diff smart_toolShed/SMART/Java/FormatsContainer.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/FormatsContainer.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 FormatsContainer {
+
+  HashMap < String, FormatType > formatTypes;
+
+
+  public FormatsContainer() {
+    this.formatTypes = new HashMap < String, FormatType > ();
+  }
+
+
+  public void addFormat(String type, String format) {
+    FormatType formatType;
+    if (formatTypes.containsKey(type)) {
+      formatType = this.formatTypes.get(type);
+    }
+    else {
+      formatType = new FormatType(type);
+      this.formatTypes.put(type, formatType);
+    }
+    formatType.addFormat(format);
+  }
+
+
+  public Vector < String > getFormatTypes () {
+    Vector < String > v = new Vector < String > ();
+    v.addAll(this.formatTypes.keySet());
+    return v;
+  }
+
+
+  public FormatType getFormats (String type) {
+    if (! formatTypes.containsKey(type)) {
+      System.out.print("Format type " + type + " is unavailable. Got: ");
+      Iterator it = formatTypes.entrySet().iterator();
+      while (it.hasNext()) {
+        Map.Entry pairs = (Map.Entry) it.next();
+        System.out.print(pairs.getKey() + " ");
+      }
+      System.out.println();
+    }
+    return formatTypes.get(type);
+  }
+
+
+  public String getFormatType (String format) {
+    for (Iterator it = formatTypes.keySet().iterator(); it.hasNext(); ) {
+      Object type       =  it.next();
+      Object formatType = formatTypes.get(type);
+      if (((FormatType) formatType).containsFormat(format)) {
+        return (String) type;
+      }
+    }
+    return null;
+  }
+}
+
+