testsrc/compbio/metadata/OptionCombinatorTester.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.metadata;\r
  20 \r
  21 import static org.testng.Assert.fail;\r
  22 \r
  23 import java.io.File;\r
  24 import java.io.FileInputStream;\r
  25 import java.io.FileNotFoundException;\r
  26 \r
  27 import javax.xml.bind.JAXBException;\r
  28 \r
  29 import org.testng.annotations.BeforeMethod;\r
  30 import org.testng.annotations.Test;\r
  31 \r
  32 import compbio.engine.conf.RunnerConfigMarshaller;\r
  33 import compbio.metadata.RunnerConfig;\r
  34 import compbio.runner.OptionCombinator;\r
  35 import compbio.runner.msa.ClustalW;\r
  36 import compbio.runner.msa.Mafft;\r
  37 import compbio.runner.msa.Muscle;\r
  38 \r
  39 public class OptionCombinatorTester {\r
  40 \r
  41         static final String mafftConfigFile = AllTestSuit.TEST_DATA_PATH\r
  42                         + "MafftParameters.xml";\r
  43 \r
  44         static final String muscleConfigFile = AllTestSuit.TEST_DATA_PATH\r
  45                         + "MuscleParameters.xml";\r
  46 \r
  47         static final String clustalConfigFile = AllTestSuit.TEST_DATA_PATH\r
  48                         + "ClustalParameters.xml";\r
  49 \r
  50         RunnerConfig<Mafft> mafftConfig = null;\r
  51         RunnerConfig<Mafft> muscleConfig = null;\r
  52         RunnerConfig<Mafft> clustalConfig = null;\r
  53 \r
  54         @BeforeMethod\r
  55         @SuppressWarnings("unchecked")\r
  56         void setup() {\r
  57                 try {\r
  58                         RunnerConfigMarshaller<Mafft> mf = new RunnerConfigMarshaller<Mafft>(\r
  59                                         RunnerConfig.class);\r
  60                         mafftConfig = mf.read(\r
  61                                         new FileInputStream(new File(mafftConfigFile)),\r
  62                                         RunnerConfig.class);\r
  63                         RunnerConfigMarshaller<Muscle> musclemarsh = new RunnerConfigMarshaller<Muscle>(\r
  64                                         RunnerConfig.class);\r
  65                         muscleConfig = musclemarsh.read(new FileInputStream(new File(\r
  66                                         muscleConfigFile)), RunnerConfig.class);\r
  67 \r
  68                         RunnerConfigMarshaller<ClustalW> clustalmarsh = new RunnerConfigMarshaller<ClustalW>(\r
  69                                         RunnerConfig.class);\r
  70                         clustalConfig = clustalmarsh.read(new FileInputStream(new File(\r
  71                                         clustalConfigFile)), RunnerConfig.class);\r
  72 \r
  73                 } catch (FileNotFoundException e) {\r
  74                         e.printStackTrace();\r
  75                         fail(e.getMessage());\r
  76                 } catch (JAXBException e) {\r
  77                         e.printStackTrace();\r
  78                         fail(e.getMessage());\r
  79                 }\r
  80         }\r
  81 \r
  82         @Test\r
  83         public void testgetAllOptions() {\r
  84                 OptionCombinator opc = new OptionCombinator(mafftConfig);\r
  85                 System.out.println(opc.getOptionsAtRandom());\r
  86                 OptionCombinator muscleOpc = new OptionCombinator(muscleConfig);\r
  87                 System.out.println("Mucle " + muscleOpc.getOptionsAtRandom());\r
  88                 OptionCombinator clustalOpc = new OptionCombinator(clustalConfig);\r
  89                 System.out.println("Clustal " + clustalOpc.getOptionsAtRandom());\r
  90 \r
  91         }\r
  92 \r
  93         @Test\r
  94         public void testgetAllParameters() {\r
  95                 OptionCombinator opc = new OptionCombinator(mafftConfig);\r
  96                 System.out.println(opc.getAllParameters());\r
  97                 OptionCombinator muscleOpc = new OptionCombinator(muscleConfig);\r
  98                 System.out.println("Muscle : " + muscleOpc.getAllParameters());\r
  99                 OptionCombinator clustalOpc = new OptionCombinator(clustalConfig);\r
 100                 System.out.println("Clustal : " + clustalOpc.getAllParameters());\r
 101         }\r
 102 }\r