Mercurial > repos > yufei-luo > s_mart
diff smart_toolShed/SMART/Java/FormatsReader.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/FormatsReader.java Thu Jan 17 10:52:14 2013 -0500 @@ -0,0 +1,83 @@ +/** + * + * 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.*; +import java.io.File; +import java.io.*; + + +public class FormatsReader { + + String fileName; + Vector < FormatType > formatTypes; + Vector < String > typeNames; + + + public FormatsReader(String fileName) { + this.fileName = fileName; + this.formatTypes = new Vector < FormatType > (); + } + + + public boolean read() { + File file = new File(this.fileName); + + try { + BufferedReader reader = new BufferedReader(new FileReader(file)); + String line = null; + String[] lineElements; + String[] formats; + String typeName; + + while ((line = reader.readLine()) != null) { + if (line.length() > 0) { + lineElements = line.split(":"); + typeName = lineElements[0].trim(); + formats = lineElements[1].split(","); + for (int i = 0; i < formats.length; i++) { + Global.formats.addFormat(typeName, formats[i].trim()); + } + } + } + + reader.close(); + } + catch (FileNotFoundException e) { + return false; + } + catch (IOException e) { + return false; + } + + return true; + } +} +