Mercurial > repos > yufei-luo > s_mart

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