test/jalview/io/ClustalFileTest.java

   1 package jalview.io;
   2
   3 import static org.testng.Assert.assertEquals;
   4 import static org.testng.Assert.assertTrue;
   5
   6 import jalview.datamodel.SequenceI;
   7
   8 import java.io.IOException;
   9
  10 import org.testng.annotations.Test;
  11
  12 public class ClustalFileTest
  13 {
  14   @Test(groups="Functional")
  15   public void testParse_withNumbering() throws IOException
  16   {
  17     //@formatter:off
  18     String data = "CLUSTAL\n\n"
  19             + "FER_CAPAA/1-8      -----------------------------------------------------------A\t1\n"
  20             + "FER_CAPAN/1-55     MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA 48\n"
  21             + "FER1_SOLLC/1-55    MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA 48\n"
  22             + "Q93XJ9_SOLTU/1-55  MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA 48\n"
  23             + "FER1_PEA/1-60      MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA 53\n\n"
  24             + "FER_CAPAA/1-8      SYKVKLI 8\n"
  25             + "FER_CAPAN/1-55     SYKVKLI 55\n"
  26             + "FER1_SOLLC/1-55    SYKVKLI 55\n"
  27             + "Q93XJ9_SOLTU/1-55  SYKVKLI 55\n"
  28             + "FER1_PEA/1-60      SYKVKLV 60\n"
  29             + "                   .*     .:....*******..** ..........**  ********...*:::*  ...\n"
  30             + "\t\t.:.::.  *\n";
  31     //@formatter:on
  32     ClustalFile cf = new ClustalFile(data, DataSourceType.PASTE);
  33     cf.parse();
  34     SequenceI[] seqs = cf.getSeqsAsArray();
  35     assertEquals(seqs.length, 5);
  36     assertEquals(seqs[0].getName(), "FER_CAPAA");
  37     assertEquals(seqs[0].getStart(), 1);
  38     assertEquals(seqs[0].getEnd(), 8);
  39     assertTrue(seqs[0].getSequenceAsString().endsWith("ASYKVKLI"));
  40   }
  41
  42   @Test(groups="Functional")
  43   public void testParse_noNumbering() throws IOException
  44   {
  45     //@formatter:off
  46     String data = "CLUSTAL\n\n"
  47             + "FER_CAPAA/1-8      -----------------------------------------------------------A\n"
  48             + "FER_CAPAN/1-55     MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA\n"
  49             + "FER1_SOLLC/1-55    MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA\n"
  50             + "Q93XJ9_SOLTU/1-55  MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA\n"
  51             + "FER1_PEA/1-60      MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA\n\n"
  52             + "FER_CAPAA/1-8      SYKVKLI\n"
  53             + "FER_CAPAN/1-55     SYKVKLI\n"
  54             + "FER1_SOLLC/1-55    SYKVKLI\n"
  55             + "Q93XJ9_SOLTU/1-55  SYKVKLI\n"
  56             + "FER1_PEA/1-60      SYKVKLV\n";
  57     //@formatter:on
  58     ClustalFile cf = new ClustalFile(data, DataSourceType.PASTE);
  59     cf.parse();
  60     SequenceI[] seqs = cf.getSeqsAsArray();
  61     assertEquals(seqs.length, 5);
  62     assertEquals(seqs[0].getName(), "FER_CAPAA");
  63     assertEquals(seqs[0].getStart(), 1);
  64     assertEquals(seqs[0].getEnd(), 8);
  65     assertTrue(seqs[0].getSequenceAsString().endsWith("ASYKVKLI"));
  66   }
  67 }