")) {
        // TODO: clean this up
        documentPath = cmdline.getOptionValue("file");
        filePath = cmdline.getOptionValue("file");

        // TEI
        if (cmdline.hasOption("tei")) {
            try {
                processWithFile();
            } catch (Exception e) {
                e.printStackTrace();
                System.exit(-1);
            }
            System.exit(0);
        }

        // Check for plain option
        if (!cmdline.hasOption("plain")) {
            logger.log(Level.WARNING, "Plain text format must be selected with file argument");
            System.exit(-1);
        }
    } else {
        logger.log(Level.WARNING, "No file argument given. Quitting.");
        formatter.printHelp("bertie", options);
        System.exit(-1);
    }

    // Make sure we have a document path
    if (documentPath == null) {
        logger.log(Level.WARNING, "Document path is empty. Quitting.");
        System.exit(-1);
    }

    // Read the document
    try {
        String encodingType = "UTF-8";

        BufferedReader fileReader = new BufferedReader(
                new InputStreamReader(new FileInputStream(documentPath), encodingType));

        StringBuilder sb = new StringBuilder();
        String line = null;

        while ((line = fileReader.readLine()) != null) {
            sb.append(line + newLine);
        }

        String input = sb.toString();
        fileReader.close();

        String output = standalone.process(input);
        if (output == null) {
            logger.log(Level.WARNING, "Empty processing result.");
            System.exit(-1);
        }

        PrintWriter fileWriter = new PrintWriter(documentPath, encodingType);
        fileWriter.write(output);
        fileWriter.close();
    } catch (Exception e) {
        e.printStackTrace();
    }
}

---

From source file:com.mycompany.mavenproject4.web.java

/**
 * @param args the command line arguments
 *///  ww  w.  j ava2  s  .c o  m
public static void main(String[] args) {
    System.out.println("Enter your choice do you want to work with \n 1.PostGreSQL \n 2.Redis \n 3.Mongodb");
    InputStreamReader IORdatabase = new InputStreamReader(System.in);
    BufferedReader BIOdatabase = new BufferedReader(IORdatabase);
    String Str1 = null;
    try {
        Str1 = BIOdatabase.readLine();
    } catch (Exception E7) {
        System.out.println(E7.getMessage());
    }

    // loading data from the CSV file 

    CsvReader data = null;

    try {
        data = new CsvReader("\\data\\Consumer_Complaints.csv");
    } catch (FileNotFoundException EB) {
        System.out.println(EB.getMessage());
    }
    int noofcolumn = 5;
    int noofrows = 100;
    int loops = 0;

    try {
        data = new CsvReader("\\data\\Consumer_Complaints.csv");
    } catch (FileNotFoundException E) {
        System.out.println(E.getMessage());
    }

    String[][] Dataarray = new String[noofrows][noofcolumn];
    try {
        while (data.readRecord()) {
            String v;
            String[] x;
            v = data.getRawRecord();
            x = v.split(",");
            for (int j = 0; j < noofcolumn; j++) {
                String value = null;
                int z = j;
                value = x[z];
                try {
                    Dataarray[loops][j] = value;
                } catch (Exception E) {
                    System.out.println(E.getMessage());
                }
                // System.out.println(Dataarray[iloop][j]);
            }
            loops = loops + 1;
        }
    } catch (IOException Em) {
        System.out.println(Em.getMessage());
    }

    data.close();

    // connection to Database 
    switch (Str1) {
    // postgre code goes here 
    case "1":

        Connection Conn = null;
        Statement Stmt = null;
        URI dbUri = null;
        String choice = null;
        InputStreamReader objin = new InputStreamReader(System.in);
        BufferedReader objbuf = new BufferedReader(objin);
        try {
            Class.forName("org.postgresql.Driver");
        } catch (Exception E1) {
            System.out.println(E1.getMessage());
        }
        String username = "ahkyjdavhedkzg";
        String password = "2f7c3_MBJbIy1uJsFyn7zebkhY";
        String dbUrl = "jdbc:postgresql://ec2-54-83-199-54.compute-1.amazonaws.com:5432/d2l6hq915lp9vi?ssl=true&sslfactory=org.postgresql.ssl.NonValidatingFactory";

        // now update data in the postgress Database 

        /*  for(int i=0;i<RowCount;i++)
           {
                try 
        {
                          
        Conn= DriverManager.getConnection(dbUrl, username, password);    
        Stmt = Conn.createStatement();
                  String Connection_String = "insert into Webdata (Id,Product,state,Submitted,Complaintid) values (' "+ Dataarray[i][0]+" ',' "+ Dataarray[i][1]+" ',' "+ Dataarray[i][2]+" ',' "+ Dataarray[i][3]+" ',' "+ Dataarray[i][4]+" ')";
         Stmt.executeUpdate(Connection_String);
                  Conn.close();
        }
        catch(SQLException E4)
                  {
           System.out.println(E4.getMessage());
        }
           }
           */
        // Quering with the Database 

        System.out.println("1. Display Data ");
        System.out.println("2. Select data based on primary key");
        System.out.println("3. Select data based on Other attributes e.g Name");
        System.out.println("Enter your Choice ");
        try {
            choice = objbuf.readLine();
        } catch (IOException E) {
            System.out.println(E.getMessage());
        }
        switch (choice) {
        case "1":
            try {
                Conn = DriverManager.getConnection(dbUrl, username, password);
                Stmt = Conn.createStatement();
                String Connection_String = " Select * from Webdata;";
                ResultSet objRS = Stmt.executeQuery(Connection_String);
                while (objRS.next()) {
                    System.out.println(" ID: " + objRS.getInt("ID"));
                    System.out.println("Product Name: " + objRS.getString("Product"));
                    System.out.println("Which state: " + objRS.getString("State"));
                    System.out.println("Sumbitted through: " + objRS.getString("Submitted"));
                    System.out.println("Complain Number: " + objRS.getString("Complaintid"));
                    Conn.close();
                }

            } catch (Exception E2) {
                System.out.println(E2.getMessage());
            }

            break;

        case "2":

            System.out.println("Enter Id(Primary Key) :");
            InputStreamReader objkey = new InputStreamReader(System.in);
            BufferedReader objbufkey = new BufferedReader(objkey);
            int key = 0;
            try {
                key = Integer.parseInt(objbufkey.readLine());
            } catch (IOException E) {
                System.out.println(E.getMessage());
            }
            try {
                Conn = DriverManager.getConnection(dbUrl, username, password);
                Stmt = Conn.createStatement();
                String Connection_String = " Select * from Webdata where Id=" + key + ";";
                ResultSet objRS = Stmt.executeQuery(Connection_String);
                while (objRS.next()) {
                    //System.out.println(" ID: " + objRS.getInt("ID"));
                    System.out.println("Product Name: " + objRS.getString("Product"));
                    System.out.println("Which state: " + objRS.getString("State"));
                    System.out.println("Sumbitted through: " + objRS.getString("Submitted"));
                    System.out.println("Complain Number: " + objRS.getString("Complaintid"));
                    Conn.close();
                }

            } catch (Exception E2) {
                System.out.println(E2.getMessage());
            }
            break;

        case "3":
            //String Name=null;
            System.out.println("Enter Complaintid to find the record");

            // Scanner input = new Scanner(System.in);
            //
            int Number = 0;
            try {
                InputStreamReader objname = new InputStreamReader(System.in);
                BufferedReader objbufname = new BufferedReader(objname);

                Number = Integer.parseInt(objbufname.readLine());
            } catch (Exception E10) {
                System.out.println(E10.getMessage());
            }
            //System.out.println(Name);
            try {
                Conn = DriverManager.getConnection(dbUrl, username, password);
                Stmt = Conn.createStatement();
                String Connection_String = " Select * from Webdata where complaintid=" + Number + ";";
                //2
                System.out.println(Connection_String);
                ResultSet objRS = Stmt.executeQuery(Connection_String);
                while (objRS.next()) {
                    int id = objRS.getInt("id");
                    System.out.println(" ID: " + id);
                    System.out.println("Product Name: " + objRS.getString("Product"));
                    String state = objRS.getString("state");
                    System.out.println("Which state: " + state);
                    String Submitted = objRS.getString("submitted");
                    System.out.println("Sumbitted through: " + Submitted);
                    String Complaintid = objRS.getString("complaintid");
                    System.out.println("Complain Number: " + Complaintid);

                }
                Conn.close();
            } catch (Exception E2) {
                System.out.println(E2.getMessage());
            }
            break;
        }
        try {
            Conn.close();
        } catch (SQLException E6) {
            System.out.println(E6.getMessage());
        }
        break;

    // Redis code goes here 

    case "2":
        int Length = 0;
        String ID = null;
        Length = 100;

        // Connection to Redis 
        Jedis jedis = new Jedis("pub-redis-13274.us-east-1-2.1.ec2.garantiadata.com", 13274);
        jedis.auth("rfJ8OLjlv9NjRfry");
        System.out.println("Connected to Redis Database");

        // Storing values in the database 

        /* 
        for(int i=0;i<Length;i++)
        { 
         //Store data in redis 
            int j=i+1;
        jedis.hset("Record:" + j , "Product", Dataarray[i][1]);
        jedis.hset("Record:" + j , "State ", Dataarray[i][2]);
        jedis.hset("Record:" + j , "Submitted", Dataarray[i][3]);
        jedis.hset("Record:" + j , "Complaintid", Dataarray[i][4]);
                
        }
        */
        System.out.println(
                "Search by \n 11.Get records through primary key \n 22.Get Records through Complaintid \n 33.Display ");
        InputStreamReader objkey = new InputStreamReader(System.in);
        BufferedReader objbufkey = new BufferedReader(objkey);
        String str2 = null;
        try {
            str2 = objbufkey.readLine();
        } catch (IOException E) {
            System.out.println(E.getMessage());
        }
        switch (str2) {
        case "11":
            System.out.print("Enter Primary Key : ");
            InputStreamReader IORKey = new InputStreamReader(System.in);
            BufferedReader BIORKey = new BufferedReader(IORKey);
            String ID1 = null;
            try {
                ID1 = BIORKey.readLine();
            } catch (IOException E3) {
                System.out.println(E3.getMessage());
            }

            Map<String, String> properties = jedis.hgetAll("Record:" + Integer.parseInt(ID1));
            for (Map.Entry<String, String> entry : properties.entrySet()) {
                System.out.println("Product:" + jedis.hget("Record:" + Integer.parseInt(ID1), "Product"));
                System.out.println("State:" + jedis.hget("Record:" + Integer.parseInt(ID1), "State"));
                System.out.println("Submitted:" + jedis.hget("Record:" + Integer.parseInt(ID1), "Submitted"));
                System.out
                        .println("Complaintid:" + jedis.hget("Record:" + Integer.parseInt(ID1), "Complaintid"));
            }
            break;

        case "22":
            System.out.print(" Enter Complaintid  : ");
            InputStreamReader IORName1 = new InputStreamReader(System.in);
            BufferedReader BIORName1 = new BufferedReader(IORName1);

            String ID2 = null;
            try {
                ID2 = BIORName1.readLine();
            } catch (IOException E3) {
                System.out.println(E3.getMessage());
            }
            for (int i = 0; i < 100; i++) {
                Map<String, String> properties3 = jedis.hgetAll("Record:" + i);
                for (Map.Entry<String, String> entry : properties3.entrySet()) {
                    String value = entry.getValue();
                    if (entry.getValue().equals(ID2)) {
                        System.out
                                .println("Product:" + jedis.hget("Record:" + Integer.parseInt(ID2), "Product"));
                        System.out.println("State:" + jedis.hget("Record:" + Integer.parseInt(ID2), "State"));
                        System.out.println(
                                "Submitted:" + jedis.hget("Record:" + Integer.parseInt(ID2), "Submitted"));
                        System.out.println(
                                "Complaintid:" + jedis.hget("Record:" + Integer.parseInt(ID2), "Complaintid"));
                    }

                }
            }

            break;

        case "33":
            for (int i = 1; i < 21; i++) {
                Map<String, String> properties3 = jedis.hgetAll("Record:" + i);
                for (Map.Entry<String, String> entry : properties3.entrySet()) {

                    System.out.println("Product:" + jedis.hget("Record:" + i, "Product"));
                    System.out.println("State:" + jedis.hget("Record:" + i, "State"));
                    System.out.println("Submitted:" + jedis.hget("Record:" + i, "Submitted"));
                    System.out.println("Complaintid:" + jedis.hget("Record:" + i, "Complaintid"));

                }
            }
            break;
        }

        break;

    // mongo db 

    case "3":
        MongoClient mongo = new MongoClient(new MongoClientURI(
                "mongodb://naikhpratik:naikhpratik@ds053964.mongolab.com:53964/heroku_6t7n587f"));
        DB db;
        db = mongo.getDB("heroku_6t7n587f");
        // storing values in the database 
        /*for(int i=0;i<100;i++)
         {
             BasicDBObject document = new BasicDBObject();
            document.put("Id", i+1);
            document.put("Product", Dataarray[i][1]);
            document.put("State", Dataarray[i][2]);    
            document.put("Submitted", Dataarray[i][3]);    
            document.put("Complaintid", Dataarray[i][4]); 
            db.getCollection("Naiknaik").insert(document);
                  
         }*/
        System.out.println("Search by \n 1.Enter Primary key \n 2.Enter Complaintid \n 3.Display");
        InputStreamReader objkey6 = new InputStreamReader(System.in);
        BufferedReader objbufkey6 = new BufferedReader(objkey6);
        String str3 = null;
        try {
            str3 = objbufkey6.readLine();
        } catch (IOException E) {
            System.out.println(E.getMessage());
        }
        switch (str3) {
        case "1":
            System.out.println("Enter the Primary Key");
            InputStreamReader IORPkey = new InputStreamReader(System.in);
            BufferedReader BIORPkey = new BufferedReader(IORPkey);
            int Pkey = 0;
            try {
                Pkey = Integer.parseInt(BIORPkey.readLine());
            } catch (IOException E) {
                System.out.println(E.getMessage());
            }
            BasicDBObject inQuery = new BasicDBObject();
            inQuery.put("Id", Pkey);
            DBCursor cursor = db.getCollection("Naiknaik").find(inQuery);
            while (cursor.hasNext()) {
                // System.out.println(cursor.next());
                System.out.println(cursor.next());
            }
            break;
        case "2":
            System.out.println("Enter the Product to Search");
            InputStreamReader objName = new InputStreamReader(System.in);
            BufferedReader objbufName = new BufferedReader(objName);
            String Name = null;
            try {
                Name = objbufName.readLine();
            } catch (IOException E) {
                System.out.println(E.getMessage());
            }
            BasicDBObject inQuery1 = new BasicDBObject();
            inQuery1.put("Product", Name);
            DBCursor cursor1 = db.getCollection("Naiknaik").find(inQuery1);
            while (cursor1.hasNext()) {
                // System.out.println(cursor.next());
                System.out.println(cursor1.next());
            }
            break;

        case "3":
            for (int i = 1; i < 21; i++) {
                BasicDBObject inQuerya = new BasicDBObject();
                inQuerya.put("_id", i);
                DBCursor cursora = db.getCollection("Naiknaik").find(inQuerya);
                while (cursora.hasNext()) {
                    // System.out.println(cursor.next());
                    System.out.println(cursora.next());
                }
            }
            break;
        }
        break;

    }

}

---

From source file:Main.java

/** Simple command-line based search demo. */
public static void main(String[] args) throws Exception {
    String usage = "Usage:\tjava SearchFiles [-index dir] [-field f] [-repeat n] [-queries file] [-query string] [-raw] [-paging hitsPerPage]\n\nSee http://lucene.apache.org/core/4_1_0/demo/ for details.";
    if (args.length > 0 && ("-h".equals(args[0]) || "-help".equals(args[0]))) {
        System.out.println(usage);
        System.exit(0);//  www . j a  va 2s .c  o m
    }

    String index = "index";
    String field = "contents";
    String queries = null;
    int repeat = 0;
    boolean raw = false;
    String queryString = null;
    int hitsPerPage = 10;

    for (int i = 0; i < args.length; i++) {
        if ("-index".equals(args[i])) {
            index = args[i + 1];
            i++;
        } else if ("-field".equals(args[i])) {
            field = args[i + 1];
            i++;
        } else if ("-queries".equals(args[i])) {
            queries = args[i + 1];
            i++;
        } else if ("-query".equals(args[i])) {
            queryString = args[i + 1];
            i++;
        } else if ("-repeat".equals(args[i])) {
            repeat = Integer.parseInt(args[i + 1]);
            i++;
        } else if ("-raw".equals(args[i])) {
            raw = true;
        } else if ("-paging".equals(args[i])) {
            hitsPerPage = Integer.parseInt(args[i + 1]);
            if (hitsPerPage <= 0) {
                System.err.println("There must be at least 1 hit per page.");
                System.exit(1);
            }
            i++;
        }
    }

    IndexReader reader = DirectoryReader.open(FSDirectory.open(new File(index)));
    IndexSearcher searcher = new IndexSearcher(reader);
    // :Post-Release-Update-Version.LUCENE_XY:
    Analyzer analyzer = new StandardAnalyzer(Version.LUCENE_4_10_0);

    BufferedReader in = null;
    if (queries != null) {
        in = new BufferedReader(new InputStreamReader(new FileInputStream(queries), StandardCharsets.UTF_8));
    } else {
        in = new BufferedReader(new InputStreamReader(System.in, StandardCharsets.UTF_8));
    }
    // :Post-Release-Update-Version.LUCENE_XY:
    QueryParser parser = new QueryParser(Version.LUCENE_4_10_0, field, analyzer);
    while (true) {
        if (queries == null && queryString == null) { // prompt the user
            System.out.println("Enter query: ");
        }

        String line = queryString != null ? queryString : in.readLine();

        if (line == null || line.length() == -1) {
            break;
        }

        line = line.trim();
        if (line.length() == 0) {
            break;
        }

        Query query = parser.parse(line);
        System.out.println("Searching for: " + query.toString(field));

        if (repeat > 0) { // repeat & time as benchmark
            Date start = new Date();
            for (int i = 0; i < repeat; i++) {
                searcher.search(query, null, 100);
            }
            Date end = new Date();
            System.out.println("Time: " + (end.getTime() - start.getTime()) + "ms");
        }

        doPagingSearch(in, searcher, query, hitsPerPage, raw, queries == null && queryString == null);

        if (queryString != null) {
            break;
        }
    }
    reader.close();
}

---

From source file:com.adobe.aem.demo.Analytics.java

public static void main(String[] args) {

    String hostname = null;//ww w .ja v  a  2s  .c o m
    String url = null;
    String eventfile = null;

    // Command line options for this tool
    Options options = new Options();
    options.addOption("h", true, "Hostname");
    options.addOption("u", true, "Url");
    options.addOption("f", true, "Event data file");
    CommandLineParser parser = new BasicParser();
    try {
        CommandLine cmd = parser.parse(options, args);

        if (cmd.hasOption("u")) {
            url = cmd.getOptionValue("u");
        }

        if (cmd.hasOption("f")) {
            eventfile = cmd.getOptionValue("f");
        }

        if (cmd.hasOption("h")) {
            hostname = cmd.getOptionValue("h");
        }

        if (eventfile == null || hostname == null || url == null) {
            System.out.println("Command line parameters: -h hostname -u url -f path_to_XML_file");
            System.exit(-1);
        }

    } catch (ParseException ex) {

        logger.error(ex.getMessage());

    }

    URLConnection urlConn = null;
    DataOutputStream printout = null;
    BufferedReader input = null;
    String u = "http://" + hostname + "/" + url;
    String tmp = null;
    try {

        URL myurl = new URL(u);
        urlConn = myurl.openConnection();
        urlConn.setDoInput(true);
        urlConn.setDoOutput(true);
        urlConn.setUseCaches(false);
        urlConn.setRequestProperty("Content-Type", "application/x-www-form-urlencoded");

        printout = new DataOutputStream(urlConn.getOutputStream());

        String xml = readFile(eventfile, StandardCharsets.UTF_8);
        printout.writeBytes(xml);
        printout.flush();
        printout.close();

        input = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));

        logger.debug(xml);
        while (null != ((tmp = input.readLine()))) {
            logger.debug(tmp);
        }
        printout.close();
        input.close();

    } catch (Exception ex) {

        logger.error(ex.getMessage());

    }

}

---

From source file:AverageCost.java

public static void main(String[] args) throws FileNotFoundException, IOException {
    //Directory of the n files
    String directory_path = "/home/gauss/rgrunitzki/Dropbox/Profissional/UFRGS/Doutorado/Artigo TRI15/SF Experiments/IQ-Learning/";
    BufferedReader reader = null;
    //Line to analyse
    String line = "";
    String csvDivisor = ";";
    int totalLines = 1002;
    int totalRows = 532;

    String filesToRead[] = new File(directory_path).list();
    Arrays.sort(filesToRead);//from w  w  w  .  j  a v  a 2 s . c o  m
    System.out.println(filesToRead.length);

    List<List<DescriptiveStatistics>> summary = new ArrayList<>();

    for (int i = 0; i <= totalLines; i++) {
        summary.add(new ArrayList<DescriptiveStatistics>());
        for (int j = 0; j <= totalRows; j++) {
            summary.get(i).add(new DescriptiveStatistics());
        }
    }

    //reads all files
    for (String file : filesToRead) {
        reader = new BufferedReader(new FileReader(directory_path + file));
        int lineCounter = 0;
        //reads all file's line
        while ((line = reader.readLine()) != null) {
            if (lineCounter > 0) {
                String[] rows = line.trim().split(csvDivisor);
                //reads all line's row
                for (int r = 0; r < rows.length; r++) {
                    summary.get(lineCounter).get(r).addValue(Double.parseDouble(rows[r]));
                }
            }
            lineCounter++;
        }

        //System.out.println(file.split("/")[file.split("/").length - 1] + csvDivisor + arithmeticMean(avgCost) + csvDivisor + standardDeviation(avgCost));
    }

    //generate mean and standard deviation;
    for (List<DescriptiveStatistics> summaryLines : summary) {
        System.out.println();
        for (DescriptiveStatistics summaryLineRow : summaryLines) {
            System.out.print(summaryLineRow.getMean() + ";" + summaryLineRow.getStandardDeviation() + ";");
        }
    }
}

---

From source file:edu.nyu.vida.data_polygamy.relationship_computation.Relationship.java

/**
 * @param args/*from   w  w w. j  a v a 2s .  c  o m*/
 * @throws ParseException 
 */
@SuppressWarnings({ "deprecation" })
public static void main(String[] args) throws IOException, InterruptedException, ClassNotFoundException {

    Options options = new Options();

    Option forceOption = new Option("f", "force", false,
            "force the computation of the relationship " + "even if files already exist");
    forceOption.setRequired(false);
    options.addOption(forceOption);

    Option scoreOption = new Option("sc", "score", true, "set threhsold for relationship score");
    scoreOption.setRequired(false);
    scoreOption.setArgName("SCORE THRESHOLD");
    options.addOption(scoreOption);

    Option strengthOption = new Option("st", "strength", true, "set threhsold for relationship strength");
    strengthOption.setRequired(false);
    strengthOption.setArgName("STRENGTH THRESHOLD");
    options.addOption(strengthOption);

    Option completeRandomizationOption = new Option("c", "complete-randomization", false,
            "use complete randomization when performing significance tests");
    completeRandomizationOption.setRequired(false);
    options.addOption(completeRandomizationOption);

    Option idOption = new Option("id", "ids", false, "output id instead of names for datasets and attributes");
    idOption.setRequired(false);
    options.addOption(idOption);

    Option g1Option = new Option("g1", "first-group", true, "set first group of datasets");
    g1Option.setRequired(true);
    g1Option.setArgName("FIRST GROUP");
    g1Option.setArgs(Option.UNLIMITED_VALUES);
    options.addOption(g1Option);

    Option g2Option = new Option("g2", "second-group", true, "set second group of datasets");
    g2Option.setRequired(false);
    g2Option.setArgName("SECOND GROUP");
    g2Option.setArgs(Option.UNLIMITED_VALUES);
    options.addOption(g2Option);

    Option machineOption = new Option("m", "machine", true, "machine identifier");
    machineOption.setRequired(true);
    machineOption.setArgName("MACHINE");
    machineOption.setArgs(1);
    options.addOption(machineOption);

    Option nodesOption = new Option("n", "nodes", true, "number of nodes");
    nodesOption.setRequired(true);
    nodesOption.setArgName("NODES");
    nodesOption.setArgs(1);
    options.addOption(nodesOption);

    Option s3Option = new Option("s3", "s3", false, "data on Amazon S3");
    s3Option.setRequired(false);
    options.addOption(s3Option);

    Option awsAccessKeyIdOption = new Option("aws_id", "aws-id", true,
            "aws access key id; " + "this is required if the execution is on aws");
    awsAccessKeyIdOption.setRequired(false);
    awsAccessKeyIdOption.setArgName("AWS-ACCESS-KEY-ID");
    awsAccessKeyIdOption.setArgs(1);
    options.addOption(awsAccessKeyIdOption);

    Option awsSecretAccessKeyOption = new Option("aws_key", "aws-id", true,
            "aws secrect access key; " + "this is required if the execution is on aws");
    awsSecretAccessKeyOption.setRequired(false);
    awsSecretAccessKeyOption.setArgName("AWS-SECRET-ACCESS-KEY");
    awsSecretAccessKeyOption.setArgs(1);
    options.addOption(awsSecretAccessKeyOption);

    Option bucketOption = new Option("b", "s3-bucket", true,
            "bucket on s3; " + "this is required if the execution is on aws");
    bucketOption.setRequired(false);
    bucketOption.setArgName("S3-BUCKET");
    bucketOption.setArgs(1);
    options.addOption(bucketOption);

    Option helpOption = new Option("h", "help", false, "display this message");
    helpOption.setRequired(false);
    options.addOption(helpOption);

    Option removeOption = new Option("r", "remove-not-significant", false,
            "remove relationships that are not" + "significant from the final output");
    removeOption.setRequired(false);
    options.addOption(removeOption);

    HelpFormatter formatter = new HelpFormatter();
    CommandLineParser parser = new PosixParser();
    CommandLine cmd = null;

    try {
        cmd = parser.parse(options, args);
    } catch (ParseException e) {
        formatter.printHelp("hadoop jar data-polygamy.jar "
                + "edu.nyu.vida.data_polygamy.relationship_computation.Relationship", options, true);
        System.exit(0);
    }

    if (cmd.hasOption("h")) {
        formatter.printHelp("hadoop jar data-polygamy.jar "
                + "edu.nyu.vida.data_polygamy.relationship_computation.Relationship", options, true);
        System.exit(0);
    }

    boolean s3 = cmd.hasOption("s3");
    String s3bucket = "";
    String awsAccessKeyId = "";
    String awsSecretAccessKey = "";

    if (s3) {
        if ((!cmd.hasOption("aws_id")) || (!cmd.hasOption("aws_key")) || (!cmd.hasOption("b"))) {
            System.out.println(
                    "Arguments 'aws_id', 'aws_key', and 'b'" + " are mandatory if execution is on AWS.");
            formatter.printHelp(
                    "hadoop jar data-polygamy.jar "
                            + "edu.nyu.vida.data_polygamy.relationship_computation.Relationship",
                    options, true);
            System.exit(0);
        }
        s3bucket = cmd.getOptionValue("b");
        awsAccessKeyId = cmd.getOptionValue("aws_id");
        awsSecretAccessKey = cmd.getOptionValue("aws_key");
    }

    boolean snappyCompression = false;
    boolean bzip2Compression = false;
    String machine = cmd.getOptionValue("m");
    int nbNodes = Integer.parseInt(cmd.getOptionValue("n"));

    Configuration s3conf = new Configuration();
    if (s3) {
        s3conf.set("fs.s3.awsAccessKeyId", awsAccessKeyId);
        s3conf.set("fs.s3.awsSecretAccessKey", awsSecretAccessKey);
        s3conf.set("bucket", s3bucket);
    }

    Path path = null;
    FileSystem fs = FileSystem.get(new Configuration());

    ArrayList<String> shortDataset = new ArrayList<String>();
    ArrayList<String> firstGroup = new ArrayList<String>();
    ArrayList<String> secondGroup = new ArrayList<String>();
    HashMap<String, String> datasetAgg = new HashMap<String, String>();

    boolean removeNotSignificant = cmd.hasOption("r");
    boolean removeExistingFiles = cmd.hasOption("f");
    boolean completeRandomization = cmd.hasOption("c");
    boolean hasScoreThreshold = cmd.hasOption("sc");
    boolean hasStrengthThreshold = cmd.hasOption("st");
    boolean outputIds = cmd.hasOption("id");
    String scoreThreshold = hasScoreThreshold ? cmd.getOptionValue("sc") : "";
    String strengthThreshold = hasStrengthThreshold ? cmd.getOptionValue("st") : "";

    // all datasets
    ArrayList<String> all_datasets = new ArrayList<String>();
    if (s3) {
        path = new Path(s3bucket + FrameworkUtils.datasetsIndexDir);
        fs = FileSystem.get(path.toUri(), s3conf);
    } else {
        path = new Path(fs.getHomeDirectory() + "/" + FrameworkUtils.datasetsIndexDir);
    }
    BufferedReader br = new BufferedReader(new InputStreamReader(fs.open(path)));
    String line = br.readLine();
    while (line != null) {
        all_datasets.add(line.split("\t")[0]);
        line = br.readLine();
    }
    br.close();
    if (s3)
        fs.close();
    String[] all_datasets_array = new String[all_datasets.size()];
    all_datasets.toArray(all_datasets_array);

    String[] firstGroupCmd = cmd.getOptionValues("g1");
    String[] secondGroupCmd = cmd.hasOption("g2") ? cmd.getOptionValues("g2") : all_datasets_array;
    addDatasets(firstGroupCmd, firstGroup, shortDataset, datasetAgg, path, fs, s3conf, s3, s3bucket);
    addDatasets(secondGroupCmd, secondGroup, shortDataset, datasetAgg, path, fs, s3conf, s3, s3bucket);

    if (shortDataset.size() == 0) {
        System.out.println("No datasets to process.");
        System.exit(0);
    }

    if (firstGroup.isEmpty()) {
        System.out.println("No indices from datasets in G1.");
        System.exit(0);
    }

    if (secondGroup.isEmpty()) {
        System.out.println("No indices from datasets in G2.");
        System.exit(0);
    }

    // getting dataset ids

    String datasetNames = "";
    String datasetIds = "";
    HashMap<String, String> datasetId = new HashMap<String, String>();
    Iterator<String> it = shortDataset.iterator();
    while (it.hasNext()) {
        datasetId.put(it.next(), null);
    }

    if (s3) {
        path = new Path(s3bucket + FrameworkUtils.datasetsIndexDir);
        fs = FileSystem.get(path.toUri(), s3conf);
    } else {
        path = new Path(fs.getHomeDirectory() + "/" + FrameworkUtils.datasetsIndexDir);
    }
    br = new BufferedReader(new InputStreamReader(fs.open(path)));
    line = br.readLine();
    while (line != null) {
        String[] dt = line.split("\t");
        all_datasets.add(dt[0]);
        if (datasetId.containsKey(dt[0])) {
            datasetId.put(dt[0], dt[1]);
            datasetNames += dt[0] + ",";
            datasetIds += dt[1] + ",";
        }
        line = br.readLine();
    }
    br.close();
    if (s3)
        fs.close();

    datasetNames = datasetNames.substring(0, datasetNames.length() - 1);
    datasetIds = datasetIds.substring(0, datasetIds.length() - 1);
    it = shortDataset.iterator();
    while (it.hasNext()) {
        String dataset = it.next();
        if (datasetId.get(dataset) == null) {
            System.out.println("No dataset id for " + dataset);
            System.exit(0);
        }
    }

    String firstGroupStr = "";
    String secondGroupStr = "";
    for (String dataset : firstGroup) {
        firstGroupStr += datasetId.get(dataset) + ",";
    }
    for (String dataset : secondGroup) {
        secondGroupStr += datasetId.get(dataset) + ",";
    }
    firstGroupStr = firstGroupStr.substring(0, firstGroupStr.length() - 1);
    secondGroupStr = secondGroupStr.substring(0, secondGroupStr.length() - 1);

    String relationshipsDir = "";
    if (outputIds) {
        relationshipsDir = FrameworkUtils.relationshipsIdsDir;
    } else {
        relationshipsDir = FrameworkUtils.relationshipsDir;
    }

    FrameworkUtils.createDir(s3bucket + relationshipsDir, s3conf, s3);

    String random = completeRandomization ? "complete" : "restricted";

    String indexInputDirs = "";
    String noRelationship = "";

    HashSet<String> dirs = new HashSet<String>();

    String dataset1;
    String dataset2;
    String datasetId1;
    String datasetId2;
    for (int i = 0; i < firstGroup.size(); i++) {
        for (int j = 0; j < secondGroup.size(); j++) {

            if (Integer.parseInt(datasetId.get(firstGroup.get(i))) < Integer
                    .parseInt(datasetId.get(secondGroup.get(j)))) {
                dataset1 = firstGroup.get(i);
                dataset2 = secondGroup.get(j);
            } else {
                dataset1 = secondGroup.get(j);
                dataset2 = firstGroup.get(i);
            }

            datasetId1 = datasetId.get(dataset1);
            datasetId2 = datasetId.get(dataset2);

            if (dataset1.equals(dataset2))
                continue;
            String correlationOutputFileName = s3bucket + relationshipsDir + "/" + dataset1 + "-" + dataset2
                    + "/";

            if (removeExistingFiles) {
                FrameworkUtils.removeFile(correlationOutputFileName, s3conf, s3);
            }
            if (!FrameworkUtils.fileExists(correlationOutputFileName, s3conf, s3)) {
                dirs.add(s3bucket + FrameworkUtils.indexDir + "/" + dataset1);
                dirs.add(s3bucket + FrameworkUtils.indexDir + "/" + dataset2);
            } else {
                noRelationship += datasetId1 + "-" + datasetId2 + ",";
            }
        }
    }

    if (dirs.isEmpty()) {
        System.out.println("All the relationships were already computed.");
        System.out.println("Use -f in the beginning of the command line to force the computation.");
        System.exit(0);
    }

    for (String dir : dirs) {
        indexInputDirs += dir + ",";
    }

    Configuration conf = new Configuration();
    Machine machineConf = new Machine(machine, nbNodes);

    String jobName = "relationship" + "-" + random;
    String relationshipOutputDir = s3bucket + relationshipsDir + "/tmp/";

    FrameworkUtils.removeFile(relationshipOutputDir, s3conf, s3);

    for (int i = 0; i < shortDataset.size(); i++) {
        conf.set("dataset-" + datasetId.get(shortDataset.get(i)) + "-agg", datasetAgg.get(shortDataset.get(i)));
    }
    for (int i = 0; i < shortDataset.size(); i++) {
        conf.set("dataset-" + datasetId.get(shortDataset.get(i)) + "-agg-size",
                Integer.toString(datasetAgg.get(shortDataset.get(i)).split(",").length));
    }
    conf.set("dataset-keys", datasetIds);
    conf.set("dataset-names", datasetNames);
    conf.set("first-group", firstGroupStr);
    conf.set("second-group", secondGroupStr);
    conf.set("complete-random", String.valueOf(completeRandomization));
    conf.set("output-ids", String.valueOf(outputIds));
    conf.set("complete-random-str", random);
    conf.set("main-dataset-id", datasetId.get(shortDataset.get(0)));
    conf.set("remove-not-significant", String.valueOf(removeNotSignificant));
    if (noRelationship.length() > 0) {
        conf.set("no-relationship", noRelationship.substring(0, noRelationship.length() - 1));
    }
    if (hasScoreThreshold) {
        conf.set("score-threshold", scoreThreshold);
    }
    if (hasStrengthThreshold) {
        conf.set("strength-threshold", strengthThreshold);
    }

    conf.set("mapreduce.tasktracker.map.tasks.maximum", String.valueOf(machineConf.getMaximumTasks()));
    conf.set("mapreduce.tasktracker.reduce.tasks.maximum", String.valueOf(machineConf.getMaximumTasks()));
    conf.set("mapreduce.jobtracker.maxtasks.perjob", "-1");
    conf.set("mapreduce.reduce.shuffle.parallelcopies", "20");
    conf.set("mapreduce.input.fileinputformat.split.minsize", "0");
    conf.set("mapreduce.task.io.sort.mb", "200");
    conf.set("mapreduce.task.io.sort.factor", "100");
    conf.set("mapreduce.task.timeout", "2400000");

    if (s3) {
        machineConf.setMachineConfiguration(conf);
        conf.set("fs.s3.awsAccessKeyId", awsAccessKeyId);
        conf.set("fs.s3.awsSecretAccessKey", awsSecretAccessKey);
        conf.set("bucket", s3bucket);
    }

    if (snappyCompression) {
        conf.set("mapreduce.map.output.compress", "true");
        conf.set("mapreduce.map.output.compress.codec", "org.apache.hadoop.io.compress.SnappyCodec");
        //conf.set("mapreduce.output.fileoutputformat.compress.codec", "org.apache.hadoop.io.compress.SnappyCodec");
    }
    if (bzip2Compression) {
        conf.set("mapreduce.map.output.compress", "true");
        conf.set("mapreduce.map.output.compress.codec", "org.apache.hadoop.io.compress.BZip2Codec");
        //conf.set("mapreduce.output.fileoutputformat.compress.codec", "org.apache.hadoop.io.compress.BZip2Codec");
    }

    Job job = new Job(conf);
    job.setJobName(jobName);

    job.setMapOutputKeyClass(PairAttributeWritable.class);
    job.setMapOutputValueClass(TopologyTimeSeriesWritable.class);
    job.setOutputKeyClass(Text.class);
    job.setOutputValueClass(Text.class);

    job.setMapperClass(CorrelationMapper.class);
    job.setReducerClass(CorrelationReducer.class);
    job.setNumReduceTasks(machineConf.getNumberReduces());

    job.setInputFormatClass(SequenceFileInputFormat.class);
    //job.setOutputFormatClass(TextOutputFormat.class);
    LazyOutputFormat.setOutputFormatClass(job, TextOutputFormat.class);

    FileInputFormat.setInputDirRecursive(job, true);
    FileInputFormat.setInputPaths(job, indexInputDirs.substring(0, indexInputDirs.length() - 1));
    FileOutputFormat.setOutputPath(job, new Path(relationshipOutputDir));

    job.setJarByClass(Relationship.class);

    long start = System.currentTimeMillis();
    job.submit();
    job.waitForCompletion(true);
    System.out.println(jobName + "\t" + (System.currentTimeMillis() - start));

    // moving files to right place
    for (int i = 0; i < firstGroup.size(); i++) {
        for (int j = 0; j < secondGroup.size(); j++) {

            if (Integer.parseInt(datasetId.get(firstGroup.get(i))) < Integer
                    .parseInt(datasetId.get(secondGroup.get(j)))) {
                dataset1 = firstGroup.get(i);
                dataset2 = secondGroup.get(j);
            } else {
                dataset1 = secondGroup.get(j);
                dataset2 = firstGroup.get(i);
            }

            if (dataset1.equals(dataset2))
                continue;

            String from = s3bucket + relationshipsDir + "/tmp/" + dataset1 + "-" + dataset2 + "/";
            String to = s3bucket + relationshipsDir + "/" + dataset1 + "-" + dataset2 + "/";
            FrameworkUtils.renameFile(from, to, s3conf, s3);
        }
    }
}

---

From source file:edu.oregonstate.eecs.mcplan.domains.toy.CliffWorld.java

public static void main(final String[] argv) throws NumberFormatException, IOException {
    final RandomGenerator rng = new MersenneTwister(42);
    final int L = 7;
    final int W = 4;
    final int F = 5;
    final State s = new State(rng, L, W, F);
    final Simulator sim = new Simulator(s, rng);

    final Actions actions = new Actions(rng);

    while (!sim.state().isTerminal()) {
        System.out.println(s);/*from   w ww. jav  a 2  s  . c  o m*/
        actions.setState(sim.state(), sim.t());
        final ArrayList<Action> action_list = Fn.takeAll(actions);
        for (int i = 0; i < action_list.size(); ++i) {
            System.out.println(i + ": " + action_list.get(i));
        }
        System.out.print(">>> ");
        final BufferedReader cin = new BufferedReader(new InputStreamReader(System.in));
        final int choice = Integer.parseInt(cin.readLine());
        final Action a = action_list.get(choice);
        sim.takeAction(new JointAction<Action>(a));
        System.out.println("Reward: " + Arrays.toString(sim.reward()));
    }
}

---

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