Mercurial > repos > yufei-luo > s_mart

comparison smart_toolShed/SMART/Java/ProgramFileReader.java @ 0:e0f8dcca02ed

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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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-1:000000000000 0:e0f8dcca02ed
1 /**
2 *
3 * Copyright INRA-URGI 2009-2010
4 *
5 * This software is governed by the CeCILL license under French law and
6 * abiding by the rules of distribution of free software. You can use,
7 * modify and/ or redistribute the software under the terms of the CeCILL
8 * license as circulated by CEA, CNRS and INRIA at the following URL
9 * "http://www.cecill.info".
10 *
11 * As a counterpart to the access to the source code and rights to copy,
12 * modify and redistribute granted by the license, users are provided only
13 * with a limited warranty and the software's author, the holder of the
14 * economic rights, and the successive licensors have only limited
15 * liability.
16 *
17 * In this respect, the user's attention is drawn to the risks associated
18 * with loading, using, modifying and/or developing or reproducing the
19 * software by the user in light of its specific status of free software,
20 * that may mean that it is complicated to manipulate, and that also
21 * therefore means that it is reserved for developers and experienced
22 * professionals having in-depth computer knowledge. Users are therefore
23 * encouraged to load and test the software's suitability as regards their
24 * requirements in conditions enabling the security of their systems and/or
25 * data to be ensured and, more generally, to use and operate it in the
26 * same conditions as regards security.
27 *
28 * The fact that you are presently reading this means that you have had
29 * knowledge of the CeCILL license and that you accept its terms.
30 *
31 */
32 import java.util.*;
33 import java.io.File;
34 import java.io.*;
35
36
37 public class ProgramFileReader {
38 String fileName;
39 Vector <Program> programs;
40
41
42 public ProgramFileReader(String fileName) {
43 this.fileName = fileName;
44 this.programs = new Vector <Program> ();
45 }
46
47
48 public boolean read() {
49 // File file = new File(this.fileName);
50 // Program program = null;
51 // int step = 0;
52 // TreeMap <String, ProgramOption> options = new TreeMap <String, ProgramOption> ();
53
54 // try {
55 // BufferedReader reader = new BufferedReader(new FileReader(file));
56 // String line = null;
57 // String section = null;
58
59 // while ((line = reader.readLine()) != null) {
60
61 // line = line.trim();
62
63 // if (line.length() == 0) {
64 // if (program != null) {
65 // programs.add(program);
66 // }
67 // program = null;
68 // step = 0;
69 // continue;
70 // }
71
72 // if ((line.charAt(0) == '[') && (line.charAt(line.length() - 1) == ']')) {
73 // section = line.substring(1, line.length() - 1).trim();
74 // continue;
75 // }
76 // switch (step) {
77 // case 0:
78 // program = new Program();
79 // program.setName(line);
80 // if (section == null) {
81 // System.out.println("Error! Section of program '" + line + "' is not set!");
82 // }
83 // program.setSection(section);
84 // step = 1;
85 // break;
86 // case 1:
87 // program.setShortName(line);
88 // step = 2;
89 // break;
90 // case 2:
91 // ProgramOption option = new ProgramOption();
92
93 // String[] elements = line.split(":");
94 // boolean input = elements[0].trim().equalsIgnoreCase("input")? true: false;
95 // String[] subElements = elements[1].split(";");
96 // String identifier = subElements[0].trim();
97
98 // option.setInput(input);
99
100 // if (input) {
101
102 // if (subElements.length < 4) {
103 // System.out.println("Line '" + line + "' is weird...");
104 // }
105
106 // String type = subElements[1].trim();
107 // String comment = subElements[2].trim();
108 // boolean compulsory = subElements[3].trim().equalsIgnoreCase("0")? false: true;
109
110 // option.setIdentifier(identifier);
111 // option.setType(type);
112 // option.setComment(comment);
113 // option.setCompulsory(compulsory);
114
115 // if ("file".compareToIgnoreCase(type) == 0) {
116 // if (subElements.length < 5) {
117 // System.out.println("Line '" + line + "' is weird...");
118 // }
119
120 // String formatIdentifier = subElements[4].trim();
121 // option.setFormatIdentifier(formatIdentifier);
122 // }
123 // else if ("choice".compareToIgnoreCase(type) == 0) {
124 // if (subElements.length < 5) {
125 // System.out.println("Line '" + line + "' is weird...");
126 // }
127
128 // String[] choices = subElements[4].trim().split(",");
129 // for (int i = 0; i < choices.length; i++) {
130 // choices[i] = choices[i].trim();
131 // }
132 // option.setChoices(choices);
133 // }
134 // options.put(identifier, option);
135 // }
136 // else {
137 // String format = subElements[1].trim();
138
139 // option.setFormat(format);
140 // option.setAssociatedOption(options.get(identifier));
141 // }
142
143 // program.addOption(option);
144
145 // break;
146 // default:
147 // return false;
148 // }
149 // }
150
151 // reader.close();
152 // }
153 // catch (FileNotFoundException e) {
154 // return false;
155 // }
156 // catch (IOException e) {
157 // return false;
158 // }
159
160 // if (program != null) {
161 // programs.add(program);
162 // }
163
164 return true;
165 }
166
167 public int getNbPrograms() {
168 return programs.size();
169 }
170
171 public Program getProgram(int i) {
172 return programs.get(i);
173 }
174 }