1 /* Copyright (c) 2009 Peter Troshin
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3 * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0
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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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19 package compbio.runner.msa;
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21 import static org.testng.Assert.assertFalse;
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22 import static org.testng.Assert.assertNotNull;
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23 import static org.testng.Assert.assertTrue;
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24 import static org.testng.Assert.fail;
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26 import java.io.File;
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27 import java.io.FileInputStream;
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28 import java.io.FileNotFoundException;
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29 import java.io.IOException;
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30 import java.util.ArrayList;
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31 import java.util.Collections;
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32 import java.util.List;
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33 import java.util.Map;
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35 import javax.xml.bind.JAXBException;
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36 import javax.xml.bind.ValidationException;
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38 import org.apache.log4j.Level;
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39 import org.apache.log4j.Logger;
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40 import org.testng.annotations.BeforeMethod;
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41 import org.testng.annotations.Test;
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43 import compbio.engine.Configurator;
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44 import compbio.engine.client.ConfiguredExecutable;
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45 import compbio.engine.client.Executable.ExecProvider;
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46 import compbio.engine.conf.RunnerConfigMarshaller;
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47 import compbio.engine.local.ExecutableWrapper;
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48 import compbio.engine.local.LocalRunner;
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49 import compbio.metadata.AllTestSuit;
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50 import compbio.metadata.JobExecutionException;
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51 import compbio.metadata.JobSubmissionException;
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52 import compbio.metadata.Option;
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53 import compbio.metadata.Parameter;
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54 import compbio.metadata.Preset;
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55 import compbio.metadata.PresetManager;
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56 import compbio.metadata.ResultNotAvailableException;
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57 import compbio.metadata.RunnerConfig;
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58 import compbio.runner.OptionCombinator;
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59 import compbio.runner.msa.ClustalW;
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60 import compbio.util.FileUtil;
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62 @Test(sequential = true)
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63 public class ClustalWParametersTester {
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65 static final String clustalConfigFile = AllTestSuit.TEST_DATA_PATH
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66 + "ClustalParameters.xml";
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68 public static String test_outfile = "TO1381.clustal.out";
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69 public static String test_error = "TO1381.clustal.error";
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70 public static String cluster_test_outfile = "TO1381.clustal.cluster.out";
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71 public static final String input = AllTestSuit.TEST_DATA_PATH
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72 + "ClustalPresets.xml";
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74 private static Logger log = Logger
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75 .getLogger(AllTestSuit.RUNNER_TEST_LOGGER);
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77 log.setLevel(Level.INFO);
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80 RunnerConfig<ClustalW> clustalConfig = null;
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81 OptionCombinator clustalOpc = null;
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82 PresetManager<ClustalW> presets = null;
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84 @BeforeMethod(groups = { AllTestSuit.test_group_runner })
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85 public void setup() {
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87 RunnerConfigMarshaller<ClustalW> clustalmarsh = new RunnerConfigMarshaller<ClustalW>(
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88 RunnerConfig.class);
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89 clustalConfig = clustalmarsh.read(new FileInputStream(new File(
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90 clustalConfigFile)), RunnerConfig.class);
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91 clustalOpc = new OptionCombinator(clustalConfig);
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94 RunnerConfigMarshaller<ClustalW> rconfigPresets = new RunnerConfigMarshaller<ClustalW>(
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95 PresetManager.class);
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96 File infile = new File(input);
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97 assertTrue(infile.exists());
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98 presets = rconfigPresets.read(new FileInputStream(infile),
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99 PresetManager.class);
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100 assertNotNull(presets);
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101 assertFalse(presets.getPresets().isEmpty());
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103 } catch (JAXBException e) {
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104 e.printStackTrace();
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105 fail(e.getLocalizedMessage());
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106 } catch (FileNotFoundException e) {
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107 e.printStackTrace();
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108 fail(e.getLocalizedMessage());
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114 public void testConfiguration() {
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116 this.clustalConfig.validate();
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117 } catch (ValidationException e) {
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118 e.printStackTrace();
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119 fail(e.getLocalizedMessage());
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120 } catch (IllegalStateException e) {
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121 e.printStackTrace();
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122 fail(e.getLocalizedMessage());
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126 @Test(groups = { AllTestSuit.test_group_runner })
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127 public void testDefaultParameters() {
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128 ClustalW clustal = new ClustalW();
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129 clustal.setInput(AllTestSuit.test_input).setOutput(test_outfile);
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132 // For local execution use relavive
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133 ConfiguredExecutable<ClustalW> confClustal = Configurator
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134 .configureExecutable(clustal);
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135 LocalRunner lr = new LocalRunner(confClustal);
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137 confClustal = (ConfiguredExecutable<ClustalW>) lr.waitForResult();
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138 assertNotNull(confClustal.getResults());
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139 } catch (JobSubmissionException e) {
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140 e.printStackTrace();
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141 fail(e.getLocalizedMessage());
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142 } catch (JobExecutionException e) {
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143 e.printStackTrace();
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144 fail(e.getLocalizedMessage());
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145 } catch (ResultNotAvailableException e) {
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146 e.printStackTrace();
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147 fail(e.getLocalizedMessage());
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151 @Test(groups = { AllTestSuit.test_group_runner })
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152 public void testOptions() {
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153 test(clustalOpc.getAllOptions());
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156 @Test(groups = { AllTestSuit.test_group_runner })
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157 public void testParameters() {
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158 List<Parameter<?>> params = clustalOpc.getAllParameters();
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159 Collections.shuffle(params);
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163 @Test(groups = { AllTestSuit.test_group_runner })
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164 public void testArguments() {
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165 List<Option<?>> options = clustalOpc.getAllOptions();
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166 options.addAll(clustalOpc.getAllParameters());
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167 Collections.shuffle(options);
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171 @Test(groups = { AllTestSuit.test_group_runner })
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172 public void testConstrainedParametersMinValues() {
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173 Map<Parameter<?>, String> params = clustalOpc
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174 .getAllConstrainedParametersWithBorderValues(true);
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178 @Test(groups = { AllTestSuit.test_group_runner })
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179 public void testConstrainedParametersMaxValues() {
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180 Map<Parameter<?>, String> params = clustalOpc
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181 .getAllConstrainedParametersWithBorderValues(false);
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185 @Test(groups = { AllTestSuit.test_group_runner })
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186 public void testConstrainedParametersRandomValues() {
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187 for (int i = 0; i < 5; i++) {
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188 Map<Parameter<?>, String> params = clustalOpc
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189 .getAllConstrainedParametersWithRandomValues();
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190 List<Parameter<?>> paramList = new ArrayList<Parameter<?>>(params
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192 Collections.shuffle(paramList);
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193 List<String> args = clustalOpc.parametersToCommandString(paramList,
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199 void test(Map<Parameter<?>, String> paramValue) {
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200 List<Parameter<?>> paramList = new ArrayList<Parameter<?>>(paramValue
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202 for (int i = 0; i < paramValue.size(); i++) {
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203 List<String> args = clustalOpc.parametersToCommandString(paramList,
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206 Collections.shuffle(paramList);
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208 log.info("NUMBER OF COBINATION TESTED: " + paramValue.size());
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211 void test(List<? extends Option<?>> params) {
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212 for (int i = 0; i < params.size(); i++) {
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213 List<String> args = clustalOpc.argumentsToCommandString(params);
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215 Collections.shuffle(params);
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217 log.info("NUMBER OF COBINATION TESTED: " + params.size());
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220 void singleTest(List<String> params) {
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222 log.info("Using arguments: " + params);
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223 ClustalW clustal = new ClustalW();
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224 clustal.setInput(AllTestSuit.test_input).setOutput(test_outfile);
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226 // For local execution use relative
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227 ConfiguredExecutable<ClustalW> confClustal = Configurator
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228 .configureExecutable(clustal, ExecProvider.Local);
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229 // Add options to the executable
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230 confClustal.addParameters(params);
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231 LocalRunner lr = new LocalRunner(confClustal);
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233 confClustal = (ConfiguredExecutable<ClustalW>) lr.waitForResult();
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234 assertNotNull(confClustal.getResults());
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235 File errors = new File(confClustal.getWorkDirectory(),
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236 ExecutableWrapper.PROC_ERR_FILE);
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237 if (errors.length() != 0) {
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238 log.error("PROBLEMS:\n " + FileUtil.readFileToString(errors));
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240 assertTrue(errors.length() == 0, "Run with arguments : " + params
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242 Collections.shuffle(params);
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243 } catch (JobSubmissionException e) {
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244 e.printStackTrace();
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245 fail(e.getLocalizedMessage());
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246 } catch (JobExecutionException e) {
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247 e.printStackTrace();
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248 fail(e.getLocalizedMessage());
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249 } catch (IOException e) {
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250 e.printStackTrace();
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251 fail(e.getLocalizedMessage());
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252 } catch (ResultNotAvailableException e) {
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253 e.printStackTrace();
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254 fail(e.getLocalizedMessage());
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258 @Test(groups = { AllTestSuit.test_group_runner })
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259 public void testPresets() {
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260 for (Preset<ClustalW> p : presets.getPresets()) {
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261 singleTest(p.getOptions());
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