Examples of CSVReader

Examples of info.unipax.bina.analysis.data.csv.CsvReader

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  {
    final File file = pageGeneData.getSelectedFile();     
    if (file != null){   
      if (controller != null)
      {       
        CsvReader reader = (CsvReader) new CsvReaderFactory().getReader(session, file);
        try
        {
          reader.readHeader(task);
          SeriesFilterSettingsEditor settingsEditor = reader.getSettingsEditor();
     
          if (settingsEditor != null)
          {
            String title = "Select settings for gene expresion data";
            final SeriesFilterSettingsDialog dialog = new SeriesFilterSettingsDialog(session.getMainWindow(), settingsEditor, title);
 
            class DialogRunner implements Runnable
            {
              private boolean approved = false;
 
              @Override
              public void run()
              {
                approved = dialog.showDialog();
              }
            }
 
            DialogRunner runner = new DialogRunner();
 
            try
            {
              SwingUtilities.invokeAndWait(runner);
            }
            catch (InterruptedException e)
            {
              e.printStackTrace();
            }
            catch (InvocationTargetException e)
            {         
              e.printStackTrace();
            }
            if (!runner.approved)
            return;
            settingsEditor.settingsApproved();
          }
          Core.getProcessManager().showDialog();
       
          //ImportConfiguration config = reader.getConfig();
          //config.setColumnTypes(new String[]{"ignore","ids","ignore","ignore","values"});
           
          reader.readData(task);
       
          if (reader.getSeries() != null) {
            seriesRegistry.registerSeries(reader.getSeries());
 
            LinearColorMapper colorMapper = new LinearColorMapper(new Color[]{Color.BLUE,Color.WHITE,Color.RED} );
            DefaultMapping mapping = new DefaultMapping(controller, "UDIS", BasicProteinComponentUI.BACKGROUNDCOLOR_MAPPING_POINT,colorMapper); 
 
            SeriesMappingConfiguration mappingConfig = new SeriesMappingConfiguration(DoubleVector.class, reader.getSeries());
            mappingConfig.setSelectedSamples(reader.getSeries().getSample(0));
            mappingConfig.setMappingTargetTranslator(controller.getMappingModel().createExternalIdentifierTranslator("NCBI-GeneID"));
           
 
            SeriesMappingValueProvider seriesMappingValueProvider = new SeriesMappingValueProvider(session, mappingConfig, controller.getMappingTargetTranslators());
            mapping.setValueProvider(seriesMappingValueProvider);
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Examples of liquibase.util.csv.CSVReader

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    @Override
    public List<RanChangeSet> getRanChangeSets() throws DatabaseException {
        FileReader reader = null;
        try {
            reader = new FileReader(this.changeLogFile);
            CSVReader csvReader = new CSVReader(reader);
            String[] line = csvReader.readNext();
            if (!line[COLUMN_ID].equals("ID")) {
                throw new DatabaseException("Missing header in file "+this.changeLogFile.getAbsolutePath());
            }

            List<RanChangeSet> returnList = new ArrayList<RanChangeSet>();
            while ((line = csvReader.readNext()) != null) {
                returnList.add(new RanChangeSet(
                        line[COLUMN_FILENAME],
                        line[COLUMN_ID],
                        line[COLUMN_AUTHOR],
                        CheckSum.parse(line[COLUMN_MD5SUM]),
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Examples of liquibase.util.csv.opencsv.CSVReader

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            for (Map.Entry<String, List<String>> entry : result.entrySet()) {
                List<String> values = new ArrayList<String>(entry.getValue());
                String columns = values.remove(0);
                for (String line : values) {
                    System.out.print("<" + entry.getKey() + " ");
                    CSVReader columnNames = new CSVReader(new StringReader(columns));
                    CSVReader columnValues = new CSVReader(new StringReader(line));
                    String[] columnValueItems = columnValues.readNext();
                    String[] columnNameItems = columnNames.readNext();

                    for (int i = 0; i < columnNameItems.length; i++) {
                        if (!columnValueItems[i].equals("NULL")) {
                            System.out.print(columnNameItems[i] + "=\"" + columnValueItems[i].replaceAll("&", "&amp;") + "\" ");
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Examples of net.datacrow.util.CSVReader

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    }
   
    @Override
    protected void initialize() throws Exception {
        InputStreamReader reader = new InputStreamReader(new FileInputStream(file), getCharacterSet());
        CSVReader csvReader = new CSVReader(reader, getSeperator());
        String[] headers = csvReader.readNext();
       
        Collection<String> fields = new ArrayList<String>();
        for (String field : headers)
            fields.add(field);
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Examples of net.datacrow.util.CSVReader

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                String characterSet = getCharacterSet();
                String seperator = getSeperator();
                seperator = seperator == null || seperator.equals("TAB") ? "\t" : seperator;
               
                InputStreamReader reader = new InputStreamReader(new FileInputStream(file), characterSet);
                CSVReader csvReader = new CSVReader(reader, seperator);

                List<String[]> lines = csvReader.readAll();                       
                listener.notifyStarted(lines.size() - 1);
               
                int counter = -1;
                for (String[] values : lines) {
                    counter++;
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Examples of net.geco.model.iocsv.CsvReader

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  private CsvWriter writer;
 
  public RegistryBuilder(Factory factory) {
    super(factory);
    this.reader = new CsvReader();
    this.writer = new CsvWriter();
  }
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Examples of net.sf.csv4j.CSVReader

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    public void init(Resource csvResource, boolean containsHeader,
      String mappingDefinition) {
  this.mappingDefinition = mappingDefinition;

  try {
      csvReader = new CSVReader(new BufferedReader(new InputStreamReader(
        csvResource.getInputStream())));
      if (containsHeader) {
    csvReader.readLine();
      }
  } catch (Exception e) {
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Examples of net.sf.jmatchparser.util.csv.CSVReader

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  @Override
  public String format(String content, PrintStream debugStream) throws IOException {
    if (content.length() == 0)
      return content;
    CSVReader csvr = new CSVReader(new StringReader(content));
    String[] row;
    StringBuilder result = new StringBuilder();
    while ((row = csvr.read()) != null) {
      for (String cell : row) {
        result.append(":" + cell + "\n");
      }
      result.append("-\n");
    }
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Examples of no.priv.garshol.duke.utils.CSVReader

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  public void setMappingFile(String filename) {
    mapping = new HashMap();
   
    // FIXME: character encoding?
    try {
      CSVReader csv = new CSVReader(new FileReader(filename));

      String[] row = csv.next();
      while (row != null) {
        mapping.put(row[0], row[1]);
        row = csv.next();
      }
     
      csv.close();
    } catch (IOException e) {
      throw new DukeException("Error loading mapping file " + filename, e);
    }
  } 
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Examples of org.apache.flink.api.java.io.CsvReader

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   *
   * @param filePath The path of the CSV file.
   * @return A CsvReader that can be used to configure the CSV input.
   */
  public CsvReader readCsvFile(String filePath) {
    return new CsvReader(filePath, this);
  }
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