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