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.List;
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22 import compbio.runner._SkeletalCommandBuilder;
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25 @see file:///(/homes/www-refine/SSPF_01/) Z:/bin/Brunak/TMHMM2/TMHMM2.0c/TMHMM2.0.html
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26 could have used decodeanhmm directly
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27 for more options @see ./decodeanhmm -h
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28 e.g. decodeanhmm -f <path>/TMHMM2.0.options -modelfile <path>/TMHMM2.0.model
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30 class Tmhmm2 extends _SkeletalCommandBuilder {
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33 * This is a standard tmhmm binary, but slightly modified the only
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34 * difference is that it will always write results in $workDirectory/TMHMM
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36 private static final String command = "/homes/www-refine/bin/Brunak/TMHMM2/TMHMM2.0c/bin/tmhmm_samedir";
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39 List<String> params;
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41 private final String workDirectory;
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43 public Tmhmm2(String workDirectory) {
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44 this.workDirectory = workDirectory;
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47 public static String getTestCommand() {
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51 public String getCommandName() {
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56 public List<String> getCreatedFiles() {
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57 // TODO Auto-generated method stub
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62 public String getInput() {
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63 // TODO Auto-generated method stub
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