Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/SMART/Java/Sav/Program.java @ 2:7c697a8bde9f
Deleted selected files
| author | yufei-luo | 
|---|---|
| date | Thu, 17 Jan 2013 11:02:49 -0500 | 
| parents | e0f8dcca02ed | 
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| rev | line source | 
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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changeset | 1 /** | 
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changeset | 2 * | 
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changeset | 3 * Copyright INRA-URGI 2009-2010 | 
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changeset | 4 * | 
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changeset | 5 * This software is governed by the CeCILL license under French law and | 
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changeset | 6 * abiding by the rules of distribution of free software. You can use, | 
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changeset | 7 * modify and/ or redistribute the software under the terms of the CeCILL | 
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changeset | 8 * license as circulated by CEA, CNRS and INRIA at the following URL | 
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changeset | 9 * "http://www.cecill.info". | 
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changeset | 10 * | 
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changeset | 11 * As a counterpart to the access to the source code and rights to copy, | 
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changeset | 12 * modify and redistribute granted by the license, users are provided only | 
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changeset | 13 * with a limited warranty and the software's author, the holder of the | 
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changeset | 14 * economic rights, and the successive licensors have only limited | 
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changeset | 15 * liability. | 
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changeset | 16 * | 
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changeset | 17 * In this respect, the user's attention is drawn to the risks associated | 
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changeset | 18 * with loading, using, modifying and/or developing or reproducing the | 
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changeset | 19 * software by the user in light of its specific status of free software, | 
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changeset | 20 * that may mean that it is complicated to manipulate, and that also | 
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changeset | 21 * therefore means that it is reserved for developers and experienced | 
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changeset | 22 * professionals having in-depth computer knowledge. Users are therefore | 
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changeset | 23 * encouraged to load and test the software's suitability as regards their | 
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changeset | 24 * requirements in conditions enabling the security of their systems and/or | 
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changeset | 25 * data to be ensured and, more generally, to use and operate it in the | 
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changeset | 26 * same conditions as regards security. | 
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changeset | 27 * | 
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changeset | 28 * The fact that you are presently reading this means that you have had | 
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changeset | 29 * knowledge of the CeCILL license and that you accept its terms. | 
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changeset | 30 * | 
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changeset | 31 */ | 
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changeset | 32 import java.util.*; | 
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changeset | 33 import java.awt.*; | 
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changeset | 34 import javax.swing.*; | 
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changeset | 35 | 
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changeset | 36 | 
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changeset | 37 public class Program { | 
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changeset | 38 String shortName; | 
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changeset | 39 String name; | 
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changeset | 40 String section; | 
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changeset | 41 String description; | 
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changeset | 42 Vector <ProgramOption> options; | 
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changeset | 43 JPanel panel; | 
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changeset | 44 JButton button; | 
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changeset | 45 | 
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changeset | 46 | 
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changeset | 47 public Program() { | 
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changeset | 48 this.shortName = null; | 
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changeset | 49 this.name = null; | 
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changeset | 50 this.options = new Vector <ProgramOption> (); | 
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changeset | 51 } | 
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changeset | 52 | 
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changeset | 53 | 
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changeset | 54 public void setShortName(String shortName) { | 
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changeset | 55 this.shortName = shortName; | 
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changeset | 56 } | 
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changeset | 57 | 
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changeset | 58 | 
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changeset | 59 public void setName(String name) { | 
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changeset | 60 this.name = name; | 
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changeset | 61 } | 
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changeset | 62 | 
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changeset | 63 | 
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changeset | 64 public void setSection(String section) { | 
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changeset | 65 this.section = section; | 
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changeset | 66 } | 
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changeset | 67 | 
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changeset | 68 public void setDescription(String description) { | 
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changeset | 69 this.description = description; | 
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changeset | 70 } | 
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changeset | 71 | 
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changeset | 72 | 
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changeset | 73 public void addOption(ProgramOption option) { | 
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changeset | 74 options.add(option); | 
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changeset | 75 } | 
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changeset | 76 | 
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changeset | 77 | 
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changeset | 78 public String getShortName() { | 
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changeset | 79 return this.shortName; | 
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changeset | 80 } | 
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changeset | 81 | 
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changeset | 82 | 
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changeset | 83 public String getName() { | 
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changeset | 84 return this.name; | 
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changeset | 85 } | 
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changeset | 86 | 
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changeset | 87 | 
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changeset | 88 public String getSection() { | 
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changeset | 89 return this.section; | 
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changeset | 90 } | 
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changeset | 91 | 
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changeset | 92 public String getDescription() { | 
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changeset | 93 return this.description; | 
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changeset | 94 } | 
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changeset | 95 | 
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changeset | 96 | 
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changeset | 97 public String checkValues() { | 
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changeset | 98 for (int i = 0; i < options.size(); i++) { | 
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changeset | 99 String comment = options.get(i).checkValue(); | 
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changeset | 100 if (comment != null) { | 
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changeset | 101 return comment; | 
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changeset | 102 } | 
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changeset | 103 } | 
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changeset | 104 return null; | 
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changeset | 105 } | 
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changeset | 106 | 
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changeset | 107 | 
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changeset | 108 public LinkedList<String> getCommand() { | 
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changeset | 109 LinkedList<String> parameterList = new LinkedList<String>(); | 
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changeset | 110 parameterList.add(Global.pythonCommand); | 
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changeset | 111 parameterList.add("Python" + java.io.File.separator + this.shortName); | 
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changeset | 112 for (int i = 0; i < options.size(); i++) { | 
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changeset | 113 ProgramOption option = options.get(i); | 
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changeset | 114 parameterList.addAll(option.getCommand()); | 
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changeset | 115 } | 
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changeset | 116 return parameterList; | 
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changeset | 117 } | 
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changeset | 118 | 
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changeset | 119 | 
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changeset | 120 public JPanel getPanel() { | 
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changeset | 121 if (this.panel != null) { | 
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changeset | 122 return this.panel; | 
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changeset | 123 } | 
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changeset | 124 | 
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changeset | 125 this.panel = new JPanel(false); | 
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changeset | 126 this.panel.setLayout(new FlowLayout()); | 
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changeset | 127 Box box = Box.createVerticalBox(); | 
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changeset | 128 | 
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changeset | 129 JPanel descriptionPanel = new JPanel(false); | 
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changeset | 130 JLabel descriptionLabel = new JLabel(this.description); | 
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changeset | 131 descriptionPanel.add(descriptionLabel); | 
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changeset | 132 box.add(descriptionPanel); | 
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changeset | 133 | 
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changeset | 134 for (int i = 0; i < options.size(); i++) { | 
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changeset | 135 ProgramOption option = options.get(i); | 
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changeset | 136 JPanel panel = option.getPanel(); | 
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changeset | 137 if (panel == null) { | 
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changeset | 138 System.out.println("Problem with Python program '" + this.shortName + "'."); | 
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changeset | 139 return null; | 
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changeset | 140 } | 
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changeset | 141 box.add(option.getPanel()); | 
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changeset | 142 } | 
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changeset | 143 | 
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changeset | 144 JPanel buttonPanel = new JPanel(false); | 
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changeset | 145 this.button = new JButton("GO!"); | 
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changeset | 146 | 
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changeset | 147 buttonPanel.add(button); | 
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changeset | 148 | 
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changeset | 149 box.add(buttonPanel); | 
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changeset | 150 | 
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changeset | 151 this.panel.add(box); | 
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changeset | 152 | 
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changeset | 153 return this.panel; | 
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changeset | 154 } | 
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changeset | 155 | 
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changeset | 156 | 
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changeset | 157 public JButton getButton() { | 
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changeset | 158 if (this.button == null) { | 
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changeset | 159 this.getPanel(); | 
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changeset | 160 } | 
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changeset | 161 return this.button; | 
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changeset | 162 } | 
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changeset | 163 | 
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changeset | 164 | 
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changeset | 165 public Vector < File > getOutputFiles() { | 
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changeset | 166 Vector < File > files = new Vector < File > (); | 
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changeset | 167 for (int i = 0; i < options.size(); i++) { | 
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changeset | 168 ProgramOption option = options.get(i); | 
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changeset | 169 if (! option.isInput()) { | 
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changeset | 170 files.add(option.getOutputFile()); | 
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changeset | 171 } | 
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changeset | 172 } | 
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changeset | 173 return files; | 
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changeset | 174 } | 
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changeset | 175 } | 
