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.assertEquals;
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22 import static org.testng.Assert.assertFalse;
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23 import static org.testng.Assert.assertNotNull;
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24 import static org.testng.Assert.assertTrue;
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25 import static org.testng.Assert.fail;
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27 import java.io.File;
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28 import java.io.FileInputStream;
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29 import java.io.FileNotFoundException;
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30 import java.util.List;
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32 import javax.xml.bind.JAXBException;
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34 import org.testng.annotations.BeforeMethod;
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35 import org.testng.annotations.Test;
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37 import compbio.engine.client.ConfExecutable;
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38 import compbio.engine.conf.RunnerConfigMarshaller;
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39 import compbio.metadata.AllTestSuit;
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40 import compbio.metadata.Limit;
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41 import compbio.metadata.LimitsManager;
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42 import compbio.metadata.PresetManager;
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43 import compbio.runner.msa.ClustalW;
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45 public class LimitTester {
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47 static final String clustalLimitsFile = AllTestSuit.TEST_DATA_PATH
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48 + "ClustalLimits.xml";
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49 static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE
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50 + "TO1381.fasta"; //
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51 static final String input = AllTestSuit.TEST_DATA_PATH
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52 + "ClustalPresets.xml";
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54 LimitsManager<ClustalW> clustalLimitConfig = null;
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55 PresetManager<ClustalW> presets = null;
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57 @BeforeMethod(groups = { AllTestSuit.test_group_runner })
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58 public void setup() {
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60 RunnerConfigMarshaller<ClustalW> clustalmarsh = new RunnerConfigMarshaller<ClustalW>(
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61 LimitsManager.class);
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62 clustalLimitConfig = clustalmarsh.read(new FileInputStream(
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63 new File(clustalLimitsFile)), LimitsManager.class);
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64 assertNotNull(clustalLimitConfig.getLimits());
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65 assertEquals(clustalLimitConfig.getLimits().size(), 3);
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67 RunnerConfigMarshaller<ClustalW> rconfigPresets = new RunnerConfigMarshaller<ClustalW>(
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68 PresetManager.class);
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69 File infile = new File(input);
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70 assertTrue(infile.exists());
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71 presets = rconfigPresets.read(new FileInputStream(infile),
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72 PresetManager.class);
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73 assertNotNull(presets);
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74 assertFalse(presets.getPresets().isEmpty());
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76 } catch (JAXBException e) {
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77 e.printStackTrace();
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78 fail(e.getLocalizedMessage());
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79 } catch (FileNotFoundException e) {
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80 e.printStackTrace();
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81 fail(e.getLocalizedMessage());
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87 public void testLoadLimits() {
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88 assertNotNull(clustalLimitConfig);
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89 List<Limit<ClustalW>> limits = clustalLimitConfig.getLimits();
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90 assertEquals(limits.size(), 3);
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91 Limit<ClustalW> limit = limits.get(0);
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92 assertNotNull(limit);
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93 assertEquals(limit.getPreset(),
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94 "Disable gap weighting (Speed-oriented)");
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95 assertEquals(limit.getSeqNumber(), 400);
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96 assertEquals(limit.getAvgSeqLength(), 600);
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97 assertFalse(limit.isDefault());
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99 limit = limits.get(1);
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100 assertNotNull(limit);
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101 assertEquals(limit.getPreset(), null);
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102 assertEquals(limit.getSeqNumber(), 1000);
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103 assertEquals(limit.getAvgSeqLength(), 400);
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104 assertTrue(limit.isDefault());
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