Example usage for java.io Reader toString

List of usage examples for java.io Reader toString

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Introduction

In this page you can find the example usage for java.io Reader toString.

Prototype

public String toString()

Source Link

Document

Returns a string representation of the object.

Usage

From source file:Main.java

/**
 * Creates a DOM from a file representation of an xml record
 * /*  w  ww.jav a2s  .  com*/
 * @param reader
 *            the xml reader
 * @return the DOM document
 */
public static Document parseDom(Reader reader) {
    try {
        DocumentBuilder builder = factory.newDocumentBuilder();
        return builder.parse(new org.xml.sax.InputSource(reader));
    } catch (Exception e) {
        throw new RuntimeException("Could not parse DOM for '" + reader.toString() + "'!", e);
    }
}

From source file:com.mmj.app.lucene.analyzer.JcsegWordAnalyzer.java

@SuppressWarnings("unused")
@Override/* w w w . ja  va 2  s.co  m*/
public List<String> splitWords(Reader input, SegMode segMode) {
    List<String> result = new ArrayList<String>();
    if (seg == null) {
        return Arrays.asList(input.toString());
    }
    // jcseg?
    Object[] paras = createParas(false);
    IWord word = null;
    try {
        seg.reset(input);
        while ((word = seg.next()) != null) {
            result.add(word.getValue());
        }
    } catch (Exception e) {
        logger.error(e.getMessage(), e);
    }
    return result;
}

From source file:com.abstratt.mdd.internal.frontend.textuml.TextUMLCompiler.java

private Start parse(Reader source, IProblemTracker problems) throws CoreException {
    ProblemBuilder<Node> problemBuilder = new ProblemBuilder<Node>(problems, new SCCTextUMLSourceMiner());
    PushbackReader in = new PushbackReader(source, 64 * 1024);
    Lexer lexer = new Lexer(in);
    Parser parser = new Parser(lexer);
    try {/*from w w  w .ja v a  2s  . co  m*/
        return parser.parse();
    } catch (ParserException e) {
        if (problems != null)
            problemBuilder.addProblem(
                    new SyntaxProblem("Found: '" + e.getToken().getText() + "'. " + e.getMessage()),
                    e.getToken());
    } catch (LexerException e) {
        if (problems != null) {
            SyntaxProblem problem = new SyntaxProblem(e.getMessage());
            problem.setAttribute(IProblem.LINE_NUMBER, SCCTextUMLSourceMiner.parseLineNumber(e.getMessage()));
            problemBuilder.addProblem(problem, null);
        }
    } catch (IOException e) {
        IStatus status = new Status(IStatus.ERROR, TextUMLConstants.PLUGIN_ID, 0,
                "Error reading source unit: " + source.toString(), e);
        throw new CoreException(status);
    } finally {
        try {
            in.close();
        } catch (IOException e) {
            // not interested in failures while closing
        }
    }
    return null;
}

From source file:org.echocat.adam.configuration.ConfigurationMarshaller.java

@Nullable
public static Configuration unmarshall(@Nonnull Reader content, @Nullable String systemId) {
    try {// w  w w.  j  av  a  2s  . com
        final Unmarshaller unmarshaller = unmarshallerFor(content, systemId);
        final InputSource source = new InputSource(content);
        source.setSystemId(systemId != null ? systemId : "<unknownSource>");
        return (Configuration) unmarshaller.unmarshal(source);
    } catch (final UnmarshalException e) {
        throw new ParseException(e, (systemId != null ? systemId : content.toString()));
    } catch (final JAXBException e) {
        throw new ConfigurationException("Could not unmarshall: " + (systemId != null ? systemId : content), e);
    }
}

From source file:org.intermine.bio.dataconversion.XenmineConverter.java

/**
 * /*w ww .  j  a va2 s . c o m*/
 * @param reader
 * @throws Exception
 * @throws ObjectStoreException
 */
private void processScaffoldMappingFile(Reader preader, String genomeBuild)
        throws Exception, ObjectStoreException {

    /*    Xenbase gene ID       
     * gene symbol    
     *  JGI Model Name    
     *  JGI Scaffold Name   
     *  JGI Scaffold Start Position   
     *  JGI Scaffold End Position   
     *  JGI Scaffold Strand    
     *  GenePageToJgiTropicalisScaffoldMapping_4.1.txt:XB-GENE-1021745   c1orf228   e_gw1.1.454.1   scaffold_1   4235   14986   -1
     */
    System.out.println("Processing scaffold file....");

    Iterator<?> tsvIter;
    try {
        tsvIter = FormattedTextParser.parseTabDelimitedReader(preader);
    } catch (Exception e) {
        throw new Exception("cannot parse file: " + preader.toString(), e);
    }

    Item organism = createItem("Organism");
    organism.setAttribute("taxonId", TAXON_ID);
    organism.setAttribute("genus", "Xenopus");
    organism.setAttribute("species", "tropicalis");
    organism.setAttribute("name", "Xenopus tropicalis");
    organism.setAttribute("shortName", "X. tropicalis");
    store(organism);

    while (tsvIter.hasNext()) {

        String[] line = (String[]) tsvIter.next();

        if (line.length < 7) {
            LOG.error("Couldn't process line. Expected 7 cols, but was " + line.length);
            continue;
        }

        String xbGeneId = line[0].trim();
        String symbol = line[1].trim();
        String jgimodelName = line[2].trim();
        String chromosome = line[3].trim();
        String start = line[4].trim();
        String end = line[5].trim();
        String strand = line[6].trim();
        String length = getLength(start, end);

        Item gene = createItem("Gene");
        gene.setAttribute("primaryIdentifier", jgimodelName);
        gene.setAttribute("secondaryIdentifier", xbGeneId);
        gene.setAttribute("symbol", symbol);
        gene.setAttribute("genomeBuild", genomeBuild);

        String chrRefId = getChromosome(chromosome, organism.getIdentifier());
        gene.setReference("chromosome", chrRefId);
        String locationRefId = getLocation(gene, chrRefId, start, end, strand);
        gene.setReference("chromosomeLocation", locationRefId);

        gene.setAttribute("jgiModelName", jgimodelName);
        gene.setReference("organism", organism);

        genes.put(xbGeneId, gene);

    }

    preader.close();

}

From source file:org.intermine.bio.dataconversion.XenmineConverter.java

/**
 * /*from www . j av a 2  s . c  o  m*/
 * @param reader
 * @throws Exception
 * @throws ObjectStoreException
 */
private void processLaevisScaffoldMappingFile(Reader preader, String genomeBuild)
        throws Exception, ObjectStoreException {

    /*    Xenbase gene ID       
     * gene symbol    
     *  JGI Model Name    
     *  JGI Scaffold Name   
     *  JGI Scaffold Start Position   
     *  JGI Scaffold End Position   
     *  JGI Scaffold Strand    
     *  XB-GENE-478732  impdh2  XeXenL6RMv10052779m.g   Scaffold87688   113849  139524  -1
     */
    System.out.println("Processing laevis scaffold file....");

    Iterator<?> tsvIter;
    try {
        tsvIter = FormattedTextParser.parseTabDelimitedReader(preader);
    } catch (Exception e) {
        throw new Exception("cannot parse file: " + preader.toString(), e);
    }

    Item organism = createItem("Organism");
    organism.setAttribute("taxonId", "8355");
    organism.setAttribute("genus", "Xenopus");
    organism.setAttribute("species", "laevis");
    organism.setAttribute("name", "Xenopus laevis");
    organism.setAttribute("shortName", "X. laevis");
    store(organism);

    while (tsvIter.hasNext()) {

        String[] line = (String[]) tsvIter.next();

        if (line.length < 7) {
            LOG.error("Couldn't process line. Expected 7 cols, but was " + line.length);
            continue;
        }

        String xbGeneId = line[0].trim();
        String symbol = line[1].trim();
        String jgimodelName = line[2].trim();
        String chromosome = line[3].trim();
        String start = line[4].trim();
        String end = line[5].trim();
        String strand = line[6].trim();
        String length = getLength(start, end);

        Item gene = createItem("Gene");
        gene.setAttribute("primaryIdentifier", jgimodelName);
        gene.setAttribute("secondaryIdentifier", xbGeneId);
        if (!symbol.equalsIgnoreCase("unnamed"))
            gene.setAttribute("symbol", symbol);
        gene.setAttribute("genomeBuild", genomeBuild);

        String chrRefId = getChromosome(chromosome, organism.getIdentifier());
        gene.setReference("chromosome", chrRefId);

        String locationRefId = getLocation(gene, chrRefId, start, end, strand);
        gene.setReference("chromosomeLocation", locationRefId);

        gene.setAttribute("jgiModelName", jgimodelName);
        gene.setReference("organism", organism);

        genes.put(xbGeneId, gene);

    }

    preader.close();

}

From source file:org.intermine.bio.dataconversion.XenmineConverter.java

/**
 * //from  w ww . jav a  2  s.c  om
 * @param reader
 * @throws Exception
 * @throws ObjectStoreException
 */
private void processNameFile(Reader preader, String genomeBuild) throws Exception, ObjectStoreException {

    /* model name     
     * Xenbase tropicalis gene ID     
     * gene symbol     
     * gene name   
     */
    System.out.println("Processing Names file....");

    Iterator<?> tsvIter;
    try {
        tsvIter = FormattedTextParser.parseTabDelimitedReader(preader);
    } catch (Exception e) {
        throw new Exception("cannot parse file: " + preader.toString(), e);
    }

    while (tsvIter.hasNext()) {

        String[] line = (String[]) tsvIter.next();

        if (line.length < 4) {
            LOG.error("Couldn't process line. Expected 4 cols, but was " + line.length);
            continue;
        }

        String jgimodelname = line[0].trim();
        String primaryIdentifier = line[1].trim();
        String symbol = line[2].trim();
        String name = line[3].trim();

        Item gene = genes.get(primaryIdentifier);

        if (gene != null) {
            gene.setAttribute("name", name);
        }

    }

    preader.close();

}

From source file:org.intermine.bio.dataconversion.XenmineConverter.java

/**
 * //from   w  ww.jav a 2  s .c  o m
 * @param reader
 * @throws Exception
 * @throws ObjectStoreException
 */
private void processNcbiProteinFile(Reader preader) throws Exception, ObjectStoreException {

    /* gi    
     * accession   
     * Xenbase gene ID     
     * gene symbol
     * 1000735 AAA84444        XB-GENE-865674  gsk3b
     */
    System.out.println("Processing NCBI-PROTEIN file....");

    Iterator<?> tsvIter;
    try {
        tsvIter = FormattedTextParser.parseTabDelimitedReader(preader);
    } catch (Exception e) {
        throw new Exception("cannot parse file: " + preader.toString(), e);
    }

    while (tsvIter.hasNext()) {

        String[] line = (String[]) tsvIter.next();

        if (line.length < 4) {
            LOG.error("Couldn't process line. Expected 4 cols, but was " + line.length);
            continue;
        }

        String gi = line[0].trim();
        String accession = line[1].trim();
        String xenbaseGeneId = line[2].trim();
        String symbol = line[3].trim();

        //System.out.println("identifier.." + gi + " accession    " + accession);
        Item gene = genes.get(xenbaseGeneId);

        if (gene != null) {
            getCrossReference(gene.getIdentifier(), gi, accession, "NCBI Protein");
        }

    }

    preader.close();

}

From source file:org.intermine.bio.dataconversion.XenmineConverter.java

/**
 * // ww  w  .  j  ava2s. c o m
 * @param reader
 * @throws Exception
 * @throws ObjectStoreException
 */
private void processUnigeneEntrezFile(Reader preader) throws Exception, ObjectStoreException {

    /* Xenbase gene ID     
     * gene symbol
     * Entrez ID
     * Unigene ID
     * XB-GENE-478054  trnt1   394602  Str.7616
     */
    System.out.println("Processing UNIGENE ENTREZ file....");

    Iterator<?> tsvIter;
    try {
        tsvIter = FormattedTextParser.parseTabDelimitedReader(preader);
    } catch (Exception e) {
        throw new Exception("cannot parse file: " + preader.toString(), e);
    }

    while (tsvIter.hasNext()) {

        String[] line = (String[]) tsvIter.next();

        if (line.length < 4) {
            LOG.error("Couldn't process line. Expected 4 cols, but was " + line.length);
            continue;
        }

        String xenbaseGeneId = line[0].trim();
        String symbol = line[1].trim();
        String entrezId = line[2].trim();
        String unigeneId = line[3].trim();

        Item gene = genes.get(xenbaseGeneId);

        if (gene != null) {
            if (StringUtils.isNotEmpty(entrezId))
                getCrossReference(gene.getIdentifier(), entrezId, "", "Entrez Gene ID");
            if (StringUtils.isNotEmpty(unigeneId))
                getCrossReference(gene.getIdentifier(), unigeneId, "", "Unigene ID");
        }

    }

    preader.close();

}

From source file:org.intermine.bio.dataconversion.XenmineConverter.java

/**
 * //w  w  w. jav a2  s . co  m
 * @param reader
 * @throws Exception
 * @throws ObjectStoreException
 */
private void processNcbiMrnaFile(Reader preader) throws Exception, ObjectStoreException {

    /* gi    
     * accession   
     * Xenbase gene ID     
     * gene symbol
     * 1000735 AAA84444        XB-GENE-865674  gsk3b
     */
    System.out.println("Processing NCBI-MRNA file....");

    Iterator<?> tsvIter;
    try {
        tsvIter = FormattedTextParser.parseTabDelimitedReader(preader);
    } catch (Exception e) {
        throw new Exception("cannot parse file: " + preader.toString(), e);
    }

    while (tsvIter.hasNext()) {

        String[] line = (String[]) tsvIter.next();

        if (line.length < 4) {
            LOG.error("Couldn't process line. Expected 4 cols, but was " + line.length);
            continue;
        }

        String gi = line[0].trim();
        String accession = line[1].trim();
        String xenbaseGeneId = line[2].trim();
        String symbol = line[3].trim();

        Item gene = genes.get(xenbaseGeneId);

        if (gene != null) {
            getCrossReference(gene.getIdentifier(), gi, accession, "NCBI mRNA");
        }

    }

    preader.close();

}