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 static org.hamcrest.MatcherAssert.assertThat;
  31 import static org.hamcrest.Matchers.equalTo;
  32
  33 import java.util.BitSet;
  34 import java.util.Hashtable;
  35 import java.util.Map;
  36
  37 import org.testng.Assert;
  38 import org.testng.annotations.BeforeClass;
  39 import org.testng.annotations.DataProvider;
  40 import org.testng.annotations.Test;
  41
  42 /**
  43  * @author jprocter
  44  *
  45  */
  46 public class SeqsetUtilsTest
  47 {
  48
  49   @BeforeClass(alwaysRun = true)
  50   public void setUpJvOptionPane()
  51   {
  52     JvOptionPane.setInteractiveMode(false);
  53     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  54   }
  55
  56   /**
  57    * test for JAL-2046 bug - duplication of sequence features on reconstructed
  58    * alignment
  59    */
  60   @Test(groups = { "Functional" })
  61   public void testSeqFeatureAddition()
  62   {
  63     SequenceI[] sqset = new SequenceI[] { new Sequence("Aseq1", "AREALSEQ"),
  64         new Sequence("Aseq2", "AREALSEQ") };
  65
  66     AlignmentI al = new Alignment(sqset);
  67     al.setDataset(null);
  68     AlignmentI ds = al.getDataset();
  69     SequenceFeature sf1 = new SequenceFeature("f1", "foo", 2, 3, "far");
  70     SequenceFeature sf2 = new SequenceFeature("f2", "foo", 2, 3, "far");
  71     ds.getSequenceAt(0).addSequenceFeature(sf1);
  72     Map<String, SeqsetUtils.SequenceInfo> unq = SeqsetUtils.uniquify(sqset, true);
  73     SequenceI[] sqset2 = new SequenceI[] {
  74         new Sequence(sqset[0].getName(), sqset[0].getSequenceAsString()),
  75         new Sequence(sqset[1].getName(), sqset[1].getSequenceAsString()) };
  76     Assert.assertSame(sqset[0].getSequenceFeatures().get(0), sf1);
  77     Assert.assertTrue(sqset2[0].getSequenceFeatures().isEmpty());
  78     ds.getSequenceAt(0).addSequenceFeature(sf2);
  79     Assert.assertEquals(sqset[0].getSequenceFeatures().size(), 2);
  80     SeqsetUtils.deuniquify(unq, sqset2);
  81     // explicitly test that original sequence features still exist because they
  82     // are on the shared dataset sequence
  83     Assert.assertEquals(sqset[0].getSequenceFeatures().size(), 2);
  84     Assert.assertEquals(sqset2[0].getSequenceFeatures().size(), 2);
  85     Assert.assertSame(sqset[0].getSequenceFeatures().get(0),
  86             sqset2[0].getSequenceFeatures().get(0));
  87     Assert.assertSame(sqset[0].getSequenceFeatures().get(1),
  88             sqset2[0].getSequenceFeatures().get(1));
  89   }
  90
  91   @DataProvider
  92   public Object[][] sequenceAndMask()
  93   {
  94     return new Object[][] {
  95       { "AAAABBBBCCCCDDDD", 0xFFFFL, "AAAABBBBCCCCDDDD" },
  96       { "AAAABBBBCCCCDDDD", 0x000FL, "AAAA" },
  97       { "---A---B---C---D", 0x8888L, "ABCD" },
  98       { "---A---B---C---D", 0x9999L, "-A-B-C-D" },
  99       { "ABCDABCDABCDABCD", 0xC5A3L, "ABBDACCD" },
 100       { "", 0xFFFFL, "" },
 101       { "AAAABBBBCCCCDDDD", 0x0000L, "" },
 102       { "AAABBBCCC", 0xFFFF, "AAABBBCCC" },
 103       { "AAAABBBB", 0xD000L, "" },
 104       { "AAAABBBB", 0xAA0AL, "AA" },
 105     };
 106   }
 107
 108   @Test(groups = {"Functional"}, dataProvider = "sequenceAndMask")
 109   public void testFilterSequence(String sequence, long mask, String expected)
 110   {
 111     BitSet bitMask = BitSet.valueOf(new long[] {mask});
 112     var result = SeqsetUtils.filterSequence(sequence.toCharArray(), bitMask);
 113     assertThat(result, equalTo(expected.toCharArray()));
 114   }
 115 }