Mercurial > repos > yufei-luo > s_mart
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 |
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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 @@ -0,0 +1,90 @@ +/** + * + * 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; + } +} + +