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;
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20 import java.util.ArrayList;
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21 import java.util.Arrays;
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22 import java.util.List;
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24 import compbio.engine.client.CommandBuilder;
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25 import compbio.engine.client.Executable;
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26 import compbio.engine.client.RunConfiguration;
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27 import compbio.metadata.Limit;
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28 import compbio.metadata.LimitsManager;
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30 public abstract class _SkeletalCommandBuilder implements
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31 Executable<_SkeletalCommandBuilder> {
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33 String tmpDirectory;
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36 List<String> params = new ArrayList<String>();
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38 public _SkeletalCommandBuilder setEmail(String email) {
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43 public _SkeletalCommandBuilder setName(String name) {
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48 public String getName() {
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52 public String getEmail() {
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56 public _SkeletalCommandBuilder addParameters(String[] parameters) {
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57 this.params.addAll(Arrays.asList(parameters));
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61 public _SkeletalCommandBuilder addParameters(List<String> parameters) {
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62 this.params.addAll(parameters);
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67 public CommandBuilder<_SkeletalCommandBuilder> getParameters(
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68 ExecProvider provider) {
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72 public _SkeletalCommandBuilder addParameter(String parameter) {
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73 params.add(parameter);
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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<_SkeletalCommandBuilder> getLimit(String presetName) {
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103 // TODO Auto-generated method stub
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108 public LimitsManager<_SkeletalCommandBuilder> getLimits() {
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109 // TODO Auto-generated method stub
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