testsrc/compbio/data/sequence/ClustalAlignmentUtilTester.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.data.sequence;\r
  20 \r
  21 import static org.testng.AssertJUnit.assertEquals;\r
  22 import static org.testng.AssertJUnit.assertNotNull;\r
  23 import static org.testng.AssertJUnit.assertTrue;\r
  24 import static org.testng.AssertJUnit.fail;\r
  25 \r
  26 import java.io.FileInputStream;\r
  27 import java.io.FileNotFoundException;\r
  28 import java.io.FileWriter;\r
  29 import java.io.IOException;\r
  30 import java.io.Writer;\r
  31 \r
  32 import org.testng.annotations.Test;\r
  33 \r
  34 import compbio.metadata.AllTestSuit;\r
  35 \r
  36 public class ClustalAlignmentUtilTester {\r
  37 \r
  38         @Test()\r
  39         public void testReadClustalFile() {\r
  40                 try {\r
  41                         readWriteClustal("TO1381.aln");\r
  42                 } catch (FileNotFoundException e) {\r
  43                         e.printStackTrace();\r
  44                         fail(e.getMessage());\r
  45                 } catch (Exception e) {\r
  46                         e.printStackTrace();\r
  47                         fail(e.getMessage());\r
  48                 }\r
  49         }\r
  50 \r
  51         static void readWriteClustal(String fname) throws IOException,\r
  52                         UnknownFileFormatException {\r
  53                 FileInputStream fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
  54                                 + fname);\r
  55                 Alignment seqAl = ClustalAlignmentUtil.readClustalFile(fio);\r
  56                 assertTrue(seqAl != null);\r
  57                 assertTrue(seqAl.getSize() == 3);\r
  58                 assertNotNull(seqAl.getSequences());\r
  59                 assertEquals(3, seqAl.getSequences().size());\r
  60 \r
  61                 // Now try to write the alignment read\r
  62                 Writer os = new FileWriter(AllTestSuit.TEST_DATA_PATH + fname\r
  63                                 + ".written");\r
  64                 ClustalAlignmentUtil.writeClustalAlignment(os, seqAl);\r
  65                 fio.close();\r
  66                 os.close();\r
  67 \r
  68                 fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + fname\r
  69                                 + ".written");\r
  70                 Alignment readseqs = ClustalAlignmentUtil.readClustalFile(fio);\r
  71                 assertTrue(readseqs != null);\r
  72                 assertTrue(readseqs.getSize() == 3);\r
  73                 fio.close();\r
  74         }\r
  75 \r
  76         @Test()\r
  77         public void testReadClustalFileShortNames() {\r
  78                 try {\r
  79                         readWriteClustal("TO1381s.aln");\r
  80                 } catch (FileNotFoundException e) {\r
  81                         e.printStackTrace();\r
  82                         fail(e.getMessage());\r
  83                 } catch (Exception e) {\r
  84                         e.printStackTrace();\r
  85                         fail(e.getMessage());\r
  86                 }\r
  87         }\r
  88 \r
  89         @Test()\r
  90         public void testReadClustalFileLongNames() {\r
  91                 try {\r
  92                         readWriteClustal("TO1381L.aln");\r
  93                 } catch (FileNotFoundException e) {\r
  94                         e.printStackTrace();\r
  95                         fail(e.getMessage());\r
  96                 } catch (Exception e) {\r
  97                         e.printStackTrace();\r
  98                         fail(e.getMessage());\r
  99                 }\r
 100         }\r
 101 \r
 102 }\r