Example usage for org.apache.commons.io LineIterator LineIterator

Introduction

In this page you can find the example usage for org.apache.commons.io LineIterator LineIterator.

Prototype

public LineIterator(final Reader reader) throws IllegalArgumentException 

Source Link

Document

Constructs an iterator of the lines for a Reader.

Usage

From source file:edu.scripps.fl.pubchem.app.CIDDownloader.java

public static void main(String[] args) throws Exception {
    CIDDownloader fetcher = new CIDDownloader();

    CommandLineHandler clh = new CommandLineHandler() {
        public void configureOptions(Options options) {
            options.addOption(OptionBuilder.withLongOpt("input_file").withType("").withValueSeparator('=')
                    .hasArg().create());
            options.addOption(OptionBuilder.withLongOpt("output_file").withType("").withValueSeparator('=')
                    .hasArg().isRequired().create());
        }/*from  ww  w.ja  v a2 s . co m*/
    };
    args = clh.handle(args);
    String inputFile = clh.getCommandLine().getOptionValue("input_file");
    String outputFile = clh.getCommandLine().getOptionValue("output_file");

    fetcher.setOutputFile(outputFile);
    Iterator<?> iterator;
    if (null == inputFile) {
        if (args.length == 0) {
            log.info("Running query to find CIDs in PCAssayResult but not in PCCompound");
            SQLQuery query = PubChemDB.getSession().createSQLQuery(
                    "select distinct r.cid from pcassay_result r left join pccompound c on r.cid = c.cid where (r.cid is not null and r.cid > 0 ) and c.cid is null order by r.cid");
            ScrollableResults scroll = query.scroll(ScrollMode.FORWARD_ONLY);
            iterator = new ScrollableResultsIterator<Integer>(Integer.class, scroll);
        } else {
            iterator = Arrays.asList(args).iterator();
        }
    } else if ("-".equals(inputFile)) {
        log.info("Reading CIDs (one per line) from STDIN");
        iterator = new LineIterator(new InputStreamReader(System.in));
    } else {
        log.info("Reading CIDs (one per line) from " + inputFile);
        iterator = new LineIterator(new FileReader(inputFile));
    }
    fetcher.process(iterator);
    System.exit(0);
}

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From source file:au.org.ala.names.util.FileUtils.java

/**
 * @param source   the source input stream
 * @param encoding the encoding used by the input stream
 * @return/* w  w w. j av a2  s. co m*/
 * @throws UnsupportedEncodingException
 */
public static LineIterator getLineIterator(InputStream source, String encoding) {
    try {
        return new LineIterator(new BufferedReader(new InputStreamReader(source, encoding)));
    } catch (UnsupportedEncodingException e) {
        throw new IllegalArgumentException("Unsupported encoding" + encoding, e);
    }
}

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From source file:de.tudarmstadt.lt.nlkg.EvaluatePreds.java

static void evaluate(String file) throws IllegalArgumentException, FileNotFoundException {
    DT dt = new DT() {
        {//from   www. ja v  a 2s  . c o m
            _mysql_dbname = "nlkg_1";
        }
    };
    LineIterator iter = new LineIterator(new FileReader(file));
    iter.nextLine(); // skip first line
    int lineno = 1;
    double tp = 0d, tn = 0d, fp = 0d, fn = 0d;
    while (iter.hasNext() && (lineno < 100 || true)) {
        lineno++;
        String line = iter.nextLine();
        if (line.trim().isEmpty())
            continue;

        String[] splits = line.split("\t");
        String x = splits[0].trim();
        String y = splits[1].trim();
        String pred_l = splits[2].trim();
        String pred_r = splits[3].trim();
        boolean entailing_trueclass = Boolean.valueOf(splits[4].trim());

        _X.add(x);
        _Y.add(y);
        _PRED_L.add(pred_l);
        _PRED_R.add(pred_r);
        _ENTAILING.add(entailing_trueclass);

        boolean entailing_predicted = predictEntailing(dt, pred_l, pred_r);
        if (lineno % 100 == 0)
            Evaluate.log_progress();

        if (entailing_predicted && entailing_trueclass) {
            Evaluate.log_true(String.format("%d %-10s %-30s %-30s %b %n", lineno, "tp", pred_l, pred_r,
                    entailing_trueclass));
            tp++;
        }
        if (!entailing_predicted && !entailing_trueclass) {
            Evaluate.log_true(String.format("%d %-10s %-30s %-30s %b %n", lineno, "tn", pred_l, pred_r,
                    entailing_trueclass));
            tn++;
        }
        if (entailing_predicted && !entailing_trueclass) {
            Evaluate.log_false(String.format("%d %-10s %-30s %-30s %b %n", lineno, "fp", pred_l, pred_r,
                    entailing_trueclass));
            fp++;
        }
        if (!entailing_predicted && entailing_trueclass) {
            Evaluate.log_false(String.format("%d %-10s %-30s %-30s %b %n", lineno, "fn", pred_l, pred_r,
                    entailing_trueclass));
            fn++;
        }

    }

    System.out.format("tp: %d; fp: %d; fn: %d; tn: %d; %n", (int) tp, (int) fp, (int) fn, (int) tn);
    System.out.println("Precision = " + (tp / (tp + fp)));
    System.out.println("Recall    = " + (tp / (tp + fn)));
    System.out.println("F1        = " + ((2 * tp) / ((2 * tp) + fn + fp)));

    dt.disconnect();

}

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From source file:edu.umd.cs.hcil.twitterreplay.GzippedFileReader.java

public void open() throws FileNotFoundException, IOException {
    FileInputStream inFileStream = new FileInputStream(mFile);
    GZIPInputStream gzippedStream = new GZIPInputStream(inFileStream, 65536);
    BufferedReader reader = new BufferedReader(new InputStreamReader(gzippedStream, Charset.forName("UTF-8")));
    mReaderIterator = new LineIterator(reader);
}

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From source file:com.lithium.flow.io.InputStreamSpliterator.java

public InputStreamSpliterator(@Nonnull InputStream in, @Nonnull Charset encoding) {
    checkNotNull(in);//from   w  w w  .j  ava  2 s.  c o  m
    checkNotNull(encoding);
    it = new LineIterator(new InputStreamReader(in, encoding));
}

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From source file:com.mewmew.fairy.v1.spell.BaseLineSpell.java

@Override
public void process(InputStream in, OutputStream out) {
    LineIterator iter = null;//from www . j  a va 2s.  c  om
    try {
        output = createOutput(out);
        pipe = createPipe();
        iter = new LineIterator(new InputStreamReader(in));
        PipeUtil.process(iter, pipe, output);
    } catch (IOException e) {
        throw new RuntimeException(e);
    } finally {
        if (iter != null) {
            iter.close();
        }
    }
}

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From source file:de.tudarmstadt.lt.lm.service.PreTokenizedStringProvider.java

@Override
public List<String>[] getNgrams(String text, String language_code) throws Exception {
    LOG.trace(String.format("Computing ngrams from text: %s", StringUtils.abbreviate(text, 200)));
    List<String>[] ngrams = null;

    text = text.trim();//from w  w w  .  ja  va2s  .  c o  m
    for (LineIterator iter = new LineIterator(new StringReader(text)); iter.hasNext();) {

        List<String> tokens = tokenizeSentence(iter.nextLine());

        LOG.trace(String.format("Current sentence: %s", StringUtils.abbreviate(tokens.toString(), 200)));
        if (tokens.size() < getLanguageModel().getOrder()) {
            LOG.trace("Too few tokens.");
            continue;
        }
        List<String>[] current_ngrams = getNgramSequenceFromSentence(tokens);

        LOG.trace(String.format("Current ngrams: %s",
                StringUtils.abbreviate(Arrays.toString(current_ngrams), 200)));
        if (ngrams == null)
            ngrams = current_ngrams;
        else
            ngrams = ArrayUtils.getConcatinatedArray(ngrams, current_ngrams);
    }
    LOG.trace(String.format("Ngrams for text: %n\t'%s'%n\t%s ", StringUtils.abbreviate(text, 200),
            StringUtils.abbreviate(Arrays.toString(ngrams), 200)));
    return ngrams;
}

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From source file:com.meltmedia.cadmium.core.meta.MimeTypeConfigProcessor.java

static void addDefaultMimeTypes(Map<String, String> mimeTypeMap)
        throws IllegalArgumentException, UnsupportedEncodingException {
    InputStream in = null;/*  w  w w  . ja  v  a  2s  . co m*/
    try {
        in = MimeTypeConfigProcessor.class.getResourceAsStream("mime.types");
        if (in == null) {
            log.warn("The default mime type file is missing.");
            return;
        }
        LineIterator lineIterator = new LineIterator(new InputStreamReader(in, "UTF-8"));
        while (lineIterator.hasNext()) {
            String line = lineIterator.next();
            line = line.replaceAll("(\\A[^#]*)(#.*)?\\Z", "$1").trim(); // kill comments.
            if (line.length() == 0)
                continue; // skip blank lines.
            String[] parts = line.split("\\s+");
            if (parts.length < 2)
                continue; // skip lines with no extensions.
            String type = parts[0];
            for (int i = 1; i < parts.length; i++) {
                mimeTypeMap.put(parts[i], type);
            }
        }
    } finally {
        IOUtils.closeQuietly(in);
    }
}

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From source file:mitm.common.postfix.PostfixMainConfigParser.java

private static List<String> normalize(Reader config) {
    List<String> lines = new LinkedList<String>();

    LineIterator it = new LineIterator(config);

    String line = "";

    try {//from w  w  w .  jav  a  2 s .co m
        while (it.hasNext()) {
            String nextLine = it.nextLine();

            Matcher matcher = CONTINUATION.matcher(nextLine);

            if (!nextLine.trim().startsWith("#") && matcher.matches()) {
                /* its a continuation line */
                line = line + LF + nextLine;
            } else {
                matcher = NAME_VALUE.matcher(nextLine);

                if (matcher.matches()) {
                    /* its a name/value line */

                    if (StringUtils.isNotEmpty(line)) {
                        /* store the previous line because it is finished */
                        lines.add(line);
                    }

                    line = nextLine;
                } else {
                    /* it's some other line like a comment */
                    if (StringUtils.isNotEmpty(line)) {
                        /* store the previous line because it is finished */
                        lines.add(line);
                    }
                    lines.add(nextLine);

                    line = "";
                }
            }
        }
        if (StringUtils.isNotEmpty(line)) {
            lines.add(line);
        }
    } finally {
        LineIterator.closeQuietly(it);
    }

    return lines;
}

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From source file:com.mewmew.fairy.v1.book.Join.java

@Override
protected ObjectPipe<Map<String, Object>, Map<String, Object>> createPipe() {
    try {/*w w w .j a  va  2  s  . c o m*/
        return new BaseObjectPipe<Map<String, Object>, Map<String, Object>>(
                new com.mewmew.fairy.v1.json.map.Join(
                        new SimpleJsonIterator(new LineIterator(new FileReader(join))), key));
    } catch (IOException e) {
        throw new RuntimeException(e);
    }
}

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