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

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Files.java	Thu Jan 17 10:52:14 2013 -0500
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+/**
+ *
+ * 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;
+  }
+}
+