test/jalview/datamodel/SequenceFeatureTest.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.datamodel;
  22
  23 import static org.testng.AssertJUnit.assertEquals;
  24 import static org.testng.AssertJUnit.assertFalse;
  25 import static org.testng.AssertJUnit.assertNull;
  26 import static org.testng.AssertJUnit.assertSame;
  27 import static org.testng.AssertJUnit.assertTrue;
  28
  29 import jalview.gui.JvOptionPane;
  30
  31 import org.testng.annotations.BeforeClass;
  32 import org.testng.annotations.Test;
  33
  34 public class SequenceFeatureTest
  35 {
  36
  37   @BeforeClass(alwaysRun = true)
  38   public void setUpJvOptionPane()
  39   {
  40     JvOptionPane.setInteractiveMode(false);
  41     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  42   }
  43
  44   @Test(groups = { "Functional" })
  45   public void testCopyConstructor()
  46   {
  47     SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
  48             12.5f, "group");
  49     sf1.setValue("STRAND", "+");
  50     sf1.setValue("Note", "Testing");
  51     Integer count = new Integer(7);
  52     sf1.setValue("Count", count);
  53
  54     SequenceFeature sf2 = new SequenceFeature(sf1);
  55     assertEquals("type", sf2.getType());
  56     assertEquals("desc", sf2.getDescription());
  57     assertEquals(22, sf2.getBegin());
  58     assertEquals(33, sf2.getEnd());
  59     assertEquals("+", sf2.getValue("STRAND"));
  60     assertEquals("Testing", sf2.getValue("Note"));
  61     // shallow clone of otherDetails map - contains the same object values!
  62     assertSame(count, sf2.getValue("Count"));
  63   }
  64
  65   /**
  66    * Tests for retrieving a 'miscellaneous details' property value, with or
  67    * without a supplied default
  68    */
  69   @Test(groups = { "Functional" })
  70   public void testGetValue()
  71   {
  72     SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
  73             12.5f, "group");
  74     sf1.setValue("STRAND", "+");
  75     assertEquals("+", sf1.getValue("STRAND"));
  76     assertNull(sf1.getValue("strand")); // case-sensitive
  77     assertEquals(".", sf1.getValue("unknown", "."));
  78     Integer i = new Integer(27);
  79     assertSame(i, sf1.getValue("Unknown", i));
  80   }
  81
  82   /**
  83    * Tests the method that returns 1 / -1 / 0 for strand "+" / "-" / other
  84    */
  85   @Test(groups = { "Functional" })
  86   public void testGetStrand()
  87   {
  88     SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f,
  89             "group");
  90     assertEquals(0, sf.getStrand());
  91     sf.setValue("STRAND", "+");
  92     assertEquals(1, sf.getStrand());
  93     sf.setValue("STRAND", "-");
  94     assertEquals(-1, sf.getStrand());
  95     sf.setValue("STRAND", ".");
  96     assertEquals(0, sf.getStrand());
  97   }
  98
  99   /**
 100    * Tests for equality, and that equal objects have the same hashCode
 101    */
 102   @Test(groups = { "Functional" })
 103   public void testEqualsAndHashCode()
 104   {
 105     SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
 106             12.5f, "group");
 107     sf1.setValue("ID", "id");
 108     sf1.setValue("Name", "name");
 109     sf1.setValue("Parent", "parent");
 110     sf1.setStrand("+");
 111     sf1.setPhase("1");
 112     SequenceFeature sf2 = new SequenceFeature("type", "desc", 22, 33,
 113             12.5f, "group");
 114     sf2.setValue("ID", "id");
 115     sf2.setValue("Name", "name");
 116     sf2.setValue("Parent", "parent");
 117     sf2.setStrand("+");
 118     sf2.setPhase("1");
 119
 120     assertFalse(sf1.equals(null));
 121     assertTrue(sf1.equals(sf2));
 122     assertTrue(sf2.equals(sf1));
 123     assertEquals(sf1.hashCode(), sf2.hashCode());
 124
 125     // changing type breaks equals:
 126     SequenceFeature sf3 = new SequenceFeature("type", "desc", 22, 33,
 127             12.5f, "group");
 128     SequenceFeature sf4 = new SequenceFeature("Type", "desc", 22, 33,
 129             12.5f, "group");
 130     assertFalse(sf3.equals(sf4));
 131
 132     // changing description breaks equals:
 133     String restores = sf2.getDescription();
 134     sf2.setDescription("Desc");
 135     assertFalse(sf1.equals(sf2));
 136     sf2.setDescription(restores);
 137
 138     // changing score breaks equals:
 139     float restoref = sf2.getScore();
 140     sf2.setScore(12.4f);
 141     assertFalse(sf1.equals(sf2));
 142     sf2.setScore(restoref);
 143
 144     // NaN doesn't match a number
 145     restoref = sf2.getScore();
 146     sf2.setScore(Float.NaN);
 147     assertFalse(sf1.equals(sf2));
 148
 149     // NaN matches NaN
 150     sf1.setScore(Float.NaN);
 151     assertTrue(sf1.equals(sf2));
 152     sf1.setScore(restoref);
 153     sf2.setScore(restoref);
 154
 155     // changing start position breaks equals:
 156     int restorei = sf2.getBegin();
 157     sf2 = new SequenceFeature(sf2, 21, sf2.getEnd(), sf2.getFeatureGroup());
 158     assertFalse(sf1.equals(sf2));
 159     sf2 = new SequenceFeature(sf2, restorei, sf2.getEnd(),
 160             sf2.getFeatureGroup());
 161
 162     // changing end position breaks equals:
 163     restorei = sf2.getEnd();
 164     sf2 = new SequenceFeature(sf2, sf2.getBegin(), 32,
 165             sf2.getFeatureGroup());
 166     assertFalse(sf1.equals(sf2));
 167     sf2 = new SequenceFeature(sf2, sf2.getBegin(), restorei,
 168             sf2.getFeatureGroup());
 169
 170     // changing feature group breaks equals:
 171     restores = sf2.getFeatureGroup();
 172     sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), "Group");
 173     assertFalse(sf1.equals(sf2));
 174     sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), restores);
 175
 176     // changing ID breaks equals:
 177     restores = (String) sf2.getValue("ID");
 178     sf2.setValue("ID", "id2");
 179     assertFalse(sf1.equals(sf2));
 180     sf2.setValue("ID", restores);
 181
 182     // changing Name breaks equals:
 183     restores = (String) sf2.getValue("Name");
 184     sf2.setValue("Name", "Name");
 185     assertFalse(sf1.equals(sf2));
 186     sf2.setValue("Name", restores);
 187
 188     // changing Parent breaks equals:
 189     restores = (String) sf1.getValue("Parent");
 190     sf1.setValue("Parent", "Parent");
 191     assertFalse(sf1.equals(sf2));
 192     sf1.setValue("Parent", restores);
 193
 194     // changing strand breaks equals:
 195     restorei = sf2.getStrand();
 196     sf2.setStrand("-");
 197     assertFalse(sf1.equals(sf2));
 198     sf2.setStrand(restorei == 1 ? "+" : "-");
 199
 200     // changing phase breaks equals:
 201     restores = sf1.getPhase();
 202     sf1.setPhase("2");
 203     assertFalse(sf1.equals(sf2));
 204     sf1.setPhase(restores);
 205
 206     // restore equality as sanity check:
 207     assertTrue(sf1.equals(sf2));
 208     assertTrue(sf2.equals(sf1));
 209     assertEquals(sf1.hashCode(), sf2.hashCode());
 210
 211     // changing status doesn't change equals:
 212     sf1.setStatus("new");
 213     assertTrue(sf1.equals(sf2));
 214   }
 215
 216   @Test(groups = { "Functional" })
 217   public void testIsContactFeature()
 218   {
 219     SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f,
 220             "group");
 221     assertFalse(sf.isContactFeature());
 222     sf = new SequenceFeature("", "desc", 22, 33, 12.5f, "group");
 223     assertFalse(sf.isContactFeature());
 224     sf = new SequenceFeature(null, "desc", 22, 33, 12.5f, "group");
 225     assertFalse(sf.isContactFeature());
 226     sf = new SequenceFeature("Disulfide Bond", "desc", 22, 33, 12.5f,
 227             "group");
 228     assertTrue(sf.isContactFeature());
 229     sf = new SequenceFeature("disulfide bond", "desc", 22, 33, 12.5f,
 230             "group");
 231     assertTrue(sf.isContactFeature());
 232     sf = new SequenceFeature("Disulphide Bond", "desc", 22, 33, 12.5f,
 233             "group");
 234     assertTrue(sf.isContactFeature());
 235     sf = new SequenceFeature("disulphide bond", "desc", 22, 33, 12.5f,
 236             "group");
 237     assertTrue(sf.isContactFeature());
 238   }
 239 }