Example usage for java.io Reader toString

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:org.intermine.bio.dataconversion.XenmineConverter.java

/**
 * //from  ww w. j  a v  a2  s  . c om
 * @param reader
 * @throws Exception
 * @throws ObjectStoreException
 */
private void processGenePageFile(Reader preader) throws Exception, ObjectStoreException {

    /* XB-GENEPAGE ID     
     * XB-GENE IDs for tropicalis and laevis   
     * The XB-GENE IDs are comma-separated
     * It seems like first one is tropicals, rest are laevis (a & b) 
     */
    System.out.println("Processing Gene Page 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 < 2) {
            LOG.error("Couldn't process line. Expected 2 cols, but was " + line.length);
            continue;
        }

        String genePageName = line[0].trim().substring(12);
        String geneIds = line[1].trim();

        if (geneIds.indexOf(",") != -1) {
            String[] refs = geneIds.split(",");
            for (int i = 0; i < refs.length; i++) {
                addGenePageId(refs[i], genePageName);
            }

        } else {
            addGenePageId(geneIds, genePageName);
        }

    }
    preader.close();

    //print out contents
    for (Map.Entry<String, HashSet> entry : genesPageName.entrySet()) {
        System.out.printf("Key : %s and Value: %s %n", entry.getKey(), entry.getValue());
    }

}

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

/**
 * //  w  w w. j  a v  a2s  .  c om
 * @param reader
 * @throws Exception
 * @throws ObjectStoreException
 */

private void processSynFile(Reader preader) throws Exception, ObjectStoreException {

    /* Xenbase gene ID     
     * gene symbol    
     *  gene name     
     *  gene function -- will store as description    
     *  gene synonyms    
     *  JGI ID  -- missing from the file --not required
     */

    System.out.println("Processing Synonym 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 < 5) {
            LOG.error("Couldn't process line. Expected 5 cols, but was " + line.length);
            continue;
        }

        String genePageId = line[0].trim().substring(12);
        String symbol = line[1].trim();
        String name = line[2].trim();
        String desc = line[3].trim();
        String synonyms = line[4].trim();

        HashSet geneIds = genesPageName.get(genePageId);
        Iterator it = geneIds.iterator();

        while (it.hasNext()) {

            String geneId = (String) it.next();
            Item gene = genes.get(geneId);

            if (gene != null) {

                if (desc != null && !StringUtils.isEmpty(desc)) {
                    gene.setAttribute("briefDescription", desc);
                }

                if (synonyms != null && !StringUtils.isEmpty(synonyms)) {

                    gene.setAttribute("alias", synonyms);

                    if (synonyms.indexOf("|") != -1) {
                        String[] syns = synonyms.split("\\|");
                        for (int i = 0; i < syns.length; i++) {
                            getSynonym(gene.getIdentifier(), syns[i]);
                        }
                    } else {
                        getSynonym(gene.getIdentifier(), synonyms);
                    }

                }

            } else {
                System.out
                        .println("gene page id for a gene that is not laoded in the prev file.." + genePageId);
            }

        }

    }

    preader.close();

}

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

public void testProcess() throws Exception {

    Reader reader = new InputStreamReader(getClass().getClassLoader().getResourceAsStream("2xpatres.txt"));
    System.out.println("***" + reader.toString());

    converter.process(reader);/*from www  .  j a va2s  . c  om*/
    converter.close();

    // uncomment to write out a new target items file
    writeItemsFile(itemWriter.getItems(), "ZfinExpression-tgt-items.xml");

    Set expected = readItemSet("ZfinExpression-tgt-items.xml");

    assertEquals(expected, itemWriter.getItems());
}