testsrc/compbio/runner/msa/LimitTester.java

   1 /* Copyright (c) 2009 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0     \r
   4  * \r
   5  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   6  *  Apache License version 2 as published by the Apache Software Foundation\r
   7  * \r
   8  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
   9  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  10  *  License for more details.\r
  11  * \r
  12  *  A copy of the license is in apache_license.txt. It is also available here:\r
  13  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  14  * \r
  15  * Any republication or derived work distributed in source code form\r
  16  * must include this copyright and license notice.\r
  17  */\r
  18 \r
  19 package compbio.runner.msa;\r
  20 \r
  21 import static org.testng.Assert.assertEquals;\r
  22 import static org.testng.Assert.assertFalse;\r
  23 import static org.testng.Assert.assertNotNull;\r
  24 import static org.testng.Assert.assertTrue;\r
  25 import static org.testng.Assert.fail;\r
  26 \r
  27 import java.io.File;\r
  28 import java.io.FileInputStream;\r
  29 import java.io.FileNotFoundException;\r
  30 import java.util.List;\r
  31 \r
  32 import javax.xml.bind.JAXBException;\r
  33 \r
  34 import org.testng.annotations.BeforeMethod;\r
  35 import org.testng.annotations.Test;\r
  36 \r
  37 import compbio.engine.client.ConfExecutable;\r
  38 import compbio.engine.conf.RunnerConfigMarshaller;\r
  39 import compbio.metadata.AllTestSuit;\r
  40 import compbio.metadata.Limit;\r
  41 import compbio.metadata.LimitsManager;\r
  42 import compbio.metadata.PresetManager;\r
  43 import compbio.runner.msa.ClustalW;\r
  44 \r
  45 public class LimitTester {\r
  46 \r
  47         static final String clustalLimitsFile = AllTestSuit.TEST_DATA_PATH\r
  48                         + "ClustalLimits.xml";\r
  49         static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
  50                         + "TO1381.fasta"; //\r
  51         static final String input =  AllTestSuit.TEST_DATA_PATH\r
  52                         + "ClustalPresets.xml";\r
  53 \r
  54         LimitsManager<ClustalW> clustalLimitConfig = null;\r
  55         PresetManager<ClustalW> presets = null;\r
  56 \r
  57         @BeforeMethod(groups = { AllTestSuit.test_group_runner })\r
  58         public void setup() {\r
  59                 try {\r
  60                         RunnerConfigMarshaller<ClustalW> clustalmarsh = new RunnerConfigMarshaller<ClustalW>(\r
  61                                         LimitsManager.class);\r
  62                         clustalLimitConfig = clustalmarsh.read(new FileInputStream(\r
  63                                         new File(clustalLimitsFile)), LimitsManager.class);\r
  64                         assertNotNull(clustalLimitConfig.getLimits());\r
  65                         assertEquals(clustalLimitConfig.getLimits().size(), 3);\r
  66                         // Load presets\r
  67                         RunnerConfigMarshaller<ClustalW> rconfigPresets = new RunnerConfigMarshaller<ClustalW>(\r
  68                                         PresetManager.class);\r
  69                         File infile = new File(input);\r
  70                         assertTrue(infile.exists());\r
  71                         presets = rconfigPresets.read(new FileInputStream(infile),\r
  72                                         PresetManager.class);\r
  73                         assertNotNull(presets);\r
  74                         assertFalse(presets.getPresets().isEmpty());\r
  75 \r
  76                 } catch (JAXBException e) {\r
  77                         e.printStackTrace();\r
  78                         fail(e.getLocalizedMessage());\r
  79                 } catch (FileNotFoundException e) {\r
  80                         e.printStackTrace();\r
  81                         fail(e.getLocalizedMessage());\r
  82                 }\r
  83 \r
  84         }\r
  85 \r
  86         @Test\r
  87         public void testLoadLimits() {\r
  88                 assertNotNull(clustalLimitConfig);\r
  89                 List<Limit<ClustalW>> limits = clustalLimitConfig.getLimits();\r
  90                 assertEquals(limits.size(), 3);\r
  91                 Limit<ClustalW> limit = limits.get(0);\r
  92                 assertNotNull(limit);\r
  93                 assertEquals(limit.getPreset(),\r
  94                                 "Disable gap weighting (Speed-oriented)");\r
  95                 assertEquals(limit.getSeqNumber(), 400);\r
  96                 assertEquals(limit.getAvgSeqLength(), 600);\r
  97                 assertFalse(limit.isDefault());\r
  98 \r
  99                 limit = limits.get(1);\r
 100                 assertNotNull(limit);\r
 101                 assertEquals(limit.getPreset(), null);\r
 102                 assertEquals(limit.getSeqNumber(), 1000);\r
 103                 assertEquals(limit.getAvgSeqLength(), 400);\r
 104                 assertTrue(limit.isDefault());\r
 105         }\r
 106 }\r