guineu.data.parser.impl.ParserXLS.java Source code

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Here is the source code for guineu.data.parser.impl.ParserXLS.java

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/*
 * Copyright 2007-2013 VTT Biotechnology
 * This file is part of Guineu.
 *
 * Guineu is free software; you can redistribute it and/or modify it under the
 * terms of the GNU General Public License as published by the Free Software
 * Foundation; either version 2 of the License, or (at your option) any later
 * version.
 *
 * Guineu is distributed in the hope that it will be useful, but WITHOUT ANY
 * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
 * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License along with
 * Guineu; if not, write to the Free Software Foundation, Inc., 51 Franklin St,
 * Fifth Floor, Boston, MA 02110-1301 USA
 */
package guineu.data.parser.impl;

import java.io.FileInputStream;
import java.io.IOException;
import java.util.Iterator;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.apache.poi.hssf.usermodel.HSSFCell;
import org.apache.poi.hssf.usermodel.HSSFCellStyle;
import org.apache.poi.hssf.usermodel.HSSFFont;
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.hssf.util.HSSFColor;
import org.apache.poi.poifs.filesystem.POIFSFileSystem;

/**
 *
 * @author scsandra
 */
public abstract class ParserXLS {

    public HSSFWorkbook openExcel(String file_name) throws IOException {
        FileInputStream fileIn = null;
        try {
            HSSFWorkbook wb;
            POIFSFileSystem fs;
            fileIn = new FileInputStream(file_name);
            fs = new POIFSFileSystem(fileIn);
            wb = new HSSFWorkbook(fs);
            return wb;
        } finally {
            if (fileIn != null) {
                fileIn.close();
            }
        }
    }

    //get the number of rows to read in the excel file
    public int getNumberRows(int init, HSSFSheet sheet) {
        Iterator rowIt = sheet.rowIterator();
        int num = 0;

        while (rowIt.hasNext()) {
            HSSFRow row = (HSSFRow) rowIt.next();
            HSSFCell cell;
            cell = row.getCell(0);
            if ((cell == null || cell.getCellType() == HSSFCell.CELL_TYPE_BLANK) && row.getRowNum() > init) {
                break;
            }
            num = row.getRowNum();
        }
        return num - init;
    }

    /*
     *return 0 if the cell is blank, boolean or its color is red
     *return 2 if the cell is string  
     *return 1 if the cell is numeric or formula
     */
    public int v_type(HSSFWorkbook wb, HSSFRow row, HSSFCell cell) {
        switch (cell.getCellType()) {
        case HSSFCell.CELL_TYPE_BLANK:
            System.out.println(" Error - Row: " + row.getRowNum() + " Cell: " + cell.getColumnIndex()
                    + "  - Cell type Blank  - " + cell.toString());
            return 0;
        case HSSFCell.CELL_TYPE_BOOLEAN:
            System.out.println(" Error - Row: " + row.getRowNum() + " Cell: " + cell.getColumnIndex()
                    + "  - Cell type boolean  - " + cell.toString());
            return 0;
        case HSSFCell.CELL_TYPE_FORMULA:
            System.out.println(" Error - Row: " + row.getRowNum() + " Cell: " + cell.getColumnIndex()
                    + "  - Cell type formula  - " + cell.toString());
            return 1;
        case HSSFCell.CELL_TYPE_NUMERIC:
            HSSFCellStyle style = cell.getCellStyle();
            HSSFFont font = wb.getFontAt(style.getFontIndex());
            if (font.getColor() == (new HSSFColor.RED().getIndex())) {
                return 0;
            }
            return 1;
        case HSSFCell.CELL_TYPE_STRING:
            style = cell.getCellStyle();
            font = wb.getFontAt(style.getFontIndex());
            if (font.getColor() == (new HSSFColor.RED().getIndex())) {
                return 0;
            }
            return 2;
        default:
            return 0;
        }
    }

    //get the name experiment from the name of the excel file
    public String getDatasetName(String file_name) {
        Pattern pat = Pattern.compile("[\\\\/]");
        Matcher matcher = pat.matcher(file_name);
        int index = 0;
        while (matcher.find()) {
            index = matcher.start();
        }
        String n = file_name.substring(index + 1, file_name.length() - 4);
        return n;
    }

    //replace all patterns in str string to string replace
    public String replace(String str, String pattern, String replace) {
        Pattern pat = Pattern.compile(pattern);
        Matcher matcher = pat.matcher(str);
        if (matcher.find()) {
            str = matcher.replaceAll(replace);
        }
        return str;
    }
}