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.engine.client.CommandBuilder;
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24 import compbio.engine.client.Executable;
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25 import compbio.engine.client.RunConfiguration;
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26 import compbio.metadata.Limit;
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27 import compbio.metadata.LimitsManager;
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30 @see http://www.cbs.dtu.dk/cgi-bin/nph-runsafe?man=netNglyc
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32 public class NetNglyc implements Executable<NetNglyc> {
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34 private static final String command = "/homes/www-refine/bin/Brunak/NOBACK/netNglyc-1.0a/netNglyc";
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36 List<String> params;
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42 public CommandBuilder<NetNglyc> getParameters(ExecProvider provider) {
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43 return null; // Arrays.asList(new String[] { "-a", "-f" }); // "-g"
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47 public static List<String> getTestArgs() {
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48 return Arrays.asList(new String[] { "-a", "-f" });
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52 public NetNglyc addParameters(List<String> parameters) {
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53 this.params = parameters;
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57 public static String getTestCommand() {
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61 public String getCommandName() {
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66 public List<String> getCreatedFiles() {
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67 // TODO Auto-generated method stub
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72 public String getInput() {
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73 // TODO Auto-generated method stub
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78 public <V> V getResults(String directory) {
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79 // TODO Auto-generated method stub
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84 public Executable<?> loadRunConfiguration(RunConfiguration rconfig) {
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85 // TODO Auto-generated method stub
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90 public String getOutput() {
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91 // TODO Auto-generated method stub
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96 public String getError() {
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97 // TODO Auto-generated method stub
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102 public Limit<NetNglyc> getLimit(String presetName) {
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103 // TODO Auto-generated method stub
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108 public LimitsManager<NetNglyc> getLimits() {
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109 // TODO Auto-generated method stub
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