test/jalview/io/ClustalFileTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.io;
  22
  23 import static org.testng.Assert.assertEquals;
  24 import static org.testng.Assert.assertTrue;
  25
  26 import jalview.datamodel.SequenceI;
  27
  28 import java.io.IOException;
  29
  30 import org.testng.annotations.Test;
  31
  32 public class ClustalFileTest
  33 {
  34   @Test(groups = "Functional")
  35   public void testParse_withNumbering() throws IOException
  36   {
  37     //@formatter:off
  38     String data = "CLUSTAL\n\n"
  39             + "FER_CAPAA/1-8      -----------------------------------------------------------A\t1\n"
  40             + "FER_CAPAN/1-55     MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA 48\n"
  41             + "FER1_SOLLC/1-55    MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA 48\n"
  42             + "Q93XJ9_SOLTU/1-55  MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA 48\n"
  43             + "FER1_PEA/1-60      MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA 53\n\n"
  44             + "FER_CAPAA/1-8      SYKVKLI 8\n"
  45             + "FER_CAPAN/1-55     SYKVKLI 55\n"
  46             + "FER1_SOLLC/1-55    SYKVKLI 55\n"
  47             + "Q93XJ9_SOLTU/1-55  SYKVKLI 55\n"
  48             + "FER1_PEA/1-60      SYKVKLV 60\n"
  49             + "                   .*     .:....*******..** ..........**  ********...*:::*  ...\n"
  50             + "\t\t.:.::.  *\n";
  51     //@formatter:on
  52     ClustalFile cf = new ClustalFile(data, DataSourceType.PASTE);
  53     cf.parse();
  54     SequenceI[] seqs = cf.getSeqsAsArray();
  55     assertEquals(seqs.length, 5);
  56     assertEquals(seqs[0].getName(), "FER_CAPAA");
  57     assertEquals(seqs[0].getStart(), 1);
  58     assertEquals(seqs[0].getEnd(), 8);
  59     assertTrue(seqs[0].getSequenceAsString().endsWith("ASYKVKLI"));
  60   }
  61
  62   @Test(groups = "Functional")
  63   public void testParse_noNumbering() throws IOException
  64   {
  65     //@formatter:off
  66     String data = "CLUSTAL\n\n"
  67             + "FER_CAPAA/1-8      -----------------------------------------------------------A\n"
  68             + "FER_CAPAN/1-55     MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA\n"
  69             + "FER1_SOLLC/1-55    MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA\n"
  70             + "Q93XJ9_SOLTU/1-55  MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA\n"
  71             + "FER1_PEA/1-60      MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA\n\n"
  72             + "FER_CAPAA/1-8      SYKVKLI\n"
  73             + "FER_CAPAN/1-55     SYKVKLI\n"
  74             + "FER1_SOLLC/1-55    SYKVKLI\n"
  75             + "Q93XJ9_SOLTU/1-55  SYKVKLI\n"
  76             + "FER1_PEA/1-60      SYKVKLV\n";
  77     //@formatter:on
  78     ClustalFile cf = new ClustalFile(data, DataSourceType.PASTE);
  79     cf.parse();
  80     SequenceI[] seqs = cf.getSeqsAsArray();
  81     assertEquals(seqs.length, 5);
  82     assertEquals(seqs[0].getName(), "FER_CAPAA");
  83     assertEquals(seqs[0].getStart(), 1);
  84     assertEquals(seqs[0].getEnd(), 8);
  85     assertTrue(seqs[0].getSequenceAsString().endsWith("ASYKVKLI"));
  86   }
  87 }