test/jalview/datamodel/SequenceFeatureTest.java

   1 package jalview.datamodel;
   2
   3 import static org.testng.AssertJUnit.assertEquals;
   4 import static org.testng.AssertJUnit.assertFalse;
   5 import static org.testng.AssertJUnit.assertNull;
   6 import static org.testng.AssertJUnit.assertSame;
   7 import static org.testng.AssertJUnit.assertTrue;
   8
   9 import org.testng.annotations.Test;
  10
  11 public class SequenceFeatureTest
  12 {
  13   @Test(groups = { "Functional" })
  14   public void testCopyConstructor()
  15   {
  16     SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
  17             12.5f, "group");
  18     sf1.setValue("STRAND", "+");
  19     sf1.setValue("Note", "Testing");
  20     Integer count = new Integer(7);
  21     sf1.setValue("Count", count);
  22
  23     SequenceFeature sf2 = new SequenceFeature(sf1);
  24     assertEquals("type", sf2.getType());
  25     assertEquals("desc", sf2.getDescription());
  26     assertEquals(22, sf2.getBegin());
  27     assertEquals(33, sf2.getEnd());
  28     assertEquals("+", sf2.getValue("STRAND"));
  29     assertEquals("Testing", sf2.getValue("Note"));
  30     // shallow clone of otherDetails map - contains the same object values!
  31     assertSame(count, sf2.getValue("Count"));
  32   }
  33
  34   /**
  35    * Tests for retrieving a 'miscellaneous details' property value, with or
  36    * without a supplied default
  37    */
  38   @Test(groups = { "Functional" })
  39   public void testGetValue()
  40   {
  41     SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
  42             12.5f, "group");
  43     sf1.setValue("STRAND", "+");
  44     assertEquals("+", sf1.getValue("STRAND"));
  45     assertNull(sf1.getValue("strand")); // case-sensitive
  46     assertEquals(".", sf1.getValue("unknown", "."));
  47     Integer i = new Integer(27);
  48     assertSame(i, sf1.getValue("Unknown", i));
  49   }
  50
  51   /**
  52    * Tests the method that returns 1 / -1 / 0 for strand "+" / "-" / other
  53    */
  54   @Test(groups = { "Functional" })
  55   public void testGetStrand()
  56   {
  57     SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f,
  58             "group");
  59     assertEquals(0, sf.getStrand());
  60     sf.setValue("STRAND", "+");
  61     assertEquals(1, sf.getStrand());
  62     sf.setValue("STRAND", "-");
  63     assertEquals(-1, sf.getStrand());
  64     sf.setValue("STRAND", ".");
  65     assertEquals(0, sf.getStrand());
  66   }
  67
  68   /**
  69    * Tests for equality, and that equal objects have the same hashCode
  70    */
  71   @Test(groups = { "Functional" })
  72   public void testEqualsAndHashCode()
  73   {
  74     SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
  75             12.5f, "group");
  76     sf1.setValue("ID", "id");
  77     sf1.setValue("Name", "name");
  78     sf1.setValue("Parent", "parent");
  79     sf1.setStrand("+");
  80     sf1.setPhase("1");
  81     SequenceFeature sf2 = new SequenceFeature("type", "desc", 22, 33,
  82             12.5f, "group");
  83     sf2.setValue("ID", "id");
  84     sf2.setValue("Name", "name");
  85     sf2.setValue("Parent", "parent");
  86     sf2.setStrand("+");
  87     sf2.setPhase("1");
  88
  89     assertFalse(sf1.equals(null));
  90     assertTrue(sf1.equals(sf2));
  91     assertTrue(sf2.equals(sf1));
  92     assertEquals(sf1.hashCode(), sf2.hashCode());
  93
  94     // changing type breaks equals:
  95     sf2.setType("Type");
  96     assertFalse(sf1.equals(sf2));
  97
  98     // changing description breaks equals:
  99     sf2.setType("type");
 100     sf2.setDescription("Desc");
 101     assertFalse(sf1.equals(sf2));
 102
 103     // changing start position breaks equals:
 104     sf2.setDescription("desc");
 105     sf2.setBegin(21);
 106     assertFalse(sf1.equals(sf2));
 107
 108     // changing end position breaks equals:
 109     sf2.setBegin(22);
 110     sf2.setEnd(32);
 111     assertFalse(sf1.equals(sf2));
 112
 113     // changing feature group breaks equals:
 114     sf2.setEnd(33);
 115     sf2.setFeatureGroup("Group");
 116     assertFalse(sf1.equals(sf2));
 117
 118     // changing ID breaks equals:
 119     sf2.setFeatureGroup("group");
 120     sf2.setValue("ID", "id2");
 121     assertFalse(sf1.equals(sf2));
 122
 123     // changing Name breaks equals:
 124     sf2.setValue("ID", "id");
 125     sf2.setValue("Name", "Name");
 126     assertFalse(sf1.equals(sf2));
 127
 128     // changing Parent breaks equals:
 129     sf2.setValue("Name", "name");
 130     sf1.setValue("Parent", "Parent");
 131     assertFalse(sf1.equals(sf2));
 132
 133     // changing strand breaks equals:
 134     sf1.setValue("Parent", "parent");
 135     sf2.setStrand("-");
 136     assertFalse(sf1.equals(sf2));
 137
 138     // changing phase breaks equals:
 139     sf2.setStrand("+");
 140     sf1.setPhase("2");
 141     assertFalse(sf1.equals(sf2));
 142
 143     // restore equality as sanity check:
 144     sf1.setPhase("1");
 145     assertTrue(sf1.equals(sf2));
 146     assertTrue(sf2.equals(sf1));
 147     assertEquals(sf1.hashCode(), sf2.hashCode());
 148
 149     // changing status doesn't change equals:
 150     sf1.setStatus("new");
 151     assertTrue(sf1.equals(sf2));
 152   }
 153 }