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 import jalview.gui.JvOptionPane;
  29
  30 import java.util.Hashtable;
  31 import java.util.Map;
  32
  33 import org.testng.Assert;
  34 import org.testng.annotations.BeforeClass;
  35 import org.testng.annotations.Test;
  36
  37 /**
  38  * @author jprocter
  39  *
  40  */
  41 public class SeqsetUtilsTest
  42 {
  43
  44   @BeforeClass(alwaysRun = true)
  45   public void setUpJvOptionPane()
  46   {
  47     JvOptionPane.setInteractiveMode(false);
  48     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  49   }
  50
  51
  52   /**
  53    * test for JAL-2046 bug - duplication of sequence features on reconstructed
  54    * alignment
  55    */
  56   @Test(groups = { "Functional" })
  57   public void testSeqFeatureAddition()
  58   {
  59     SequenceI[] sqset = new SequenceI[] {
  60         new Sequence("Aseq1", "AREALSEQ"),
  61         new Sequence("Aseq2", "AREALSEQ") };
  62
  63     AlignmentI al = new Alignment(sqset);
  64     al.setDataset(null);
  65     AlignmentI ds = al.getDataset();
  66     SequenceFeature sf1 = new SequenceFeature("f1", "foo", 2, 3, "far");
  67     SequenceFeature sf2 = new SequenceFeature("f2", "foo", 2, 3, "far");
  68     ds.getSequenceAt(0).addSequenceFeature(sf1);
  69     Map<String, SeqsetUtils.SequenceInfo> unq = SeqsetUtils.uniquify(sqset, true);
  70     SequenceI[] sqset2 = new SequenceI[] {
  71         new Sequence(sqset[0].getName(), sqset[0].getSequenceAsString()),
  72         new Sequence(sqset[1].getName(), sqset[1].getSequenceAsString()) };
  73     Assert.assertSame(sqset[0].getSequenceFeatures().get(0), sf1);
  74     Assert.assertTrue(sqset2[0].getSequenceFeatures().isEmpty());
  75     ds.getSequenceAt(0).addSequenceFeature(sf2);
  76     Assert.assertEquals(sqset[0].getSequenceFeatures().size(), 2);
  77     SeqsetUtils.deuniquify(unq, sqset2);
  78     // explicitly test that original sequence features still exist because they
  79     // are on the shared dataset sequence
  80     Assert.assertEquals(sqset[0].getSequenceFeatures().size(), 2);
  81     Assert.assertEquals(sqset2[0].getSequenceFeatures().size(), 2);
  82     Assert.assertSame(sqset[0].getSequenceFeatures().get(0), sqset2[0]
  83             .getSequenceFeatures().get(0));
  84     Assert.assertSame(sqset[0].getSequenceFeatures().get(1), sqset2[0]
  85             .getSequenceFeatures().get(1));
  86   }
  87 }