Example usage for java.lang String indexOf

List of usage examples for java.lang String indexOf

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Introduction

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

Prototype

public int indexOf(String str)

Source Link

Document

Returns the index within this string of the first occurrence of the specified substring.

Usage

From source file:com.cyberway.issue.util.SurtPrefixSet.java

/**
 * Allow class to be used as a command-line tool for converting 
 * URL lists (or naked host or host/path fragments implied
 * to be HTTP URLs) to implied SURT prefix form. 
 * //  w  ww  .  j  a v a2s. com
 * Read from stdin or first file argument. Writes to stdout. 
 *
 * @param args cmd-line arguments: may include input file
 * @throws IOException
 */
public static void main(String[] args) throws IOException {
    InputStream in = args.length > 0 ? new BufferedInputStream(new FileInputStream(args[0])) : System.in;
    PrintStream out = args.length > 1 ? new PrintStream(new BufferedOutputStream(new FileOutputStream(args[1])))
            : System.out;
    BufferedReader br = new BufferedReader(new InputStreamReader(in));
    String line;
    while ((line = br.readLine()) != null) {
        if (line.indexOf("#") > 0)
            line = line.substring(0, line.indexOf("#"));
        line = line.trim();
        if (line.length() == 0)
            continue;
        out.println(prefixFromPlain(line));
    }
    br.close();
    out.close();
}

From source file:edu.cmu.lti.oaqa.annographix.apps.SolrQueryApp.java

public static void main(String[] args) {
    Options options = new Options();

    options.addOption("u", null, true, "Solr URI");
    options.addOption("q", null, true, "Query");
    options.addOption("n", null, true, "Max # of results");
    options.addOption("o", null, true, "An optional TREC-style output file");
    options.addOption("w", null, false, "Do a warm-up query call, before each query");

    CommandLineParser parser = new org.apache.commons.cli.GnuParser();

    BufferedWriter trecOutFile = null;

    try {/*w w w .j av a  2s. co  m*/
        CommandLine cmd = parser.parse(options, args);
        String queryFile = null, solrURI = null;

        if (cmd.hasOption("u")) {
            solrURI = cmd.getOptionValue("u");
        } else {
            Usage("Specify Solr URI");
        }

        SolrServerWrapper solr = new SolrServerWrapper(solrURI);

        if (cmd.hasOption("q")) {
            queryFile = cmd.getOptionValue("q");
        } else {
            Usage("Specify Query file");
        }

        int numRet = 100;

        if (cmd.hasOption("n")) {
            numRet = Integer.parseInt(cmd.getOptionValue("n"));
        }

        if (cmd.hasOption("o")) {
            trecOutFile = new BufferedWriter(new FileWriter(new File(cmd.getOptionValue("o"))));
        }

        List<String> fieldList = new ArrayList<String>();
        fieldList.add(UtilConst.ID_FIELD);
        fieldList.add(UtilConst.SCORE_FIELD);

        double totalTime = 0;
        double retQty = 0;

        ArrayList<Double> queryTimes = new ArrayList<Double>();

        boolean bDoWarmUp = cmd.hasOption("w");

        if (bDoWarmUp) {
            System.out.println("Using a warmup step!");
        }

        int queryQty = 0;
        for (String t : FileUtils.readLines(new File(queryFile))) {
            t = t.trim();
            if (t.isEmpty())
                continue;
            int ind = t.indexOf('|');
            if (ind < 0)
                throw new Exception("Wrong format, line: '" + t + "'");
            String qID = t.substring(0, ind);
            String q = t.substring(ind + 1);

            SolrDocumentList res = null;

            if (bDoWarmUp) {
                res = solr.runQuery(q, fieldList, numRet);
            }

            Long tm1 = System.currentTimeMillis();
            res = solr.runQuery(q, fieldList, numRet);
            Long tm2 = System.currentTimeMillis();
            retQty += res.getNumFound();
            System.out.println(qID + " Obtained: " + res.getNumFound() + " entries in " + (tm2 - tm1) + " ms");
            double delta = (tm2 - tm1);
            totalTime += delta;
            queryTimes.add(delta);
            ++queryQty;

            if (trecOutFile != null) {

                ArrayList<SolrRes> resArr = new ArrayList<SolrRes>();
                for (SolrDocument doc : res) {
                    String id = (String) doc.getFieldValue(UtilConst.ID_FIELD);
                    float score = (Float) doc.getFieldValue(UtilConst.SCORE_FIELD);
                    resArr.add(new SolrRes(id, "", score));
                }
                SolrRes[] results = resArr.toArray(new SolrRes[resArr.size()]);
                Arrays.sort(results);

                SolrEvalUtils.saveTrecResults(qID, results, trecOutFile, TREC_RUN, results.length);
            }
        }
        double devTime = 0, meanTime = totalTime / queryQty;
        for (int i = 0; i < queryQty; ++i) {
            double d = queryTimes.get(i) - meanTime;
            devTime += d * d;
        }
        devTime = Math.sqrt(devTime / (queryQty - 1));
        System.out.println(String.format("Query time, mean/standard dev: %.2f/%.2f (ms)", meanTime, devTime));
        System.out.println(String.format("Avg # of docs returned: %.2f", retQty / queryQty));

        solr.close();
        trecOutFile.close();
    } catch (ParseException e) {
        Usage("Cannot parse arguments");
    } catch (Exception e) {
        System.err.println("Terminating due to an exception: " + e);
        System.exit(1);
    }

}

From source file:client.MultiplexingClient.java

public static void main(String[] args) throws Exception {
    // Prepare to parse the command line
    Options options = new Options();
    Option sslOpt = new Option("s", "ssl", false, "Use SSL");
    Option debugOpt = new Option("d", true,
            "Debug level (NONE, FINER, FINE, CONFIG, INFO, WARNING, SEVERE. Default INFO.");
    Option numConnectionsOpt = new Option("n", true, "Number of connections to establish. [Default: 1]");
    Option numPcktOpt = new Option("p", true, "Number of packets to send in each connection. [Default: 20]");
    Option pcktMaxSizeOpt = new Option("m", true, "Maximum size of packets. [Default: 4096]");
    Option help = new Option("h", "print this message");

    options.addOption(help);/* ww w  .j  a va  2 s .  c  o  m*/
    options.addOption(debugOpt);
    options.addOption(numConnectionsOpt);
    options.addOption(numPcktOpt);
    options.addOption(pcktMaxSizeOpt);
    options.addOption(sslOpt);
    CommandLineParser parser = new PosixParser();
    // parse the command line arguments
    CommandLine line = parser.parse(options, args);

    if (line.hasOption(help.getOpt()) || line.getArgs().length < 1) {
        showUsage(options);
        return;
    }

    if (line.hasOption(sslOpt.getOpt())) {
        channelFactory = new SSLChannelFactory(true, TRUSTSTORE, TRUSTSTORE_PASSWORD);
    } else {
        channelFactory = new PlainChannelFactory();
    }

    if (line.hasOption(numConnectionsOpt.getOpt())) {
        connectionCount = Integer.parseInt(line.getOptionValue(numConnectionsOpt.getOpt()));
    } else {
        connectionCount = 1;
    }

    if (line.hasOption(numPcktOpt.getOpt())) {
        packetsToSend = Integer.parseInt(line.getOptionValue(numPcktOpt.getOpt()));
    } else {
        packetsToSend = 20;
    }

    if (line.hasOption(pcktMaxSizeOpt.getOpt())) {
        maxPcktSize = Integer.parseInt(line.getOptionValue(pcktMaxSizeOpt.getOpt()));
    } else {
        maxPcktSize = 4096;
    }

    InetSocketAddress remotePoint;
    try {
        String host = line.getArgs()[0];
        int colonIndex = host.indexOf(':');
        remotePoint = new InetSocketAddress(host.substring(0, colonIndex),
                Integer.parseInt(host.substring(colonIndex + 1)));
    } catch (Exception e) {
        showUsage(options);
        return;
    }

    // Setups the logging context for Log4j
    //     NDC.push(Thread.currentThread().getName());

    st = new SelectorThread();
    for (int i = 0; i < connectionCount; i++) {
        new MultiplexingClient(remotePoint);
        // Must sleep for a while between opening connections in order
        // to give the remote host enough time to handle them. Otherwise,
        // the remote host backlog will get full and the connection
        // attemps will start to be refused.
        Thread.sleep(100);
    }
}

From source file:de.mpg.escidoc.services.edoc.BatchUpdate.java

/**
 * @param args/*from w w  w  . ja  va2 s . co m*/
 */
public static void main(String[] args) throws Exception {
    CORESERVICES_URL = PropertyReader.getProperty("escidoc.framework_access.framework.url");

    String userHandle = AdminHelper.loginUser("import_user", "");

    logger.info("Querying core-services...");
    HttpClient httpClient = new HttpClient();
    String filter = "<param><filter name=\"http://escidoc.de/core/01/structural-relations/context\">"
            + IMPORT_CONTEXT
            + "</filter><order-by>http://escidoc.de/core/01/properties/creation-date</order-by><limit>0</limit></param>";

    logger.info("Filter: " + filter);

    PostMethod postMethod = new PostMethod(CORESERVICES_URL + "/ir/items/filter");

    postMethod.setRequestBody(filter);

    ProxyHelper.executeMethod(httpClient, postMethod);

    //        GetMethod getMethod = new GetMethod(CORESERVICES_URL + "/ir/item/escidoc:100220");
    //        getMethod.setRequestHeader("Cookie", "escidocCookie=" + userHandle)ProxyHelper.executeMethod(httpClient, getMethod)hod(httpClient, getMethod);

    String response = postMethod.getResponseBodyAsString();
    logger.info("...done!");

    System.out.println(response);

    while (response.contains("<escidocItem:item")) {

        int startPos = response.indexOf("<escidocItem:item");
        int endPos = response.indexOf("</escidocItem:item>");

        String item = response.substring(startPos, endPos + 19);

        response = response.substring(endPos + 19);

        startPos = item.indexOf("xlink:href=\"");
        endPos = item.indexOf("\"", startPos + 12);

        String objId = item.substring(startPos + 12, endPos);

        System.out.print(objId);

        if (item.contains("escidoc:22019")) {
            item = item.replaceAll("escidoc:22019", "escidoc:55222");

            PutMethod putMethod = new PutMethod(CORESERVICES_URL + objId);

            putMethod.setRequestHeader("Cookie", "escidocCookie=" + userHandle);
            putMethod.setRequestEntity(new StringRequestEntity(item));
            ProxyHelper.executeMethod(httpClient, putMethod);

            String result = putMethod.getResponseBodyAsString();

            //System.out.println(item);

            startPos = result.indexOf("last-modification-date=\"");
            endPos = result.indexOf("\"", startPos + 24);
            String modDate = result.substring(startPos + 24, endPos);
            //System.out.println("modDate: " + modDate);
            String param = "<param last-modification-date=\"" + modDate
                    + "\"><url>http://pubman.mpdl.mpg.de/pubman/item/" + objId.substring(4) + "</url></param>";
            postMethod = new PostMethod(CORESERVICES_URL + objId + "/assign-version-pid");
            postMethod.setRequestHeader("Cookie", "escidocCookie=" + userHandle);
            postMethod.setRequestEntity(new StringRequestEntity(param));
            ProxyHelper.executeMethod(httpClient, postMethod);
            result = postMethod.getResponseBodyAsString();
            //System.out.println("Result: " + result);

            startPos = result.indexOf("last-modification-date=\"");
            endPos = result.indexOf("\"", startPos + 24);
            modDate = result.substring(startPos + 24, endPos);
            //System.out.println("modDate: " + modDate);
            param = "<param last-modification-date=\"" + modDate
                    + "\"><comment>Batch repair of organizational unit identifier</comment></param>";
            postMethod = new PostMethod(CORESERVICES_URL + objId + "/submit");
            postMethod.setRequestHeader("Cookie", "escidocCookie=" + userHandle);
            postMethod.setRequestEntity(new StringRequestEntity(param));
            ProxyHelper.executeMethod(httpClient, postMethod);
            result = postMethod.getResponseBodyAsString();
            //System.out.println("Result: " + result);

            startPos = result.indexOf("last-modification-date=\"");
            endPos = result.indexOf("\"", startPos + 24);
            modDate = result.substring(startPos + 24, endPos);
            //System.out.println("modDate: " + modDate);
            param = "<param last-modification-date=\"" + modDate
                    + "\"><comment>Batch repair of organizational unit identifier</comment></param>";
            postMethod = new PostMethod(CORESERVICES_URL + objId + "/release");
            postMethod.setRequestHeader("Cookie", "escidocCookie=" + userHandle);
            postMethod.setRequestEntity(new StringRequestEntity(param));
            ProxyHelper.executeMethod(httpClient, postMethod);
            result = postMethod.getResponseBodyAsString();
            //System.out.println("Result: " + result);
            System.out.println("...changed");
        } else {
            System.out.println("...not affected");
        }
    }

}

From source file:com.joliciel.lefff.Lefff.java

/**
 * @param args//w w  w.j a  va  2 s  .com
 */
public static void main(String[] args) throws Exception {
    long startTime = (new Date()).getTime();
    String command = args[0];

    String memoryBaseFilePath = "";
    String lefffFilePath = "";
    String posTagSetPath = "";
    String posTagMapPath = "";
    String word = null;
    List<String> categories = null;
    int startLine = -1;
    int stopLine = -1;

    boolean firstArg = true;
    for (String arg : args) {
        if (firstArg) {
            firstArg = false;
            continue;
        }
        int equalsPos = arg.indexOf('=');
        String argName = arg.substring(0, equalsPos);
        String argValue = arg.substring(equalsPos + 1);
        if (argName.equals("memoryBase"))
            memoryBaseFilePath = argValue;
        else if (argName.equals("lefffFile"))
            lefffFilePath = argValue;
        else if (argName.equals("startLine"))
            startLine = Integer.parseInt(argValue);
        else if (argName.equals("stopLine"))
            stopLine = Integer.parseInt(argValue);
        else if (argName.equals("posTagSet"))
            posTagSetPath = argValue;
        else if (argName.equals("posTagMap"))
            posTagMapPath = argValue;
        else if (argName.equals("word"))
            word = argValue;
        else if (argName.equals("categories")) {
            String[] parts = argValue.split(",");
            categories = new ArrayList<String>();
            for (String part : parts) {
                categories.add(part);
            }
        } else
            throw new RuntimeException("Unknown argument: " + argName);
    }

    final LefffServiceLocator locator = new LefffServiceLocator();
    locator.setDataSourcePropertiesFile("jdbc-live.properties");

    TalismaneServiceLocator talismaneServiceLocator = TalismaneServiceLocator.getInstance();

    final LefffService lefffService = locator.getLefffService();
    if (command.equals("load")) {
        if (lefffFilePath.length() == 0)
            throw new RuntimeException("Required argument: lefffFile");
        final LefffLoader loader = lefffService.getLefffLoader();
        File file = new File(lefffFilePath);
        if (startLine > 0)
            loader.setStartLine(startLine);
        if (stopLine > 0)
            loader.setStopLine(stopLine);

        loader.LoadFile(file);
    } else if (command.equals("serialiseBase")) {
        if (memoryBaseFilePath.length() == 0)
            throw new RuntimeException("Required argument: memoryBase");
        if (posTagSetPath.length() == 0)
            throw new RuntimeException("Required argument: posTagSet");
        if (posTagMapPath.length() == 0)
            throw new RuntimeException("Required argument: posTagMap");

        PosTaggerServiceLocator posTaggerServiceLocator = talismaneServiceLocator.getPosTaggerServiceLocator();
        PosTaggerService posTaggerService = posTaggerServiceLocator.getPosTaggerService();
        File posTagSetFile = new File(posTagSetPath);
        PosTagSet posTagSet = posTaggerService.getPosTagSet(posTagSetFile);

        File posTagMapFile = new File(posTagMapPath);
        LefffPosTagMapper posTagMapper = lefffService.getPosTagMapper(posTagMapFile, posTagSet);

        Map<PosTagSet, LefffPosTagMapper> posTagMappers = new HashMap<PosTagSet, LefffPosTagMapper>();
        posTagMappers.put(posTagSet, posTagMapper);

        LefffMemoryLoader loader = new LefffMemoryLoader();
        LefffMemoryBase memoryBase = loader.loadMemoryBaseFromDatabase(lefffService, posTagMappers, categories);
        File memoryBaseFile = new File(memoryBaseFilePath);
        memoryBaseFile.delete();
        loader.serializeMemoryBase(memoryBase, memoryBaseFile);
    } else if (command.equals("deserialiseBase")) {
        if (memoryBaseFilePath.length() == 0)
            throw new RuntimeException("Required argument: memoryBase");

        LefffMemoryLoader loader = new LefffMemoryLoader();
        File memoryBaseFile = new File(memoryBaseFilePath);
        LefffMemoryBase memoryBase = loader.deserializeMemoryBase(memoryBaseFile);

        String[] testWords = new String[] { "avoir" };
        if (word != null) {
            testWords = word.split(",");
        }

        for (String testWord : testWords) {
            Set<PosTag> possiblePosTags = memoryBase.findPossiblePosTags(testWord);
            LOG.debug("##### PosTags for '" + testWord + "': " + possiblePosTags.size());
            int i = 1;
            for (PosTag posTag : possiblePosTags) {
                LOG.debug("### PosTag " + (i++) + ":" + posTag);
            }

            List<? extends LexicalEntry> entriesForWord = memoryBase.getEntries(testWord);
            LOG.debug("##### Entries for '" + testWord + "': " + entriesForWord.size());
            i = 1;
            for (LexicalEntry entry : entriesForWord) {
                LOG.debug("### Entry " + (i++) + ":" + entry.getWord());
                LOG.debug("Category " + entry.getCategory());
                LOG.debug("Predicate " + entry.getPredicate());
                LOG.debug("Lemma " + entry.getLemma());
                LOG.debug("Morphology " + entry.getMorphology());
            }

            List<? extends LexicalEntry> entriesForLemma = memoryBase.getEntriesForLemma(testWord, "");
            LOG.debug("##### Entries for '" + testWord + "' lemma: " + entriesForLemma.size());
            for (LexicalEntry entry : entriesForLemma) {
                LOG.debug("### Entry " + entry.getWord());
                LOG.debug("Category " + entry.getCategory());
                LOG.debug("Predicate " + entry.getPredicate());
                LOG.debug("Lemma " + entry.getLemma());
                LOG.debug("Morphology " + entry.getMorphology());
                for (PredicateArgument argument : entry.getPredicateArguments()) {
                    LOG.debug("Argument: " + argument.getFunction() + ",Optional? " + argument.isOptional());
                    for (String realisation : argument.getRealisations()) {
                        LOG.debug("Realisation: " + realisation);
                    }
                }
            }
        }

    } else {
        System.out.println("Usage : Lefff load filepath");
    }
    long endTime = (new Date()).getTime() - startTime;
    LOG.debug("Total runtime: " + ((double) endTime / 1000) + " seconds");
}

From source file:hk.hku.cecid.corvus.http.AS2EnvelopQuerySender.java

/**
 * The main method is for CLI mode./*from  www. j a  v  a 2  s .co  m*/
 */
public static void main(String[] args) {
    try {
        java.io.PrintStream out = System.out;

        if (args.length < 2) {
            out.println("Usage: as2-envelop [config-xml] [log-path]");
            out.println();
            out.println("Example: as2-envelop ./config/as2-envelop/as2-request.xml ./logs/as2-envelop.log");
            System.exit(1);
        }

        out.println("------------------------------------------------------");
        out.println("       AS2 Envelop Queryer       ");
        out.println("------------------------------------------------------");

        // Initialize the logger.
        out.println("Initialize logger .. ");
        // The logger path is specified at the last argument.
        FileLogger logger = new FileLogger(new File(args[args.length - 1]));

        // Initialize the query parameter.
        out.println("Importing AS2 administrative sending parameters ... ");
        AS2AdminData acd = DataFactory.getInstance()
                .createAS2AdminDataFromXML(new PropertyTree(new File(args[0]).toURI().toURL()));

        boolean historyQueryNeeded = false;
        AS2MessageHistoryRequestData queryData = new AS2MessageHistoryRequestData();
        if (acd.getMessageIdCriteria() == null || acd.getMessageIdCriteria().trim().equals("")) {

            historyQueryNeeded = true;

            // print command prompt
            out.println("No messageID was specified!");
            out.println("Start querying message repositry ...");

            String endpoint = acd.getEnvelopQueryEndpoint();
            String host = endpoint.substring(0, endpoint.indexOf("/corvus"));
            host += "/corvus/httpd/as2/msg_history";
            queryData.setEndPoint(host);
        } /*
            If the user has entered message id but no messagebox, 
            using the messageid as serach criteria and as 
            user to chose his target message
          */
        else if (acd.getMessageBoxCriteria() == null || acd.getMessageBoxCriteria().trim().equals("")) {

            historyQueryNeeded = true;

            // print command prompt
            out.println("Message Box value haven't specified.");
            out.println("Start query message whcih matched with messageID: " + acd.getMessageIdCriteria());

            String endpoint = acd.getEnvelopQueryEndpoint();
            String host = endpoint.substring(0, endpoint.indexOf("/corvus"));
            host += "/corvus/httpd/as2/msg_history";

            queryData.setEndPoint(host);
            queryData.setMessageId(acd.getMessageIdCriteria());
        }
        //Debug Message
        System.out.println("history Endpoint: " + queryData.getEndPoint());
        System.out.println("Repositry Endpoint: " + acd.getEnvelopQueryEndpoint());

        if (historyQueryNeeded) {
            List msgList = listAvailableMessage(queryData, logger);

            if (msgList == null || msgList.size() == 0) {
                out.println();
                out.println();
                out.println("No stream data found in repositry...");
                out.println("Please view log for details .. ");
                return;
            }

            int selection = promptForSelection(msgList);

            if (selection == -1) {
                return;
            }

            String messageID = (String) ((List) msgList.get(selection)).get(0);
            String messageBox = (String) ((List) msgList.get(selection)).get(1);
            acd.setMessageIdCriteria(messageID);
            acd.setMessageBoxCriteria(messageBox.toUpperCase());
            out.println();
            out.println();
            out.println("Start download targeted message envelop ...");
        }

        // Initialize the sender.
        out.println("Initialize AS2 HTTP data service client... ");
        AS2EnvelopQuerySender sender = new AS2EnvelopQuerySender(logger, acd);

        out.println("Sending    AS2 HTTP Envelop Query request ... ");
        sender.run();

        out.println();
        out.println("                    Sending Done:                   ");
        out.println("----------------------------------------------------");
        out.println("The Message Envelope : ");
        InputStream eins = sender.getEnvelopStream();
        if (eins.available() == 0) {
            out.println("No stream data found.");
            out.println("The message envelop does not exist for message id " + sender.getMessageIdToDownload()
                    + " and message box " + sender.getMessageBoxToDownload());
        } else
            IOHandler.pipe(sender.getEnvelopStream(), out);

        out.println("Please view log for details .. ");
    } catch (Exception e) {
        e.printStackTrace(System.err);
    }
}

From source file:MainClass.java

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

    ParserGetter kit = new ParserGetter();
    HTMLEditorKit.Parser parser = kit.getParser();

    URL u = new URL("http://www.java2s.com");
    InputStream in = u.openStream();
    InputStreamReader r = new InputStreamReader(in);
    String remoteFileName = u.getFile();
    if (remoteFileName.endsWith("/")) {
        remoteFileName += "index.html";
    }//from  w w w  .  ja  v a  2s.  c o  m
    if (remoteFileName.startsWith("/")) {
        remoteFileName = remoteFileName.substring(1);
    }
    File localDirectory = new File(u.getHost());
    while (remoteFileName.indexOf('/') > -1) {
        String part = remoteFileName.substring(0, remoteFileName.indexOf('/'));
        remoteFileName = remoteFileName.substring(remoteFileName.indexOf('/') + 1);
        localDirectory = new File(localDirectory, part);
    }
    if (localDirectory.mkdirs()) {
        File output = new File(localDirectory, remoteFileName);
        FileWriter out = new FileWriter(output);
        HTMLEditorKit.ParserCallback callback = new PageSaver(out, u);
        parser.parse(r, callback, false);
    }

}

From source file:MainClass.java

public static void main(String[] args) throws Exception {
    Document document = new Document(PageSize.A6);
    PdfWriter.getInstance(document, new FileOutputStream("2.pdf"));
    document.open();//from   w ww  .j av a  2  s  .  co m
    document.add(new Paragraph("Hello World"));
    document.add(new Paragraph("Hello People"));
    document.close();

    PdfReader reader = new PdfReader("2.pdf");
    PdfDictionary page = reader.getPageN(1);
    PRIndirectReference objectReference = (PRIndirectReference) page.get(PdfName.CONTENTS);
    PRStream stream = (PRStream) PdfReader.getPdfObject(objectReference);
    byte[] streamBytes = PdfReader.getStreamBytes(stream);
    String contentStream = new String(streamBytes);
    System.out.println(contentStream);
    PRTokeniser tokenizer = new PRTokeniser(streamBytes);
    while (tokenizer.nextToken()) {
        if (tokenizer.getTokenType() == PRTokeniser.TK_STRING) {
            System.out.println(tokenizer.getStringValue());
        }
    }
    StringBuffer buf = new StringBuffer();
    int pos = contentStream.indexOf("Hello World") + 11;
    buf.append(contentStream.substring(0, pos));
    buf.append("Hello");
    buf.append(contentStream.substring(pos));
    String hackedContentStream = buf.toString();
    document = new Document(PageSize.A6);
    PdfWriter writer = PdfWriter.getInstance(document, new FileOutputStream("HelloWorldStreamHacked.pdf"));
    document.open();
    PdfContentByte cb = writer.getDirectContent();
    cb.setLiteral(hackedContentStream);
    document.close();
}

From source file:edu.msu.cme.rdp.classifier.train.validation.distance.TaxaSimilarityMain.java

/**
 * This calculates the average similarity (Sab score or pairwise alignment) between taxa at given ranks and plot the box and whisker plot and accumulation curve. 
 * The distances associate to a given rank contains the distances between different child taxa. It does not include the distances within the same child taxa.
 * For example, if a query and it's closest match are from the same genus, the distance value is added to that genus.
 * If there are from different genera but the same family, the distance value is added to that family, etc.
 * @param args/*ww  w .j  ava2  s.  c  om*/
 * @throws IOException 
 */
public static void main(String[] args) throws IOException, OverlapCheckFailedException {
    String usage = "Usage: taxonfile trainset.fasta query.fasta outdir kmersize rankFile sab|pw \n"
            + "  This program calculates the average similarity (Sab score, or pairwise alignment) within taxa\n"
            + "  and plot the box and whisker plot and accumulation curve plot. \n"
            + "  rankFile: a file contains a list of ranks to be calculated and plotted. One rank per line, no particular order required. \n"
            + "  Note pw is extremely slower, recommended only for lower ranks such as species, genus and family. ";

    if (args.length != 7) {
        System.err.println(usage);
        System.exit(1);
    }
    List<String> ranks = readRanks(args[5]);
    File outdir = new File(args[3]);
    if (!outdir.isDirectory()) {
        System.err.println("outdir must be a directory");
        System.exit(1);
    }
    int kmer = Integer.parseInt(args[4]);
    GoodWordIterator.setWordSize(kmer);
    TaxaSimilarityMain theObj = new TaxaSimilarityMain(ranks);

    String plotTitle = new File(args[2]).getName();
    int index = plotTitle.indexOf(".");
    if (index != -1) {
        plotTitle = plotTitle.substring(0, index);
    }
    if (args[6].equalsIgnoreCase("sab")) {
        theObj.calSabSimilarity(args[0], args[1], args[2]);
    } else {
        theObj.calPairwiseSimilaritye(args[0], args[1], args[2]);
    }

    theObj.createPlot(plotTitle, outdir);

}

From source file:cht.Parser.java

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

    // TODO get from google drive
    boolean isUnicode = false;
    boolean isRemoveInputFileOnComplete = false;
    int rowNum;/*from  w w  w . j  ava 2 s.c  om*/
    int colNum;
    Gson gson = new GsonBuilder().setPrettyPrinting().create();

    Properties prop = new Properties();

    try {
        prop.load(new FileInputStream("config.txt"));
    } catch (IOException ex) {
        ex.printStackTrace();
    }

    String inputFilePath = prop.getProperty("inputFile");
    String outputDirectory = prop.getProperty("outputDirectory");
    System.out.println(outputDirectory);
    // optional
    String unicode = prop.getProperty("unicode");
    String removeInputFileOnComplete = prop.getProperty("removeInputFileOnComplete");

    inputFilePath = inputFilePath.trim();
    outputDirectory = outputDirectory.trim();

    if (unicode != null) {
        isUnicode = Boolean.parseBoolean(unicode.trim());
    }
    if (removeInputFileOnComplete != null) {
        isRemoveInputFileOnComplete = Boolean.parseBoolean(removeInputFileOnComplete.trim());
    }

    Writer out = null;
    FileInputStream in = null;
    final String newLine = System.getProperty("line.separator").toString();
    final String separator = File.separator;
    try {
        in = new FileInputStream(inputFilePath);

        Workbook workbook = new XSSFWorkbook(in);

        Sheet sheet = workbook.getSheetAt(0);

        rowNum = sheet.getLastRowNum() + 1;
        colNum = sheet.getRow(0).getPhysicalNumberOfCells();

        for (int j = 1; j < colNum; ++j) {
            String outputFilename = sheet.getRow(0).getCell(j).getStringCellValue();
            // guess directory
            int slash = outputFilename.indexOf('/');
            if (slash != -1) { // has directory
                outputFilename = outputFilename.substring(0, slash) + separator
                        + outputFilename.substring(slash + 1);
            }

            String outputPath = FilenameUtils.concat(outputDirectory, outputFilename);
            System.out.println("--Writing " + outputPath);
            out = new OutputStreamWriter(new FileOutputStream(outputPath), "UTF-8");
            TreeMap<String, Object> map = new TreeMap<String, Object>();
            for (int i = 1; i < rowNum; i++) {
                try {
                    String key = sheet.getRow(i).getCell(0).getStringCellValue();
                    //String value = "";
                    Cell tmp = sheet.getRow(i).getCell(j);
                    if (tmp != null) {
                        // not empty string!
                        value = sheet.getRow(i).getCell(j).getStringCellValue();
                    }
                    if (!key.equals("") && !key.startsWith("#") && !key.startsWith(".")) {
                        value = isUnicode ? StringEscapeUtils.escapeJava(value) : value;

                        int firstdot = key.indexOf(".");
                        String keyName, keyAttribute;
                        if (firstdot > 0) {// a.b.c.d 
                            keyName = key.substring(0, firstdot); // a
                            keyAttribute = key.substring(firstdot + 1); // b.c.d
                            TreeMap oldhash = null;
                            Object old = null;
                            if (map.get(keyName) != null) {
                                old = map.get(keyName);
                                if (old instanceof TreeMap == false) {
                                    System.out.println("different type of key:" + key);
                                    continue;
                                }
                                oldhash = (TreeMap) old;
                            } else {
                                oldhash = new TreeMap();
                            }

                            int firstdot2 = keyAttribute.indexOf(".");
                            String rootName, childName;
                            if (firstdot2 > 0) {// c, d.f --> d, f
                                rootName = keyAttribute.substring(0, firstdot2);
                                childName = keyAttribute.substring(firstdot2 + 1);
                            } else {// c, d  -> d, null
                                rootName = keyAttribute;
                                childName = null;
                            }

                            TreeMap<String, Object> object = myPut(oldhash, rootName, childName);
                            map.put(keyName, object);

                        } else {// c, d  -> d, null
                            keyName = key;
                            keyAttribute = null;
                            // simple string mode
                            map.put(key, value);
                        }

                    }

                } catch (Exception e) {
                    // just ingore empty rows
                }

            }
            String json = gson.toJson(map);
            // output json
            out.write(json + newLine);
            out.close();
        }
        in.close();

        System.out.println("\n---Complete!---");
        System.out.println("Read input file from " + inputFilePath);
        System.out.println(colNum - 1 + " output files ate generated at " + outputDirectory);
        System.out.println(rowNum + " records are generated for each output file.");
        System.out.println("output file is ecoded as unicode? " + (isUnicode ? "yes" : "no"));
        if (isRemoveInputFileOnComplete) {
            File input = new File(inputFilePath);
            input.deleteOnExit();
            System.out.println("Deleted " + inputFilePath);
        }

    } catch (FileNotFoundException e) {
        e.printStackTrace();
    } catch (IOException e) {
        e.printStackTrace();
    } finally {
        if (in != null) {
            in.close();
        }
    }

}