test/jalview/analysis/SeqsetUtilsTest.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.analysis;
  22
  23 import jalview.datamodel.Alignment;
  24 import jalview.datamodel.AlignmentI;
  25 import jalview.datamodel.Sequence;
  26 import jalview.datamodel.SequenceFeature;
  27 import jalview.datamodel.SequenceI;
  28
  29 import java.util.Hashtable;
  30
  31 import org.testng.Assert;
  32 import org.testng.annotations.Test;
  33
  34 /**
  35  * @author jprocter
  36  *
  37  */
  38 public class SeqsetUtilsTest
  39 {
  40   /**
  41    * test for JAL-2046 bug - duplication of sequence features on reconstructed
  42    * alignment
  43    */
  44   @Test(groups = { "Functional" })
  45   public void testSeqFeatureAddition()
  46   {
  47     SequenceI[] sqset = new SequenceI[] {
  48         new Sequence("Aseq1", "AREALSEQ"),
  49         new Sequence("Aseq2", "AREALSEQ") };
  50
  51     AlignmentI al = new Alignment(sqset);
  52     al.setDataset(null);
  53     AlignmentI ds = al.getDataset();
  54     SequenceFeature sf1 = new SequenceFeature("f1", "foo", "bleh", 2, 3,
  55             "far"), sf2 = new SequenceFeature("f2", "foo", "bleh", 2, 3,
  56             "far");
  57     ds.getSequenceAt(0).addSequenceFeature(sf1);
  58     Hashtable unq = SeqsetUtils.uniquify(sqset, true);
  59     SequenceI[] sqset2 = new SequenceI[] {
  60         new Sequence(sqset[0].getName(), sqset[0].getSequenceAsString()),
  61         new Sequence(sqset[1].getName(), sqset[1].getSequenceAsString()) };
  62     Assert.assertTrue(sqset[0].getSequenceFeatures()[0] == sf1);
  63     Assert.assertEquals(sqset2[0].getSequenceFeatures(), null);
  64     ds.getSequenceAt(0).addSequenceFeature(sf2);
  65     Assert.assertEquals(sqset[0].getSequenceFeatures().length, 2);
  66     SeqsetUtils.deuniquify(unq, sqset2);
  67     // explicitly test that original sequence features still exist because they
  68     // are on the shared dataset sequence
  69     Assert.assertEquals(sqset[0].getSequenceFeatures().length, 2);
  70     Assert.assertEquals(sqset2[0].getSequenceFeatures().length, 2);
  71     Assert.assertTrue(sqset[0].getSequenceFeatures()[0] == sqset2[0]
  72             .getSequenceFeatures()[0]);
  73     Assert.assertTrue(sqset[0].getSequenceFeatures()[1] == sqset2[0]
  74             .getSequenceFeatures()[1]);
  75   }
  76 }