fr.ens.transcriptome.aozan.io.CasavaDesignXLSReader.java Source code

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Here is the source code for fr.ens.transcriptome.aozan.io.CasavaDesignXLSReader.java

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/*
 *                  Aozan development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU General Public License version 3 or later 
 * and CeCILL. This should be distributed with the code. If you 
 * do not have a copy, see:
 *
 *      http://www.gnu.org/licenses/gpl-3.0-standalone.html
 *      http://www.cecill.info/licences/Licence_CeCILL_V2-en.html
 *
 * Copyright for this code is held jointly by the Genomic platform
 * of the Institut de Biologie de l'cole Normale Suprieure and
 * the individual authors. These should be listed in @author doc
 * comments.
 *
 * For more information on the Aozan project and its aims,
 * or to join the Aozan Google group, visit the home page at:
 *
 *      http://www.transcriptome.ens.fr/aozan
 *
 */

package fr.ens.transcriptome.aozan.io;

import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;

import org.apache.poi.hssf.usermodel.HSSFCell;
import org.apache.poi.hssf.usermodel.HSSFRow;
import org.apache.poi.hssf.usermodel.HSSFSheet;
import org.apache.poi.hssf.usermodel.HSSFWorkbook;
import org.apache.poi.poifs.filesystem.POIFSFileSystem;
import org.apache.poi.ss.usermodel.Cell;
import org.apache.poi.ss.usermodel.Row;

import com.google.common.math.DoubleMath;

import fr.ens.transcriptome.eoulsan.illumina.CasavaDesign;
import fr.ens.transcriptome.eoulsan.illumina.io.AbstractCasavaDesignTextReader;

/**
 * This class reads a Casava design file in xls format.
 * @since 0.1
 * @author Laurent Jourdren
 */
public class CasavaDesignXLSReader extends AbstractCasavaDesignTextReader {

    private final InputStream is;

    @Override
    public CasavaDesign read() throws IOException {

        // create a POIFSFileSystem object to read the data
        final POIFSFileSystem fs = new POIFSFileSystem(this.is);

        // Create a workbook out of the input stream
        final HSSFWorkbook wb = new HSSFWorkbook(fs);

        // Get a reference to the worksheet
        final HSSFSheet sheet = wb.getSheetAt(0);

        // When we have a sheet object in hand we can iterator on
        // each sheet's rows and on each row's cells.
        final Iterator<Row> rows = sheet.rowIterator();
        final List<String> fields = new ArrayList<>();

        while (rows.hasNext()) {
            final HSSFRow row = (HSSFRow) rows.next();
            final Iterator<Cell> cells = row.cellIterator();

            while (cells.hasNext()) {
                final HSSFCell cell = (HSSFCell) cells.next();
                while (fields.size() != cell.getColumnIndex()) {
                    fields.add("");
                }

                // Convert cell value to String
                fields.add(parseCell(cell));
            }

            // Parse the fields
            if (!isFieldsEmpty(fields)) {
                parseLine(fields);
            }
            fields.clear();

        }

        this.is.close();

        return getDesign();
    }

    /**
     * Parse the content of a cell.
     * @param cell cell to parse
     * @return a String with the cell content
     */
    private static String parseCell(final HSSFCell cell) {

        if (cell.getCellType() == Cell.CELL_TYPE_NUMERIC) {
            final double doubleValue = cell.getNumericCellValue();

            if (DoubleMath.isMathematicalInteger(doubleValue)) {
                return Long.toString((long) doubleValue);
            }
        }

        return cell.toString();
    }

    /**
     * Test if all the elements of a list are empty.
     * @param list the list to test
     * @return true if all the elements of the list are empty
     */
    private static boolean isFieldsEmpty(final List<String> list) {

        if (list == null) {
            return true;
        }

        for (final String e : list) {
            if (e != null && !"".equals(e.trim())) {
                return false;
            }
        }

        return true;
    }

    //
    // Constructors
    //

    /**
     * Public constructor.
     * @param is InputStream to use
     */
    public CasavaDesignXLSReader(final InputStream is) {

        if (is == null) {
            throw new NullPointerException("InputStream is null");
        }

        this.is = is;
    }

    /**
     * Public constructor.
     * @param file File to use
     */
    public CasavaDesignXLSReader(final File file) throws FileNotFoundException {

        if (file == null) {
            throw new NullPointerException("File is null");
        }

        if (!file.isFile()) {
            throw new FileNotFoundException("File not found: " + file.getAbsolutePath());
        }

        this.is = new FileInputStream(file);
    }

    /**
     * Public constructor.
     * @param filename Filename to use
     */
    public CasavaDesignXLSReader(final String filename) throws FileNotFoundException {

        this(new File(filename));
    }

}