1 /* Copyright (c) 2009 Peter Troshin
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3 * Jalview Web Services @version: 2.0
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5 * This library is free software; you can redistribute it and/or modify it under the terms of the
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6 * Apache License version 2 as published by the Apache Software Foundation
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8 * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
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9 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
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10 * License for more details.
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12 * A copy of the license is in apache_license.txt. It is also available here:
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13 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
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15 * Any republication or derived work distributed in source code form
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16 * must include this copyright and license notice.
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18 package compbio.runner._impl;
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20 import java.util.Arrays;
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21 import java.util.List;
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23 import compbio.runner._SkeletalCommandBuilder;
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26 * TODO this needs fixing! Executable does not work
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31 public class OB extends _SkeletalCommandBuilder {
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33 // $obdir/OB.pl -i $fa -p $obdir/databases/GES_hydrophobicity.dat -m
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34 // $obdir/databases/GES_zmat2.dat -n -o $outdir/OB.dat"
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35 // where $obdir= /homes/www-refine/SSPF_TO1/TarO_newclus/
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36 private static final String commandName = "OB";
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37 private static final String command = "/homes/www-refine/SSPF_TO1/TarO_newclus/OB_runner.sh";
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39 String workDirectory;
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42 // TODO Auto-generated constructor stub
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45 public OB(String workDirectory) {
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46 this.workDirectory = workDirectory;
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49 public static String getTestCommand() {
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55 public List<String> getTestArgs() {
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56 return Arrays.asList(new String[] { "" });
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59 public static void main(String[] args) {
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64 public List<String> getCreatedFiles() {
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65 // TODO Auto-generated method stub
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70 public String getInput() {
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71 // TODO Auto-generated method stub
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