+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-\r
-package compbio.metadata;\r
-\r
-import static org.testng.Assert.fail;\r
-\r
-import java.io.File;\r
-import java.io.FileInputStream;\r
-import java.io.FileNotFoundException;\r
-\r
-import javax.xml.bind.JAXBException;\r
-\r
-import org.testng.annotations.BeforeMethod;\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.engine.conf.RunnerConfigMarshaller;\r
-import compbio.metadata.RunnerConfig;\r
-import compbio.runner.OptionCombinator;\r
-import compbio.runner.msa.ClustalW;\r
-import compbio.runner.msa.Mafft;\r
-import compbio.runner.msa.Muscle;\r
-\r
-public class OptionCombinatorTester {\r
-\r
- static final String mafftConfigFile = AllTestSuit.TEST_DATA_PATH\r
- + "MafftParameters.xml";\r
-\r
- static final String muscleConfigFile = AllTestSuit.TEST_DATA_PATH\r
- + "MuscleParameters.xml";\r
-\r
- static final String clustalConfigFile = AllTestSuit.TEST_DATA_PATH\r
- + "ClustalParameters.xml";\r
-\r
- RunnerConfig<Mafft> mafftConfig = null;\r
- RunnerConfig<Mafft> muscleConfig = null;\r
- RunnerConfig<Mafft> clustalConfig = null;\r
-\r
- @BeforeMethod\r
- @SuppressWarnings("unchecked")\r
- void setup() {\r
- try {\r
- RunnerConfigMarshaller<Mafft> mf = new RunnerConfigMarshaller<Mafft>(\r
- RunnerConfig.class);\r
- mafftConfig = mf.read(\r
- new FileInputStream(new File(mafftConfigFile)),\r
- RunnerConfig.class);\r
- RunnerConfigMarshaller<Muscle> musclemarsh = new RunnerConfigMarshaller<Muscle>(\r
- RunnerConfig.class);\r
- muscleConfig = musclemarsh.read(new FileInputStream(new File(\r
- muscleConfigFile)), RunnerConfig.class);\r
-\r
- RunnerConfigMarshaller<ClustalW> clustalmarsh = new RunnerConfigMarshaller<ClustalW>(\r
- RunnerConfig.class);\r
- clustalConfig = clustalmarsh.read(new FileInputStream(new File(\r
- clustalConfigFile)), RunnerConfig.class);\r
-\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (JAXBException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
- @Test\r
- public void testgetAllOptions() {\r
- OptionCombinator opc = new OptionCombinator(mafftConfig);\r
- System.out.println(opc.getOptionsAtRandom());\r
- OptionCombinator muscleOpc = new OptionCombinator(muscleConfig);\r
- System.out.println("Mucle " + muscleOpc.getOptionsAtRandom());\r
- OptionCombinator clustalOpc = new OptionCombinator(clustalConfig);\r
- System.out.println("Clustal " + clustalOpc.getOptionsAtRandom());\r
-\r
- }\r
-\r
- @Test\r
- public void testgetAllParameters() {\r
- OptionCombinator opc = new OptionCombinator(mafftConfig);\r
- System.out.println(opc.getAllParameters());\r
- OptionCombinator muscleOpc = new OptionCombinator(muscleConfig);\r
- System.out.println("Muscle : " + muscleOpc.getAllParameters());\r
- OptionCombinator clustalOpc = new OptionCombinator(clustalConfig);\r
- System.out.println("Clustal : " + clustalOpc.getAllParameters());\r
- }\r
-}\r