annotate smart_toolShed/SMART/Java/Files.java @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

/**
 *
 * Copyright INRA-URGI 2009-2010
 * 
 * This software is governed by the CeCILL license under French law and
 * abiding by the rules of distribution of free software. You can use,
 * modify and/ or redistribute the software under the terms of the CeCILL
 * license as circulated by CEA, CNRS and INRIA at the following URL
 * "http://www.cecill.info".
 * 
 * As a counterpart to the access to the source code and rights to copy,
 * modify and redistribute granted by the license, users are provided only
 * with a limited warranty and the software's author, the holder of the
 * economic rights, and the successive licensors have only limited
 * liability.
 * 
 * In this respect, the user's attention is drawn to the risks associated
 * with loading, using, modifying and/or developing or reproducing the
 * software by the user in light of its specific status of free software,
 * that may mean that it is complicated to manipulate, and that also
 * therefore means that it is reserved for developers and experienced
 * professionals having in-depth computer knowledge. Users are therefore
 * encouraged to load and test the software's suitability as regards their
 * requirements in conditions enabling the security of their systems and/or
 * data to be ensured and, more generally, to use and operate it in the
 * same conditions as regards security.
 * 
 * The fact that you are presently reading this means that you have had
 * knowledge of the CeCILL license and that you accept its terms.
 *
 */
import java.util.*;

public class Files {
  HashMap <String, File> files;  

  public Files () {
    files = new HashMap < String, File> ();
  }

  public void addFile(String fileName, String type, String format) {
    this.addFile(new File(fileName, type, format));
  }

  public void addFile(File file) {
    files.put(file.name, file);
  }

  public void clear() {
    files.clear();
  }

  public String getType(String fileName) {
    if (fileName == null) {
      System.out.println("Error! Looking for format of empty file name!");
    }
    if (! files.containsKey(fileName)) {
      System.out.println("Oops! Format type of file " + fileName + " is not found!");
      return null;
    }
    return files.get(fileName).formatType;
  }

  public String getFormat(String fileName) {
    if (fileName == null) {
      System.out.println("Error! Looking for format of empty file name!");
    }
    if (! files.containsKey(fileName)) {
      System.out.println("Oops! Format of file " + fileName + " is not found!");
      return null;
    }
    return files.get(fileName).format;
  }
}