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.io.IOException;
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31 import java.util.List;
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33 import javax.xml.bind.JAXBException;
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35 import org.testng.annotations.BeforeMethod;
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36 import org.testng.annotations.Test;
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38 import compbio.data.sequence.FastaSequence;
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39 import compbio.data.sequence.SequenceUtil;
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40 import compbio.engine.conf.RunnerConfigMarshaller;
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41 import compbio.metadata.AllTestSuit;
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42 import compbio.metadata.Limit;
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43 import compbio.metadata.LimitsManager;
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44 import compbio.metadata.PresetManager;
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46 public class LimitTester {
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48 static final String clustalLimitsFile = AllTestSuit.TEST_DATA_PATH
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49 + "ClustalLimits.xml";
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50 static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE
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51 + "TO1381.fasta"; //
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52 static final String input = AllTestSuit.TEST_DATA_PATH
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53 + "ClustalPresets.xml";
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55 LimitsManager<ClustalW> clustalLimitConfig = null;
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56 PresetManager<ClustalW> presets = null;
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58 @BeforeMethod(groups = { AllTestSuit.test_group_runner })
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59 public void setup() {
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61 RunnerConfigMarshaller<ClustalW> clustalmarsh = new RunnerConfigMarshaller<ClustalW>(
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62 LimitsManager.class);
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63 clustalLimitConfig = clustalmarsh.read(new FileInputStream(
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64 new File(clustalLimitsFile)), LimitsManager.class);
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65 assertNotNull(clustalLimitConfig.getLimits());
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66 assertEquals(clustalLimitConfig.getLimits().size(), 3);
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68 RunnerConfigMarshaller<ClustalW> rconfigPresets = new RunnerConfigMarshaller<ClustalW>(
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69 PresetManager.class);
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70 File infile = new File(input);
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71 assertTrue(infile.exists());
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72 presets = rconfigPresets.read(new FileInputStream(infile),
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73 PresetManager.class);
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74 assertNotNull(presets);
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75 assertFalse(presets.getPresets().isEmpty());
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77 } catch (JAXBException e) {
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78 e.printStackTrace();
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79 fail(e.getLocalizedMessage());
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80 } catch (FileNotFoundException e) {
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81 e.printStackTrace();
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82 fail(e.getLocalizedMessage());
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88 public void testLoadLimits() {
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89 assertNotNull(clustalLimitConfig);
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90 List<Limit<ClustalW>> limits = clustalLimitConfig.getLimits();
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91 assertEquals(limits.size(), 3);
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92 Limit<ClustalW> limit = limits.get(0);
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93 assertNotNull(limit);
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94 assertEquals(limit.getPreset(),
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95 "Disable gap weighting (Speed-oriented)");
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96 assertEquals(limit.getSeqNumber(), 400);
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97 assertEquals(limit.getAvgSeqLength(), 600);
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98 assertFalse(limit.isDefault());
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100 limit = limits.get(1);
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101 assertNotNull(limit);
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102 assertEquals(limit.getPreset(), null);
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103 assertEquals(limit.getSeqNumber(), 1000);
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104 assertEquals(limit.getAvgSeqLength(), 400);
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105 assertTrue(limit.isDefault());
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109 public void testLimitExceeded() {
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111 String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE
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112 + "testlimit.fasta";
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114 FileInputStream fio;
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116 fio = new FileInputStream(test_input);
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117 List<FastaSequence> data = SequenceUtil.readFasta(fio);
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119 assertNotNull(data);
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120 assertEquals(data.size(), 6);
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121 assertEquals(Limit.getAvgSequenceLength(data), 20486);
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122 Limit small = new Limit(40, 500, "default");
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124 assertTrue(small.isExceeded(data));
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126 Limit large = new Limit(500, 500, "default");
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127 assertFalse(large.isExceeded(data));
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129 Limit numSeqOnly = new Limit(6, 0, "default");
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130 assertFalse(numSeqOnly.isExceeded(data));
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132 Limit exnumSeqOnly = new Limit(5, 0, "default");
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133 assertTrue(exnumSeqOnly.isExceeded(data));
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135 Limit numSeq3 = new Limit(5, 1000000, "default");
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136 assertTrue(numSeq3.isExceeded(data));
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138 } catch (FileNotFoundException e) {
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139 e.printStackTrace();
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140 fail(e.getMessage());
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141 } catch (IOException e) {
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142 e.printStackTrace();
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143 fail(e.getMessage());
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